Key Microbial Taxa in Streams: Bacteria, Fungi, and Diatoms

Methodological Constraints and Major Bacterial Phyla. Our understanding of important microbial taxa in streams is constrained by both available data sets and the drastic evolution of methodological approaches over time. While modern molecular sequencing is now the standard, this makes historical comparisons difficult. A meta-analysis of stream bacteria by Zeglin [4] identified 11 dominant phyla, yet as noted in Table 1, the physiological coherence within these groups varies dramatically [24-32]. Consequently, a high-level taxonomic identity often reveals little about an organism's specific ecological function. Studies focusing specifically on biofilm habitats consistently show that these communities are dominated by the Proteobacteria (primarily Beta- and Alphaproteobacteria) and Bacteroidetes phyla [33], providing a foundational view of stream benthic life.

Table 1. Common bacteria phyla found in streams with very general statements about their characteristics

The Dominant and Diverse Proteobacteria. The Proteobacteria are a widespread, abundant, and highly diverse group across many ecosystems, including many known pathogens and metabolically versatile species. Within this phylum, Betaproteobacteria are often the most abundant and ecologically significant subgroup in freshwater systems. However, Alphaproteobacteria are also critically important, particularly due to their tendency to thrive in low-nutrient conditions [29]. Given the immense diversity within this phylum, simply quantifying its abundance provides limited ecological insight. There is a pressing need for more detailed phylogenetic analysis, coupled with transcriptomics, to effectively link the phylogenetic identity of these organisms to their specific functional roles in stream ecosystems.

The Functionally Defined Aquatic Hyphomycetes. Among stream fungi, the most extensively studied group is the aquatic hyphomycetes, which are defined by their functional role and unique sporulation structures rather than representing a single phylogenetic taxon. Most of these fungi belong to the phylum Ascomycota and are crucial decomposers of plant litter, such as fallen leaves, in stream environments. As described by Grossart and Rojas-Jimenez [34], the importance and true diversity of these organisms require further study, hampered by methodological limitations in quantifying specific taxa and their physiology. Enhancing the representation of fungal diversity in molecular studies often requires using different sets of primers to target individual groups effectively [35].

Fungal Ecology on Decomposing Leaves. Several studies have specifically investigated the role of hyphomycetes in the decomposition of leaf litter in streams. One study found that fungal biomass and diversity on decomposing leaves were higher than bacterial biomass, though these fungal communities did not significantly differ among various leaf types [36]. Conversely, other research has demonstrated that leaf chemical properties and environmental conditions are key drivers of microbial community composition. For instance, Wymore et al. [37] found that leaf tannin, lignin, and nitrogen content were negatively correlated with overall microbial diversity, highlighting the complex interplay between substrate quality and microbial assembly.

Diatoms and Protozoans: Alternative Approaches and Challenges. Diatoms are ubiquitous in streams and have traditionally been identified via microscopy, as their silica-based cell walls allow for precise morphological classification. They are widely used as bioindicators of stream health, though recent efforts are shifting toward using molecular methods like metabarcoding to assess their diversity [39]. However, challenges remain, including efficiently extracting adequate DNA [38] and standardizing these molecular approaches for reliable application in governmental biomonitoring programs [40]. The diversity of protozoans is even less studied, but molecular methods are also being applied. A study by Dopheide et al. [41] using ciliate-specific primers found them inadequate for capturing full protozoan diversity, indicating a need for more refined, taxon-specific primers.

Conclusion: A Rapidly Advancing Field. In summary, the advent and application of molecular methods, particularly high-throughput sequencing, have profoundly impacted nearly all aspects of microbial ecology. Despite these advances, certain ecosystems like streams and specific microbial taxa remain relatively understudied. The field is currently in a dynamic phase of rapid advancement, steadily improving our understanding of the immense microbial diversity within stream environments and its critical connection to ecosystem function.