Biogenic calcium carbonate (coral skeleton, foraminifera shell, bivalve shell, otolith, etc.) is one of the best archives of the past changes of aquatic environment that includes ocean, river, and lake. I have dedicated myself to the development and application of the environmental proxies such as trace element, stable isotope, and radiogenic isotope in calcium carbonate of marine organisms to study paleoclimate, paleoceanography, marine carbon cycle, and calcification processes of them. In this manuscript, I focus on boron isotope proxy of skeleton of marine calcifiers, coral and foraminifera, that are often used in paleoclimatology. Boron isotopes can record pH of the seawater, from which atmospheric carbon dioxide concentration can be estimated, thus it has been recognized as a holy grail in marine carbon cycle study. First, I review the mechanism of boron isotope as seawater pH proxy, history in technical development in the isotope measurement, issues with regard to fractionation factor between boric acid and borate ion in seawater, reconsideration of the boron incorporation mechanism into calcium carbonate skeleton, and recent findings. Then I overview my recent marine carbon cycle studies using boron isotope proxy in different timescales, since the Industrial Revolution (since 1750 C.E.) and since the last glacial period (since ～20,000 years ago).The boron isotopic composition was determined in high precision and accuracy by using thermal ionization mass spectrometry and multi-collector inductively-coupled plasma mass spectrometry in Japan Agency for Marine–Earth Science and Technology.

Long-chain alkenones, unique class of lipid biomarker produced by members of the Isochrysidales haptophytes, have been widely used for reconstructing past sea surface temperature (SST) from marine sediment cores. In recent decades, alkenones have also been discovered from some freshwater and saline lakes. The application of alkenone paleothermometer in lakes and some marginal seas are often hindered by the potential occurrence of species different from the typical marine alkenone producers: different species often exhibit significantly different temperature calibrations. Recent molecular biological studies updated the overall view of diversity in the alkenone producers, dividing Isochrysidales into three major groups: Group I consists of uncultured sequences occur in freshwater lakes, Group II includes Isochrysidaceae haptophytes often found in saline lakes and marginal sea, and Group III consists of Noëlaerhabdaceae haptophytes (ocean species).Laboratory culture experiments of Group II species highlight significant chemotaxonomic variations in both biomarker compositions and temperature calibrations, reflecting a wider phylogenetic diversity compared to Group III. Recent field studies also suggest the conserved characteristics in alkenone and temperature responses in Group I haptophytes. A combination of environmental DNA analysis and chemotaxonomic profiling is essential for the identification of alkenone producers and improved applications of alkenone-based indices for paleoclimate and paleoenvironmental research.