Quantifying biological carbon pump pathways with a data-constrained mechanistic model ensemble approach

The ability to constrain the mechanisms that transport organic carbon into the deep ocean is complicated by the multiple physical, chemical, and ecological processes that intersect to create, transform, and transport particles in the ocean. In this manuscript we develop and parameterize a data-assimilative model of the multiple pathways of the biological carbon pump (NEMUROBCP). The mechanistic model is designed to represent sinking particle flux, active transport by vertically migrating zooplankton, and passive transport by subduction and vertical mixing, while also explicitly representing multiple biological and chemical properties measured directly in the field (including nutrients, phytoplankton and zooplankton taxa, carbon dioxide and oxygen, nitrogen isotopes, and 234Thorium). Using 30 different data types (including standing stock and rate measurements related to nutrients, phytoplankton, zooplankton, and non-living organic matter) from Lagrangian experiments conducted on 11 cruises from four ocean regions, we conduct an objective statistical parameterization of the model and generate one million different potential parameter sets that are used for ensemble model simulations. The model simulates in situ parameters that were assimilated (net primary production and gravitational particle flux) and parameters that were withheld (234Thorium and nitrogen isotopes) with reasonable accuracy. Model results show that gravitational flux of sinking particles and vertical mixing of organic matter from the surface ocean are more important biological pump pathways than active transport by vertically-migrating zooplankton. However, these processes are regionally variable, with sinking particles most important in oligotrophic areas of the Gulf of Mexico and California, sinking particles and vertical mixing roughly equivalent in productive regions of the CCE and the subtropical front in the Southern Ocean, and active transport an important contributor in the Eastern Tropical Pacific. We further find that mortality at depth is an important component of active transport when mesozooplankton biomasses are high, but that it is negligible in regions with low mesozooplankton biomass. Our results also highlight the high degree of uncertainty, particularly amongst mesozooplankton functional groups, that is derived from uncertainty in model parameters, with important implications from results that rely on non-ensemble model outputs. We also discuss the implications of our results for other data assimilation approaches.

Reconstructed Paleodiets and Subsistence Strategies of the Central Ciscaucasian Population (1000 BC to 1000 AD), Based on Collagen Isotope Analysis of Bone Samples from the Kichmalka II Burial Ground

Settlement and economy patterns of the Iron Age and early medieval population of the Central North Caucasus evidence complex cultural processes in the region. The ecological approach including the evaluation of carbon and nitrogen isotopes in the local biota opens up new prospects in the study of environments, climate, anthropogenic effect, land use, and nutrition. We analyze the isotopic composition of collagen in 19 human and 11 animal bone samples from Kichmalka II—a cemetery successively used by the Koban people, those of the Sarmatian stage, and Alans. The isotopic composition of the Alanian sample indicates a heavy predominance of plants with the C3-type photosynthesis in the diet of humans and animals. People who lived during the Koban and Sarmatian stages consumed also C4-plants, such as common millet (Panicum miliaceum), suggesting the rise of the trophic step for carbon (Δδ13Chuman-animal). Statistically signifi cant differences in the isotopic composition of carbon were found within the Koban population, apparently evidencing two dietary models. The Δδ15Nhuman-animal values fall within the trophic step, mirroring a focus on meat and dairy products in the diet of all groups. Comparison with respective data on the Klin-Yar III cemetery revealed differences in isotopic signatures in the diet of both humans and domestic animals during the Koban period. The possible reason is climatic change in the Iron Age and the variable share of millet in the diet of the Koban people. The low proportion of δ15N (below 4 ‰) in the bone collagen of goat, sheep, and horse of the Alanian period may attest to vertical transhumance.

Supplemental Material: Linkages between nitrogen cycling, nitrogen isotopes, and environmental properties in paleo-lake basins

Raw data.<br>

Supplemental Material: Linkages between nitrogen cycling, nitrogen isotopes, and environmental properties in paleo-lake basins

Raw data.<br>

Ultralight ultrafast enzymes

Inorganic materials depleted of heavy stable isotopes are known to deviate strongly in some physico-chemical properties from their isotopically natural (native) counterparts; however, in biotechnology such effects have not been investigated yet. Here we explored for the first time the effect of simultaneous depletion of the heavy carbon, hydrogen, oxygen and nitrogen isotopes on the bacterium E. coli and the enzymes expressed in it. Bacteria showed faster growth, with proteins exhibiting higher thermal stability, while for recombinant enzymes expressed in ultralight media, faster kinetics was discovered. At room temperature, luciferase, thioredoxin and dihydrofolate reductase showed a 40-250% increase in activity compared to the native counterparts. The efficiency of ultralight Pfu DNA polymerase in polymerase chain reaction was also significantly higher than that of the normal enzyme. At 10 °C, the advantage factor of ultralight enzymes typically increased by 50%, which points towards the reduction in structural entropy as the main factor explaining the kinetic effect of heavy isotope depletion. Ultralight enzymes may find an application where extreme reaction rates are required.

Impact of intensifying nitrogen limitation on ocean net primary production is fingerprinted by nitrogen isotopes

The open ocean nitrogen cycle is being altered by increases in anthropogenic atmospheric nitrogen deposition and climate change. How the nitrogen cycle responds will determine long-term trends in net primary production (NPP) in the nitrogen-limited low latitude ocean, but is poorly constrained by uncertainty in how the source-sink balance will evolve. Here we show that intensifying nitrogen limitation of phytoplankton, associated with near-term reductions in NPP, causes detectable declines in nitrogen isotopes (δ15N) and constitutes the primary perturbation of the 21st century nitrogen cycle. Model experiments show that ~75% of the low latitude twilight zone develops anomalously low δ15N by 2060, predominantly due to the effects of climate change that alter ocean circulation, with implications for the nitrogen source-sink balance. Our results highlight that δ15N changes in the low latitude twilight zone may provide a useful constraint on emerging changes to nitrogen limitation and NPP over the 21st century.

Isotope data from amino acids indicate Darwin’s ground sloth was not an herbivore

Fossil sloths are regarded as obligate herbivores for reasons including peculiarities of their craniodental morphology and that all living sloths feed exclusively on plants. We challenge this view based on isotopic analyses of nitrogen of specific amino acids, which show that Darwin’s ground sloth Mylodon darwinii was an opportunistic omnivore. This direct evidence of omnivory in an ancient sloth requires reevaluation of the ecological structure of South American Cenozoic mammalian communities, as sloths represented a major component of these ecosystems across the past 34 Myr. Furthermore, by analyzing modern mammals with known diets, we provide a basis for reliable interpretation of nitrogen isotopes of amino acids of fossils. We argue that a widely used equation to determine trophic position is unnecessary, and that the relative isotopic values of the amino acids glutamate and phenylalanine alone permit reliable reconstructions of trophic positions of extant and extinct mammals.