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We discuss the climatic and environmental changes during the last millennium in NE Europe based on a ca. 8-m long high-resolved and well-dated marine sediment record from the deepest basin of Gullmar Fjord (SW Sweden). According to the 210Pb- and 14C-datings, the record includes the period of the late Holocene characterised by anomalously cold summers and well-known as the Little Ice Age (LIA). Using benthic foraminiferal stratigraphy, lithology, bulk sediment geochemistry and stable carbon isotopes we reconstruct various phases of the cold period, identify its timing in the study area and discuss the land–sea interactions occurring during that time. The onset of the LIA is indicated by an increase in cold-water foraminiferal species Adercotryma glomerata at ~ 1350 AD The first phase of the LIA was characterised by a stormy climate and higher productivity, which is indicated by a foraminiferal unit of Nonionella iridea and Cassidulina laevigata. Maximum abundances of N. iridea probably mirror a short and abrupt warming event at ~ 1600 AD. It is likely that due to land use changes in the second part of the LIA there was an increased input of terrestrial organic matter to the fjord, which is indicated by lighter δ13C values and an increase of detritivorous and omnivorous species such as Textularia earlandi and Eggerelloides scaber. The climate deterioration during the climax of the LIA (1675–1704 AD), as suggested by the increase of agglutinated species, presence of Hyalinea balthica, and a decline of N. iridea may have driven the decline in primary productivity during this time period.

It is expected that the calcification of foraminifera will be negatively affected by the ongoing acidification of the oceans. Compared to the open oceans, these organisms are subjected to much more adverse carbonate system conditions in coastal and estuarine environments such as the southwestern Baltic Sea, where benthic foraminifera are abundant. This study documents the seasonal changes of carbonate chemistry and the ensuing response of the foraminiferal community with bi-monthly resolution in Flensburg Fjord. In comparison to the surface pCO2 , which is close to equilibrium with the atmosphere, we observed large seasonal fluctuations of pCO2 in the bottom and sediment pore waters. The sediment pore water pCO2 was constantly high during the entire year ranging from 1244 to 3324 μatm. Nevertheless, in contrast to the bottom water, sediment pore water was slightly supersaturated with respect to calcite as a consequence of higher alkalinity (AT ) for most of the year. Foraminiferal assemblages were dominated by two calcareous species, Ammonia aomoriensis and Elphidium incertum, and the agglutinated Ammotium cassis. The one-year cycle was characterised by seasonal community shifts. Our results revealed that there is no dynamic response of foraminiferal population density and diversity to elevated sediment pore water pCO2 . Surprisingly, the fluctuations of sediment pore water undersaturation (Ωcalc ) co-vary with the population densities of living Ammonia aomoriensis. Further, we observed that most of the tests of living calcifying foraminifera were intact. Only Ammonia aomorienis showed dissolution and recalcification structures on the tests, especially at undersaturated conditions. Therefore, the benthic community is subjected to high pCO2 and tolerates elevated levels as long as sediment pore water remains supersaturated. Model calculations inferred that increasing atmospheric CO2 concentrations will finally lead to a perennial undersaturation in sediment pore waters. Whereas benthic foraminifera indeed may cope with a high sediment pore water pCO2 , the steady undersaturation of sediment pore waters would likely cause a significant higher mortality of the dominating Ammonia aomoriensis. This shift may eventually lead to changes in the benthic foraminiferal communities in Flensburg Fjord, as well as in other regions experiencing naturally undersaturated Ωcalc levels.

Over the past several decades, there has been increasing interest in using foraminifera as environmental indicators for coastal marine environments. Foraminifera provide equally good environmental quality status assessment as compared to large invertebrates (macrofauna), which are currently used as biological quality elements. However, foraminifera offer several distinct advantages as bioindicators, including short response and generation times, a high number of individuals per small sample volume, and hard and fossilizing shells with a potential of paleoecological record. One of the major challenges in foraminifera identification is the reliance on manual morphological methods, which are not only time-consuming and error-prone but also highly dependent on the expertise of taxonomic specialists. Deep learning, a subfield of machine learning (ML), has emerged as a promising solution to this challenge, since a neural network can learn to recognize subtle differences in shell morphology that may be difficult for the human eye to distinguish. In addition, the speed and ease afforded by deep learning methods would allow experts and non-experts alike to use foraminifera more extensively in their work, thus helping to integrate the use of foraminifera in biomonitoring programs by agencies and industry. This study focuses on benthic foraminifera from several Skagerrak fjords, including Gullmar Fjord, Hakefjord, Sannäs Fjord, and Idefjord (Fig. 1a). Sediment archives from these fjords provide extensive records of past and ongoing climate and environmental changes. Fjord foraminifera mounted on microslides were imaged using a stereomicroscope (3003 images), and individual foraminifera were labeled using the Roboflow online platform (22 138 individuals). Using the labeled images, we trained a You Only Look Once (YOLO) v7 deep learning model, which demonstrates state-of-the-art speed and performance for object detection as of the time of writing. The models can distinguish among 29 species with 90.3 % and 78.8 % mean average precision in the best- and the worst-performing models, respectively. Even though the imaging and labeling was done in a short amount of time (∼ 300 h over a course of 2 months), the results show that even a relatively small dataset can be used for training a reliable deep learning species identification model.

Synthetic antibiotics are medicinal substances crucial for human and animal health and welfare. Recently they have been expansively used in the food industry for reducing bacterial infections in livestock, poultry, and aquaculture. Due to their extensive use, antibiotics are increasingly accumulating in coastal marine ecosystems and cause damage to marine organisms. In this study we investigated the influence of antibiotics on benthic foraminifera, which are widespread marine protists. Foraminifera are often used as bioindicators to define the health state of coastal ecosystems. To gain deeper insights into the ecology of foraminifera and enhance their use as bioindicators, numerous studies have conducted laboratory experiments, with some employing antibiotics to prevent bacterial infections in the cultures. However, for decades it remained unresolved whether antibiotics have either a negative or a positive effect on foraminifera. In this study we tested the influence of three commonly used antibiotics (ampicillin, chloramphenicol, and tetracycline) as well as a mixture of the three on nutrient uptake of two benthic foraminifera, temperate fjord species Nonionella sp. T1 and large tropical species Heterostegina depressa. Our results showed that tetracycline present alone or in mixture has the most negative influence on the nutrition uptake of foraminifera, and under light conditions it may completely inactivate foraminiferal activity. Ampicillin showed a less negative impact, likely caused by a hydrolysis of this drug in seawater over days. Finally, chloramphenicol reduced the nutrient uptake of the symbiont-bearing H. depressa but not that of Nonionella sp. T1, which indicates that this antibiotic exerts a species-specific effect. However, given that the applied antibiotic concentrations were high following the supplier's recommendation for laboratory cultures, an extrapolation of these results to antibiotic concentrations occurring in coastal waters is difficult.

We present 2500 years of reconstructed bottom water temperatures (BWT) using a fjord sediment archive from the north-east Atlantic region. The BWT represent winter conditions due to the fjord hydrography and the associated timing and frequency of bottom water renewals. The study is based on a ca. 8 m long sediment core from Gullmar Fjord (Sweden), which was dated by 210Pb and AMS 14C and analysed for stable oxygen isotopes (δ18O) measured on shallow infaunal benthic foraminiferal species Cassidulina laevigata d'Orbigny 1826. The BWT, calculated using the palaeotemperature equation from McCorkle et al. (1997), range between 2.7 and 7.8 ∘C and are within the annual temperature variability that has been instrumentally recorded in the deep fjord basin since the 1890s. The record demonstrates a warming during the Roman Warm Period (∼350 BCE–450 CE), variable BWT during the Dark Ages (∼450–850 CE), positive BWT anomalies during the Viking Age/Medieval Climate Anomaly (∼850–1350 CE) and a long-term cooling with distinct multidecadal variability during the Little Ice Age (∼1350–1850 CE). The fjord BWT record also picks up the contemporary warming of the 20th century (presented here until 1996), which does not stand out in the 2500-year perspective and is of the same magnitude as the Roman Warm Period and the Medieval Climate Anomaly.

Small leisure boat harbours have important aesthetic and recreational values in any country with a coastline. In Sweden, there are about 860 000 leisure boats, which is one of the world's highest numbers in relation to the country's population. However, small boat harbours also present a wide range of environmental problems, including the introduction of alien species and high pollution. In this study, we investigated the ecological quality status (EcoQS) of the Hinsholmskilen small boat harbour, located southwest of the city of Gothenburg (Sweden). We performed a reconnaissance survey of the harbour's previously unstudied benthic foraminiferal communities and analysed surface sediment (0–2 cm) samples for potentially toxic elements: copper (Cu), zinc (Zn), lead (Pb), cobalt (Co), nickel (Ni), chromium (Cr), mercury (Hg), and arsenic (As). The results show that, based on the total benthic foraminiferal distribution (dead and live specimens), the assemblages in Hinsholmskilen harbour represent a typical European estuarine community with highly abundant Ammonia and Elphidium species. Based on molecular and morphological data, we report the presence of two alien and putatively invasive species likely originating from Asia: Trochammina hadai and Ammonia confertitesta (phylotype T6). Both species have recently been identified elsewhere on the Swedish west coast based on molecular and morphological data but do not have a well-known distribution. The sediment analysis for potentially toxic elements showed that the harbour has good to high EcoQS corresponding to no or little deviation from reference conditions for Cd, Co, Ni, and Pb distribution. Some of the contaminants (Pb, As, Zn, and Cr) showed poor to bad EcoQS in the innermost harbour in proximity to high-pressure cleaning plants, where boats are usually lifted, cleaned, and prepared for winter storage on land. Finally, Cu and Hg showed consistently bad and poor EcoQS all over the harbour, reflecting the use of both metals as biocides in antifouling boat paints.

Many benthic organisms show aggregated distribution patterns due to the spatial heterogeneity of niches or food availability. In particular, high-abundance patches of benthic foraminifera have been reported that extend from centimetres to metres in diameter in salt marshes or shallow waters. The dimensions of spatial variations of shelf or deep-sea foraminiferal abundances have not yet been identified. Therefore, we studied the distribution of Globobulimina turgida dwelling in the 0–3 cm surface sediment at 118m water depth in the Alsbäck Deep, Gullmar Fjord, Sweden. Standing stock data from 58 randomly replicated samples depicted a log-normal distribution of G. turgida with weak evidence for an aggregated distribution on a decimetre scale. A model simulation with different patch sizes, outlines, and impedances yielded no significant correlation with the observed variability of G. turgida standing stocks. Instead, a perfect match with a random log-normal distribution of population densities was obtained. The data–model comparison revealed that foraminiferal populations in the Gullmar Fjord were not moulded by any underlying spatial structure beyond 10 cm diameter. Log-normal population densities also characterise data from contiguous, gridded, or random sample replicates reported in the literature. Here, a centimetre-scale heterogeneity was found and interpreted to be a result of asexual reproduction events and restricted mobility of juveniles. Standing stocks of G. turgida from the Alsbäck Deep temporal data series from 1994 to 2021 showed two distinct cohorts of samples of either high or low densities. These cohorts are considered to represent two distinct ecological settings: hypoxic and well-ventilated conditions in the Gullmar Fjord. Environmental forcing is therefore considered to impact the population structure of benthic foraminifera rather than their reproduction dynamics.

A comprehensive multi-proxy study on two sediment cores from the western and central Skagerrak was performed in order to detect the variability and causes of marine primary productivity changes in the investigated region over the last 1100 years. The cores were dated by Hg pollution records and AMS 14C dating and analysed for palaeoproductivity proxies such as total organic carbon, δ13C, total planktonic foraminifera, benthic foraminifera (total assemblages as well as abundance of Brizalina skagerrakensis and other palaeoproductivity taxa) and palaeothermometers such as Mg∕Ca and δ18O. Our results reveal two periods with changes in productivity in the Skagerrak region: (i) a moderate productivity at ∼ CE 900–1700 and (ii) a high productivity at ∼ CE 1700–present. During ∼ CE 900–1700, moderate productivity was likely driven by the nutrients transported with the warm Atlantic water inflow associated with a tendency for a persistent positive NAO phase during the warm climate of the Medieval Climate Anomaly, which continues into the LIA until ∼ CE 1450. The following lower and more variable temperature period at ∼ CE 1450–1700 was likely caused by a reduced contribution of warm Atlantic water, but stronger deep-water renewal, due to a generally more negative NAO phase and a shift to the more variable and generally cooler climate conditions of the Little Ice Age. The productivity and fluxes of organic matter to the seafloor did not correspond to the temperature and salinity changes recorded in the benthic Melonis barleeanus shells. For the period from ∼ CE 1700 to the present day, our data point to an increased nutrient content in the Skagerrak waters. This increased nutrient content was likely caused by enhanced inflow of warm Atlantic water, increased Baltic outflow, intensified river runoff, and enhanced human impact through agricultural expansion and industrial development. Intensified human impact likely increased nutrient transport to the Skagerrak and caused changes in the oceanic carbon isotope budget, known as the Suess effect, which is clearly visible in our records as a negative shift in δ13C values from ∼ CE 1800. In addition, a high appearance of S. fusiformis during the last 70 years at both studied locations suggests increased decaying organic matter at the sea floor after episodes of enhanced primary production.

A non-indigenous species (NIS) of benthic foraminifera was first identified in a core collected in 1993 in San Francisco Bay, California, USA, and subsequently identified as Trochammina hadai Uchio, 1962. Archived samples and literature reviews were used to determine that the species, which is native to Asia, arrived in San Francisco Bay between the early 1960s and 1983. Through molecular analyses of specimens, archived samples and literature reviews from 1930–1983, and site surveys of harbors and estuaries along the western North American seaboard in 1994–2024, in total more than 2500 samples, we documented the presence of T. hadai at 73 locations in the USA and four in Canada. Trochammina hadai has also been recovered at nine sites in Sweden, two in France, three in Brazil, and two locations at one site in Australia. The rapid temporal and geographic spread of the NIS T. hadai in a non-native location is illustrated by a time series from 1930 to 2024 in San Francisco Bay. Between 1980 and 1986, the species' range expanded from low abundance (1.5 %) at a single site to cover nearly the entire South Bay with > 70 % abundance at some locations. By 1995 and continuing into 2010, the species expanded its range into the central and northern portions of San Francisco Bay, commonly with abundances of > 30 % and sometimes exceeding 70 %. This expansion may predate 1995, but a lack of samples makes it difficult to be more precise. Unfortunately, two Pb-210 and Cs-137-dated cores (BC01 and BC02) recovered from northern South Bay and Central Bay did not clarify this point, but additional cores may. Trochammina hadai is an infaunal opportunist that thrives in polluted locations. We surmise the species was introduced along the west coast of the USA in Puget Sound between 1902 and the 1920s, with cultivated oysters and oyster larvae and associated plant matter and residual sediment. This probably also happened in some areas of France, Sweden, and Brazil, where Japanese oysters were introduced in 1966, 1970, and 1975, respectively. After World War II, commercial shipping expanded dramatically and, with it, the release of ballast water and sediment in receiving ports, which introduced NIS worldwide. This primary vector of introduction occurred in large industrial harbors in several countries, sometimes followed by secondary introductions in small industrial centers and marinas by mud attached to the anchors and anchor chains of smaller boats.