Photovoltaic Shading Alters Water Quality and Sustains Diatom-Dominated Microbial Communities in Shrimp–Crab Aquaculture Ponds

Fishery–photovoltaic systems are expanding rapidly in coastal China, yet their effects on pond water quality and microbial communities remain poorly understood. We compared three PV-shaded and three unshaded (NPV) earthen ponds co-culturing Pacific white shrimp (Litopenaeus vannamei) and mud crab (Scylla paramamosain) in August and September 2025. Water quality measurements and 16S and 18S rRNA gene amplicon sequencing were conducted on 60 samples. PV ponds had lower temperature (28.9 vs. 31.2 °C), turbidity (31.6 vs. 40.9 NTU), dissolved oxygen (5.76 vs. 6.91 mg L−1), and ammonium, nitrite, phosphate, total nitrogen and total phosphorus concentrations. Shading explained 8.0% and 10.4% of bacterial and eukaryotic community variation respectively, while alpha diversity remained largely unchanged. Diatom relative abundance was higher under shading (46.2% vs. 26.7%), whereas dinoflagellate abundance was lower. From August to September, NPV communities shifted from diatom to ciliate dominance, with ciliate abundance increasing from 2.1% to 45.4% and Vibrio from 0.6% to 9.8%. In contrast, diatom abundance remained stable and Vibrio remained below 2.5% in PV ponds. Shaded communities exhibited lower dispersion and broader niche breadth, although assembly processes did not differ between treatments. Cross-kingdom networks contained fewer bacteria–eukaryote associations under shading, but cohesion and resampled network topology remained comparable. Overall, PV shading was associated with cooler, less nutrient-rich water and persistent diatom dominance; however, reduced dissolved oxygen highlights the importance of aeration management in fishery–PV systems.