Microbial Ecology in Streams: Biofilms, Functions, and Environmental Drivers

Introduction to Stream Microbial Ecology. The study of microbial ecology in streams remains a comparatively underdeveloped field relative to research in marine or soil environments. Scientific emphasis has historically been placed on microbe-mediated ecosystem functions rather than on the detailed community or population ecology of these organisms. The available information also varies significantly among different microbial taxa, with bacteria being the most extensively studied group. This focus arises from their ubiquitous distribution and their critically important roles in other, better-characterized ecosystems. Consequently, many foundational examples in stream microbiology are derived from bacterial studies, highlighting a knowledge gap for other microorganisms.

The Central Role of Microbes in Stream Biogeochemistry. Microorganisms, particularly bacteria, are fundamental drivers of key biogeochemical processes in stream ecosystems. They mediate essential functions including denitrification, the anaerobic reduction of nitrate to nitrogen gases (N₂ or N₂O), and the decomposition of both dissolved and particulate organic matter. While environmental drivers clearly influence both the structure and function of these microbial communities, the precise interdependence of function on community composition is complex and difficult to discern. Rapid methodological advancements, especially the advent of high-throughput sequencing, have revolutionized the field but also complicate historical study comparisons. These technological advances are ultimately expected to provide a more mechanistic understanding of the structure-function relationship in stream microbial ecology.

The Unique Physicochemical Template of Streams. Streams present a distinct set of physical and chemical conditions that shape the life of their microbial inhabitants. Defining characteristics include unidirectional water flow, a tight hydrological and ecological connection to the surrounding watershed, and a high susceptibility to anthropogenic disturbance. These specific physicochemical conditions directly influence the ecology of the microorganisms and, by extension, their functional roles within the ecosystem. The activities of these microbial communities, in turn, have a profound feedback effect on overall stream biogeochemistry and water quality, creating a dynamic and interconnected system.

Fundamentals of Stream Ecology and Habitat. The unidirectional flow and four-dimensional nature of streams—longitudinal, lateral, vertical, and temporal—create a unique environmental template that governs the biota and biogeochemistry, as reviewed by Allan and Castillo [1]. This constant flow delivers dissolved nutrients and organic matter to organisms but also poses a challenge for retaining position. Consequently, stream ecosystems are largely benthic dominated, with true planktonic food webs typically restricted to larger rivers. This benthic emphasis means that nearly all submerged surfaces are coated with complex microbial biofilms, which are consortia of microbial cells embedded in a matrix of extracellular polymeric substances.

Biofilm terminology has evolved and varies among researchers; terms like periphyton (algal-based biofilms) and epilithon (biofilms on rocks) are common. For consistency, this article uses the overarching term biofilm to refer to all such matrix-enclosed communities. These biofilms develop on diverse physical substrates available for colonization, including rocks, wood, sand, and leaf litter, each offering a distinct microhabitat.

Hydrological and Temporal Dynamics. The unidirectional flow means that conditions at any point in a stream are heavily influenced by upstream processes. Flowing water promotes mixing, which introduces oxygen and generally prevents the prolonged thermal stratification seen in lakes. Streams also extend vertically into the hyporheic zone, a saturated region below and alongside the stream bed that harbors diverse microorganisms and exhibits spatially variable redox conditions. Furthermore, streams are highly dynamic over time, experiencing diurnal changes (e.g., in light availability), seasonal shifts (e.g., temperature and leaf litter inputs), and annual variations driven by climate and hydrology.

Watershed Connectivity and Anthropogenic Impact. Streams are intrinsically linked to their watersheds, which act as sources of water, dissolved and particulate materials, and organisms. This connectivity means the stream's microbial community is continuously seeded by microbes entering from the surrounding landscape. These introductions can be natural or significantly amplified by human land use, such as through agricultural erosion, or from point sources like sewage outfalls. This intimate connection also renders streams highly vulnerable to anthropogenic impacts, including channel modification, reservoir construction, and effluent from wastewater treatment plants (WWTPs). Given that streams are used for drinking water, waste disposal, and recreation, understanding and preserving water quality is of paramount importance.

Conclusion: Seeking Generalities in a Complex System. The unique features of the microbial community in lotic ecosystems are a direct reflection of the stream's character. As in any ecological field, drawing broad generalities is confounded by methodological differences and variations in ecosystem properties. To help guide this search for unifying principles, several review articles have been sought to depict the central features of microbial ecology in streams [2-4]. These works are essential for synthesizing knowledge and directing future research into these critical and dynamic ecosystems.