Abstract
BackgroundAlthough the common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. An understanding of the biology of these species may provide insights into sustainable control methods. The animal-associated microbiome plays an important role in host health. Characterization of the carp microbiome and the factors that affect its composition is an important step toward understanding the biology and interrelationships between these species and their environments.ResultsWe compared the fecal microbiomes of common, silver, and bighead carps from wild and laboratory environments using Illumina sequencing of bacterial 16S ribosomal RNA (rRNA). The fecal bacterial communities of fish were diverse, with Shannon indices ranging from 2.3 to 4.5. The phyla Proteobacteria, Firmicutes, and Fusobacteria dominated carp guts, comprising 76.7 % of total reads. Environment played a large role in shaping fecal microbial community composition, and microbiomes among captive fishes were more similar than among wild fishes. Although differences among wild fishes could be attributed to feeding preferences, diet did not strongly affect microbial community structure in laboratory-housed fishes. Comparison of wild- and lab-invasive carps revealed five shared OTUs that comprised approximately 40 % of the core fecal microbiome.ConclusionsThe environment is a dominant factor shaping the fecal bacterial communities of invasive carps. Captivity alters the microbiome community structure relative to wild fish, while species differences are pronounced within habitats. Despite the absence of a true stomach, invasive carp species exhibited a core microbiota that warrants future study.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0190-1) contains supplementary material, which is available to authorized users.
Highlights
The common, silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America
Student’s t test comparison between the gut microbiome of river and laboratory-housed invasive carps showed that common carp exhibited significantly higher richness (p ≤ 0.0001) and diversity in wild fish (p = 0.002)
We examined the operational taxonomic unit (OTU) that were present across wild and lab fish of the same species, and five OTUs emerged as the dominant bacteria of the core gut microbiota of invasive carps (Table 2)
Summary
Silver, and bighead carps are native and sparsely distributed in Eurasia, these fish have become abundant and invasive in North America. Characterization of the carp microbiome and the factors that affect its composition is an important step toward understanding the biology and interrelationships between these species and their environments. The potential ecosystem impacts of silver and bighead carp are not well known, as large filter feeders they could potentially affect native fish species directly by inducing changes in zooplankton communities [7, 8]. While the management of common carp has occasionally been successful through poisoning entire lakes or manipulating weaknesses in their life history characteristics (e.g., manipulation of predators in spawning habitats) [9], no control strategies have been successful in reducing the population of silver and bighead carps.
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