The microbial food web refers to the combined trophic interactions among microbes in aquatic environments. These microbes include viruses, bacteria, algae, heterotrophic protists (such as ciliates and flagellates). In aquatic ecosystems, microbial food webs are essential because they form the basis for the cycling of nutrients and energy. These webs are vital to the stability and production of ecosystems in a variety of aquatic environments, including lakes, rivers, and oceans. By converting dissolved organic carbon (DOC) and other nutrients into biomass that larger organisms may eat, microbial food webs maintain higher trophic levels. Thus, these webs are crucial for energy flow and nutrient cycling in both freshwater and marine ecosystems.

In aquatic environments, microbes constitute the base of the food web. Single celled photosynthetic organisms such as diatoms and cyanobacteria are generally the most important primary producers in the open ocean. Many of these cells, especially cyanobacteria, are too small to be captured and consumed by small crustaceans and planktonic larvae. Instead, these cells are consumed by phagotrophic protists which are readily consumed by larger organisms.

Viruses

Aquatic ecosystems are full of viruses, which are essential for managing microbial populations. They release organic matter back into the environment by infecting and lysing planktonic algae (phycoviruses) and bacterial cells (bacteriophages). This mechanism, called the viral shunt, promotes nutrient recycling and aids in the control of microbial populations. Viral particles and dissolved organic carbon (DOC), which can be further used by other microorganisms, are released when bacterial cells are lysed. Viruses can infect and break open bacterial cells and (to a lesser extent), planktonic algae (a.k.a. phytoplankton). Therefore, viruses in the microbial food web act to reduce the population of bacteria and, by lysing bacterial cells, release particulate and dissolved organic carbon (DOC).

Bacteria

In the microbial food web, bacteria play a crucial role in breaking down organic materials and recycling nutrients. They transform DOC into bacterial biomass so that protists and other higher trophic levels can consume it. Additionally, bacteria take part in the nitrogen and carbon cycles, among other biogeochemical cycles.

Algae

In aquatic ecosystems, single-celled photosynthetic organisms like cyanobacteria and diatoms are the main producers. Through the process of photosynthesis, they transform sunlight into chemical energy and create organic matter, which is the foundation of the food chain. Particularly significant in nutrient-poor environments are cyanobacteria because of their capacity to fix atmospheric nitrogen. When vital nutrients like nitrogen and phosphorus are scarce during periods of uneven development, algal cells have the potential to produce DOC. DOC may also be released into the environment by algal cells. One of the reasons phytoplankton release DOC termed "unbalanced growth" is when essential nutrients (e.g. nitrogen and phosphorus) are limiting. Therefore, carbon produced during photosynthesis is not used for the synthesis of proteins (and subsequent cell growth), but is limited due to a lack of the nutrients necessary for macromolecules. Excess photosynthate, or DOC is then released, or exuded.