Spatially explicit habitat mapping and modeling enables consideration of patterns of microhabitat patches and their potential importance for fluvial ecological functions. Patch spatial patterns likely change with discharge, yet no framework for investigating this exists. In this study, new concepts and methods were developed to characterize spatial patterns of microhabitat patches and discharge-dependent patch behaviors. The five patch behaviors were disappearance, expansion, contraction, aggregation, and segmentation. Patch analyses were applied to 12 km of adult rainbow trout habitat along a confined river in the Sierra Mountains of California. Depth and velocity habitat suitability curves were coupled with 2D hydrodynamic modeling to map microhabitat patches at 7 discharges (baseflow to modest flooding). Area of high-quality microhabitat, patch count, and patch size were analyzed by discharge. Patch behaviors were tallied for 46-56 patches among 5 patch size classes (0.25-2.5, 2.5-25, 25-250, 250-2500, and ≥ 2500 m2) for each discharge increase between the 7 flows. Three different regimes in flow-dependent patch size change were found along with a gradual decrease in patch persistence with discharge. The occurrence of patch behaviors had a trend explaining patch size and persistence change. Expansion and aggregation behavior had the largest count at low flows and decreased as discharge increased. Conversely, contraction and segmentation behaviors had the minimum count at low flow and increased with discharge. Some behaviors indicated the emergence of high-quality patches during floods, controlled by geomorphic features. Overall, patch analysis enriches ecohydraulics and river management.

The gut microbiota confers host protection against pathogen colonization early after infection. Several mechanisms underlying the protection have been described, but the contributions of nutrient competition versus direct inhibition are controversial. Using an ex vivo model of Salmonella growth in the mouse cecum with its indigenous microbes, we find that nutrient limitation and typical inhibitory factors alone cannot prevent pathogen growth. However, the addition of certain amino acids markedly reverses the microbiota's ability to suppress pathogen growth. Enhanced Salmonella colonization after antibiotic treatment is ablated by exclusion of dietary protein, which requires the presence of the microbiota. Thus, dietary protein and amino acids are important regulators of colonization resistance.