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Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras.Hitherto, ancient frozen soils have proved excellent in preservingDNAmolecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a fewmetres fromthe sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNAfromlake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here,we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progressmade up to the present.Weargue that aDNAanalyses add newand additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments.

Living benthic foraminifera, known as environmental bio-indicators of both natural and anthropogenic conditions in marine environments, were investigated in the coastal environment of Roscoff Aber Bay (Brittany, France). Eight sampling sites subject to natural variations (freshwater inputs, tides) and/or anthropogenic impacts (pollution, eutrophication) were studied over four seasons in 2021–2022 (November, February, May, August). We sought to understand the spatial distribution of foraminiferal populations within and between sampling sites over the different seasons and to identify sensitive species and those tolerant to anthropogenic impacts. To this end, sedimentary and biogeochemical characteristics of the sediments were examined by measuring grain size, temperature, oxygen, salinity, pH, environmental pigment concentration (chl a and phaeopigments), total organic carbon (TOC), isotopic ratios of carbon (δ 13 C), nitrogen (δ 15 N) and sulfide (δ 34 S), and chl a fluorescence. Considering these parameters as potential driving factors, four environments were distinguished among the sampling sites: open water, terrestrial, oligotrophic and eutrophic. These showed an increasing gradient of organic supply as well as very different microbial activities, highlighted by carbon and sulfide isotopic ratios. Foraminiferal population study revealed the dominant species characterising these main environments. The lowest abundance but highest diversity of foraminifera was found in the harbour site, associated with the dominance of Haynesina germanica , suggesting this species is tolerant to eutrophic environments and anthropogenic impacts. Open water was dominated by Ammonia beccarii and Elphidium crispum , while Quinqueloculina seminula was the most abundant species in the site with the greatest terrestrial influence. Interestingly, the observed organic enrichment of the harbour due to anthropogenic activities (fisheries, waste deposits, etc.) does not seem to significantly affect foraminiferal diversity. Overall, the benthic foraminiferal species in Roscoff Aber Bay appear to be an excellent proxy for marine environmental conditions under various natural and anthropogenic influences.

Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.

Microbial life in marine sediment contributes substantially to global biomass and is a crucial component of the Earth system. Subseafloor sediment includes both aerobic and anaerobic microbial ecosystems, which persist on very low fluxes of bioavailable energy over geologic time. However, the taxonomic diversity of the marine sedimentary microbial biome and the spatial distribution of that diversity have been poorly constrained on a global scale. We investigated 299 globally distributed sediment core samples from 40 different sites at depths of 0.1 to 678 m below the seafloor. We obtained ~47 million 16S ribosomal RNA (rRNA) gene sequences using consistent clean subsampling and experimental procedures, which enabled accurate and unbiased comparison of all samples. Statistical analysis reveals significant correlations between taxonomic composition, sedimentary organic carbon concentration, and presence or absence of dissolved oxygen. Extrapolation with two fitted species–area relationship models indicates taxonomic richness in marine sediment to be 7.85 × 10³ to 6.10 × 10⁵ and 3.28 × 10⁴ to 2.46 × 10⁶ amplicon sequence variants for Archaea and Bacteria, respectively. This richness is comparable to the richness in topsoil and the richness in seawater, indicating that Bacteria are more diverse than Archaea in Earth’s global biosphere.

Microplastics are ubiquitous in estuarine, coastal, and deep sea sediments. The impacts of microplastics on sedimentary microbial ecosystems and biogeochemical carbon and nitrogen cycles, however, have not been well reported. To evaluate if microplastics influence the composition and function of sedimentary microbial communities, we conducted a microcosm experiment using salt marsh sediment amended with polyethylene (PE), polyvinyl chloride (PVC), polyurethane foam (PUF) or polylactic acid (PLA) microplastics. We report that the presence of microplastics alters sediment microbial community composition and nitrogen cycling processes. Compared to control sediments without microplastic, PUF- and PLA-amended sediments promote nitrification and denitrification, while PVC amendment inhibits both processes. These results indicate that nitrogen cycling processes in sediments can be significantly affected by different microplastics, which may serve as organic carbon substrates for microbial communities. Considering this evidence and increasing microplastic pollution, the impact of plastics on global ecosystems and biogeochemical cycling merits critical investigation. Plastic pollution has infiltrated every ecosystem, but few studies have quantified the biogeochemical or ecological effects of plastic. Here the authors show that microplastics in ocean sediment can significantly alter microbial community structure and nitrogen cycling.

A fourth of the global seabed sediment volume is buried at depths where temperatures exceed 80 °C, a previously proposed thermal barrier for life in the subsurface. Here, we demonstrate, utilizing an extensive suite of radiotracer experiments, the prevalence of active methanogenic and sulfate-reducing populations in deeply buried marine sediment from the Nankai Trough subduction zone, heated to extreme temperature (up to ~120 °C). The small microbial community subsisted with high potential cell-specific rates of energy metabolism, which approach the rates of active surface sediments and laboratory cultures. Our discovery is in stark contrast to the extremely low metabolic rates otherwise observed in the deep subseafloor. As cells appear to invest most of their energy to repair thermal cell damage in the hot sediment, they are forced to balance delicately between subsistence near the upper temperature limit for life and a rich supply of substrates and energy from thermally driven reactions of the sedimentary organic matter. In the deep sedimentary biosphere, 80 °C has been proposed as an upper thermal barrier for life. Using a suite of radiotracer experiments, this study reports active methanogenic and sulfate-reducing microbial populations with high cell-specific metabolic rates in deeply buried marine sediments from the Nankai Trough subduction zone, which reach temperatures up to 120 °C.

The production of bifaces is a central feature of the Acheulian culture, reflecting complex planning, material selectivity, and skilled execution. At Gesher Benot Ya'aqov (GBY), a key early Middle Pleistocene site situated within the tectonically active northern segment of the Dead Sea Transform, basalt served as a significant raw material used for the manufacture of giant cores, bifaces (handaxes and cleavers), and associated debris. However, the geological instability of the region, together with the burial and erosion of basalt flows, complicates the identification of the sources exploited by GBY hominins. Here we apply a set of geochemical analyses including major elements, trace elements, rare earth elements, and multivariate statistical approaches to basalt artifacts and regional geological samples, including subsurface drill cores. These data reveal the compositional range of basalts available around GBY and allow the mapping of archaeological specimens onto this geochemical landscape. The results demonstrate that most artifacts were produced from basalt flows immediately surrounding the site, while a subset of tools particularly some cleavers reflect the use of additional flows not currently exposed at the surface. Together, these findings clarify the raw-material procurement strategies employed by GBY hominins and highlight a selective, structured approach to basalt exploitation within a dynamically changing landscape. The integration of geological and archaeological evidence offers new insights into the planning depth, technological behavior, and adaptive strategies of Acheulian populations in the Jordan Valley.

Studies of marine benthic archaeal communities are updating our view of their taxonomic composition and metabolic versatility. However, large knowledge gaps remain with regard to community assembly processes and inter taxa associations. Here, using 16S rRNA gene amplicon sequencing and qPCR, we investigated the spatiotemporal dynamics, assembly processes, and co-occurrence relationships of the archaeal community in 58 surface sediment samples collected in both summer and winter from across ~1500 km of the eastern Chinese marginal seas. Clear patterns in spatiotemporal dynamics in the archaeal community structure were observed, with a more pronounced spatial rather than seasonal variation. Accompanying the geographic variation was a significant distance-decay pattern with varying contributions from different archaeal clades, determined by their relative abundance. In both seasons, dispersal limitation was the most important process, explaining ~40% of the community variation, followed by homogeneous selection and ecological drift, that made an approximately equal contribution (~30%). This meant that stochasticity rather than determinism had a greater impact on the archaeal community assembly. Furthermore, we observed seasonality in archaeal co-occurrence patterns: closer inter-taxa connections in winter than in summer, and unmatched geographic patterns between community composition and co-occurrence relationship. These results demonstrate that the benthic archaeal community was assembled under a seasonal-consistent mechanism but the co-occurrence relationships changed over the seasons, indicating complex archaeal dynamic patterns in coastal sediments of the eastern Chinese marginal seas.

Low phosphorus burial in shallow marine sedimentary rocks before about 750 million years ago implies a change in the global phosphorus cycle, coinciding with the end of what may have been a stable low-oxygen world. A history of phosphorus limitation It is thought that the nutrient phosphorus limits marine primary productivity on geological timescales, but it is not clear whether phosphorus limitation has persisted throughout Earth's history. On the basis of a compilation of phosphorus abundances in marine sedimentary rocks spanning the past 3.5 billion years, and a biogeochemical model, Christopher Reinhard, Noah Planavsky and colleagues suggest that a prolonged period of phosphorus biolimitation was followed by a fundamental shift in the phosphorus cycle during the late Proterozoic eon (between 800 million and 635 million years ago). This is coincident with a previously inferred shift in marine redox states, severe perturbations to Earth's climate system, and the emergence of animals. The macronutrient phosphorus is thought to limit primary productivity in the oceans on geological timescales 1 . Although there has been a sustained effort to reconstruct the dynamics of the phosphorus cycle over the past 3.5 billion years 2 , 3 , 4 , 5 , it remains uncertain whether phosphorus limitation persisted throughout Earth’s history and therefore whether the phosphorus cycle has consistently modulated biospheric productivity and ocean–atmosphere oxygen levels over time. Here we present a compilation of phosphorus abundances in marine sedimentary rocks spanning the past 3.5 billion years. We find evidence for relatively low authigenic phosphorus burial in shallow marine environments until about 800 to 700 million years ago. Our interpretation of the database leads us to propose that limited marginal phosphorus burial before that time was linked to phosphorus biolimitation, resulting in elemental stoichiometries in primary producers that diverged strongly from the Redfield ratio (the atomic ratio of carbon, nitrogen and phosphorus found in phytoplankton). We place our phosphorus record in a quantitative biogeochemical model framework and find that a combination of enhanced phosphorus scavenging in anoxic, iron-rich oceans 6 , 7 and a nutrient-based bistability in atmospheric oxygen levels could have resulted in a stable low-oxygen world. The combination of these factors may explain the protracted oxygenation of Earth’s surface over the last 3.5 billion years of Earth history 8 . However, our analysis also suggests that a fundamental shift in the phosphorus cycle may have occurred during the late Proterozoic eon (between 800 and 635 million years ago), coincident with a previously inferred shift in marine redox states 9 , severe perturbations to Earth’s climate system 10 , and the emergence of animals 11 , 12 .

Cyanobacterial blooms frequently occur in freshwater lakes, subsequently, substantial amounts of decaying cyanobacterial bloom biomass (CBB) settles onto the lake sediments where anaerobic mineralization reactions prevail. Coupled Fe/S cycling processes can influence the mobilization of phosphorus (P) in sediments, with high releases often resulting in eutrophication. To better understand eutrophication in Lake Taihu (PRC), we investigated the effects of CBB and temperature on phosphorus cycling in lake sediments. Results indicated that added CBB not only enhanced sedimentary iron reduction, but also resulted in a change from net sulfur oxidation to sulfate reduction, which jointly resulted in a spike of soluble Fe(II) and the formation of FeS/FeS2. Phosphate release was also enhanced with CBB amendment along with increases in reduced sulfur. Further release of phosphate was associated with increases in incubation temperature. In addition, CBB amendment resulted in a shift in P from the Fe-adsorbed P and the relatively unreactive Residual-P pools to the more reactive Al-adsorbed P, Ca-bound P and organic-P pools. Phosphorus cycling rates increased on addition of CBB and were higher at elevated temperatures, resulting in increased phosphorus release from sediments. These findings suggest that settling of CBB into sediments will likely increase the extent of eutrophication in aquatic environments and these processes will be magnified at higher temperatures.