Size fractionated chlorophyll a data (total and less than 20 µm) analysed using high performance liquid chromatography (HPLC). Underway samples were taken using a seawater line in the oceanographic lab on RSV Aurora Australis (approx. depth 4 m). CTD samples were taken using Niskin bottles attached to a CTD rosette. Six depths were sampled per station, based on fluorescence profiles from the CTD. Two of the two of six samples always included both near-surface (approximately 10 m) and the depth of the chlorophyll maximum where applicable. HPLC analyses were conducted according to the method of Wright et al. (2010). Column chlorophylls (µg L-1) and integrated chlorophylls (mg m-2) are shown in two separate tabs within the Excel spreadsheet.

Processed CTD instrument data - Corrected fluorescence profiles at the Southern Kerguelen Plateau, Indian Sector of the Southern Ocean. The fluorometer was calibrated through the regression of burst measurements against in situ chlorophyll a measured at the same depths and sites using high performance liquid chromatography (Wright et al. 2010). Zero chlorophyll a reference points were included in the regression and were obtained through averaging fluorometry data over 200-300 m bins. The resulting linear equation used to convert flourometry data was: chlorophyll = 0.262*fluorescence + 0.101. Column measurements (µg L-1) and integrated data (0-150 m, mg m-2) for each CTD station are provided.

Gross Primary Production Six depths were sampled per CTD station ranging from near-surface to 125 m. Sample depths were based on downward fluorescence profiles and two of six samples always included both near-surface (approximately 5-10 m) and the depth of the chlorophyll maximum where applicable. Photosynthetic rates were determined using radioactive NaH14CO3. Incubations were conducted according to the method of Westwood et al. (2011). Cells were incubated for 1 hour at 21 light intensities ranging from 0 to 1200 µmol m-2 s-1 (CT Blue filter centred on 435 nm). Carbon uptake rates were corrected for in situ chlorophyll a (chl a) concentrations (µg L-1) measured using high performance liquid chromatography (HPLC, Wright et al. 2010), and for total dissolved inorganic carbon availability, analysed according to Dickson et al. (2007). Photosynthesis-irradiance (P-I) relationships were then plotted in R and the equation of Platt et al. (1980) used to fit curves to data using robust least squares non-linear regression. Photosynthetic parameters determined included light-saturated photosynthetic rate [Pmax, mg C (mg chl a)-1 h-1], initial slope of the light-limited section of the P-I curve [α, mg C (mg chl a)-1 h-1 (µmol m-2 s-1)-1], light intensity at which carbon-uptake became maximal (calculated as Pmax/ α = Ek, µmol m-2 s-1), intercept of the P-I curve with the carbon uptake axis [c, mg C (mg chl a)-1 h-1] , and the rate of photoinhibition where applicable [β, mg C (mg chl a)-1 h-1 (µmol m-2 s-1)-1]. Gross primary production rates were modelled using R. Depth interval profiles (1 m) of chl a from the surface to 200 m were constructed through the conversion of up-cast fluorometry data measured at each CTD station. For conversions, pooled fluorometry burst data from all sites and depths was linearly regressed against in situ chl a determined using HPLC. Gross daily depth-integrated water-column production was then calculated using chl a depth profiles, photosynthetic parameters (Pmax, α , β, see above), incoming climatological PAR, vertical light attenuation (Kd), and mixed layer depth. Climatological PAR was based on spatially averaged (49 pixels, approx. 2 degrees) 8 day composite Aqua MODIS data (level 3, 2004-2017) obtained for Julian day 34. Summed incoming light intensities throughout the day equated to mean total PAR provided by Aqua MODIS. Kd for each station was calculated through robust linear regression of natural logarithm-transformed PAR data with depth. In cases where CTD stations were conducted at night, Kd was calculated from a linear relationship established between pooled chlorophyll a concentrations and Kd’s determined at CTD stations conducted during the day (Kd = -0.0421 chl a * -0.0476). Mixed layer depths were calculated as the depth where density (sigma) changed by 0.05 from a 10 m reference point. Gross primary production was calculated at 0.1 time steps throughout the day (10 points per hour) and summed.

Sampling Samples were collected on board the RSV Aurora Australis between 22 January and 17 February 2016. The cruise surveyed the region south of the Kerguelen Plateau including the Princess Elizabeth Trough and BANZARE Bank in a series of eight transects covering 8165 km. Plankton communities were collected at 45 conductivity temperature depth (CTD) stations and seven additional underway stations, with biological replicates collected at two stations (52 independent sites). Surface water was sampled from 4 plus or minus 2 m depth using the uncontaminated seawater line. Deep Chlorophyll Maximum (DCM, 10-74 m) water samples were obtained using 10 L Niskin bottles mounted on a Seabird 911+ CTD. Plankton communities were size-fractionated by sequentially filtering 10 L seawater through 25 mm 20 micron (nylon) and 5 micron filters (PVDF), and 0.45 micron Sterivex filters (PVDF). Filters were stored frozen at -80 °C. DNA extraction and high-throughput sequencing DNA was extracted from half of each filter using the MoBio PowerSoil DNA Isolation kit at the Australian Genome Research Facility (AGRF, Adelaide, Australia; http://www.agrf.org.au). The V4 region of the 18S rDNA (approximately 380 bp excluding primers) was PCR-amplified using universal eukaryotic primers from all extracts and sequenced on an Illumina MiSeq v2 (2 x 250 bp paired-end) following the Ocean Sampling Day protocol (Piredda et al. 2017). Amplicon library preparation and high-throughput sequencing were carried out at the Ramaciotti Centre for Genomics (Sydney, Australia). Sequence analysis, OTU picking and assignment followed the Biomes of Australian Soil Environments (BASE) workflow (Bissett et al. 2016). Taxonomy was assigned to OTUs based on the PR2 database using the ‘classify.seqs’ command in mothur version 1.31.2 with default settings and a bootstrap cut-off of 60%. OTUs representing any terrestrial contaminants (e.g. human) and samples with low sequencing coverage (less than 7000 reads) were removed from the dataset. The date of sea ice melt for each station was estimated from daily SSM/I-derived sea-ice spatial concentration from the National Snow and Ice Data Centre (NSIDC) at 25 x 25 km resolution. Days since melt was considered to be the number of days between the date on which sea ice concentration first fell below 15% and the date of sampling. Other environmental variables included are in situ chlorophyll a, as an indicator of biological production, and near-surface salinity (mean over the upper 10 m) as an indicator for recent sea ice melt. Both environmental measurements were taken from the associated CTD seawater samples. The surface chlorophyll a in seawater (1-2 L) collected in Niskin bottles was analysed by high performance liquid chromatography (HPLC, provided by Karen Westwood and Imojen Pearce, Australian Antarctic Division, doi:10.4225/15/5a94c701b98a8). Sampling times are given in UTC.

Midwater fish nitrogen isotope data from the Kerguelen Axis ecosystem study (AAS_4344): These data are based on samples collected as part of the Kerguelen Axis marine ecosystem study (AAS_4344), chief scientist Andrew Constable. This research was supported by the Australian government under the (i) Cooperative Research Centre Program through the Antarctic Climate and Ecosystems Cooperative Research Centre (ACE CRC), (ii) Australian Antarctic Science Program (Projects 4343, 4344, 4347 and 4366), and (iii) Australian Research Council’s Special Research Initiative for Antarctic Gateway Partnership (Project ID SR140300001). The preferred citation is: Walters et al. Food sources and trophic structure of deep sea midwater (fish) food webs in the Southern Ocean as inferred from nitrogen isotopic compositions. Midwater fish samples were collected on board the R.S.V. Aurora Australis during the austral summer of 2016 (22 January-17 February) as part of the Kerguelen Axis marine ecosystem study (AAS_4344). Samples were collected from 9 sampling stations along one transect from the Antarctic continental shelf to the BANZARE Bank over the Kerguelen Plateau. Midwater fish were sampled from the surface to 1000 m depth using an IYGPT (International Young Gadoid Pelagic Trawl) net equipped with a MIDOC (Mid-water Open Close) multiple cod-end device. Analyses focused on mesopelagic and bathypelagic fish taxa. The nitrogen isotopic composition of individual amino acids was measured in muscle tissue from each fish. As of 2022-09-30, these data were still being worked up for publication.

Mesopelagic fish gut content data from the Kerguelen Axis ecosystem study (AAS_4344): These data are based on samples collected as part of the Kerguelen Axis marine ecosystem study (AAS_4344), chief scientist Andrew Constable. This research was supported by the Australian government under the (i) Cooperative Research Centre Program through the Antarctic Climate and Ecosystems Cooperative Research Centre (ACE CRC), (ii) Australian Antarctic Science Program (Projects 4343, 4344, 4347 and 4366), and (iii) Australian Research Council’s Special Research Initiative for Antarctic Gateway Partnership (Project ID SR140300001). The preferred citation is: Riaz, J., Walters, A., Trebilco, R., Bestley, S., Lea, M-A. (2019) Stomach content analysis of mesopelagic fish from the southern Kerguelen Axis. Deep Sea Research Part II: Topical Studies in Oceanography. Samples for gut content analysis were collected on board the R.S.V Aurora Australis during the austral summer of 2016 (22 January-17 February) during the Kerguelen Axis marine ecosystem survey (AAS_4344). Analyses focused on four of the most common and widespread Southern Ocean mesopelagic fish species: three myctophids (Electrona antarctica, Gymnoscopelus braueri, Krefftichthys anderssoni), and one bathylagid (Bathylagus antarcticus). Species were sampled across a broad range of size classes to investigate the influence of predator size on predator and prey size relationships. Fish were collected from six sampling stations along the major south-to-north transect of the Kerguelen Axis. Three sampling sites were located in subpolar waters south of the Southern Boundary (SB) of the Antarctic Circumpolar Current (ACC) over the Princess Elizabeth Trough. The other three sampling sites were located north of the Southern Antarctic Circumpolar Circulation Front (SACCF) over the Banzare Bank on the southern Kerguelen Plateau.The contribution and relative importance of prey taxa to stomach contents was quantified with four traditional metrics of dietary composition (Hyslop 1980). These were calculated for each fish species separately at northern and southern sampling stations, and across species within all stations. Hyslop, E. J. (1980) Stomach contents analysis-a review of methods and their application. Journal of Fish Biology 17:411.

Mesopelagic fish bulk stable isotope data from the Kerguelen Axis ecosystem study (AAS_4344): These data are based on samples collected as part of the Kerguelen Axis marine ecosystem study (AAS_4344), chief scientist Andrew Constable. This research was supported by the Australian government under the (i) Cooperative Research Centre Program through the Antarctic Climate and Ecosystems Cooperative Research Centre (ACE CRC), (ii) Australian Antarctic Science Program (Projects 4343, 4344, 4347 and 4366), and (iii) Australian Research Council’s Special Research Initiative for Antarctic Gateway Partnership (Project ID SR140300001). The preferred citation is: Woods, B., Walters, A., Hindell, M.A., Trebilco, R. (2019) Isotopic insights into mesopelagic niche space and energy pathways on the southern Kerguelen Plateau. Deep Sea Research Part II: Topical Studies in Oceanography Samples for stable isotope analysis were collected on board the R.S.V Aurora Australis during the austral summer of 2016 (22 January – 17 February) as part of the Kerguelen Axis marine ecosystem study (AAS_4344). Samples were collected from 15 sampling stations along two transects from the Antarctic continental shelf to the BANZARE Bank over the Kerguelen Plateau and in an east to west direction across the Kerguelen Plateau. Mesopelagic fish were sampled from the surface to 1000 m depth using an IYGPT (International Young Gadoid Pelagic Trawl) net equipped with a MIDOC (Mid-water Open Close) multiple cod-end device. Analyses focused on an assemblage including genera from the family Myctophidae (Electrona, Gymnoscopelus, Krefftichthys and Protomyctophum), and the genus Bathylagus from the family Bathylagidae, as these are dominant genera in the Southern Ocean (Pusch et al., 2004; Hulley and Duhamel, 2011; Collins et al., 2012). Muscle tissue from each fish was analysed for δ15N and δ13C. Collins, M. A., Stowasser, G., Fielding, S., Shreeve, R., Xavier, J. C., Venables, H. J., . . . Van de Putte, A. (2012). Latitudinal and bathymetric patterns in the distribution and abundance of mesopelagic fish in the Scotia Sea. Deep-Sea Research Part Ii-Topical Studies in Oceanography, 59, 189-198. doi:10.1016/j.dsr2.2011.07.003 Hulley, P. A., and Duhamel, G. (2011). Aspects of lanternfish distribution in the Kerguelen Plateau region. The Kerguelen Plateau: marine ecosystems and fisheies. G. Duhamel and DC Welsford, Editors, 183-195. Pusch, C., Hulley, P. A., and Kock, K. H. (2004). Community structure and feeding ecology of mesopelagic fishes in the slope waters of King George Island (South Shetland Islands, Antarctica). Deep-Sea Research Part I-Oceanographic Research Papers, 51(11), 1685-1708. doi:10.1016/j.dsr.2004.06.008

During the K-Axis marine voyage from mid Jan-late Feb 2016, a diverse range of sampling techniques were employed to collect specimens and data. Each sampling event was recorded by scientists and technical support staff in a logbook that was kept in the operations room on board the Aurora Australis. This is a direct digital copy/transcription of the paper logbook. event_number: A unique event identifier in the log, in the order that the events were written down (usually but not always chronologically) event_type: The code defined and used by each research project to identify the types of equipment deployed or samples collected for an event. event_type_prefix: A non-mandatory prefix field used by some research projects to identify the type of an event event_type_number: A sequential number or alphanumeric-number combination defined and used by each research project to identify unique equipment deployment or sample collection events station_number: A universal (voyage-wide) station number used across all projects to identify a nominal lat/lon position defined during voyage planning leg: A nominally straight-line section of the voyage track defined during voyage planning. The voyage track was planned as a series of roughly N-S and E-W transects that intersected in some locations. Legs start at a station and continue through more stations to a vertex-station which is the start of the next leg. Legs are numbered consecutively. waypoint: A GPS waypoint used by Aurora Australis crew, AAD science technical support and researchers to identify target lat/lon positions in the voyage. Some waypoints correspond with station numbers. start_date_utc: The start date of the event in UTC start_time_utc: The start time of the event in UTC start_lat_deg: The latitude (whole degrees) of the vessel at the beginning of the event start_lat_min: The latitude (minutes) of the vessel at the beginning of the event start_lat_dec_deg: The latitude (decimal degrees) of the vessel at the beginning of the event start_lon_deg: The longitude (whole degrees) of the vessel at the beginning of the event start_lon_min: The longitude (minutes) of the vessel at the beginning of the event start_lon_dec_deg: The longitude (decimal degrees) of the vessel at the beginning of the event end_date_utc: The end date of the event in UTC end_time_utc: The end time of the event in UTC end_lat_deg: The latitude (whole degrees) of the vessel at the end of the event end_lat_min: The latitude (minutes) of the vessel at the end of the event end_lat_dec_deg: The latitude (decimal degrees) of the vessel at the end of the event end_lon_deg: The longitude (whole degrees) of the vessel at the end of the event end_lon_min: The longitude (minutes) of the vessel at the end of the event end_lon_dec_deg: The longitude (decimal degrees) of the vessel at the end of the event remarks: Comments/remarks written by researchers when completing the paper log transcribe_comments: Comments/remarks made by the transcriber when the log was digitised

During the K-Axis marine voyage from mid Jan-late Feb 2016, a diverse range of sampling techniques were employed to collect specimens and data. Each sampling event was recorded by scientists and technical support staff in a logbook that was kept in the operations room on board the Aurora Australis. This is a PDF of the scanned original document, compiled on paper during the voyage. event_number: A unique event identifier in the log, in the order that the events were written down (usually but not always chronologically) event_type: The code defined and used by each research project to identify the types of equipment deployed or samples collected for an event. event_type_prefix: A non-mandatory prefix field used by some research projects to identify the type of an event event_type_number: A sequential number or alphanumeric-number combination defined and used by each research project to identify unique equipment deployment or sample collection events station_number: A universal (voyage-wide) station number used across all projects to identify a nominal lat/lon position defined during voyage planning leg: A nominally straight-line section of the voyage track defined during voyage planning. The voyage track was planned as a series of roughly N-S and E-W transects that intersected in some locations. Legs start at a station and continue through more stations to a vertex-station which is the start of the next leg. Legs are numbered consecutively. waypoint: A GPS waypoint used by Aurora Australis crew, AAD science technical support and researchers to identify target lat/lon positions in the voyage. Some waypoints correspond with station numbers. start_date_utc: The start date of the event in UTC start_time_utc: The start time of the event in UTC start_lat_deg: The latitude (whole degrees) of the vessel at the beginning of the event start_lat_min: The latitude (minutes) of the vessel at the beginning of the event start_lat_dec_deg: The latitude (decimal degrees) of the vessel at the beginning of the event start_lon_deg: The longitude (whole degrees) of the vessel at the beginning of the event start_lon_min: The longitude (minutes) of the vessel at the beginning of the event start_lon_dec_deg: The longitude (decimal degrees) of the vessel at the beginning of the event end_date_utc: The end date of the event in UTC end_time_utc: The end time of the event in UTC end_lat_deg: The latitude (whole degrees) of the vessel at the end of the event end_lat_min: The latitude (minutes) of the vessel at the end of the event end_lat_dec_deg: The latitude (decimal degrees) of the vessel at the end of the event end_lon_deg: The longitude (whole degrees) of the vessel at the end of the event end_lon_min: The longitude (minutes) of the vessel at the end of the event end_lon_dec_deg: The longitude (decimal degrees) of the vessel at the end of the event remarks: Comments/remarks written by researchers when completing the paper log

During the K-Axis marine voyage from mid Jan-late Feb 2016, a diverse range of sampling techniques were employed to collect specimens and data. Each sampling event was recorded by scientists and technical support staff in a logbook that was kept in the operations room on board the Aurora Australis. This is a direct digital transcription of the paper logbook with interpolated lat/lon from underway data to supplement start times as recorded in the log. The method used to obtain the supplementary position is described in the associated eventlog_matchup.html file. event_number: A unique event identifier in the log, in the order that the events were written down (usually but not always chronologically) event_type: The code defined and used by each research project to identify the types of equipment deployed or samples collected for an event. event_type_prefix: A non-mandatory prefix field used by some research projects to identify the type of an event event_type_number: A sequential number or alphanumeric-number combination defined and used by each research project to identify unique equipment deployment or sample collection events station_number: A universal (voyage-wide) station number used across all projects to identify a nominal lat/lon position defined during voyage planning leg: A nominally straight-line section of the voyage track defined during voyage planning. The voyage track was planned as a series of roughly N-S and E-W transects that intersected in some locations. Legs start at a station and continue through more stations to a vertex-station which is the start of the next leg. Legs are numbered consecutively. waypoint: A GPS waypoint used by Aurora Australis crew, AAD science technical support and researchers to identify target lat/lon positions in the voyage. Some waypoints correspond with station numbers. start_date_utc: The start date of the event in UTC start_time_utc: The start time of the event in UTC start_lat_deg: The latitude (whole degrees) of the vessel at the beginning of the event start_lat_min: The latitude (minutes) of the vessel at the beginning of the event start_lat_dec_deg: The latitude (decimal degrees) of the vessel at the beginning of the event start_lon_deg: The longitude (whole degrees) of the vessel at the beginning of the event start_lon_min: The longitude (minutes) of the vessel at the beginning of the event start_lon_dec_deg: The longitude (decimal degrees) of the vessel at the beginning of the event end_date_utc: The end date of the event in UTC end_time_utc: The end time of the event in UTC end_lat_deg: The latitude (whole degrees) of the vessel at the end of the event end_lat_min: The latitude (minutes) of the vessel at the end of the event end_lat_dec_deg: The latitude (decimal degrees) of the vessel at the end of the event end_lon_deg: The longitude (whole degrees) of the vessel at the end of the event end_lon_min: The longitude (minutes) of the vessel at the end of the event end_lon_dec_deg: The longitude (decimal degrees) of the vessel at the end of the event remarks: Comments/remarks written by researchers when completing the paper log transcribe_comments: Comments/remarks made by the transcriber when the log was digitised utc: The start date and time of the event in UTC start_lon_dec_deg_interp: The latitude (decimal degrees) of the vessel at the beginning of the event interpolated from the vessel underway data start_lat_dec_deg_interp: The longitude (decimal degrees) of the vessel at the beginning of the event interpolated from the vessel underway data