June 2018 Adélie penguin scats were collected from Signy Island (South Orkney Islands) during crèche (December/January) 2014/15 and 2015/16 and stored in 80% Ethanol. DNA was extracted from ~30 mg of faecal material using a Promega ‘Maxwell 16' instrument and a Maxwell® 16 Tissue DNA kit. A total of 450 samples were analysed: 30 extractions per week for 2015 and 60 per week for samples collected in 2016. Three DNA markers providing different taxonomic information were amplified from penguin faecal DNA. First, ALL faecal DNA samples were characterised using a highly conserved metazoan primer set that amplifies a region of the nuclear 18S gene. In addition, a subset of faecal samples from each year were also characterised with two other primer pairs that amplify a region of the mtDNA 16S gene to allow species-level identification for most fish (16S_Fish) and krill (16S_Krill) species respectively. During amplification of markers, the products were tagged with a unique pair of index primers allowing samples to be pooled and sequenced (2x150bp) on a MiSeq high-throughput DNA sequencer. - See Adelie Pengiun Diet CCAMLR paper for all of the primer/PCR details - See BAS Adelie 18s Krill and Fish subset excel spreadsheet for sample details. - See BAS Adelie 18s ALL samples fastq for 18s fastq files - See BAS Adelie 16s Krill subset fastq for 16s krill fastq files - See BAS Adelie Fish subset fastq for 16s fish fastq files ##################################################################################### November 2018 In addition we also amplified all 450 samples with the 16S_Fish marker. - See Adelie Experiment Details 16s Fish for sample details, plate layout, first and second round PCR and miseq sheet. - See BAS Adelie Fish ALL Samples fastq for 16s fish fastq files

Raw and processed acoustic data were collected in East Antarctica from the RSV Aurora Australis during two surveys: the Krill Availability, Community Trophodynamics and AMISOR Surveys (KACTAS) and the Krill Acoustics and Oceanography Survey (KAOS) in the East Antarctic. Seabed alias example file used to make Figure 3. 38_false_bottom.sv.csv (file size: 10.7 MB) This file is an example of seabed aliasing (false bottom echo) that occurred during the KAOS survey. The data in this file are acoustic (mean volume backscattering strength, Sv) sample-by-sample and in a CSV format. Ping_index - ping number Distance_GPS - along track distance from the vessel’s GPS (nautical miles). Distance_vl - along track distance from the vessel’s log (nautical miles). Not used here, so is populated by Echoview’s ‘don’t care’ value (-9.90E+37) to keep the file format consistent. Ping_date - format yyyy-mm-dd Ping_time - format hh:mm:ss Ping_milliseconds - format (integer; ms) Latitude - position from the vessel’s GPS (degrees) Longitude position from the vessel’s GPS (degrees) Depth_start - start depth of vessel echosounder logging range (m) Depth_stop - stop depth of vessel echosounder logging range (m) Range_start - start range of vessel echosounder logging range (m) Range_stop - stop range of vessel echosounder logging range (m) Sample_count number of samples in a ping. Acoustic Sv samples follow in column-wise vector (dB re 1 m-1) Transect metadata all_transects.csv (file size: 14.8 K) This is the transect metadata for both the KACTAS and KAOS surveys: Transect - transect number startDate - start date of transect dd/mm/yyyy startTime - start time of transect hh:mm endDate - end date of transect dd/mm/yyyy endTime - end time of transect dd/mm/yyyy Ping_subset - a ping subset specified between two timestamps to isolate acoustic data that occurred on transect , i.e start timestamp to stop timestamp (yyyy-mm-dd hh:mm = yyyy-mm-dd hh:mm). Direction - Direction traveled along the transect (N - north or S- south). Light - day or night when transect was observed Survey - Either KACTAS or KAOS Leg - Krill box 1 or 2 (there were two surveys only during the KAOS voyage). Pass - Sampling bout for a transect in a given direction. Example R-code FigureAndDataprocessingExample.R (12KB) This R-code provides examples of scripting acoustic data processing using EchoviewR, specifically, using ping-subsets to isolate acoustic data along a transect of interest, detecting schools and exporting echo integrations for 38, 120 and 200 kHz. The R-code for making the figures in the paper is also given. GPS vessel positions for both the KACTAS and KAOS surveys KACTASandKAOS_GPS.csv (3 MB) This CSV file gives the vessel track for both the KACTAS and KAOS surveys. GPS_date - dd/mm/yyyy GPS_time - HH:MM:SS GPS_milliseconds - integer Latitude - position from the vessel’s GPS (degrees) Longitude - position from the vessel’s GPS (degrees) x - relative grid position (x) used for plotting Figure 1 y - relative grid position (y) used for plotting Figure 1 Survey - either: KACTAS_Krillbox, KAOS_Krillbox1, or KACTAS_Krillbox2 Krill swarms for both the KACTAS and KAOS surveys KACTASandKAOSswarms.csv (2.1 MB) Krill swarms descriptors for the KACTAS and KAOS surveys in CSV format (see Table 2 for description of the data fields). Echoview file for the KACTAS survey KACTAS-survey.EV (21.8 MB) An Echoview file (version 12.0) for the KACTAS acoustic data analysis KACTAS EK60 scientific echosounder calibration values KACTAS_EK500_calibration.ecs 3,623 16/05/2022 21:21 -a-- An Echoview format calibration file for the KACTAS survey (see Table 3 for calibration values and Demer et al.20 for a description of the calibration parameters). Echoview file for the KAOS survey KAOS-survey.EV (16.4MB) An Echoview file (version 12.0) for the KAOS acoustic data analysis KAOS EK60 scientific echosounder calibration values KAOS_EK60_calibration.ecs 5,711 01/11/2021 04:36 -a– An Echoview format calibration file for the KAOS survey (see Table 3 for calibration values and Demer et al. (2015) for a description of the calibration parameters).

Demersal fish form an important component of sub-Antarctic ecosystems. While understanding the distribution of key commercial species is the subject of much current research, patterns in the distribution of benthic fish assemblages as a whole and associated diversity has received less attention. Here we combine Australian (source: AAD Random Stratified Trawl Surveys) and French (source: POKER 2006, 2010, 2013) demersal fish datasets with synoptic environmental data to quantify and predict the distribution of fish assemblages across the Kerguelen Plateau. We achieve this by applying a recently developed method, called Regions of Common Profile (RCP), which quantifies distinct environmental regions containing a similar profile of species. The RCP method directly models species simultaneously (rather than dissimilarities or single species at a time) and offers advantages over previous methods in the areas of model diagnostics, the interpretability of model outputs, and providing estimates of uncertainty. We define the contents, environmental correlates and spatial extent of several assemblages across the plateau. The files provided here are the outputs of the RCP analyses. Files KP_RCP_Predictions.csv: Region of Common Profile (RCP) spatial predictions for entire Kerguelen Plateau. The resolution of the grid is 0.1 x 0.1 degrees (Long, Lat, WGS84) and predictions were restricted to depths shallower than 1200 m. The probability of each grid cell belonging to each RCP is reported (RCP_1 - RCP_7) as well as the most likely RCP (HClass) and the most likely RCP's probability of occurrence (HClass_prob) RCP_Species_Composition_Average.xls: Average (standard deviation) of probability of occurrence for each species in each RCP. Statistics calculated by taking 500 bootstrap samples of model parameters, generating expected probability of occurrences for each species in each RCP for each level of the sampling factor Year/Season/Gear and summarising over the 3500 (7 levels of sampling effect x 500 bootstraps) values. RCP_Species_Composition_SampEff.xls: Average (Standard deviation) probability of occurrence of species for each RCP for each level of the sampling factor (Year/Season/Gear). Marginal_env_plots (Folder): Marginal plots of the response of each RCP to depth (m), chl-a yearly mean (mg/m3) and surface temperature yearly mean (degrees Celsius). Plots were generated by predicting RCP membership for each trawl site based on its environmental covariates only and plotting. Interactive maps showing the predicted spatial distribution of the RCP groups, as well as the species profile and environmental conditions characterising each group, and the coverage of the HIMI Marine reserve can be found at doi: 10.4225/15/58169d06ee8fc. Contains the above results in an interactive map with the following layers: 1) Assemblage maps: Species Profile: Map of the most likely RCP group. The pop up graphic shows pictures of the four most likely species to occur in this assemblage as well as the expected occurrence of all species (the species profile). 2) Assemblage maps: Environment Characteristics: Map of the most likely RCP group. The pop up graphic shows the response of each assemblage to depth, surface temperature yearly mean and chl-a yearly mean. These inform us of the environmental characteristics of each RCP group. Plots were generated by predicting RCP group membership for each trawl site based only on its environmental covariates. 3) Group Membership: Map of the most likely RCP group and the uncertainty associated with this group. 4) HIMI Reserve Coverage: Location of Heard and McDonald Islands Marine Reserve with pop-up table of the proportion of each RCP group contained within the reserve. Proportion calculated within the Australian EEZ only.

Geoscience Australia and the Australian Antarctic Division conducted a benthic community survey using underwater still photographs on the shelf around the Mertz Glacier region. The purpose of the work was to collect high resolution still photographs of the seafloor across the shelf to address three main objectives: 1. to investigate benthic community composition in the area previously covered by the Mertz Glacier tongue and to the east, an area previously covered by fast ice 2. to investigate benthic community composition (or lack thereof) in areas of known iceberg scours 3. to investigate the lateral extent of cold water coral communities in canyons along the shelf break. Benthic photos were captured using a Canon EOS 20D SLR 8 megapixel stills camera fitted with a Canon EF 35mm f1.4 L USM lens in a 2500m rated flat port anodised aluminium housing. Two Canon 580EX Speedlight strobes were housed in 6000m rated stainless steel housings with hemispherical acrylic domes. The camera and strobes were powered with a 28V 2.5Ah cyclone SLA battery pack fitted in the camera housing and connected using Brantner Wetconn series underwater connectors. The results were obtained with 100 ASA and a flash compensation value of +2/3 of a stop. The focus was set manually to 7m and the image was typically exposed at f2.8 and a shutter speed of 1/60 sec. The interval between photos was set to 10 or 15 seconds. The camera was fitted to either the CTD frame or the beam trawl frame and lowered to approximately 4-5 m from the bottom. Two laser pointers, set 50 cm apart, were used for scale. The camera was deployed at 93 stations, 7 using the beam trawl frame and 86 using the CTD frame. The stations were named by: 1. Camera deployment frame (e.g. CTD or beam trawl, BT) 2. Frame sequence number (e.g. CTD53) 3. Instrument (e.g. camera = CAM) 4. Sequence of camera deployments through the survey overall (e.g. first deployment = CAM01, second deployment = CAM02 etc). For example, BT5_CAM16 is the sixteenth camera deployment of the survey overall, and was the fifth deployment using the beam trawl frame. From the 93 stations, there were 75 successful camera deployments. There were no photos captured at 9 stations. This was due to the camera or strobes malfunctioning, the camera being too far from the bottom, or the camera or strobes being in the mud at the bottom. The photos at a further 9 stations are considered poor due to the camera being out of focus, the camera being a little too far from the bottom or because very few photos were captured of the bottom. The benthic photo will be used to document the fauna and communities associated with representative habitats in the study area. The post-cruise analysis of the benthic photos will involve recording seabed geology and biology (class or order, and whatever is significant for the habitat) for each image

Copies of the event logs/station lists taken from the Aurora Australis, Astrolabe and Umitaka Maru during their CEAMARC cruises (collaborative East Antarctic Marine Census).

Untreated, macerated wastewater effluent has been discharged to the sea at Davis Station since 2005, when the old wastewater treatment infrastructure was removed. This environmental assessment was instigated to guide the choice of the most suitable wastewater treatment facility at Davis. The assessment will support decisions that enable Australia to meet the standards set for the discharge of wastewaters in Antarctica in national legislation (Waste Management Regulations of the Antarctic Treaty Environmental Protection Act - ATEP) and to meet international commitments (the Madrid Protocol) and to meet Australia's aspirations to be a leader in Antarctic environmental protection. The overall objective was to provide environmental information in support of an operational infrastructure project to upgrade wastewater treatment at Davis. This information is required to ensure that the upgrade satisfies national legislation (ATEP/Waste Management Regulations), international commitments (the Madrid Protocol) and maintain the AAD's status as an international leader in environmental management. The specific objectives were to: 1. Wastewater properties: Determine the properties of discharged wastewater (contaminant levels, toxicity, microbiological hazards) as the basis for recommendations on the required level of treatment and provide further consideration of what might constitute adequate dilution and dispersal for discharge to the nearshore marine environment 2. Dispersal and dilution characteristics of marine environment: Assess the dispersing characteristics of the immediate nearshore marine environment in the vicinity of Davis Station to determine whether conditions at the existing site of effluent discharge are adequate to meet the ATEP requirement of initial dilution and rapid dispersal. 3. Environmental impacts: Describe the nature and extent of impacts to the marine environment associated with present wastewater discharge practices at Davis and determine whether wastewater discharge practices have adversely affected the local environment. 4. Evaluate treatment options: Evaluate the different levels of treatment required to mitigate and/or prevent various environmental impacts and reduce environmental risks.