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Abstract DNA‐based aquatic biomonitoring methods show promise to provide rapid, standardized, and efficient biodiversity assessment to supplement and in some cases replace current morphology‐based approaches that are often less efficient and can produce inconsistent results. Despite this potential, broad‐scale adoption of DNA‐based approaches by end‐users remains limited, and studies on how these two approaches differ in detecting aquatic biodiversity across large spatial scales are lacking. Here, we present a comparison of DNA metabarcoding and morphological identification, leveraging national‐scale, open‐source, ecological datasets from the National Ecological Observatory Network (NEON). Across 24 wadeable streams in North America with 179 paired sample comparisons, we found that DNA metabarcoding detected twice as many unique taxa than morphological identification overall. The two approaches showed poor congruence in detecting the same taxa, averaging 59%, 35%, and 23% of shared taxa detected at the order, family, and genus levels, respectively. Importantly, the two approaches detected different proportions of indicator taxa like %EPT and %Chironomidae. DNA metabarcoding detected far fewer Chironomid and Trichopteran taxa than morphological identification, but more Ephemeropteran and Plecopteran taxa, a result likely due to primer choice. Overall, our results showed that DNA metabarcoding and morphological identification detected different benthic macroinvertebrate communities. Despite these differences, we found that the same environmental variables were correlated with invertebrate community structure, suggesting that both approaches can accurately detect biodiversity patterns across environmental gradients. Further refinement of DNA metabarcoding protocols, primers, and reference libraries–as well as more standardized, large‐scale comparative studies–may improve our understanding of the taxonomic agreement and data linkages between DNA metabarcoding and morphological approaches. 

Abstract Ecosystems that are coupled by reciprocal flows of energy and nutrient subsidies can be viewed as a single “meta‐ecosystem.” Despite these connections, the reciprocal flow of subsidies is greatly asymmetrical and seasonally pulsed. Here, we synthesize existing literature on stream–riparian meta‐ecosystems to quantify global patterns of the amount of subsidy consumption by organisms, known as “allochthony.” These resource flows are important since they can comprise a large portion of consumer diets, but can be disrupted by human modification of streams and riparian zones. Despite asymmetrical subsidy flows, we found stream and riparian consumer allochthony to be equivalent. Although both fish and stream invertebrates rely on seasonally pulsed allochthonous resources, we find allochthony varies seasonally only for fish, being nearly three times greater during the summer and fall than during the winter and spring. We also find that consumer allochthony varies with feeding traits for aquatic invertebrates, fish, and terrestrial arthropods, but not for terrestrial vertebrates. Finally, we find that allochthony varies by climate for aquatic invertebrates, being nearly twice as great in arid climates than in tropical climates, but not for fish. These findings are critical to understanding the consequences of global change, as ecosystem connections are being increasingly disrupted.