Globally, habitat loss in coastal marine systems is a major driver of species decline, and estuaries are particularly susceptible to loss. Along the United States Pacific coast, monospecific eelgrass (Zostera marina) beds form the major estuarine vegetated habitat. In Morro Bay, California, eelgrass experienced an unprecedented decline of > 95%, from 139 ha in 2007 to < 6 ha by 2017. Fish populations were compared before and after the eelgrass decline using trawl surveys. Beach seines surveys were also conducted during the post-decline period to characterize species within and outside of remnant eelgrass beds.While the estuary-wide loss of eelgrass did not result in fewer fish or less biomass, it led to changes in species composition. The post-eelgrass decline period was characterized by increases in flatfish (mainly Citharichthys stigmaeus) and staghorn sculpin (Leptocottus armatus), and decreases in habitat specialists including bay pipefish (Syngnathus leptorhynchus) and shiner perch (Cymatogaster aggregata). There were similar trends inside and outside of remnant eelgrass patches. These findings support evidence across multiple ecosystems suggesting that the predominance of habitat-specialists predicts whether or not habitat loss leads to an overall decline in fish abundance. In addition, loss of critical habitats across seascapes can restrict population connectivity and lead to range contraction. For bay pipefish, the loss of eelgrass in Morro Bay is likely to create a population biogeographic divide. Currently, Morro Bay is dominated by flatfish and sculpins, and the longevity of this new ecosystem state will depend on future eelgrass recovery dynamics supported by ecosystem-based management approaches.



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