Biogeochemistry covers a variety of topics in biogeochemical cycles. Because biogeochemical studies generally require interdisciplinary approaches, biogeochemists often face difficulty in figuring out a conference session that is suitable for presenting their research. Although the past annual meetings of the geochemical society of Japan have widely opened the door to such biogeochemists, the research topics presented in the corresponding session seemed unintentionally biased. The aim of this special issue Biogeochemistry is to broaden biogeochemical perspectives and to encourage more biogeochemists to consider joining and collaborating with the members of the geochemical society of Japan.

Phosphorus (P) is one of the most important nutrients for all living organisms. Recently, not only inorganic P but also organic P has been focused because of the development of an analytical technique— ³¹P nuclear magnetic resonance (NMR) spectroscopy. In the current paper, we reviewed historical backgrounds of the P analysis with the reason for using NMR and the limitation. Furthermore, we discussed the processes of sediment and suspended particles in lakes in the recent studies. The processes are complex, including physical, chemical, and biological aspects (i.e. diffusion, resuspension, adsorption/desorption, and enzymatic hydrolysis). Because P is present majorly as particulate forms, it is affected by physical processes compared with carbon and nitrogen. We shed light on how the processes of physical, chemical, and biological aspects affect P behavior in sediment and suspended particles in shallow and deep lakes.

Adsorption chemistry of Fe(III) oxyhydroxides is one of the important topics because of their considerable impacts on trace element geochemistry in the surface environment. Although inorganic Fe(III) oxyhydroxides have been used as an absorbent for laboratory studies, there is a growing recognition that biogenic iron oxyhydroxides (BIOS) are dominant in the environment. The microbial organic materials in BIOS can dramatically change mineralogical and adsorptive characteristics of Fe(III) oxyhydroxides, but the details and their differences from inorganic Fe(III) oxyhydroxides have not been specified well. In this review, we introduce our recent findings of BIOS especially focusing on their crystal structure, mineral transformation during early diagenesis, and trace element adsorption. The microbe-mineral interactions in BIOS (i) change the mineral structure of ferrihydrite, (ii) limit the ratio of BIOS reduced under anoxic condition, and (iii) enhance adsorption of cesium cation whereas inhibit anion adsorption of selenate and selenite ions compared to inorganic Fe(III) oxyhydroxides. These results will provide new insight into the geochemical role of BIOS and also contribute to other scientific fields such as environmental engineering, environmental microbiology, and ore geology.

Biogeochemistry is the study of how organisms alter the earth's surface geochemical processes. Meanwhile, ecosystem ecology is the study of how materials and energy flow and are stored among organisms and environments. Although there is significant crossover between these two fields, some research topics are not overlapped. For instance, chemoautotrophic microorganisms that harness energy from redox reactions and gain carbon from inorganic carbon substances are of geochemical interest because of their catalytic effects on biogeochemical reactions, whereas those communities have not seemed to get much ecological attentions. Two reasons can potentially explain this; 1) the main target organisms in ecology have been flora and fauna, and their carbon storage and cycling is a cornerstone concept of ecosystem ecology; 2) the difficulty in oveservation and isolation of chemoautotrophic microorganisms have long inhibited the progress of their ecological understanding. In bringing together the biogeochemical and ecological perspectives, however, recent studies have accelerated our understanding the interactions between the ecology of chemolithoautotrophs and material flows for the last decade.

Surface oceans absorb a part of anthropogenic CO₂, and it induces changes in carbonate equilibrium of seawater. The seawater is gradually acidified, and saturation status of calcium carbonate is being lowered. These changes in carbonate chemistry would be serious threats for marine organisms (e.g., calcifying organisms). Ecosystems around submarine CO₂ vents; CO₂ seep, would be natural analogues of ocean acidification (OA) in coastal area, and ecosystem-level studies have been carried out so far. Drastic changes in species composition of primary producers have been reported in several CO₂ seep. Common features are decrease in calcifying organisms such as coral and calcifying algae, and increase in mat-forming turf algae and seagrass. Considering such shift of benthic flora, change in primary production in coastal ecosystem is expected. However, there are limited number of direct measurements for photosynthesis, and their reports had focused on only some species living both in/out of CO₂ seep. Therefore, the knowledges are limited to the physiological response of the primary producers to OA. In order to quantify the impact on the primary production at ecosystem level, consideration on the shift of flora and estimation per unit community area will be required.

The elemental composition of diatom frustules has not been treated as an intensive object of scientific research and it has been lain aside without being fully understood. In this commentary paper some observed evidences are shown for the presence of aluminum at a sub % level. The presence of aluminum in frustules at a certain amount directly indicates that diatoms incorporate some elements from terrigenous particles. It is argued that the presence of aluminum in diatom frustules can be relevant to some outstanding problems, which include a problem of the glacial-interglacial cycles.

With recent advantages in accelerator mass spectrometry techniques, natural and anthropogenic ²³⁶U (T_1/2=2.34×10⁷ y, α-decay) concentrations and ²³⁶U/²³⁸U atomic ratios have been excessively measured in various environmental samples, and have been an emerging isotopic tracer in the geochemical and environmental sciences, most notably in oceanographic studies. Here, we reviewed the publications on 1) natural and anthropogenic sources of ²³⁶U in the environment, 2) the levels, distribution and behavior of ²³⁶U in normal and accidental areas, and ²³⁶U as oceanic tracer.