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Aphids live in symbiosis with a variety of bacteria, including the obligate symbiont  Buchnera aphidicola  and diverse facultative symbionts. The symbiotic associations for one aphid species, especially for polyphagous species, often differ across populations. In the present study, by using high-throughput 16S rRNA sequencing, we surveyed in detail the microbiota in natural populations of the cotton aphid  Aphis gossypii  in China and assessed differences in bacterial diversity with respect to host plant and geography. The microbial community of  A. gossypii  was dominated by a few heritable symbionts.  Arsenophonus  was the most dominant secondary symbiont, and  Spiroplasma  was detected for the first time. Statistical tests and ordination analyses showed that host plants rather than geography seemed to have shaped the associated symbiont composition. Special symbiont communities inhabited the Cucurbitaceae-feeding populations, which supported the ecological specialization of  A. gossypii  on cucurbits from the viewpoint of symbiotic bacteria. Correlation analysis suggested antagonistic interactions between  Buchnera  and coexisting secondary symbionts and more complicated interactions between different secondary symbionts. Our findings lend further support to an important role of the host plant in structuring symbiont communities of polyphagous aphids and will improve our understanding of the interactions among phytophagous insects, symbionts, and environments.   Electronic supplementary material  The online version of this article (10.1007/s00248-019-01435-2) contains supplementary material, which is available to authorized users.

The Bacterial Flora Associated with the Polyphagous Aphid Aphis gossypii Glover (Hemiptera: Aphididae) Is Strongly Affected by Host Plants