From the Surface Ocean to the Seafloor: Linking Modern and Paleo-Genetics at the Sabrina Coast, East Antarctica (IN2017_V01)

This project was supported through funding from the Australian Government’s Australian Antarctic Science Grant Programs (AAS 4333 and AAS 4419) and the Australian Research Council’s Discovery Projects funding scheme (DP170100557). We thank the team at the Australian Centre for Ancient DNA (ACAD), The Univer- sity of Adelaide, especially Corinne Preuss and Steve Johnson for their techni- cal help during the sedaDNA laboratory work. LA was funded by an Australian Research Council Discovery Early Career Researcher Award (ARC DECRA DE210100929). The modern molecular data analysis was supported by an ARC Grant awarded to IP (FL140100021). KAL is supported by an Australian Research Training Program (RTP) scholarship. We acknowledge the use of imagery from the NASA Worldview application (https://worldview.earthdata. nasa.gov), part of the NASA Earth Observing System Data and Information System (EOSDIS). Open access publish- ing facilitated by University of Tasmania, as part of the Wiley - University of Tasmania agreement via the Council of Australian University Librarians.With ongoing climate change, research into the biological changes occurring in particularly vulnerable ecosystems, such as Antarctica, is critical. The Totten Glacier region, Sabrina Coast, is currently experiencing some of the highest rates of thinning across all East Antarctica. An assessment of the microscopic organisms supporting the ecosystem of the marginal sea-ice zone over the continental rise is important, yet there is a lack of knowledge about the diversity and distribution of these organisms throughout the water column, and their occurrence and/or preservation in the underlying sediments. Here, we provide a taxonomic overview of the modern and ancient marine bacterial and eukaryotic communities of the Totten Glacier region, using a combination of 16S and 18S rRNA amplicon sequencing (modern DNA) and shotgun metagenomics (sedimentary ancient DNA, sedaDNA). Our data show considerable differences between eukaryote and bacterial signals in the water column versus the sediments. Proteobacteria and diatoms dominate the bacterial and eukaryote composition in the upper water column, while diatoms, dinoflagellates, and haptophytes notably decrease in relative abundance with increasing water depth. Little diatom sedaDNA is preserved in the sediments, which are instead dominated by Proteobacteria and Retaria. We compare the diatom microfossil and sedaDNA record and link the weak preservation of diatom sedaDNA to DNA degradation while sinking through the water column to the seafloor. This study provides the first assessment of DNA transfer from ocean waters to sediments and an overview of the microscopic communities occurring in the climatically important Totten Glacier region.Australian Government's Australian Antarctic Science Grant Programs AAS 4419, DP170100557Australian Research Council FL140100021Australian Research Training Program (RTP) scholarshipAAS 4333ARC DECRA DE21010092

Assessment of welfare indicators in dairy farms offering pasture at differing levels.

In terms of animal welfare, farming systems of dairy cows are perceived positively by consumers when compared to pigs or poultry. A main reason is that the majority of consumers associate dairy farming with pasture, which in turn they relate with benefits for animal health and welfare. However, holistic scientific assessments of the effects of pasturing on animal welfare are rare. Hence, it was the aim to study the animal welfare level in 61 German loose housing dairy farms by using the measures of the Welfare Quality® protocol for dairy cattle (WQP). Data were collected twice per farm at the end of the pasture season (July to October) and approximately 6 months later at the end of the barn season (December to April). Farms were classified based on the duration cows had access to pasture per day during the pasture season: group 1 (G1)>10 h; group 2 (G2) 6 to 10 h; group 3 (G3)<6 h and group 4 (G4) without pasture access. The average herd size was 129 Holstein-Friesian or Red-Holstein cows (range 58 to 527). In addition to WQP data, performance data were gathered from routine herd data recordings. The indicators were aggregated to criteria applying the scoring system of the WQP. G4 received lower scores at the first than at the second visit for the criterion absence of hunger, while there were no differences between visits in the other groups (P=0.58 – group×farm visit effect). All pasturing groups were scored better at the end of the pasture season than G4 for the criterion comfort around resting (P<0.01). Compared with G1 for both farm visits and G2 for the end of the barn season, G4 reached inferior scores for the criterion absence of injuries, including indicators such as hairless patches, lesions, and swellings and lameness. At both assessments G2 was scored higher than the other groups for the criterion absence of diseases (P=0.04). In conclusion, pasture access had positive effects only on selected welfare indicators, however, these effects were not maintained throughout the barn season

Ancient marine sediment DNA reveals diatom transition in Antarctica

Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency. Sedimentary ancient DNA (sedaDNA) analysis can provide such insights into past ecosystem-wide changes. Here we present authenticated (through extensive contamination control and sedaDNA damage analysis) metagenomic marine eukaryote sedaDNA from the Scotia Sea region acquired during IODP Expedition 382. We also provide a marine eukaryote sedaDNA record of ~1 Mio. years and diatom and chlorophyte sedaDNA dating back to ~540 ka (using taxonomic marker genes SSU, LSU, psbO). We find evidence of warm phases being associated with high relative diatom abundance, and a marked transition from diatoms comprising <10% of all eukaryotes prior to ~14.5 ka, to ~50% after this time, i.e., following Meltwater Pulse 1A, alongside a composition change from sea-ice to open-ocean species. Our study demonstrates that sedaDNA tools can be expanded to hundreds of thousands of years, opening the pathway to the study of ecosystem-wide marine shifts and paleo-productivity phases throughout multiple glacial-interglacial cycles

The Community Ecology of Herbivore Regulation in an Agroecosystem: Lessons from Complex Systems

AbstractWhether an ecological community is controlled from above or below remains a popular framework that continues generating interesting research questions and takes on especially important meaning in agroecosystems. We describe the regulation from above of three coffee herbivores, a leaf herbivore (the green coffee scale, Coccus viridis), a seed predator (the coffee berry borer, Hypothenemus hampei), and a plant pathogen (the coffee rust disease, caused by Hemelia vastatrix) by various natural enemies, emphasizing the remarkable complexity involved. We emphasize the intersection of this classical question of ecology with the burgeoning field of complex systems, including references to chaos, critical transitions, hysteresis, basin or boundary collision, and spatial self-organization, all aimed at the applied question of pest control in the coffee agroecosystem

Antiphased dust deposition and productivity in the Antarctic Zone over 1.5 million years

The Southern Ocean paleoceanography provides key insights into how iron fertilization and oceanic productivity developed through Pleistocene ice-ages and their role in influencing the carbon cycle. We report a high-resolution record of dust deposition and ocean productivity for the Antarctic Zone, close to the main dust source, Patagonia. Our deep-ocean records cover the last 1.5 Ma, thus doubling that from Antarctic ice-cores. We find a 5 to 15-fold increase in dust deposition during glacials and a 2 to 5-fold increase in biogenic silica deposition, reflecting higher ocean productivity during interglacials. This antiphasing persisted throughout the last 25 glacial cycles. Dust deposition became more pronounced across the Mid-Pleistocene Transition (MPT) in the Southern Hemisphere, with an abrupt shift suggesting more severe glaciations since ~0.9 Ma. Productivity was intermediate pre-MPT, lowest during the MPT and highest since 0.4 Ma. Generally, glacials experienced extended sea-ice cover, reduced bottom-water export and Weddell Gyre dynamics, which helped lower atmospheric CO2 levels

Interactions of the Totten Glacier with the Southern Ocean through multiple glacial cycles (IN2017-V01): Post-survey report

The authors wish to thank the CSIRO Marine National Facility (MNF) for its support in the form of sea time on RV Investigator, support personnel, scientific equipment and data management. All data and samples acquired on the voyage are made publicly available in accordance with MNF Policy. All raw and processed data acquired by MNF equipment on MNF voyages will be archived by MNF data support staff in the enduring CSIRO Data Access Portal, https://data.csiro.au. Metadata records will be made publicly available at http://www.marlin.csiro.au. Processed data and data products will be made publicly available through Data Trawler http://www.cmar.csiro.au/data/trawler/index.cfm, the MNF web data access tool http://www.cmar.csiro.au/data/underway/, and/or from national or world data centres most suitable for the dissemination of particular data types.Other Australian Program Support Smaller projects have attracted funding to support research activities post-cruise these include the following: 1. Australian and New Zealand IODP Committee (ANZIC) Special Analytical Support Grant. Project Title: Using ancient phytoplankton communities and genes to illuminate future ocean responses. Researchers involved: L. Armand, L. Armbrecht, M. Ostrowski, & S. George. 2. Australian Antarctic Division Australian Antarctic Science Grant (#4320). Project Title: Characterising East Antarctic seabed habitats. Researchers involved: Post, A.L., & Smith, J. 3. Australian Antarctic Division Australian Antarctic Science Grant (#4419). Project Title: Response of the Totten Glacier to past climate warming. Researchers involved: Noble, T., Armand, L., Chase, Z., & Halpin, J.The Sabrina Sea Floor Survey was a major marine geoscience expedition to the Antarctic margin which took place between 14 January and 7 March 2017. It sailed on the Australian Marine National Facility vessel RV Investigator. This document describes survey activities, data collected on the ship and important metadata. Some preliminary results are included and the location of samples and data sets reported for future use. The report also provides information on data ownership and acknowledgement for future use and publication. It is intended as an aid to future research and use of results and has not been rigorously edited and peer-reviewed.Australian Research Council (DP170100557), Australian Antarctic Science Grant Program (AAS #4333), Italian Antarctic program support PNRA TYTAN Project (PdR 14_00119), Spanish Ministry of Economy and Competitivity (MINECO) (CTM2015-60451-C2-1-P & CTM2015-60451-C2-2-P), United States National Science Foundation's Polar Program - Antarctic Integrated System Science. #1143834, 1143836, 1143837, 1143843, 1313826

A database of marine phytoplankton abundance, biomass and species composition in Australian waters

There have been many individual phytoplankton datasets collected across Australia since the mid 1900s, but most are unavailable to the research community. We have searched archives, contacted researchers, and scanned the primary and grey literature to collate 3,621,847 records of marine phytoplankton species from Australian waters from 1844 to the present. Many of these are small datasets collected for local questions, but combined they provide over 170 years of data on phytoplankton communities in Australian waters. Units and taxonomy have been standardised, obviously erroneous data removed, and all metadata included. We have lodged this dataset with the Australian Ocean Data Network (http://portal.aodn.org.au/) allowing public access. The Australian Phytoplankton Database will be invaluable for global change studies, as it allows analysis of ecological indicators of climate change and eutrophication (e.g., changes in distribution; diatom:dinoflagellate ratios). In addition, the standardised conversion of abundance records to biomass provides modellers with quantifiable data to initialise and validate ecosystem models of lower marine trophic levels

Miocene to present oceanographic variability in the Scotia Sea and Antarctic Ice Sheet dynamics: Insight from revised seismic-stratigraphy following IODP Expedition 382

Scotia Sea and the Drake Passage is key towards understanding the development of modern oceanic circulation patterns and their implications for ice sheet growth and decay. The sedimentary record of the southern Scotia Sea basins documents the regional tectonic, oceanographic and climatic evolution since the Eocene. However, a lack of accurate age estimations has prevented the calibration of the reconstructed history. The upper sedimentary record of the Scotia Sea was scientifically drilled for the first time in 2019 during International Ocean Discovery Program (IODP) Expedition 382, recovering sediments down to ∼643 and 676 m below sea floor in the Dove and Pirie basins respectively. Here, we report newly acquired high resolution physical properties data and the first accurate age constraints for the seismic sequences of the upper sedimentary record of the Scotia Sea to the late Miocene. The drilled record contains four basin-wide reflectors – Reflector-c, -b, -a and -a' previously estimated to be ∼12.6 Ma, ∼6.4 Ma, ∼3.8 Ma and ∼2.6 Ma, respectively. By extrapolating our new Scotia Sea age model to previous morpho-structural and seismic-stratigraphic analyses of the wider region we found, however, that the four discontinuities drilled are much younger than previously thought. Reflector-c actually formed before 8.4 Ma, Reflector-b at ∼4.5/3.7 Ma, Reflector-a at ∼1.7 Ma, and Reflector-a' at ∼0.4 Ma. Our updated age model of these discontinuities has major implications for their correlation with regional tectonic, oceanographic and cryospheric events. According to our results, the outflow of Antarctic Bottom Water to northern latitudes controlled the Antarctic Circumpolar Current flow from late Miocene. Subsequent variability of the Antarctic ice sheets has influenced the oceanic circulation pattern linked to major global climatic changes during early Pliocene, Mid-Pleistocene and the Marine Isotope Stage 11

Ancient marine sediment DNA reveals diatom transition in Antarctica

Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency. Sedimentary ancient DNA (sedaDNA) analysis can provide such insights into past ecosystem-wide changes. Here we present authenticated (through extensive contamination control and sedaDNA damage analysis) metagenomic marine eukaryote sedaDNA from the Scotia Sea region acquired during IODP Expedition 382. We also provide a marine eukaryote sedaDNA record of ~1 Mio. years and diatom and chlorophyte sedaDNA dating back to ~540 ka (using taxonomic marker genes SSU, LSU, psbO). We find evidence of warm phases being associated with high relative diatom abundance, and a marked transition from diatoms comprising <10% of all eukaryotes prior to ~14.5 ka, to ~50% after this time, i.e., following Meltwater Pulse 1A, alongside a composition change from sea-ice to open-ocean species. Our study demonstrates that sedaDNA tools can be expanded to hundreds of thousands of years, opening the pathway to the study of ecosystem-wide marine shifts and paleo-productivity phases throughout multiple glacial-interglacial cycles

Antiphased dust deposition and productivity in the Antarctic Zone over 1.5 million years

The Southern Ocean paleoceanography provides key insights into how iron fertilization and oceanic productivity developed through Pleistocene ice-ages and their role in influencing the carbon cycle. We report a high-resolution record of dust deposition and ocean productivity for the Antarctic Zone, close to the main dust source, Patagonia. Our deep-ocean records cover the last 1.5 Ma, thus doubling that from Antarctic ice-cores. We find a 5 to 15-fold increase in dust deposition during glacials and a 2 to 5-fold increase in biogenic silica deposition, reflecting higher ocean productivity during interglacials. This antiphasing persisted throughout the last 25 glacial cycles. Dust deposition became more pronounced across the Mid-Pleistocene Transition (MPT) in the Southern Hemisphere, with an abrupt shift suggesting more severe glaciations since ~0.9 Ma. Productivity was intermediate pre-MPT, lowest during the MPT and highest since 0.4 Ma. Generally, glacials experienced extended sea-ice cover, reduced bottom-water export and Weddell Gyre dynamics, which helped lower atmospheric CO2 levels