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Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it is challenging to produce fast and accurate depiction of ecosystems due to methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative abundances of genes that may not correctly represent living communities from environmental DNA assessed with morphological methods. However, it has the potential to deliver fast descriptions of living communities provided that it is interpreted with validated species‐specific calibrations and reference databases. Here, we developed a quantitative approach to retrieve from metabarcoding data the assemblages of living large benthic foraminifera (LBF), photosymbiotic calcifying protists, from Indonesian coral reefs that are under increasing anthropogenic pressure. To depict the diversity, we calculated taxon‐specific correction factors to reduce biological biases by comparing surface area, biovolume and calcite volume, and the number of mitochondrial gene copies in seven common LBF species. To validate the approach, we compared calibrated datasets of morphological communities from mock samples with bulk reef sediment; both sample types were metabarcoded. The calibration of the data significantly improved the estimations of genus relative abundance, with a difference of ±5% on average, allowing for comparison of past morphological datasets with future molecular ones. Our results also highlight the application of our quantitative approach to support reef monitoring operations by capturing fine‐scale processes, such as seasonal and pollution‐driven dynamics, that require high‐throughput sampling treatment. [ABSTRACT FROM AUTHOR]

This paper introduces ForametCeTera, a pioneering dataset designed to address the challenges associated with automating the analysis of benthic foraminifera in sediment cores. Foraminifera are sensitive sentinels of environmental change and are a crucial component of carbonate-denominated ecosystems, such as coral reefs. Studying their prevalence and characteristics is imperative in understanding climate change. However, analysis of foraminifera contained in core samples currently requires washing, sieving and manual quantification. These methods are thus time-consuming and require trained experts. To overcome these limitations, we propose an alternative workflow utilizing 3D X-ray computational tomography (CT) for fully automated analysis, saving time and resources. Despite recent advancements in automation, a crucial lack of methods persists for segmenting and classifying individual foraminifera from 3D scans. In response, we present ForametCeTera, a diverse dataset featuring 436 3D CT scans of individual foraminifera and non-foraminiferan material following a high-throughput scanning workflow. ForametCeTera serves as a foundational resource for generating synthetic digital core samples, facilitating the development of segmentation and classification methods of entire core sample CT scans. [ABSTRACT FROM AUTHOR]

Reef cores are a powerful tool for investigating temporal changes in reef communities. Radiometric dating facilitates the determination of vertical accretion rates, which has allowed for examination of local-regional controlling factors, such as subsidence and sea level changes. Coral reefs must grow at sufficient rates to keep up with sea level rise, or risk 'drowning.' As sea level is expected to rise significantly in the next 100 years and beyond, it is important to understand whether reefs will be able to survive. Historical records of reef accretion rates extracted from cores provide valuable insights into extrinsic controlling factors of reef growth and are instrumental in helping predict if future reefs can accrete at rates needed to overcome predicted sea level changes. While extensive research exists at local and regional scales, limited attention has been given to identifying global patterns and drivers. To address this, we present "RADReef": A global dataset of dated Holocene reef cores. RADReef serves as a foundation for further research on past, present and future reef accretion. [ABSTRACT FROM AUTHOR]

Although Pliocene temperature and pCO2 are similar to those predicted in the IPPC RCP4.5 scenario, the distribution of coral reefs in the center of maximum coral diversity, the Coral Triangle, during this period has not been explored. We discovered a significantly lower occurrence of reefs during the Pliocene, which we refer to as the Pliocene Reef Gap, but this decrease was not associated with a drop in coral genus richness. While some of the multiple local causes that drove this decline, such as sea level rise, are analogs to drivers of Anthropocene reef decline, neither warming nor increasing pCO2 are among them. [ABSTRACT FROM AUTHOR]

In order to preserve diversity it is essential to understand how assemblages change across space. Despite this fact, we still know very little about how marine diversity is spatially distributed, especially among lesser-studied invertebrate taxa. In the present study beta-diversity patterns of sea urchins, sponges, mushroom corals and larger foraminifera were assessed in the Spermonde Archipelago (Indonesia). Using ordinations we showed that the inshore zone (<5 km offshore), midshore zone (5 < x < 30 km offshore) and distance offshore zone (>30 km offshore) all contained distinct assemblages of sponges and corals, while only foraminifera assemblages from the inshore (<5 km offshore) zone were distinct. There was a significant spatial pattern of community similarity for all taxa surveyed, but this pattern proved to be wholly related to environmental variables for sponges and foraminifera, and primarily for mushroom corals and sea urchins. The lack of a pure spatial component suggests that these taxa may not be dispersal limited within the spatial scales of this study ( c. 1600 km2). The analyses of the corals and foraminifera were additionally tested at two spatial scales of sampling. Both taxa were primarily associated with local-scale environmental variables at the local scale and larger-scale variables at the larger scale. Mean inter-plot similarity was also higher and variation lower at the larger scale. The results suggest that substantial variation in similarity can be predicted using simple locally assessed environmental variables combined with remotely sensed parameters. [ABSTRACT FROM AUTHOR]

Abstract: Most studies of Cenozoic shallow-water, mixed carbonate–siliciclastic depositional systems have focused on their sedimentology. To date, however, comprehensive analyses of biotas and biofacies of Indo-West Pacific reefs that developed in mixed carbonate–siliciclastic systems are lacking. This study describes the palaeoenvironment and biodiversity of a late Burdigalian patch reef that developed in a mixed carbonate–siliciclastic depositional system. The studied exposure is located at the northeast margin of the Kutai Basin near Bontang (Indonesia), and is approximately 80m wide and 25m thick. Multi-taxon analysis of the most abundant fossil groups, including larger benthic foraminifera, corals, coralline algae, and bryozoans, aims to provide a model for environmental interpretation that will allow comparison with similar deposits of Indo-West Pacific region. Based on fossil content and lithology, five different facies types have been distinguished: foraminiferal packstone (FP), bioclastic packstone with foralgal communities (BP), thin-platy coral sheetstone (CS), platy-tabular coral platestone (CP), and shales (S). Among larger benthic foraminifera, smaller and more robust forms dominate in the FP and BP facies, while larger and flatter forms are the most abundant in the CS and CP facies. Thin-platy corals are dominant in the CS facies and gradually change into thicker platy-tabular forms in the CP facies. Assemblages and growth forms of coralline algae show no major differences between the facies types and are dominated by melobesioids and Sporolithon. The majority of bryozoan species are encrusting and were found only in the CS facies. Light-dependent organisms occurring in the reef indicate low light conditions typical for mesophotic reefs. The relatively small size of this reef complex and quite distinct vertical changes in the facies types, combined with the high siliciclastic content in most of the units, points to strong terrigenous input affecting water transparency as the main factor controlling the reef growth. [Copyright &y& Elsevier]