Standardization of processing methods is the key point of ARMS research and allows for the comparability of marine biodiversity assessments. Step by step protocols are described for each part of the process, from ARMS assembly to the bioinformatics of ARMS molecular data. Click on each category below to get more information and download protocols or download the access the overview schematics of ARMS processing.
Overview
ARMS Protocol: Overview
Assembly
ARMS Protocol: Assembly
Deployment
ARMS Protocol: Deployment
Retrieval
ARMS Protocol: Retrieval
Lab Preparation
Because the DNA of the ARMS communities will be extracted and analyzed as bulk samples, great care must be taken during the processing steps to not introduce exogenous DNA. Gloves must be worn at all times and the laboratory environment should be as free as possible from potential contaminations. It is also important to bleach all the material between ARMS or to use single-use supplies when bleaching is not possible…
Disassembly
Make sure that all the containers and tools used have been bleached and rinsed between ARMS processing. Wear gloves at all times; do not touch the water with bare skin…
Photographing Plates
Make sure that all the containers and tools used have been bleached and rinsed between ARMS processing. Wear gloves at all times; do not touch the water or the plates with bare skin…
Plate Subsampling (Sessiles)
Sessile taxa of interest can be individually subsampled and vouchered for morphological study or DNA barcoding. Doing so can also help with future identification of metabarcoding sequences and plate photo analysis…
Fraction Sieving
This step will separate the motile organisms from the ARMS disassembly water tub into three size fractions. The 106µm - 500µm fraction and the 500µm - 2 mm fractions will be bulk fixed during this step while the >2 mm fractions will be processed during the next step…
Big Organisms Vouchering
During this step, the organisms > 2-mm are morphosorted and individually vouchered. Typically, an ARMS unit yields 50 to 150 organisms depending on deployment time and types of habitat…
Plate Scraping
During this step, all sessile communities will be bulk collected from all the ARMS plates to assess their overall taxonomic diversity using next-generation sequencing. Bulk samples must be treated with care as to not introduce exogenous DNA in these fractions…
Bulk Samples Preparation for Extraction
Bulk fractions need to be prepared before DNA extractions. Sessile fractions need to be homogenized and weighed; motile fractions need to be decanted in order to remove sediments and weighed…
DNA Extraction and Cleanup of Bulk Samples
We are using a modified version of the DNeasy PowerMax Soil Kit (Qiagen) protocol. In order to avoid the sheering of genomic DNA, we have replaced Step 4 of the DNeasy PowerMax Soil Kit protocol with an overnight proteinase K digestion as described below…
Cytochrome C Oxidase Subunit I (COI) Metabarcoding
This protocol is designed to amplify the mini-COI barcode (313bp) as described in Leray et al (2014). The primer set (mlCOIintF and jgHCO2198) is successfully amplifying a wide range of marine invertebrate phyla. Multiplexing is made possible by a variation of the initial primers tailed on the 5’ end with a 6 bp “tag”…
18S Metabarcoding
ARMS Protocol: 18S Metabarcoding
16S Metabarcoding
ARMS Protocol: 16S Metabarcoding
Plate Photos Analysis
Plate photos are analyzed the same way than settlement tiles. Several options are possible: quantification of the grey areas to get a measure of percent cover – annotation of functional groups – annotation at the lower taxonomic levels. The following guidelines are only provided to help you design your plate photo analysis. Depending on the specific question, protocols can be modified by the user…
