Metabolic ‘fingerprints’ and aquatic food webs

Author: Dr Paul McInerney

Food webs describe ‘who-eats-what’ within biological communities. Food consumed by organisms has several uses: generation of energy, growth and reproduction. In particular, food webs define the pathways along which energy is transferred from resource to consumer. The strength and direction of these energy transfers are sensitive to impacts from changes to river flows and landscapes.

River flows and flooding can influence the productivity of food webs by bringing organic matter into rivers, which provides food for microbes. The microbes are then consumed by small animals called zooplankton. River flows also allow fish to move, forage and spawn and support the growth of zooplankton and small water bugs, and in turn, enable birds and fish to feed and grow. Understanding how food webs respond to environmental flows is critical for understanding the responses of animals at the top of food webs, such as birds and fish.

Recent flooding has generated new growth in the Paroo River along the rivers edge. Photo: Siwan Lovett.

Productivity in an ecosystem

Productivity refers to primary production by organisms that obtain energy from the sun – plants and algae (called autotrophs) and to secondary production, which refers to organisms that obtain energy from other organisms, such as bacteria, fungi and animals (called heterotrophs). Production describes the rate of generation of new biomass in an ecosystem, usually expressed as biomass change per volume of water or surface area over time. Biomass refers to the total amount of living matter in an ecosystem and is often used as a source of energy for other living organisms.

Floodplain inundation in Barmah forest. Water that returns from floodplains to rivers can carry dissolved carbon that can fuel foodwebs. Photo credit: Paul McInerney.

The Bottom of the Food Web – primary production

In ecology, the organisms at the bottom of the food web are known as primary producers. They are called primary producers as they are the first receivers of energy from the sun and convert the sun’s rays into energy that can be consumed by organisms higher up the food chain. These organisms include plants and algae (which are also known as aquatic autotrophs). The rate of primary production (how much energy is produced) is primarily influenced by the availability of sunlight, water and nutrients and the temperature of the atmosphere. Plants and algae need sunlight and water to grow, however, they need a balanced amount of both. Too much, or not enough light and water, can significantly reduce the ability of aquatic autotrophs to grow and produce energy.

Primary production in rivers is relatively easy to measure, since it can be calculated from daily changes in the amount of oxygen in the water. This is because plants produce oxygen through photosynthesis, so high amounts of oxygen in rivers indicate high energy production. However, primary production on its own is not necessarily a good predictor of the benefit of flows for secondary production, as plants and algae are not the only food resources for consumers. Aquatic animals also eat food that comes from outside rivers, such as land-based leaf litter, plants and animals.

Plants and algae also rely on the right mix of nutrients in the aquatic ecosystem for their energy production levels to be the most efficient. Flooding is one mechanism by which environmental water flows can stimulate primary productivity, as it liberates nutrients from floodplains into the river system.

Large clumps of flourishing lignum post flood - lignum is an important floodplain plant providing habitat and food for birds and other organisms. Photo credit: Siwan Lovett.

Moving up the Food Web – secondary production

Secondary productivity can be more complex, but fundamentally it is governed by the availability of carbon (energy) at the bottom of the food web. This carbon can be supplied from terrestrial (land) sources liberated from floodplains by flows, or from aquatic autotrophs that fix carbon via photosynthesis. Once incorporated into the food web (via bacterial microbes, zooplankton and other animals) passage of this carbon to the top of the food chain can be influenced by competition, interactions between predators and prey and the efficiency of energy transfer (e.g. losses via respiration and excretion) between trophic (food chain) levels along with a host of abiotic variables (e.g. sustained flow, habitat, connectivity). Estimating secondary production of every species within a riverine food web is therefore extremely difficult and must account for the amount of food that is consumed, how much of it is assimilated (used), how much is lost via respiration and excretion, rates of biomass generation and the mortality of animals.

Stream metabolism

We can, however, measure carbon generation and consumption in rivers by estimating stream metabolism. Stream metabolism is comprised of two key ecological processes: gross primary production (GPP) and ecosystem respiration (ER), which generate and recycle organic matter respectively. Healthy aquatic ecosystems need both processes to generate new biomass (the biomass becomes food for organisms higher up the food web) and to break down plant and animal remnants to recycle nutrients to enable growth to occur. These processes have a profound effect on ecosystem character and condition through their influence on the capacity of plants to complete their life cycles and the ability of animals to acquire the food resources needed to survive and reproduce.

Stream metabolism can be measured by calculating changes in dissolved oxygen; this provides information on the sources and utilisation of organic carbon by river ecosystem food webs. Net ecosystem production (NEP), the difference between GPP and ER, is considered a measure of the overall carbon balance, and frequently used as an estimate of the basal food resource supply.

Leaf litter and snags in rivers supply a surface for autotrophs (algae) and heterotrophs (bacteria, fungi, animals) to reside. These resources supply the basal energy at the base of food webs. Photo credit: Paul McInerney.

Metabolic fingerprints

The Flow MER Food web theme seeks to improve our understanding of metabolic responses to flow and has adopted a ‘metabolic fingerprinting’ approach (see Figure 1 below). Metabolic fingerprints are an emerging method for visualising and measuring changes in ecosystem metabolism and can be used as a diagnostic tool for comparing annual patterns of metabolism across rivers or across years for the same rivers. A significant challenge when interpreting responses of ecosystem metabolism to flows is determining what is ‘desirable’ and ‘undesirable’ productivity.

For example, a large overbank flow event has the potential to liberate substantial quantities of organic carbon from floodplains that can generate large increases in heterotrophic in-channel productivity (measured as ER). However, such large productivity responses may be undesirable if they occur with small GPP responses, potentially leading to blackwater events, where more oxygen is consumed from the water column than is produced, ultimately leading to hypoxia for aquatic animals (large brown arrow in Figure 1).

Equally, at the other extreme a ‘Cease to flow/Base flow’ event (depicted by the dark green arrow in Figure 1) coupled with high light and high nutrient concentrations has the potential to generate high rates of GPP during daylight hours, and similarly high rates of ER overnight. However, if this occurs as a blue green algae bloom, it is also a non-desired productivity response that may be harmful to aquatic animal and human health.

Figure 1: Conceptual model of the Flow MER Water Quality and Food web basin-scale theme’s approach to measuring metabolic responses to Commonwealth Environmental Water. We use a metabolic fingerprinting approach (Bernhardt et al. 2018), an emerging tool for visualising and measuring change in ecosystem metabolism across time or space and in response to hypothesised drivers.


The Flow MER Food web theme is working on improving our knowledge of how to generate environmental flows that promote desirable metabolic responses where gross primary production (GPP) and Ecosystem Responses (ER) remain well-balanced and produce successful outcomes for aquatic food webs.  Stay in touch to find out more as our metabolic fingerprinting work continues.

Our work in the Food webs & water quality Basin Theme

Food webs show how food and energy resources such as microbes, algae and reeds are connected with consumers such as waterbugs, fish and waterbirds. Water quality and stream metabolism provide the oxygen and environment for aquatic plants and animals to thrive, and both respond to flow management to provide the energy that fuels riverine food webs. Our work will investigate how Commonwealth environmental water impacts food webs and water quality in the rivers, floodplains and wetlands of the Murray-Darling Basin.

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