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Endosymbionts and intracellular parasites are common in arthropod hosts. As a consequence, (co)amplification of untargeted bacterial sequences has been occasionally reported as a common problem in DNA barcoding. While identifying amphipod species with universal COI primers, we unexpectedly detected rickettsial endosymbionts belonging to the Torix group. To map the distribution and diversity of  Rickettsia  species among amphipod hosts, we conducted a nationwide molecular screening of seven families of New Zealand freshwater amphipods. In addition to uncovering a diversity of Torix  Rickettsia  species across multiple amphipod populations from three different families, our research indicates that: (1) detecting Torix  Rickettsia  with universal primers is not uncommon, (2) obtaining ‘ Rickettsia  COI sequences’ from many host individuals is highly likely when a population is infected, and (3) obtaining ‘host COI’ may not be possible with a conventional PCR if an individual is infected. Because  Rickettsia  COI is highly conserved across diverse host taxa, we were able to design blocking primers that can be used in a wide range of host species infected with Torix  Rickettsia . We propose the use of blocking primers to circumvent problems caused by unwanted amplification of  Rickettsia  and to obtain targeted host COI sequences for DNA barcoding, population genetics, and phylogeographic studies.

Widespread Torix Rickettsia in New Zealand amphipods and the use of blocking primers to rescue host COI sequences