Collection and morphological sorting of macrofauna
The macrofauna grab collected at each station was transferred to a
sealed plastic bin and transported to an onshore sieving station. A
portion of each sediment sample was transferred to a 1 mm mesh sieve
table and washed gently with running water. Once the sediment was washed
through the sieve, macrofauna were gently removed with tweezers and
transferred to a 500 ml container containing 95% ethanol. This process
was carried out until the entire grab sample from each station was
sieved. In cases where excess debris (e.g. ’shellhash’ or rocks)
remained on the sieve that might influence the search for macrofauna,
this debris was collected into containers with ethanol for further
sorting in the lab.
Macrofauna specimens from each grab were sorted into morphospecies. We
only analyzed vermiform macrofauna (e.g. Polychaeta), which comprised
the majority of total macrofauna abundance across the aquaculture sites.
All individuals of each morphospecies from each grab were separated for
counting and downstream DNA barcoding. This was done by one person to
maximize consistency. Morphospecies were photographed and defined when
first encountered to allow recognition across all farms and grabs.
Morphospecies were defined with the aid of taxonomic references
(Banse & Hobson,
1974; Dutch et al., 2014; Hobson & Banse, 1981) and/or were identified
by Leslie Harris from the Los Angeles County Museum via specimen images
uploaded to the iNaturalist platform
(https://www.inaturalist.org/).
After initial sorting of all stations, each morphospecies was
re-examined across all farms and stations to confirm consistency of
morphospecies assignment. Generally, one or two specimens from each
morphospecies at each station were picked for DNA barcoding; however, in
cases where morphospecies delineation was less clear, additional
specimens were picked for genetic confirmation.