Streams play vital roles in surrounding communities and provide essential ecosystem services. The protection of streams is important, they are legally protected under the Clean Water Act, and they can be monitored through the continuous analyses of biological data, such as algal or other aquatic communities. The goals of this study were to analyze the long-term recovery of Tobler Creek, a recovering agricultural stream on the site of a National Historic Landmark, and yield comparisons to a local low-impact stream, Murder Creek, located within the Oconee National Forest. In 2011, Tobler Creek exceeded reference criteria values for total phosphorus (TP) but met the nitrate nitrogen criteria. With an 11-year recovery period, Tobler Creek met both nutrient reference criteria. In 2022, periphyton samples were collected according to standard protocols, confirming that diatoms are the dominant algal group in the community. With recovery, Tobler Creek showed an increase in diatom species richness (χ2 = 116.11, df = 5, p < 0.01) but this was significantly lower than the values documented in Murder Creek. The multi-metric index (MMI), calculated using diatom community analysis to estimate ecological health, indicated that Tobler Creek experienced degradation from 2011 to 2022 (χ2 = 55.97, df = 5, p < 0.05) and is below the regional 25th percentile. The percentage of sediment-tolerant taxa (surirelloid, naviculoid, and nitzschoid) was significantly higher in Tobler Creek in 2022 (χ2 = 500.96, df = 5, p < 0.01) compared to Murder Creek in 2022 (t = −4.67, df = 10, p < 0.01). Despite a reduction in nutrients given the 42-year recovery period, the diatom community in Tobler Creek was significantly different than other regional protected streams. Ecological degradation of the habitat was likely driven by sedimentation due to run-off in the recovering agriculture stream. These findings highlight the importance of protecting water quality, as the recovery of nutrients can be a decades-long process overlayed with many potentially new stressors influencing aquatic organisms.

Gomphonema parvulum is a cosmopolitan freshwater diatom that is used as an indicator in water quality biomonitoring. In this study, we report the culturing of two geographically separated isolates from southeastern North America, their morphology, and the sequencing and assembly of their mitochondrial and chloroplast genomes. Morphologically, both strains fit G. parvulum sensu lato, but the frustules from a protected habitat in South Carolina were smaller than those cited in the historic data of this species from the same location as well as a second culture from Virginia. Phylogenetic analyses using the rbcL gene placed both within a clade with G. parvulum. Genetic markers, including full chloroplast and mitochondrial genomes and the nuclear small subunit rRNA gene region were assembled from each isolate. The organellar genomes of the two strains varied slightly in size due to small differences in intergenic regions with chloroplast genomes of 121,035 bp and 121,482 bp and mitochondrial genomes of 34,639 bp and 34,654 bp. The intraspecific pairwise identities of the chloroplast and mitochondrial genomes of these two isolates were 97.9% and 95.4%, respectively. Multigene phylogenetic analysis demonstrated a close relationship between G. parvulum, Gomphoneis minuta, and Didymosphenia geminata.