Plain Language Summary Earth scientists often study the same planet on radically different timescales, yet treat their observations as though they were directly comparable. They are not. A microbial reaction measured over hours, a climate trend observed over decades, and a geological archive spanning millions of years record different parts of the Earth system and preserve different kinds of evidence. This article argues that progress in geoscience depends on confronting these temporal mismatches rather than smoothing them away.

Microbial communities in the subsurface biosphere remain poorly characterized because many taxa lack cultured representatives and genomic references, limiting the accuracy of taxonomy inferred from short-read 16S ribosomal RNA gene sequencing. We tested the hypothesis that long-read 16S sequencing improves taxonomic resolution and detection of rare lineages compared with short-read approaches in low-biomass, diversity-rich sediments. Microbial communities from a sediment core of Lake Arnon (Switzerland) were analyzed using both long-and short-read sequencing, and community composition, diversity metrics, and taxonomic resolution were compared. Sequencing technology influenced observed community structure, but sediment depth also exerted a strong effect. Taxonomic profiles were broadly consistent across methods for most bacterial groups, whereas archaeal diversity was underrepresented in long-read datasets due to primer mismatches. When detected, long reads provided higher taxonomic resolution, frequently to species level, improving ecological interpretation and inference of metabolic potential. Finer-scale analyses, including species contributions to beta diversity and co-occurrence networks, showed greater specificity with long reads. These results demonstrate that long-read sequencing can substantially enhance subsurface microbial characterization, provided that primer design is optimized, and highlight its potential to improve assessments of microbial identity, structure, and function in low-biomass environments.

The Tibetan Plateau, with an average elevation of 4000 m above sea level, is the highest plateau on Earth. It is the third largest store of ice after the Arctic and Antarctic and is often referred to as the ‘Third Pole’. It is an area sensitive to climate shifts and is expected to go through significant warming in the future. Nam Co in central Tibet is located in the modern monsoon regime and was recently drilled as part of the ICDP NamCore drilling project, which aims to reconstruct the Quaternary climate history of the region. Lake sediments act as paleoenvironmental archives; with minerals forming in the water column reflecting the prevailing environmental conditions, which then become part of the sediment package after deposition. However, post-depositional processes, such as early diagenesis, can cause alteration in mineralogy, structure and/or chemistry of deposited sediments. This can happen through sediment compaction, fluid circulation and physico-chemical changes, often mediated by microbial activity in situ. We report results about authigenic minerals and mineral evolution in Nam Co. The aim is to target different diagenetic formation pathways of pyrite by combining detailed structural and compositional data, such as high-resolution X-ray computed micro-tomography (μCT), X-ray fluorescence scanning, and sulphur isotope analyses. We hypothesise the formation of pyrite in Nam Co happens because of diagenetic processes and pathways driven by changes in hydrology and limnology, tectonically induced fluid flow, and microbial activity. The overarching aim is to disentangle these different formation processes, and to assess whether we can use the sulphur isotope composition of pyrite to discriminate between environmental and tectonic controls.

The subsurface biosphere remains poorly characterized, with many resident microorganisms uncultured and lacking genomic references. Despite the growing accessibility of shotgun metagenomics, 16S rRNA gene sequencing remains a standard tool for microbial community profiling, often relying on sequence similarity to reference databases such as SILVA to infer taxonomy and potential function. However, in environments with low biomass and high proportions of unknown lineages, such as deeper sedimentary environments, the accuracy of these inferences and our ability to capture rare taxa remain uncertain. A better inference of these rare taxa may now be possible with the advent of accurate long-read applications that have recently become available. Here we provide a comparison of long-read (PacBio) and short-read (Illumina NextSeq) 16S rRNA approaches for microbial communities from a sediment core of Lake Arnon (Switzerland). We compared community composition in environmental samples and mock controls to evaluate the strengths and limitations of each method. While sequencing technology significantly influenced observed community structure, sediment depth had an even stronger effect. Taxonomic profiles were broadly consistent across methods for most bacterial groups, but archaeal diversity was underrepresented in the long-read data, likely due to primer mismatch. When detected, long-read sequencing offered more accurate taxonomic resolution, often down to the species level, enabling better inference of metabolic potential. Beta diversity patterns were similar at broad taxonomic levels between methods, though more detailed metrics such as species contributions to beta diversity (SCBD) and co-occurrence networks showed enhanced resolution and specificity in long-read datasets. Our results highlight the critical importance of primer design, in particular for capturing archaeal taxa that play important roles in the deep biosphere. With improved primer coverage and continued cost reductions, long-read sequencing holds strong potential for advancing our understanding of subsurface microbial identity, structure and function. ### Competing Interest Statement The authors have declared no competing interest.

ABSTRACTFossilization, or the transition of an organism from the biosphere to the geosphere, is a complex mechanism involving numerous biological and geological variables. Bacteria are one of the most significant biotic players to decompose organic matter in natural environments, early on during fossilization. However, bacterial processes are difficult to characterize as many different abiotic conditions can influence bacterial efficiency in degrading tissues. One potentially important variable is the composition and nature of the sediment on which a carcass is deposited after death. We experimentally examined this by decaying the marine shrimpPalaemon variansunderwater on three different clay sediments. Samples were then analyzed using 16S ribosomal RNA sequencing to identify the bacterial communities associated with each clay system. Results show that samples decaying on the surface of kaolinite have a lower bacterial diversity than those decaying on the surface of bentonite and montmorillonite, which could explain the limited decay of carcasses deposited on this clay. However, this is not the only role played by kaolinite, as a greater proportion of gram-negative over gram-positive bacteria is observed in this system. Gram-positive bacteria are generally thought to be more efficient at recycling complex polysaccharides such as those forming the body walls of arthropods. This is the first experimental evidence of sediments shaping an entire bacterial community. Such interaction between sediments and bacteria might have contributed to arthropods’ exquisite preservation and prevalence in kaolinite-rich Lagerstätten of the Cambrian Explosion.

For long time in the history of Earth, ferruginous conditions governed the oceans. With the rise of oxygen during the Proterozoic era and the subsequent evolution of living organisms, worldwide deposition of iron formations occurred. These sedimentary units reveal the transition into oxic oceans, passing by local and transitory euxinic conditions, especially in coastal shelves. Constraining the iron cycle and the biogeochemical processes occurring in present and past ferruginous basins helps answering some of the question regarding global oxygenation, the evolution of life and past climate changes. Therefore, Fe speciation and Fe isotopes in both Proterozoic and recent sedimentary records have been widely used to reconstruct past basin dynamics and redox conditions in the sediment–water interface. However, sedimentation and early diagenesis can alter paleoredox proxies and their primary climate signals. In this work, we disentangled alteration processes occurring at the redox front below the sediment–water interface of a ventilated deep-water lake (Lago Fagnano, Argentina/Chile). A sequential extraction protocol was applied to characterize two reactive Fe pools: Fe oxyhydroxides and reduced iron. Subsequently, Fe isotopes were constrained to determine the main processes mobilizing Fe. At the redox front, ferric minerals reach a δ56Fe value of − 1.3‰ resulting from oxidation of dissolved Fe likely following a Rayleigh distillation effect. Dissolved Fe is produced right below via Fe reduction, as shown by the low ferric Fe content. Our observations delineate a redox cycle and a redox horizon undergoing constant upward migration, initiated by regular sedimentation. However, during events of increased rapid sedimentation (e.g., seismites) this dynamic cycle is interrupted inducing full or partial preservation of the Fe-rich redox front. In such case, oxidation of dissolved Fe is interrupted and can be recycled in ferrous minerals, such as Fe monosulfides and amorphous phases with δ56Fe values down to − 1.7 ‰. These findings have significant implications for the recording of biogeochemical cycles in the geological past, the use of Fe isotopes in freshwater-lake sediments for paleoclimate studies, and the progress of our knowledge regarding the geochemistry of past oceans.

Microbial mats and microbialites are essential tools for reconstructing early life and its environments. To better understand microbial trace element cycling, a microbial mat was collected from the sinkhole systems of the western shores of the Dead Sea, a dynamic environment exhibiting diverse extreme environments. Intense arsenic enrichment (up to 6.5 million times higher than current water concentrations, and 400 times the bulk concentration in the mat) was measured. Arsenic was dominantly found as As(V) in organic molecules, as shown by XANES spectra and high-resolution elemental mapping. Arsenic cycling genes obtained from metagenomic analysis were associated with arsenic detoxification, supporting an active mechanism of As(V) uptake, As(III) efflux and organo-arsenic accumulation in microbial mat extracellular polymeric substances. Thus, we propose that such localized enrichment of As can be attributed to a transient increase in As(V) concentrations in the circulating subsurface water of the Dead Sea shore and its subsequent incorporation in organoarsenic molecules through microbial detoxification processes. Our dataset supports the possibility of metalloid enrichments recorded in very localized facies due to rapid geogenic fluctuations in chemistry of the water flowing over a biofilm. In this context, this example calls for caution when interpreting metal(loid) enrichment in organic matter-rich layers and microbialites of Paleoproterozoic origins. Arsenic signatures in Precambrian organic matter and carbonate rocks may host biosignatures, including evidence of extracellular polymeric susbtances, As-binding and detoxification processes, without supporting arsenotrophy. They do, however, provide clues to better assess paleoenvironmental conditions at the time of microbial mat formation and sedimentation.

Silicic caldera volcanoes present major volcanic and seismic hazards but also host dynamic hydrothermal and groundwater systems and a rich but largely unexplored subsurface biosphere. Many of these volcanoes are hosted in rift settings. The intricate connections and feedbacks among magmatism, rifting, hydrothermal processes, and the biosphere in these complex systems remain poorly understood, necessitating subsurface joint observations that are only enabled by scientific drilling. The CALDERA (Connections Among Life, geo-Dynamics and Eruptions in a Rifting Arc caldera) project workshop funded by the International Continental Scientific Drilling Program (ICDP) gathered multi-disciplinary international experts in January 2023 to advance planning of a scientific drilling project within one of these dynamic, rift-hosted calderas, the Okataina Volcanic Centre (OVC), Aotearoa New Zealand. The OVC's high eruption rate, frequent unrest events and earthquake swarms, location in a densely faulted rapidly extending rift, abundant groundwater–geothermal fluid circulations, and diverse surface hot spring microbiota make it an ideal location for exploring a connected geo-hydro-biosphere via scientific drilling and developing a test bed for novel volcano monitoring approaches. Drilling configurations with at least two boreholes (∼ 200 and ∼ 1000–1500 m deep) were favoured to achieve the multi-disciplinary objectives of the CALDERA project. Decadal monitoring including biosphere activity and composition has the potential to evaluate the response of the hydro-bio system to volcano-tectonic activity. In addition to the OVC caldera-scale datasets already available, site surveys will be conducted to select the best drilling locations. The CALDERA project at the OVC would provide, for the first time, an understanding of volcanic–tectonic–hydrological–biological connections in a caldera–rift system and a baseline for global comparisons with other volcanoes, rifts, and hydrothermal systems. CALDERA would serve as an unprecedented model system to understand how and how quickly the subsurface biosphere responds to geologic activities. Discoveries will improve assessment of volcanic and seismic hazards, guide the sustainable management and/or conservation of groundwater and geothermal resources and microbial ecosystems, and provide a forum for interweaving mātauranga Māori and Western knowledge systems.

This qualitative study examines perceptions of open access from focus groups including thirty-eight faculty who identify as Black, Indigenous, and People of Color (BIPOC). In responses, BIPOC faculty reflect on the culture and support of open access within their departments, institutions, and professional associations. It was at a time of increased discussion about knowledge equity, the impact of access to research during the 2020 pandemic, and a precursor to the 2022 U.S. Office of Science and Technology Policy Memo to expand access to data and publications sponsored by all federal funding agencies. In general, BIPOC faculty face compounded risks with open access and inequities in scholarly publishing. However, participants believe open publishing processes allow more flexibility and connection to communities. The investigators use the grounded theory method for analysis, provide themes as well as direct quotes from the data, and discuss practical applications for supporting BIPOC scholars with engagement in open access.

Sedimentologika is a community-driven Diamond Open Access scientific journal for the publication of work in the broad area of sedimentology and stratigraphy. The journal aims to provide a platform to the academic community and broader society, offering and guaranteeing permanent free publication and free access to peer-reviewed scientific studies focusing on all types of sedimentary processes, deposits, and environments across all spatial and temporal scales, on Earth or any other planetary body. It will publish high-quality research that will advance the field of sedimentary science (through multidisciplinarity, new teaching practices, tools and methods, and progress in accessibility to science). Sedimentologika is part of an ongoing broader Diamond Open Access movement in geosciences aspiring freedom from the financial barriers and pressures of private publishing houses, to provide direct and equal access to science for all citizens, scientists, and institutions worldwide. The published material will include research, review, methodology and opinion articles, which will be free to share, as the authors will retain the copyright on all the submitted material. Manuscripts will be published in English. Authors can attach a second abstract in the language of their choice, further allowing local communities, students, or decisional bodies to access, at least, a summary of the latest research, thus reducing potential language barriers. Sedimentologika follows Open Science principles to promote ethical dissemination and accessibility of science and knowledge, following high equity, diversity and inclusion standards. Sedimentologika emerged as a solution for the scientific community to sidestep structural inequality of the academic publishing system that is becoming financially unsustainable to its payers (authors, funding agencies), and to commit to bibliodiversity. The objective is to ensure that scientific findings remain accessible to all in order to keep advancing research and informing society on how we understand sedimentology and stratigraphy in the world around us. Sedimentologika is driven by the academic and scientific community for the community and society, promoting self-governance and adapting to the needs expressed by the community.

Introduction: This article reports results from a survey of faculty members with editorial responsibilities. The survey explored what publishing services and platform functionalities respondents found most valuable in their work as editors, how satisfied they were with the services provided by commercial publishers, and to what extent they were aware of alternative publishing practices. Method: The authors used data collected from a survey instrument that was distributed to a sample (n = 515) of faculty members with editorial responsibilities at their institution. Results: Collected data suggest that faculty editors value specific publishing services (e.g., coordination of peer review and copyediting) and platform functionality (e.g., submission and peer-review management) more than others, recognize several challenges facing academic publishing in their disciplines (including the transition to open access publishing models), and are mostly aware of common forms of open access research dissemination such as open access journals and institutional repositories. Discussion: The survey results may be helpful to library publishers in making decisions about what publishing services and platform functionalities to prioritize in the development of their publishing programs. In addition to utilizing the survey data to assess the needs of editors, the authors also identified a number of expanded uses of the survey related to marketing and outreach. Conclusion: Insofar as faculty editors are key stakeholders that library publishers seek to build partnerships with, it is important to understand their needs and preferences as editors. This article provides some insight into these questions that may prove helpful to library publishers.

The hypersaline Dead Sea and its sediments are natural laboratories for studying extremophile microorganism habitat response to environmental change. In modern times, increased freshwater runoff to the lake surface waters resulted in stratification and dilution of the upper water column followed by microbial blooms. However, whether these events facilitated a microbial response in the deep lake and sediments is obscure. Here we investigate archived evidence of microbial processes and changing regional hydroclimate conditions by reconstructing deep Dead Sea chemical compositions from pore fluid major ion concentration and stable S, O, and C isotopes, together with lipid biomarkers preserved in the hypersaline deep Dead Sea ICDP-drilled core sediments dating to the early Holocene (ca. 10,000 years BP). Following a significant negative lake water balance resulting in salt layer deposits at the start of the Holocene, there was a general period of positive net water balance at 9500–8300 years BP. The pore fluid isotopic composition of sulfate exhibit evidence of intensified microbial sulfate reduction, where both δ 34 S and δ 18 O of sulfate show a sharp increase from estimated base values of 15.0‰ and 13.9‰ to 40.2‰ and 20.4‰, respectively, and a δ 34 S vs. δ 18 O slope of 0.26. The presence of the n -C 17 alkane biomarker in the sediments suggests an increase of cyanobacteria or phytoplankton contribution to the bulk organic matter that reached the deepest parts of the Dead Sea. Although hydrologically disconnected, both the Mediterranean Sea and the Dead Sea microbial ecosystems responded to increased freshwater runoff during the early Holocene, with the former depositing the organic-rich sapropel 1 layer due to anoxic water column conditions. In the Dead Sea prolonged positive net water balance facilitated primary production and algal blooms in the upper waters and intensified microbial sulfate reduction in the hypolimnion and/or at the sediment–brine interface.

Changing redox conditions in water columns or sediment–water interfaces of lakes are captured as sedimentary archives, and are often influenced by climate. Their study therefore permits the reconstruction of past climate change on (sub‐) annual to longer timescales. In Lago Fagnano (54°S Argentina/Chile), a large oligotrophic and deep‐oxygenated lake, alternations of light grey clay and dark greenish and black laminae are preserved throughout the Holocene sedimentary record. This study aims to clarify the mechanism of laminae formation and preservation in Lago Fagnano, and their relation to changing redox conditions in the lake. High‐resolution major element scanning and mapping along with detailed mineralogical analyses of sediment cores allowed identifying Fe‐oxides, Mn‐oxides and Fe‐(mono) sulphides as responsible for the lamination. Based on the interpretation of redox processes at the current sedimentary redox boundary and of buried palaeo‐redox fronts underlying mass‐transported deposits, the greenish laminae enriched in Fe‐oxides are interpreted as palaeo‐redox fronts. The preservation of such former interfaces in Lago Fagnano sediments is most likely promoted by rapid increases of sedimentation due to higher runoff related to stronger Southern Hemisphere Westerlies. The formation of black laminae, showing only traces of Fe‐(mono) sulphides and organic matter, is obscured by oxidation and early diagenetic processes, i.e. degradation and partial pyritization. These layers were presumably generated by small changes in bottom‐water oxygenation due to reduced mixing and/or higher productivity. This study highlights the value of high‐resolution sediment−geochemical analyses to better understand redox and diagenetic processes in oligotrophic mixed lakes.

Exopolymeric Substances (EPS) form biofilms in which the vast majority of prokaryotic organisms develop and thrive. They are ubiquitous, harbor metal and chemical species binding properties and can be the matrix for bio/orgamineralizations. Because of these properties, EPS have also been proposed as some of the most ancient traces of microbial life on Earth. They form sedimentary structures diagnostic of biological activity in some of the most ancient sedimentary rocks of the Archean. However, the metabolisms hosted by such ecosystems remain poorly understood given poor preservation and specificity of the available molecular, isotopic or fossilized signatures. Deep time paleobiological research therefore needs for new ways to unlock the history of the rare and variably preserved sedimentary rocks of these ages, by looking for new proxies that could help characterizing microbial ecosystems and better understand the co-evolution of the geosphere and the biosphere. We here attempt to describe trace metal signatures of a modern, arsenic-rich lacustrine microbial mat fueled by oxygenic and anoxygenic photosynthesis as an analog to better understand how microbial mats and their sedimentary and chemical signatures can be preserved in the Archean sedimentary record. We coupled in-situ imaging of a microbial mat from modern Dead Sea shore with SEM, Raman spectroscopy, and X-ray mapping, to (meta)genomics data and chemical analyses. Arsenic enrichments in the anoxygenic photosynthetic layer of the mat reached a 10’000-fold level, and was associated to Mg-Si-rich EPS. The latter ultimately mineralized into aragonite clusters with a co-enrichment of Sr, Mn and Mo. At the mat scale, the mineralized zone (rich in Fe, Sr and Ca from authigenic calcium carbonates and detrital clay) is clearly located above the As-enrichment layer, in association with Mn. These data support a chemically dynamic microbial mat where microbial activity, EPS chemical affinity and environmental processes lead to specific organic and mineralized chemical signatures linked to metabolic activity. Metagenomics and synchrotron-based speciation analyses shall confirm the links between elemental enrichments and the microbial metabolic pathways. We parallel this study to a well characterized microbial system of the Archean, the stromatolitic units of the Tumbiana Lake (2.72 Ga, Pilbara, Western Australia). In this environment, microbial mat accretionary behaviour has formed limestone stromatolites harboring layered nanopyrites embedded in carbonaceous material and chlorite (Marin-Carbonne et al., 2018). C, N and S isotopes of mineral fractions have suggested a connection of photosynthetic activity, sulfate reduction and methane cycling, potentially influenced by arsenotrophy (e.g. Thomazo et al., 2009; Sforna et al., 2014; Lepot et al., 2019). This is likely the most diverse undisputed microbial environment of the Archean. Our trace-elemental mapping using PIXE suggests co-enrichment of Mo and As in association to the nanopyrite-OM layer, that could be attributed to arsenotrophic and anoxygenic photosynthetic activity, in a similar fashion than argued for in the Dead Sea mat. Simulated diagenesis experiments are planned and should be able to provide chemical insights into the transformation of microbial mats to their fossilized counterparts at the microscale, to further validate the promises of metal biosignatures for reconstructing Archean ecosystems.

In recent years resulting investigations in living microbialites have provided significant data that have been critical to disentangle the role of the various biotic and abiotic processes contributing to their development. Despite these efforts separating the impact and magnitude of these processes remain a difficult task. At present the Maquinchao Basin in northeastern Patagonia, Argentina, contains both fossil and living microbialites. Thus, the region provides a unique opportunity to investigate the impact of intrinsic and extrinsic parameters in carbonate precipitation. Early investigations (Austral summer 2011) in living microbialites concluded that organomineralization was related to both photosynthetic activity in the more surficial layer (green), and sulfate-reduction in the lower part (beige). Field investigations in the same area four years later showed that the pounds previously containing abundant active mats had dried out, and in general revealed the absence of globular structured clusters of minerals in the microbial mats. Here we present microscale investigations using optical microscopy and SEM along with the 16SrRNA gene sequence diversity, and the physico-chemical parameters of the hosting waters. They were carried out in successive seasonal samplings in November 2015, April-May 2016, August 2016, February 2017, and March 2018. All microbialite samples show regular occurrences of sulfate reducing bacteria (SRB) along with filaments of unknown origin. Carbonates are observed associated with erect filaments in shallow and active running water locations whereas the mineral phase is located below organic matter film in comparatively deeper and calmer water areas. Additionally, seasonal changes in the physico-chemical properties of the hosting waters indicate that extrinsic parameters, especially evaporation, might play a more substantial role in the precipitation of these carbonates than previously proposed. The environmental differences between 2011 and 2015 in meteorological conditions, regional volcanic activity and associated deposits in the basin are analyzed. We concluded that they are likely responsible of the decrease of the mineralization processes, and particularly those associated with photosynthetic activity. These results call for caution when interpreting the degree of biological impact on the formation of microbialites in the geological record. Local extrinsic factors might have a changeable impact over time switching mineral precipitation from biotic to abiotic and vice-versa, which can be undistinguishable in fossilized microbialites.

The Office of Digital Research and Scholarship partners with members of the scholarly community at FSU and beyond to engage with and act on innovative ideas in teaching, research, and creative activity. We privilege marginalized voices and unique contributions to scholarly discourse. We support interdisciplinary inquiry in our shared pursuit of research excellence. We work with scholars to explore and implement new modes of scholarship that emphasize broad impact and access.Our dream is to create an environment where our diverse scholarly community is rewarded for engaging in innovative modes of research and scholarship. We envision a system of research communication that is rooted in open, academy-owned infrastructure, that privileges marginalized voices, and that values all levels and aspects of intellectual labor. In addition to the accomplishments related to our core work areas outlined in this report, we also developed an Anti-Racist Action Plan in 2020 and continue to work on enacting and periodically revising and updating the goals outlined therein.