Complete Crassulacean acid metabolism (CAM) pathway was found in a metagenomic assembly genome afflitied as Sphingomonadaceae bacteria, the completeness and contamination were 96.14 and 0.243, respectively. Is this CAM pathway also existed in bacteria or it just a contamination from phytoplankton?
Most probably it is contamination. But you can explore if your bug is phototrophic.
I agree, very likely another member of the metagenome. Even if it is a >5 % of the community, if you have very high sequence depth, full pathways out of it can be detected. Also: As in the metagenomic assembly you mentioned that the majority of the reads are binning with a Sphingomonadaceae, there is a great chance you may get the strain in pure culture. Then you may ensure this lack or host of such completely unexpected content by genome sequencing or by PCR testing.
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