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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, DP170100557, Australian Research Council FL140100021, Australian Research Training Program (RTP) scholarship, AAS 4333, ARC DECRA DE210100929

Current glacier melt rates in West Antarctica substantially exceed those around the East Antarctic margin. The exception is Wilkes Land, where for example Totten Glacier underwent significant retreat between 2000 and 2012, underlining its sensitivity to climate change. This process is strongly influenced by ocean dynamics, which in turn changes in accordance with the evolution of the ice caps. Here, we present new oceanographic data (temperature, salinity, and dissolved oxygen) collected during austral summer 2017 offshore the Sabrina Coast (East Antarctica) from the continental shelf break to ca 3000 m depth. This area is characterized by very few oceanographic in situ observations. The main water masses of the study area, identified by analysing thermohaline properties, are the Antarctic Surface Water with potential temperature θ>-1.5 ∘C and salinity S (σθ kg m−3), the Winter Water with -1.92<θ<-1.75 ∘C and 34.00 ∘C and S>34.5 (σθ>27.7 kg m−3), and Antarctic Bottom Water with -0.50<θ<0 ∘C and 34.6328.30 kg m−3). The latter is a mixture of dense waters from the Ross Sea and Adélie Land continental shelves. Such waters are influenced by the mixing processes they undergo as they move westward along the Antarctic margin, also interacting with the warmer Circumpolar Deep Water. The spatial distribution of water masses offshore the Sabrina Coast also appears to be strongly linked with the complex morpho-bathymetry of the slope and rise area, supporting the hypothesis that downslope processes contribute to shaping the architecture of the distal portion of the continental margin. Oceanographic data presented here can be downloaded from https://doi.org/10.25919/yyex-t381 (CSIRO; Van Graas, 2021).

Four combinations of sedaDNA extraction treatments using marine sediments collected at a water depth of 104 m off Maria Island in Tasmania are compared. These methods contrast frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution. All four methods worked to varying degrees; see paper for recommended shotgun library preparation

Early Pleistocene Marine Isotope Stage (MIS)-31 (1.081–1.062 Ma) is a unique interval of extreme global warming, including evidence of a West Antarctic Ice Sheet (WAIS) collapse. Here we present a new 1,000-year resolution, spanning 1.110–1.030 Ma, diatom-based reconstruction of primary productivity, relative sea surface temperature changes, sea-ice proximity/open ocean conditions and diatom species absolute abundances during MIS-31, from the Scotia Sea (59°S) using deep-sea sediments collected during International Ocean Discovery Program (IODP) Expedition 382. The lower Jaramillo magnetic reversal (base of C1r.1n, 1.071 Ma) provides a robust and independent time-stratigraphic marker to correlate records from other drill cores in the Antarctic Zone of the Southern Ocean (AZSO). An increase in open ocean species Fragilariopsis kerguelensis in early MIS-31 at 53°S (Ocean Drilling Program Site 1,094) correlates with increased obliquity forcing, whereas at 59°S (IODP Site U1537; this study) three progressively increasing, successive peaks in the relative abundance of F. kerguelensis correlate with Southern Hemisphere-phased precession pacing. These observations reveal a complex pattern of ocean temperature change and sustained sea surface temperature increase lasting longer than a precession cycle within the Atlantic sector of the AZSO. Timing of an inferred WAIS collapse is consistent with delayed warmth (possibly driven by sea-ice dynamics) in the southern AZSO, supporting models that indicate WAIS sensitivity to local sub-ice shelf melting. Anthropogenically enhanced impingement of relatively warm water beneath the ice shelves today highlights the importance of understanding dynamic responses of the WAIS during MIS-31, a warmer than Holocene interglacial., SI

Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size-selection of low molecular-weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead-beating, DNA binding in silica-solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post-library LMW size-selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data-processing protocol should improve quantitative paleo-monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments.

In-depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo-genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human-induced global changes.

Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121–130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.

International Ocean Discovery Program (IODP) Expedition 382, Iceberg Alley and Subantarctic Ice and Ocean Dynamics, investigated the long-term climate history of Antarctica, seeking to understand how polar ice sheets responded to changes in insolation and atmospheric CO2 in the past and how ice sheet evolution influenced global sea level and vice versa. Five sites (U1534–U1538) were drilled east of the Drake Passage: two sites at 53.2°S at the northern edge of the Scotia Sea and three sites at 57.4°–59.4°S in the southern Scotia Sea. We recovered continuously deposited late Neogene sediments to reconstruct the past history and variability in Antarctic Ice Sheet (AIS) mass loss and associated changes in oceanic and atmospheric circulation. The sites from the southern Scotia Sea (Sites U1536–U1538) will be used to study the Neogene flux of icebergs through “Iceberg Alley,” the main pathway along which icebergs calved from the margin of the AIS travel as they move equatorward into the warmer waters of the Antarctic Circumpolar Current (ACC). In particular, sediments from this area will allow us to assess the magnitude of iceberg flux during key times of AIS evolution, including the middle Miocene glacial intensification of the East Antarctic Ice Sheet, the mid-Pliocene warm period, the late Pliocene glacial expansion of the West Antarctic Ice Sheet, the mid-Pleistocene transition (MPT), and the “warm interglacials” and glacial terminations of the last 800 ky. We will use the geochemical provenance of iceberg-rafted detritus and other glacially eroded material to determine regional sources of AIS mass loss. We will also address interhemispheric phasing of ice sheet growth and decay, study the distribution and history of land-based versus marine-based ice sheets around the continent over time, and explore the links between AIS variability and global sea level. By comparing north–south variations across the Scotia Sea between the Pirie Basin (Site U1538) and the Dove Basin (Sites U1536 and U1537), Expedition 382 will also deliver critical information on how climate changes in the Southern Ocean affect ocean circulation through the Drake Passage, meridional overturning in the region, water mass production, ocean–atmosphere CO2 transfer by wind-induced upwelling, sea ice variability, bottom water outflow from the Weddell Sea, Antarctic weathering inputs, and changes in oceanic and atmospheric fronts in the vicinity of the ACC. Comparing changes in dust proxy records between the Scotia Sea and Antarctic ice cores will also provide a detailed reconstruction of changes in the Southern Hemisphere westerlies on millennial and orbital timescales for the last 800 ky. Extending the ocean dust record beyond the last 800 ky will help to evaluate dust-climate couplings since the Pliocene, the potential role of dust in iron fertilization and atmospheric CO2 drawdown during glacials, and whether dust input to Antarctica played a role in the MPT. The principal scientific objective of Subantarctic Front Sites U1534 and U1535 at the northern limit of the Scotia Sea is to reconstruct and understand how intermediate water formation in the southwest Atlantic responds to changes in connectivity between the Atlantic and Pacific basins, the “cold water route.” The Subantarctic Front contourite drift, deposited between 400 and 2000 m water depth on the northern flank of an east–west trending trough off the Chilean continental shelf, is ideally situated to monitor millennial- to orbital-scale variability in the export of Antarctic Intermediate Water beneath the Subantarctic Front. During Expedition 382, we recovered continuously deposited sediments from this drift spanning the late Pleistocene (from ~0.78 Ma to recent) and from the late Pliocene (~3.1–2.6 Ma). These sites are expected to yield a wide array of paleoceanographic records that can be used to interpret past changes in the density structure of the Atlantic sector of the Southern Ocean, track migrations of the Subantarctic Front, and give insights into the role and evolution of the cold water route over significant climate episodes, including the most recent warm interglacials of the late Pleistocene and the intensification of Northern Hemisphere glaciation.

Harmful algal blooms (HABs) have significantly impacted the seafood industry along the Tasmanian east coast over the past three decades, and are expected to change in frequency and magnitude due to climate change induced changing oceanographic conditions. To investigate the long-term history of regional HABs, a combination of palynological and sedimentary ancient DNA (sedaDNA) analyses was applied to marine sediment cores from inshore (up to 145 years old) and offshore (up to ~9,000 years) sites at Maria Island, southeast Tasmania. Analyses focused Paralytic Shellfish Toxin (PST) producing dinoflagellates Alexandrium catenella and Gymnodinium catenatum, and the red-tide dinoflagellate Noctiluca scintillans, which were specifically targeted using a hybridization capture sedaDNA technique. Identification of primulin-stained A. catenella cysts throughout the inshore sediment core, together with sedaDNA evidence of a bloom-phase of Alexandrium ~15 years ago, indicates recent stimulation of a cryptic endemic population. Morphologically similar but unstained Alexandrium cysts were observed throughout the offshore core, with sedaDNA confirming the presence of A. catenella from ~8,300 years ago to present. Gymnodinium catenatum cysts were detected only in inshore surface sediments from 30 years ago to present, supporting previous evidence of a 1970s introduction via shipping ballast water. sedaDNA confirmed the presence of G. catenatum-related sequences in the inshore and offshore cores, however, unambiguous species identification could not be achieved due to limited reference sequence coverage of Gymnodinium. Our hybridization capture sedaDNA data also confirmed the historically recent dispersal of the non-fossilizing dinoflagellate Noctiluca scintillans, detected inshore from ~30 years ago, matching first observations of this species in Tasmanian waters in 1994. At the offshore site, N. scintillans sedaDNA was detected only in surface sediments, confirming a recent climate-driven range expansion this species. This study provides new insights into the distribution and abundance of three HAB species in the Tasmanian region, including clues to past bloom phases. Further research into paleo-environmental conditions and paleo-community structure are required to identify the factors driving bloom phases through time and predict plankton community responses under different future climate scenarios.HighlightsDinocyst and sedaDNA analyses were applied to marine sediments off TasmaniaAlexandrium catenella has been endemic to Australia for at least ~9,000 yearsRecent A. catenella blooms are likely induced by climate and oceanographic changeGymnodinium catenatum cysts in recent (~30y) sediments confirm a 1970s introductionNoctiluca scintillans sedaDNAin recent (~30y) sediments matches a 1994 introduction

International Ocean Discovery Program (IODP) Expedition 382 in the Scotia Sea’s Iceberg Alley recovered among the most continuous and highest resolution stratigraphic records in the Southern Ocean near Antarctica spanning the last 3.3 Myr. Sites drilled in Dove Basin (U1536/U1537) have well-resolved magnetostratigraphy and a strong imprint of orbital forcing in their lithostratigraphy. All magnetic reversals of the last 3.3 Myr are identified, providing a robust age model independent of orbital tuning. During the Pleistocene, alternation of terrigenous versus diatomaceous facies shows power in the eccentricity and obliquity frequencies comparable to the amplitude modulation of benthic δ18O records. This suggests that variations in Dove Basin lithostratigraphy during the Pleistocene reflect a similar history as globally integrated ice volume at these frequencies. However, power in the precession frequencies over the entire ∼3.3 Myr record does not match the amplitude modulation of benthic δ18O records, suggesting Dove Basin contains a unique record at these frequencies. Comparing the position of magnetic reversals relative to local facies changes in Dove Basin and the same magnetic reversals relative to benthic δ18O at North Atlantic IODP Site U1308, we demonstrate Dove Basin facies change at different times than benthic δ18O during intervals between ∼3 and 1 Ma. These differences are consistent with precession phase shifts and suggest climate signals with a Southern Hemisphere summer insolation phase were recorded around Antarctica. If Dove Basin lithology reflects local Antarctic ice volume changes, these signals could represent ice sheet precession-paced variations not captured in benthic δ18O during the 41-kyr world.

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture ‘baits’ technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, ‘Planktonbaits1’; and harmful algal bloom taxa, ‘HABbaits1’), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool ‘HOPS’ to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, “% eukaryote sedaDNA damage”, that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.

Highlights • Core-log-seismic correlation allows to assign ages to the Scotia Sea seismic record. • Major implications are derived on the relation between regional and global events. • The main stratigraphic events are much younger than previously proposed. • Three major phases for the regional oceanography are observed from late Miocene. • These phases appear to be closely linked to the Antarctic Ice Sheet dynamics. 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.

Sedimentary ancient DNA (sedaDNA) offers a novel approach to investigating past marine ecosystems—from the smallest bacteria to phytoplankton and their predators—over geological timescales. Knowledge about such paleo-food webs can provide broad-scale biological context to paleoceanographic and environmental reconstructions. However, the field of marine sedaDNA research is still in its infancy; community reconstructions are complicated by the minuscule amounts of ancient DNA preserved in the sediments. Consequently, the identification of most prokaryotes and eukaryotes in sedaDNA is difficult, and sedaDNA sampling, extraction, and analysis require optimized procedures and rigorous contamination control to ensure that the sedaDNA signal is authentic and not overridden by modern environmental DNA. This article describes some of the latest developments in marine sedaDNA research, including the use of metagenomics to study past marine food webs, and new experimental and computational techniques to maximize taxonomic resolution, particularly that of eukaryotes. An example of bioinformatic techniques designed to increase taxonomic insight is presented, demonstrating the breadth of paleogenetic signals that could be extracted from marine sediments. With ongoing improvements in genetic reference databases, sedaDNA extraction techniques, species-specific enrichment approaches, and computational tools, marine sedaDNA will continue to improve our understanding of how marine ecosystems evolved in concert with changing environmental conditions.

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)

To investigate whether farm animal welfare comes at the cost of dairy farm performance, and the role that pasture-access thereby plays, we analyse a rich sample of 45 dairy farms in Germany with a scientific measure of farm animal welfare. Based on directional efficiency measure that acknowledges sequential preferences such that farm animal welfare becomes relevant after technical efficiency, we cannot find a trade-off between farm animal welfare and technical milk efficiency. Pasture-based production systems can be at least as efficient or even more efficient compared to confinement systems, despite lower milk yields. Neglecting sequential preferences would bias efficiency in provision of farm animal welfare by pasture-systems. Farms from all types of dairy systems determine the efficient frontier, where efficiency increases with herd size, and is linked with higher profits. We conclude that pasture-access may help but does not guarantee higher levels of animal welfare. These results question governmental support for pasture access regarding the provision of farm animal welfare.

The Earth is currently experiencing climatic changes that will result in similar environmental conditions to those experienced during the mid-Pliocene (5.3–3.6 million years ago [Ma]), such as similar atmospheric CO2 concentrations, elevated sea surface temperature, and higher sea-levels due to polar ice melt. Studying the temporal distribution of Antarctic diatoms and silicoflagellates from this epoch provides insights into environmental conditions and sea-ice configurations during that time, and remains the only way to realistically estimate future phytoplankton community responses and Southern Ocean sea-ice extent during large-scale transient changes of similar magnitude to that anticipated by anthropogenic causes. In this study, we identified and quantified diatoms and silicoflagellates in a sediment core section obtained from the Antarctic Wilkes Land margin (IODP Expedition 318, Hole U1361A), spanning four glacial and interglacial cycles around the Gauss/Gilbert geochron boundary (3.6 Ma) between about 3.69 and 3.56 Ma. Two major abundance peaks (around 79.66 and 76.86 mbsf; representing time intervals around 3.65 Ma and 3.58 Ma, respectively) were identified. Both peaks temporally match previously determined high productivity warm intervals (interglacials). Diatom and silicoflagellate assemblages in these two interglacial periods differed: the abundance peak in the older sediments is dominated by the pennate diatoms Fragilariopsis barronii, Rouxia naviculoides and Rouxia antarctica; indicative of seasonal, meltwater associated stratification. The abundance peak in the younger sediments is composed principally of Chaetoceros resting spores, suggesting higher productivity, strong stratification and prolonged ice-free, open water conditions. Analysing highly abundant diatoms and environmental indicator species from this IODP Site in relation to the previously determined palaeo-productivity proxy Ba/Al allowed us to refine the age model. Our study provides orbital-scale insights into the variability of Antarctic diatom and silicoflagellate assemblages during the mid-Pliocene, thereby offering a reference for future predictions of extant diatom responses to ongoing climate change.

Tintinnid ciliates are an important link in marine food webs as they feed on phytoplankton and bacteria while providing nutrients to higher trophic levels. Tintinnids are known to agglutinate mineral particles or dead biogenic material such as diatom frustules to their shell-like housing (lorica), however, reasons for this agglutination remain questioned. We report on our observation of agglomeration of the living diatoms Fragilariopsis curta, F. cylindrus, F. pseudonana and F. rhombica to loricae of the Antarctic tintinnid ciliates Laackmanniella naviculaefera and Codonellopsis gaussi. These unusual associations between living diatoms and tintinnids were exclusively observed south of 63.59°S. We discuss the significance of our new finding and generate hypotheses to be tested by future research. It remains unclear where these living diatom–tintinnid associations are initially formed (in or near sea ice or also further north when abundances of L. naviculaefera, C. gaussi, F. curta, F. cylindrus, F. pseudonana and F. rhombica happen to be relatively high); who the beneficiary is in this association; what the exact benefits are; and how they might influence the Southern Ocean carbon cycle. Nevertheless, our observation provides a key step forward towards illuminating the largely unknown ecology of two Southern Ocean-endemic tintinnid species.

International Ocean Discovery Program (IODP) Expedition 382, Iceberg Alley and Subantarctic Ice and Ocean Dynamics, investigated the long-term climate history of Antarctica, seeking to understand how polar ice sheets responded to changes in insolation and atmospheric CO2 in the past and how ice sheet evolution influenced global sea level and vice versa. Five sites (U1534–U1538) were drilled east of the Drake Passage: two sites at 53.2°S at the northern edge of the Scotia Sea and three sites at 57.4°–59.4°S in the southern Scotia Sea. We recovered continuously deposited late Neogene sediment to reconstruct the past history and variability in Antarctic Ice Sheet (AIS) mass loss and associated changes in oceanic and atmospheric circulation. The sites from the southern Scotia Sea (Sites U1536–U1538) will be used to study the Neogene flux of icebergs through “Iceberg Alley,” the main pathway along which icebergs calved from the margin of the AIS travel as they move equatorward into the warmer waters of the Antarctic Circumpolar Current (ACC). In particular, sediments from this area will allow us to assess the magnitude of iceberg flux during key times of AIS evolution, including the following: The middle Miocene glacial intensification of the East Antarctic Ice Sheet, The mid-Pliocene warm period, The late Pliocene glacial expansion of the West Antarctic Ice Sheet, The mid-Pleistocene transition (MPT), and The “warm interglacials” and glacial terminations of the last 800 ky. We will use the geochemical provenance of iceberg-rafted detritus and other glacially eroded material to determine regional sources of AIS mass loss. We will also address interhemispheric phasing of ice sheet growth and decay, study the distribution and history of land-based versus marine-based ice sheets around the continent over time, and explore the links between AIS variability and global sea level. By comparing north–south variations across the Scotia Sea between the Pirie Basin (Site U1538) and the Dove Basin (Sites U1536 and U1537), Expedition 382 will also deliver critical information on how climate changes in the Southern Ocean affect ocean circulation through the Drake Passage, meridional overturning in the region, water mass production, ocean–atmosphere CO2 transfer by wind-induced upwelling, sea ice variability, bottom water outflow from the Weddell Sea, Antarctic weathering inputs, and changes in oceanic and atmospheric fronts in the vicinity of the ACC. Comparing changes in dust proxy records between the Scotia Sea and Antarctic ice cores will also provide a detailed reconstruction of changes in the Southern Hemisphere westerlies on millennial and orbital timescales for the last 800 ky. Extending the ocean dust record beyond the last 800 ky will help to evaluate dust-climate couplings since the Pliocene, the potential role of dust in iron fertilization and atmospheric CO2 drawdown during glacials, and whether dust input to Antarctica played a role in the MPT. The principal scientific objective of Subantarctic Front Sites U1534 and U1535 at the northern limit of the Scotia Sea is to reconstruct and understand how ocean circulation and intermediate water formation responds to changes in climate with a special focus on the connectivity between the Atlantic and Pacific basins, the “cold water route.” The Subantarctic Front contourite drift, deposited between 400 and 2000 m water depth on the northern flank of an east–west trending trough off the Chilean continental shelf, is ideally situated to monitor millennial- to orbital-scale variability in the export of Antarctic Intermediate Water beneath the Subantarctic Front. During Expedition 382, we recovered continuously deposited sediments from this drift spanning the late Pleistocene (from ~0.78 Ma to recent) and from the late Pliocene (~3.1–2.6 Ma). These sites are expected to yield a wide array of paleoceanographic records that can be used to interpret past changes in the density structure of the Atlantic sector of the Southern Ocean, track migrations of the Subantarctic Front, and give insights into the role and evolution of the cold water route over significant climate episodes, including the following: The most recent warm interglacials of the late Pleistocene and The intensification of Northern Hemisphere glaciation.

The marine diatom Leptocylindrus is a major component of phytoplankton blooms in coastal ecosystems and upwelling regions worldwide, however, little is known about this genus in the southern hemisphere. Whilst Leptocylindrus danicus has been reported from south-eastern (SE) Australia since the 1930s, there has been neither unequivocal species identification nor focused examination of the temporal abundance of Leptocylindrus in this region. Such investigations are crucial in the context of climate change and the strengthening of the East Australian Current, which is expected to result in alterations to the seasonal abundance and distribution of Leptocylindrus along the east Australian coast. Thus we also describe the temporal distribution of Leptocylindrus based on 50 years of records, revealing that this diatom is a key component of the seasonal phytoplankton cycle, with greatest abundance in the austral spring and summer. Using light and transmission electron microscopy and molecular phylogenetics based ...

Jean-Francois Rontani, Lukas Smik, Simon T.Belt, Frederic Vaultier, Linda Armbrecht, Amy Leventerd, Leanne K. Armand

The coastline of Australia spans tropical to temperate latitudes and encompasses a highly diverse phytoplankton community. Yet little is known about environmental driving forces of compositional and distributional patterns in natural phytoplankton communities of Australia. We investigate the relationships of phytoplankton (pico-, nano-, microphytoplankton, determined by microscopy and CHEMTAX) with a variety of environmental variables along cross-shelf gradients. Case studies were conducted in two highly distinct oceanographic regions of Australia (2010/2012): the tropical-temperate Coffs Harbour region (~ 30°S, 153°E), where the shelf is narrow (~ 30 km), and the tropical Kimberley region (~ 16°S, 122°E), where the shelf is wide (~ 200 km). We distinguished three water masses in both study regions: relatively cold, nutrient-rich inshore waters; oligotrophic, stratified offshore waters; and cold, nutrient-rich deep waters. Most phytoplankton taxa (cyanobacteria, cryptophytes, dinoflagellates, haptophytes and prasinophytes) showed group-specific relationships with similar environmental variables in both regions. Diatoms occurred in nutrient-rich inshore waters in the Kimberley, whereas they were widely spread across the narrow continental shelf at Coffs Harbour. Off Coffs Harbour, a senescent bloom of the diatom Leptocylindrus danicus probably caused shelf-scale surface nutrient depletion. While microphytoplankton clearly increased, pico- and nanophytoplankton decreased with distance from the coast over the wide shelf in the Kimberley region. In contrast, the abundance of individual phytoplankton size-classes remained relatively constant across the narrow Coffs Harbour shelf. We conclude that general similarities exist between the relationship of phytoplankton and cross-shelf environmental variables in the two sites and assign differences primarily to the varying spatial resolution of our case studies.

Strengths of numerical relationships between phytoplankton abundance estimates made by microscopy and CHEMTAX have often been tested using regression analysis. To specifically test agreement, where data points lie along a line of equality, the Bland and Altman technique is commonly used in the medical literature and applied here to phytoplankton analysis for the first time (simultaneously with regression). Our analyses are based on a sample set collected off Coffs Harbour (∼ 30°S), Eastern Australia. While comparing abundance estimates of different phytoplankton pigment-types derived from microscopy and CHEMTAX we specifically aim at: (1) determining the usefulness of the Bland and Altman technique in comparing phytoplankton abundance estimates made by both quantification techniques, and (2) identifying the lowest taxonomic level (i.e., interclass or intraclass level) at which phytoplankton abundance estimates agree. Our results suggest that Bland and Altman analysis is highly suited to compare phytoplankton abundance estimates made by microscopy and CHEMTAX. It delivered a quantifiable difference of chlorophyll a concentrations between abundance estimates, which may benefit the future calibration of phytoplankton quantification techniques. Both Bland and Altman and regression analyses were suited to resolve imbalances between phytoplankton abundance estimates made by microscopy and CHEMTAX. Best agreement was found within dinoflagellates (class-level), poor agreement within three diatom pigment-types (intraclass level). We attributed the poor agreement within diatom abundance estimates to classification errors of microscopically determined taxa into pigment-types. Intraspecific pigment composition seems more variable than generally assumed, calling for studies resolving this variation to further conform abundance estimates made by microscopy and CHEMTAX.

The East Australian Current (EAC) has been shown to be warming rapidly, which is expected to cause latitudinal shifts in phytoplankton abundance, distribution and composition along the east Australian coast. Yet a lack of phytoplankton information exists northward of 34°S. Here, we provide the first detailed taxonomic time-series survey (monthly sampling for about one annual cycle, 2011–2012) in the east Australian tropical-temperate transition zone (~ 30°S, upstream of the EAC separation point at ~ 31–32°S). All phytoplankton (categorised depending on their association with specific water-types) show a seasonal signal with abundance maxima (minima) during summer (winter). This seasonal signal is most pronounced in the seasonal/bloom category and least expressed by deep-water taxa, which prefer cold, saline and dense bottom water independent of the season. Different extents of EAC encroachment onto the continental shelf drive the cross-shelf phytoplankton composition and distribution, such that a weak EAC is associated with phytoplankton community being organised along ‘depth’ and ‘distance from the coast’ gradients with high phytoplankton abundances inshore. A strong EAC favours the occurrence of warm-water taxa offshore and an increase in diatom abundance on the mid-shelf (53% shelf width). We conclude that the phytoplankton community in the tropical-temperate transition zone of Eastern Australia is driven by an interaction of intrinsic seasonal cycles and primarily EAC-driven oceanic forcing. Our findings benefit studies located in Western Boundary Current systems worldwide, in which warming and strengthening of these currents are predicted to severely impact phytoplankton dynamics.

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files made available in this article., Chlorophyll a is the most commonly used indicator of phytoplankton biomass in the marine environment. It is relatively simple and cost effective to measure when compared to phytoplankton abundance and is thus routinely included in many surveys. Here we collate 173, 333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys and ocean voyages into a single repository. This dataset includes the chlorophyll a values as measured from samples analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). The Australian Chlorophyll a database is freely available through the Australian Ocean Data Network portal (https://portal.aodn.org.au/). These data can be used in isolation as an index of phytoplankton biomass or in combination with other data to provide insight into water quality, ecosystem state, and relationships with other trophic levels such as zooplankton or fish.

The aim of this study was to examine effects of pasturing in dairy cows on claw condition (claw length, hardness) and on the prevalence of claw diseases. At claw trimming, a total of 240 Holstein-Friesian or Red-Holstein cows from 20 German farms were examined twice, at the end of the pasture and barn season. Each individual claw was trimmed at both assessments. Farms were classified based on animals' pasture access during pasture season into: group 1 (G1)10 hours pasture access per day, group 2 (G2) 6-10 hours, group 3 (G3)6 hours and group 4 (G4) without pasture access. Greater values for hardness were associated with lower scores (=prevalence×severity level) of sole ulcers, white line disease, sole haemorrhage, heel horn erosion and interdigital hyperplasia. In pasture groups, heel horn erosion showed lower frequencies in summer compared with winter, while it was vice versa in G4. In G1 and G3, lower frequencies of white line disease were found in summer compared with winter. Overall, pasture access had positive effects in particular for claw diseases that are related to moist environments. Nevertheless, appropriate free-stall design and claw trimming routine might have a greater influence.

Creative Commons This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0 Metadata associated with this Data Descriptor is available at http://www.nature.com/sdata/ and is released under the CC0 waiver to maximize reuse., 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.

The study of ancient DNA (aDNA) from sediments (sedaDNA) offers great potential for paleoclimate interpretation, and has recently been applied as a tool to characterise past marine life and environments from deep ocean sediments over geological timescales. Using sedaDNA, palaeo-communities have been detected, including prokaryotes and eukaryotes that do not fossilise, thereby revolutionising the scope of marine micropalaeontological research. However, many studies to date have not reported on the measures taken to prove the authenticity of sedaDNA-derived data from which conclusions are drawn. aDNA is highly fragmented and degraded and extremely sensitive to contamination by non-target environmental DNA. Contamination risks are particularly high on research vessels, drilling ships and platforms, where logistics and facilities do not yet allow for sterile sediment coring, and due consideration needs to be given to sample processing and analysis following aDNA guidelines. This review clarifies the use of aDNA terminology, discusses common pitfalls and highlights the urgency behind adopting new standards for marine sedaDNA research, with a focus on sampling optimisation to facilitate the incorporation of routine sedaDNA research into International Ocean Discovery Program (IODP) operations. Currently available installations aboard drilling ships and platforms are reviewed, improvements suggested, analytical approaches detailed, and the controls and documentation necessary to support the authenticity of aDNA retrieved from deep-sea sediment cores is outlined. Beyond practical considerations, concepts relevant to the study of past marine biodiversity based on sedaDNA, and the applicability of the new guidelines to the study of other contamination-susceptible environments (permafrost and outer space) are discussed.

article i nfo Autolysed cytoplasm Diatom cell death Polysaccharide layer Silicic acid limitation SYTOX® Green Transparent exopolymer particles The demise phase of diatom blooms following nutrient exhaustion is characterised by the formation of aggre- gateswith high sinkingratesthatfacilitate carbon export to the seafloor. However,the nature of thebindingsub- stances involved and the physiological status of the phytoplankton during aggregation are not well established. Transparent Exopolymer Particles (TEP), exudated by living cells, have been proposed as a binding agent of ag- gregates but autolysed cytoplasm released after cell death might also play such a role. To differentiate these pro- cesseswe studied theresponseof cultures of the mucilageand TEP-producing giant diatom Coscinodiscus wailesii to nutrient, in particular silicic acid, limitation. Two staining methods were applied: SYTOX® Green to follow cell viability and cell death and Alcian Blue (AB) to quantify the production of TEP. Large aggregates formed exclu- sively in cultures with high cell densities in which the SYTOX® Green signal increased during the senescence phase. TEP-production under nutrient replete (f/2 treatment) and nitrate reduced growth conditions (f/2-N treatment) with high cell densities was comparatively low, indicating reduced photosynthetic activity in the stationary and senescent phases. In contrast, TEP-production was enhanced in low-density Si-limited cultures (f/2-Si treatment), probably as a means to discharge excess photosynthate, as the cells were densely packed with chloroplasts. The C/N ratios of aggregated and solitary cells did not differ significantly indicating that the binding agent was not mainly polysaccharidic. We propose that aggregate formation in C. wailesii is a conse- quence of cell lysis after cell death and that autolysed cytoplasm is the binding agent rather than TEP. This would imply that cell lysis plays a substantial role in bloom termination and mucilage formation in C. wailesii, which would in turn influence biogeochemical cycling in regions where this diatom thrives.

Phytoplankton abundance and distribution along the east coast of Australia are driven primarily by the southward flowing East Australian Current (EAC), which transports tropical water masses to temperate latitudes. The Solitary Islands Marine Park (SIMP, � 301S) is located north of the EAC separation point (� 321S) in this tropical–temperate transition zone. In this study, we describe the oceanographic context (wind, current and nutrient load) during a wind-driven downwelling and a current-driven upwelling event, both sampled in austral winter only ten days apart. We investigate the effect of these contrasting oceanographic conditions on phytoplankton abundance, composition and distribution along a cross-shelf transect. During downwelling we find a cross-shelf transition in microphytoplankton composition from an offshore- to an inshore-community associated with nutrient gradients (nitrate and silicate). Strong vertical mixing leads to increased occurrences of benthic diatoms in near-shore surface waters. During upwelling conditions, elevated nutrient availability results in maximum microphytoplankton abundances (mainly oceanic diatoms) and increased species richness on the mid-shelf. An increase in dinoflagellates and silicoflagellates (mid-shelf) and the appearance of tropical phytoplankton (especially picoplankton and dinoflagellates, offshore) signals a strong impact of the EAC across all shelf communities. Nanoplankton are a major part of the winter phytoplankton community during both oceanographic regimes (� 40–50% of TChl a). Our findings provide evidence of EAC-driven, nutrient-rich, slope water intrusion in the SIMP as expressed by cross-shelf phytoplankton variability. We suggest that rapid (� weekly) changes in phytoplankton composition along the east Australian coast are likely to be enhanced by the climate change-induced warming/strengthening of the EAC.

Scientific Data 3:160043 doi:10.1038/sdata.2016.43 (2016); Published 21 Jun 2016; Updated 6 Dec 2016 A series of errors in our database were brought to our attention by readers, and have been corrected in an updated version of this database, which is accessible via the AODN at the following link: https://portal.

Studies incorporating sedimentary ancient DNA (sedaDNA) analyses to investigate paleo-environments have increased considerably over the last few years, and the possibility of utilizing archived sediment cores from previous field campaigns could unlock an immense resource of sampling material for such paleo-investigations. However,sedaDNA research is at a high risk of contamination by modern environmental DNA, as sub-optimal sediment storage conditions may allow for contaminants (e.g., fungi) to grow and become dominant over preservedsedaDNA in the sample. Here, we test the feasibility ofsedaDNA analysis applied to archive sediment material from five sites in the North Atlantic, collected between 1994 and 2013. We analyzed two samples (one younger and one older) per site using a metagenomic shotgun approach and were able to recover eukaryoticsedaDNA from all samples. We characterized the authenticity of each sample throughsedaDNA fragment size and damage analyses, which allowed us to disentanglesedaDNA and contaminant DNA. Although we determined that contaminant sequences originated mainly from Ascomycota (fungi), most samples were dominated byEmiliania huxleyi, a haptophyte species that commonly blooms in the study region. We attribute the presence of contaminants to non-ideal sampling and sample storage conditions of the investigated samples. Therefore, while we demonstrate thatsedaDNA analysis of archival North Atlantic seafloor sediment samples are generally achievable, we stress the importance of best-practice ship-board sampling techniques and storage conditions to minimize contamination. We highly recommend the application of robust bioinformatic tools that help distinguish ancient genetic signals from modern contaminants, especially when working with archive material.