Kevin J Flynn

• PhD
• Researcher at Plymouth Marine Laboratory

Photosynthetic organisms have an enormous influence on our environment through their effects on the development of other life on Earth and the way they alter the planet's geology and geochemistry. This book takes a unique approach by examining the evolutionary history of the major groups of aquatic photoautotrophs in the context of the ecophysiolog...

Marine plankton that are capable of photosynthesis and also predation (termed “mixoplankton”) comprise up to 50% of those organisms traditionally termed phytoplankton. Many harmful bloom species are mixoplantonic. However, marine environmental management policies issued by governments, including the MSFD by the EU, have been designed assuming a str...

Plankton phototrophy consumes CO2, increasing seawater pH, while heterotrophy does the converse. Elevation of pH (>8.5) during coastal blooms becomes increasingly deleterious for plankton. Mixoplankton, which can be important bloom-formers, engage in both photoautotrophy and phagoheterotrophy; in theory, this activity could create a relatively stab...

Prorocentrum comprises a diverse group of bloom-forming dinophytes with a worldwide distribution. Although photosynthetic, mixoplanktonic phagotrophy has also been described. Recently, the small P. cf. balticum was shown to use a remarkable feeding strategy by crafting globular mucus traps to capture and immobilize potential prey. Here we present e...

An error in our original work prompts a revisitation of factors constraining photoautotrophic plankton growth rates (μmax). Ribulose-1,5-bisphosphate Carboxylase-Oxygenase does not itself provide that constraint, but we identify other factors that result in our previously suggested value of ~2 doublings per day still likely being representative of...

Analysis of trait trade-offs, through which physiological traits requiring common resources are ‘traded’ to optimize competitive advantage, provides a route to simplify and more readily understand the complexities of ecology. The concept of trait trade-offs has found favour in plankton research, especially directed at phytoplankton, defined here as...

With climate change, oceans are becoming increasingly nutrient limited, favouring growth of prokaryotic picoplankton at the expense of the larger protist plankton whose growth support higher trophic levels. Constitutive mixoplankton (CM), microalgal plankton with innate phototrophic capability coupled with phagotrophy, graze on these picoplankton,...

Protist plankton are major members of open-water marine food webs. Traditionally divided between phototrophic phytoplankton and phagotrophic zooplankton, recent research shows many actually combine phototrophy and phagotrophy in the one cell; these protists are the 'mixoplankton'. Under the mixoplankton paradigm, 'phytoplankton' are incapable of ph...

Digital twins (DT) are simulation models that so closely replicate reality in their behaviour that experts may believe model output to be real. Plankton offer worthy yet tractable biological targets for digital twinning, due to their relatively simply physiology and significant role in ecology from theoretical studies through to planetary scale bio...

Rapid virus proliferation can exert a powerful control on phytoplankton host populations, playing a significant role in marine biogeochemistry and ecology. We explore how marine lytic viruses impact phytoplankton succession, affecting host and nonhost populations. Using an in silico food web we conducted simulation experiments under a range of diff...

The traditional separation between primary producers (autotrophs) and consumers (heterotrophs) at the base of the marine food web is being increasingly replaced by the paradigm that mixoplankton, planktonic protists with the nutritional ability to use both phago(hetero)trophy and photo(auto)trophy to access energy are widespread globally. Thus, man...

The dinoflagellate Dinophysis is responsible for causing diarrhetic shellfish poisoning impacting shellfish aquaculture globally. Dinophysis species are invariably plastidic specialist non-constitutive mixoplankton (pSNCM), combining phagotrophy with acquired phototrophy. Dinophysis acquires phototrophy from another pSNCM, the ciliate Mesodinium ,...

A manual for the isolation and maintenance of mixoplankton is provided that offer guidelines to assist students and scientists initiating studies of mixoplankton. The manual contains specific information on: • Facilities required, including temperature regulated rooms or cabinets, instruments and consumables • Growth media and aseptic precautions •...

It remains unclear as to how mixoplankton (coupled phototrophy and phagotrophy in one cell) affects the estimation of grazing rates obtained from the widely used dilution grazing technique. To address this issue, we prepared laboratory-controlled dilution experiments with known mixtures of phyto-, protozoo-, and mixoplankton, operated under differe...

Projecting ocean biogeochemistry and fisheries resources under climate change requires confidence in simulation models. Core to such models is the description of consumer dynamics relating prey abundance to capture, digestion efficiency and growth rate. Capture is most commonly described as a linear function of prey encounter or by rectangular hype...

Long-term (2004–2020) studies showed yearly summer/autumn blooms in the NE Black Sea dominated by large (cell volume > 5000 μm3) diatoms (Pseudosolenia calcar-avis and Proboscia alata). This phenomenon is characterized by high (>250 W m−2 photosynthetically active radiation, PAR) insolation, and low phosphorus concentrations (to analytical zero). T...

This manual, brings together the different novel approaches developed within MixITiN for investigating marine mixoplankton activity. It comprises four sections, de facto chapters, as follows:• Section 2 Genomic sampling protocols for application to mixoplankton• Section 3 Development and validation of new methods for measuring predation rates in m...

Mixoplankton are now recognised as a major group of protist plankton, encompassing many traditionally labeled 'phytoplankton' and 'protozooplankton'. A key is given to help identify HAB species within the mixoplankton functional types.

A Simple N-based Mixoplankton Model. This work is an output of the MixITiN project (see www.mixotroph.org). It describes the construction and example deployment of a simple model describing the growth of mixoplankton for education purposes. The book is supported by a free-to-end-user model to operate on Powersim Cockpit, and an editable model in Po...

A mechanistic system dynamics description is developed of the interactions between a single lytic-virus – phytoplankton-host couple. The model has state variables for virus, uninfected and infected host biomass, and describes virus and host allometry and physiology. The model, analogous to experimental laboratory virus-host systems but more amenabl...

While traditional microplankton community assessments focus primarily on phytoplankton and protozooplankton, the last decade has witnessed a growing recognition of photo-phago mixotrophy (performed by mixoplankton) as an important nutritional route among plankton. However, the trophic classification of plankton and subsequent analysis of the trophi...

Different hypotheses have been proposed explaining plankton community assembly and how changes in biodiversity can impact ecosystem function. Mixoplankton (photo-phago-trophs) are important members of the plankton, but science lacks a clear understanding of their role in plankton succession. Here, we used a modelling approach to evaluate the season...

The aim of this book is to provide the reader with a text to enable them to explore the models and simulations provided in the textbook, Dynamic Ecology (Flynn, 2018) using a free-to-end-user software platform, namely GNU Octave.

Evolution has direct and indirect consequences on species–species interactions and the environment. However, Earth systems models describing planktonic activity invariably fail to explicitly consider organism evolution. Here we simulate the evolution of the single most important physiological characteristic of any organism as described in models—it...

A bibliographic database of scientific papers published by authors affiliated worldwide, especially focused in Europe and in the European Atlantic Area, and containing the keywords “microalga(e)” or “phytoplankton” was built. A corpus of 79,020 publications was obtained and analyzed using the Orbit Intellixir software to highlight the evolution of...

Protist plankton comprise phytoplankton (incapable of phagotrophy), protozooplankton (incapable of phototrophy) and mixoplankton (capable of phototrophy and phagotrophy). Of these, only phytoplankton and zooplankton are typically described in models. Over the last decade, however, the importance of mixoplankton across all marine biomes has risen to...

There is increasing concern that accelerating environmental change attributed to human-induced warming of the planet may substantially alter the patterns, distribution and intensity of Harmful Algal Blooms (HABs). Changes in temperature, ocean acidification, precipitation, nutrient stress or availability, and the physical structure of the water col...

Many protist plankton are mixotrophs, combining phototrophy and phagotrophy. Their role in freshwater and marine ecology has emerged as a major developing feature of plankton research over recent decades. To better aid discussions, we suggest these organisms are termed “mixoplankton”, as “planktonic protist organisms that express, or have potential...

On land, plants make their own food by photosynthesis and animals live by eating. However, in the microscopic world in the oceans, it is not that simple. Many microscopic so-called plants (phytoplankton) can also eat like animals and many microscopic so-called animals (microzooplankton) can also photosynthesize like plants! More amazingly, some of...

Aim Most protist plankton are mixotrophic, with potential to engage in photoautotrophy and phagotrophy; however, the ecology of these organisms has been misdiagnosed for over a century. A large proportion of these organisms are constitutive mixotrophs (CMs), with an innate ability to photosynthesize. Here, for the first time, an analysis is present...

Microalgae production for high added value compounds is identified as a business sector with high growth potential in the near future, especially in the Atlantic Area. Whereas scientific knowledge about microalgae production and applications in different areas (nutritio-nal, cosmetic, pharmaceutical, aquaculture...) has steadily developed in the la...

Mixotrophy is widespread among protist plankton displaying diverse functional forms within a wide range of sizes. However, little is known about the niches of different mixotrophs and how they affect nutrient cycling and trophodynamics in marine ecosystems. Here we built a plankton food web model incorporating mixotrophic functional diversity. A di...

Results from a dynamic mathematical model are presented simulating the growth of the harmful algal bloom (HAB) mixotrophic dinoflagellate Karlodinium veneficum and its algal prey, Rhodomonas salina. The model describes carbon-nitrogen-phosphorus-based interactions within the mixotroph, interlinking autotrophic and phagotrophic nutrition. The model...

From the Preface … This book aims to provide the biologist, and indeed the non-biologist (mathematician), with an introduction to dynamic ecology. The construction and operation of simulation platforms (models) provides an excellent test of understanding while also generating insight into how real complex processes in ecology operate over time. The...

Stable isotope ratios (SIR) are widely used to estimate food-web trophic levels (TLs). We built systems dynamic N-biomass-based models of different levels of complexity, containing explicit descriptions of isotope fractionation and of trophic level. The values of δ¹⁵N and TLs, as independent and emergent properties, were used to test the potential...

This chapter explores the limitations and potentials for the simplifications to serve useful roles in the management and mitigation of harmful algal blooms (HAB). The utilization of "biological rules" in ecosystem models, which include concepts of allometric scaling and "trait trade‐offs", may be viewed as of particular concern. The chapter present...

The traditional view of the planktonic food web is simplistic: nutrients are consumed by phytoplankton that, in turn, support zooplankton, which ultimately support fish. This structure is the foundation of most models used to explore fisheries production, biogeochemical cycling, and climate change. In recent years, however, the importance of mixotr...

Nutrient acquisition is a critical determinant for the competitive advantage for auto- and osmohetero- trophs alike. Nutrient limited growth is commonly described on a whole cell basis through reference to a maximum growth rate (Gmax) and a half-saturation constant (KG). This empirical application of a Michaelis-Menten like description ignores the...

Information on supplementary figures. (DOCX)

As S4 Fig, but for diatoms with Gmax = 1.386 d-1. (TIF)

Schematic showing the theoretical relationship between substrate concentration at the site of the transporter. Shown is the activity of a single transporter protein (T1), with kcat = 1 (units of transporter-specific activity per time) and half saturation KT = 1 (units of substrate concentration at the transporter site), and the collective activity...

As S3 Fig but for diatoms. The dashed black curve assumes sedimentation as allometrically defined by Eq 13. (TIF)

Values of Tmax for the transport of ammonium or nitrate in Emiliania huxleyi and Heterosigma carterae. Increasing N-stress is indicated by the declining mass ratio of N:C. The grey line, labelled “Growth”, indicates the rate of N-transport required to support steady state growth rate at a given level of cellular N:C; this assumes that the growth ra...

Relationship between N-source substrate concentration and N-specific transport rate for different protist sizes. Protists are considered of ESD 5, 20 or 60μm, with Gmax = 0.693 d-1. The left-hand column of plots assumes the value of Tmax increases with deteriorating N-status; TRDmax was assumed 0.4 pgN μm-2 d-1. The right-hand column of plots assum...

As S3 Fig, but for protists with Gmax = 1.386 d-1. (TIF)

Photosynthesis by marine diatoms plays a major role in the global carbon cycle, although the precise mechanisms of dissolved inorganic carbon (DIC) uptake remain unclear. A lack of direct measurements of carbonate chemistry at the cell surface has led to uncertainty over the underlying membrane transport processes and the role of external carbonic...

Algal biofuels have been offered as an alternative to fossil fuels, based on claims that microalgae can provide a highly productive source of compounds as feedstocks for sustainable transport fuels. Life cycle analyses identify algal productivity as a critical factor affecting commercial and environmental viability. Here, we use mechanistic modelli...

In marine science numerical models, and especially ecosystem models, have developed into an important tool for policy advice and environmental management applications (Rose et al., 2010; Holt et al., 2014; Robson, 2014; Lynam et al., 2016). The predictive capabilities of these models, in particular under changing environmental conditions, naturally...

Microalgal biotechnology has yielded a range of products for different consumer markets, but large scale production for bulk commodities is limited by the cost and environmental impact of production. Nutrient requirements for large-scale production contribute significantly to the cost and environmental impact of microalgal biomass production and sh...

This first comprehensive analysis of the global biogeography of marine protistan plankton with acquired phototrophy shows these mixotrophic organisms to be ubiquitous and abundant; however, their biogeography differs markedly between different functional groups. These mixotrophs, lacking a constitutive capacity for photosynthesis (i.e., non-constit...

We explore approaches to minimise impacts of zooplanktonic pests upon commercial microalgal crops using system dynamics models to describe algal growth controlled by light and nutrient availability and zooplankton growth controlled by crop abundance and nutritional quality. Losses of microalgal crops are minimised when their growth is fastest and,...

Most biogeochemical/ecological models divide planktonic protists between phototrophs (phytoplankton) and heterotrophs (zooplankton). However, a large number of planktonic protists are able to combine several mechanisms of carbon and nutrient acquisition. Not representing these multiple mechanisms in biogeochemical/ecological models describing eutro...

Mixotrophy, i.e., the ability to combine phototrophy and phagotrophy in one organism, is now recognized to be widespread among photic-zone protists and to potentially modify the structure and functioning of planktonic ecosystems. However, few biogeochemical/ecological models explicitly include this mode of nutrition, owing to the large diversity of...

Various innovative photobioreactor designs have been proposed to increase production of algae-derived biomass. Computer models are often employed to test these designs prior to construction. In the drive to optimise conversion of light energy to biomass, efforts to model the profile of irradiance levels within a microalgal culture can lead to highl...

The EPSRC-funded MACROBIOCRUDE project seeks to provide an innovative technology pipeline for the utilisation of an underused, but sustainable biomass in the form of Macroalgae for energy. All Treatments were proven successful with enhanced Carbohydrates, Proteins and Lipids content for a long day light regime and the treatments involving a nutrien...

Rectangular hyperbolic type 2 (RHt2; Michaelis-Menten or Monod-like) functions are commonly used to describe predation kinetics in plankton models, either alone or together with a prey selectivity algorithm deploying the same half-saturation constant for all prey types referenced to external prey biomass abundance. We present an analysis that indic...

Knowing the potential maximum photoautotrophic growth rate for planktonic primary producers is fundamental to our understanding of trophic and biogeochemical processes, and of importance in applied phycology. When day-integrated C-specific growth is considered over natural light:dark cycles, plausible RuBisCO activity (Kcat coupled with cellular Ru...

Assessments of the combined ecological impacts of ocean acidification and warming (OAW) and their social and economic consequences can help develop adaptive and responsive management strategies in the most sensitive regions. Here, available observational and experimental data, theoretical, and modelling approaches are combined to project and quanti...

Ecology involves the transfer of elements between organisms and the environment. Inevitably, and as exemplified in ‘stoichiometric ecology’, imbalances in the transfer pathways have potential to disturb trophic dynamics. It is also clear, though, that those disturbances are not simply (linearly, so to speak) related to imbalances in elemental stoic...

Coccolithophorids are enigmatic plankton that produce calcium carbonate coccoliths, which over geological time have buried atmospheric CO 2 into limestone, changing both the atmosphere and geology of the Earth. However , the role of coccoliths for the proliferation of these organisms remains unclear; suggestions include roles in anti-predation, enh...

The critical role played by copepods in ocean ecology and biogeochemistry warrants an understanding of how these animals may respond to ocean acidification (OA). Whilst an appreciation of the potential direct effects of OA, due to elevated pCO2, on copepods is improving, little is known about the indirect impacts acting via bottom-up (food quality)...

Seawater carbonate chemistry. (DOCX)

Trophic transfer efficiencies of adult female Acartia tonsa. (DOCX)

Detailed methodology. (DOCX)

Detailed methodology. (DOCX)

Arranging organisms into functional groups aids ecological research by grouping organisms (irrespective of phylogenetic origin) that interact with environmental factors in similar ways. Planktonic protists traditionally have been split between photoautotrophic “phytoplankton” and phagotrophic “microzooplankton”. However, there is a growing recognit...

The critical role played by copepods in ocean ecology and biogeochemistry warrants an understanding of how these animals may respond to ocean acidification (OA). Whilst an appreciation of the potential direct effects of OA, due to elevated pCO2, on copepods is improving, little is known about the indirect impacts acting via bottom-up(food quality)...

Phosphorus (P) is a critical element for life on Earth. However, readily extractable ores are being exhausted rapidly and a combination of increasing usage, rising costs and numerous geopolitical problems are expected to impact food security and industry sectors within the next few decades. This hence represents another great anthropogenic challeng...

Many phytoplankton exploit phosphorus (P) from organic sources when dissolved inorganic P (DIP) is depleted. This process is, however, rarely considered in ecological and biogeochemical models. We present a mechanistic model describing explicitly the ability of phytoplankton to use dissolved organic P (DOP) when DIP is limiting, by synthesizing alk...

We propose definitions in terminology to enhance ongoing collaborations between biologists and modellers on plankton ecology. Organism "functional type" should refer to commonality in ecology not biogeochemistry; the latter is largely an emergent property of the former, while alignment with ecology is also consistent with usage in terrestrial scien...

The MACROBIOCRUDE project seeks to provide an innovative technology pipeline for the utilisation of an underused, but sustainable biomass in the form of macroalgae, for the manufacture of hydrocarbon fuels. The project involves 6 Universities within the UK (Durham lead) plus 7 non-academic project collaborators, partners and consultants. One of the...

Human activity causes ocean acidification (OA) though the dissolution of anthropogenically generated CO 2 into seawater, and eutrophication through the addition of inorganic nutrients. Eutrophication increases the phytoplankton biomass that can be supported during a bloom, and the resultant uptake of dissolved inorganic carbon during photosynthesis...