AO30-1_DNA_Fish
metagenome
env_broad_scale
marine coastal environment
env_local_scale
shoreline
depth
2m
host
marine environmental DNA
isolation_source
seawater
collection_date
2021-10-14
geo_loc_name
New Zealand:Milford Sound, Southland
lat_lon
44.67 S 167.92 E
ref_biomaterial
marine environmental DNA
samp_collect_device
cruising speed net (20 μm mesh size and a cod-end) at ~2-3 knots for about 3-5 mins, filtered through a 5 μm pore Smith Root self-preserving filter pack using Smith Root eDNA citizen scientist sampler
samp_mat_process
extraction, PCR, metabarcoding
samp_size
12,121 L
Filtering_method
ANDe
Filter_preservation_method
shield
Sound
Milford Sound
Gene_marker
16S_fish
Environmental_Nucleic_Acid
DNA
Sampling_Station
30
replicate
30.1
Bioinformatics Applied
Cuadapt was used to remove primer sequences, allowing a single mismatch. Trimmed sequences then underwent processing with the 'DADA2' package in R. Reads were truncated 160 and 160 bp for the forward and reverse reads, respectively and filtered with a default maximum number of “expected errors” (maxEE), reads not meeting this threshold were discarded. A parametric error matrix was constructed, and sequence variants for the forward and reverse reads were dereplicated. Singletons were discarded, and paired-end reads were merged with no mismatch and a minimum overlap of 10 bp. Finally, chimeric sequences were eliminated using the consensus option in the removeBimeraDenovo function.
BioSampleModel
Metagenome or environmental