The Role of Microbial Ecology in Stream Biogeochemistry and Nutrient Cycling

Microorganisms are fundamental drivers of the biogeochemical cycling of essential elements like carbon, nitrogen, and phosphorus within stream ecosystems. Due to the intrinsic connection between land and water, significant research focuses on nutrients that limit primary production. This area of study is critically important because excess nutrients can lead to the eutrophication of downstream waters, causing harmful algal blooms and anaerobic dead zones. Consequently, understanding microbial processes in streams is key to managing water quality and ecosystem health.

The movement of nutrients through a stream is not linear but occurs in a spiral pattern. This process is formally described by the nutrient-spiraling concept, which quantifies the cycling and downstream displacement of atoms by the unidirectional flow of water. Metrics derived from this concept serve as vital measures of stream ecosystem function, particularly for assessing nutrient retention efficiency. These measures allow scientists to compare the processing capacity of different streams and their roles in watershed-scale biogeochemistry.

Biofilms play a uniquely important role in these stream processes. As reviewed by Leff et al. and Battin et al., the biofilm's structure, characterized by closely spaced cells and an extracellular matrix, facilitates small-scale biogeochemical interactions while providing protection from hydraulic forces. This environment effectively retains cells, organic and inorganic compounds, and extracellular enzymes, leading to greater microbial biomass and metabolic activity than found in the free-flowing water column. The formation and function of a biofilm are heavily influenced by the underlying substrate and light availability, which governs its suitability for algal growth.

A central question in microbial ecology is whether ecosystem function is linked to the composition of the microbial community. The concepts of functional redundancy, where different species perform the same role, and plasticity, where a single taxon can perform multiple functions, challenge a direct structure-function connection. Further limitations in analytical scale and resolution complicate this; for instance, detecting a gene does not confirm its expression, and common rRNA gene sequences may be too coarse to reveal meaningful functional differences among organisms.

Organic Carbon Dynamics in Stream Ecosystems.The dominant pool of organic carbon in streams is Dissolved Organic Carbon (DOC), a key component of Dissolved Organic Matter (DOM). From a microbial standpoint, DOC is crucial because microorganisms transform this otherwise inaccessible resource into biomass, making it available to higher trophic levels. Organic matter also exists as Fine Particulate Organic Matter (FPOM) and Coarse Particulate Organic Matter (CPOM), all of which require enzymatic degradation by microbes. These materials can originate externally from the watershed (allochthonous) or be produced within the stream itself (autochthonous).

The bioavailability of organic matter is highly variable and depends on its source and physical form. Generally, algal-derived autochthonous material is more labile, or easily decomposed, than terrestrial plant material. This means that even when autochthonous production is limited, it can play a disproportionately large role in the stream's food web. The physical form also dictates the decomposer community; for example, fungi are typically more important than bacteria in the initial decomposition of CPOM, such as leaves (Figure 2). Both groups employ extracellular enzymes to break down complex organic polymers into usable compounds.

Figure 2. Processing of organic matter via the microbial loop in streams

The production of these extracellular enzymes is central to decomposition and is a widely assayed process in stream ecology. Common assays target enzymes like phenol oxidase, β-D-glucosidase, phosphatases, and cellobiohydrolase. However, these assays typically measure the total pool of enzymes without identifying their specific biological sources, which can include bacteria, fungi, and algae. Researchers use these enzymatic profiles to compare ecosystems, with studies suggesting that similarities between freshwater and terrestrial systems are driven by environmental factors like temperature and pH, while differences from marine systems may stem from distinct microbial communities.

Leaves represent a particularly relevant form of allochthonous organic matter, serving as both a carbon source and a physical substrate. Their decomposition is a synergistic process involving microbes and invertebrates known as shredders. Quantifying the relative contribution of each component is complex, but studies have concluded that shredders often account for the largest fraction of decomposition, while bacteria contribute the smallest. The role of fungi, especially aquatic hyphomycetes, is typically dominant in microbial decomposition, often accounting for over 94% of microbial production on leaves. These fungi penetrate leaf tissue, which can facilitate subsequent bacterial colonization, resulting in a relationship that can be both synergistic and competitive.

Ultimately, the rate and outcome of decomposition are influenced by stream conditions. For instance, microbial biomass and respiration on leaves are enhanced by elevated nutrient concentrations in the water. This interplay between resource quality and environmental conditions highlights the sensitivity of stream ecosystem processes to external changes, such as nutrient pollution.

The Microbial Loop in Stream Food Webs.Within streams, the microbial loop is a critical pathway that makes organic matter available to higher trophic levels. This loop describes the flow of energy and carbon through the microbial components of the food web. It begins with dissolved organic matter, which is assimilated by bacteria and other microbes. These microbes are then consumed by protozoa, which in turn are preyed upon by larger organisms, thus redirecting carbon back into the main food web.

In streams, protozoa are a major source of bacterial mortality and serve as an essential link to higher trophic levels. Although studies on this process in lotic systems are less common than in lakes, existing research demonstrates its significance. One study found that protozoa cleared an average of 16% of the water column of bacteria daily. These protozoa are then consumed by filter-feeding macroinvertebrates. Seasonal estimates from the Butron River in Spain indicated that flagellates grazed 43-65% of bacterial production in the water column.

While ciliates often have higher individual consumption rates than flagellates, their typically lower abundances in rivers make them a less significant source of overall bacterial mortality. This consumption is not limited to the water column; benthic bacteria attached to sediments and organic matter are also heavily grazed. In White Clay Creek, Pennsylvania, protozoans were estimated to consume about 80% of the annual benthic bacterial production, underscoring the immense trophic importance of the microbial loop in stream benthic habitats.