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Only a few palaeo-records extend beyond the Holocene in Yakutia, eastern Siberia, since most of the lakes in the region are of Holocene thermokarst origin. Thus, we have a poor understanding of the long-term interactions between terrestrial and aquatic ecosystems and their response to climate change. The Lake Khamra region in southwestern Yakutia is of particular interest because it is in the transition zones from discontinuous to sporadic permafrost and from summergreen to evergreen boreal forests. Our multiproxy study of Lake Khamra sediments reaching back to the Last Glacial Maximum 21 cal ka BP, includes analyses of organic carbon, nitrogen, XRF-derived elements, sedimentary ancient DNA amplicon sequencing of aquatic and terrestrial plants and diatoms, as well as classical counting of pollen and non-pollen palynomorphs (NPP). The palaeogenetic approach revealed 45 diatom, 191 terrestrial plant, and 65 aquatic macrophyte taxa. Pollen analyses identified 34 pollen taxa and 28 NPP taxa. The inferred terrestrial ecosystem of the Last Glacial comprises tundra vegetation dominated by forbs and grasses, likely inhabited by megaherbivores. By 18.4 cal ka BP a lake had developed with a high abundance of macrophytes and dominant fragilarioid diatoms, while shrubs expanded around the lake. In the Bølling-Allerød at 14.7 cal ka BP both the terrestrial and aquatic systems reflect climate amelioration, alongside lake water-level rise and woodland establishment, which was curbed by the Younger Dryas cooling. In the Early Holocene warmer and wetter climate led to taiga development and lake water-level rise, reflected by diatom composition turnover from only epiphytic to planktonic diatoms. In the Mid-Holocene the lake water level decreased at ca. 8.2 cal ka BP and increased again at ca. 6.5 cal ka BP. At the same time mixed evergreen-summergreen forest expanded. In the Late Holocene, at ca. 4 cal ka BP, vegetation cover similar to modern conditions established. This stu

Current global warming results in rising sea-water temperatures, and the loss of sea ice in Arctic and subarctic oceans impacts the community composition of primary producers with cascading effects on the food web and potentially on carbon export rates. This study analyzes metagenomic shotgun and diatom rbcL amplicon sequencing data from sedimentary ancient DNA of the subarctic western Bering Sea that records phyto- and zooplankton community changes over the last glacial-interglacial cycles, including the last interglacial period (Eemian). Our data show that interglacial and glacial plankton communities differ, with distinct Eemian and Holocene plankton communities. The generally warm Holocene period is dominated by picosized cyanobacteria and bacteria-feeding heterotrophic protists, while the Eemian period is dominated by eukaryotic picosized chlorophytes and Triparmaceae. By contrast, the glacial period is characterized by microsized phototrophic protists, including sea ice-associated diatoms in the family Bacillariaceae and co-occurring diatom-feeding crustaceous zooplankton. Our deep-time record of plankton community changes reveals a long-term decrease in phytoplankton cell size coeval with increasing temperatures, resembling community changes in the currently warming Bering Sea. The phytoplankton community in the warmer-than-present Eemian period is distinct from modern communities and limits the use of the Eemian as an analog for future climate scenarios. However, under enhanced future warming, the expected shift toward the dominance of small-sized phytoplankton and heterotrophic protists might result in an increased productivity, whereas the community's potential of carbon export will be decreased, thereby weakening the subarctic Bering Sea's function as an effective carbon sink.

Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.

Sedimentary ancient DNA (sedaDNA) has proven to be a useful tool for palaeoenvironmental studies, but only a handful of studies exist so far for tropical regions. In this study we used sedaDNA to study the temporal succession of Brachionus spp. rotifer mitochondrial DNA haplotypes using two sediment cores from two climatically different alkaline-saline crater lakes from the Kenyan Rift Valley. Data were retrieved from a sediment core (dating back to AD 1800) from Lake Kageinya, located in the remote, hot and hyper-arid Suguta Valley. sedaDNA was used to study the temporal succession of mitochondrial DNA haplotypes of Brachionus spp. rotifers. The results were compared to previously published data from Lake Sonachi, a well-studied lake in the humid and colder mountainous region of Kenya near the town of Naivasha, now supported by a 210Pb age chronology. Both records extend back before the onset of substantial anthropogenic impact in these regions. The results revealed that climate—rather than anthropogenic impact—was most strongly correlated with haplotype changes in both lakes. During prolonged dry periods (such as from AD 1910 to the late AD 1960s), certain haplotypes persisted. Sudden changes and the emergence of alter native haplotypes were observed when climate became more humid or during episodes of highly variable climate (before AD 1910 and from AD 1960s onwards). Progressive changes in prevailing haplotypes during periods with variable climate could reflect local adaptation and/or be the result of immigration of new haplotypes after the eradication of previous populations during extreme environmental conditions (high temperatures, UV irradiation, pH and salinity). The results indicate that, despite adverse chemical conditions, sedaDNA in tropical lake sediments is preserved for at least a few hundred years. Therefore, its analysis provides a useful complementary palaeoenvironmental proxy for palaeolimnological reconstructions and novel insights on changes in

Ancient environmental DNA (aeDNA) data are close to enabling insights into past global-scale biodiversity dynamics at unprecedented taxonomic extent and resolution. However, achieving this potential requires solutions that bridge bioinformatics and paleoecoinformatics. Essential needs include support for dynamic taxonomic inferences, dynamic age inferences, and precise stratigraphic depth. Moreover, aeDNA data are complex and heterogeneous, generated by dispersed researcher networks, with methods advancing rapidly. Hence, expert community governance and curation are essential to building high-value data resources. Immediate recommendations include uploading metabarcoding-based taxonomic inventories into paleoecoinformatic resources, building linkages among open bioinformatic and paleoecoinformatic data resources, harmonizing aeDNA processing workflows, and expanding community data governance. These advances will enable transformative insights into global-scale biodiversity dynamics during large environmental and anthropogenic changes.

The study of environmental ancient DNA provides us with the unique opportunity to link environmental with ecosystem change over a millennial timescale. Paleorecords such as lake sediments contain genetic pools of past living organisms that are a valuable source of information to reconstruct how ecosystems were and how they changed in response to climate in the past. Here, we report on paleometagenomics of a sedimentary record in northern Siberia covering the past 6700 years. We integrated taxonomic with functional gene analysis, which enabled to shed light not only on community compositions but also on eco-physiological adaptations and ecosystem functioning. We reconstructed the presence of an open boreal forest 6700 years ago that over time was gradually replaced by tundra. This vegetation change had major consequences on the environmental microbiome, primarily enriching bacterial and archaeal ammonia oxidizers (e.g., Nitrospira, Nitrosopumilus, and Ca. Nitrosocosmicus) in the tundra ecosystem. We identified a core microbiome conserved through time and largely consisting of heterotrophic bacteria of the Bacteroidetes phylum (e.g., Mucilaginibacter) harboring numerous functional genes for degradation of plant-biomass and abiotic and biotic stress resistance. Archaea were also a key functional guild, involved in nitrogen and carbon cycling, not only methanogenesis but possibly also degradation of plant material via enzymes such as cellulases and amylases. Overall, the paleo-perspective offered by our study can have a profound impact on modern climate change biology, by helping to explain and predict the ecological interplay among multiple ecosystem levels based on past experiences.

Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.

Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Macrophytes are especially good environmental indicators, thus their environmental DNA palaeorecord might shed light on past postglacial environments. Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding and metabarcoding markers, in order to explore how each of these methods can be used to capture aquatic vegetation diversity and change. We then investigate the extent to which such a record can be leveraged for reconstructing local environmental conditions, using a case study based on macrophyte ecological niches. We find that, with state-of-the-art DNA barcode reference libraries, using metabarcoding to target the P6 loop region of the chloroplast trnL (UAA) intron is optimal to maximise taxonomic resolution and the diversity of past macrophyte communities. Shotgun sequencing also retrieves a high proportion of aquatic macrophyte diversity, but has the lowest taxonomic resolution, and targeted capture needs to be more widely applied before comparisons can be made. From our case study, we infer past aquatic habitats from sedimentary ancient DNA records of macrophyte taxa. We reconstructed Holocene thermal range, continentality, water pH, trophic status, and light conditions in northern Fennoscandia. We show an overall stability since 9,000 years ago, even though individual lakes display different trends and variation in local climatic and physico-chemical conditions. Combined with the availability of near-exhaustive barcode and traits databases, metabarcoding data can support wider ecological reconstructions that are not limited to aquatic plant taxonomic inventories but can also be used to infer past changes in water conditions and their environmental drivers. Sedimentary DNA is also a powerful tool to measure present diversity, as well as to reconstruct past lacustrine and fluvial commu

This study is based on multiproxy data gained from a 14C-dated 6.5 m long sediment core and a 210Pb-dated 23 cm short core retrieved from Lake Rauchuagytgyn in Chukotka, Arctic Russia. Our main objectives are to reconstruct the environmental history and ecological development of the lake during the last 29 kyr and to investigate the main drivers behind bioproduction shifts. The methods comprise age-modeling, accumulation rate estimation, and light microscope diatom species analysis of 74 samples, as well as organic carbon, nitrogen, and mercury analysis. Diatoms have appeared in the lake since 21.8 ka cal BP and are dominated by planktonic Lindavia ocellata and L. cyclopuncta. Around the Pleistocene–Holocene boundary, other taxa including planktonic Aulacoseira, benthic fragilarioid (Staurosira), and achnanthoid species increase in their abundance. There is strong correlation between variations of diatom valve accumulation rates (DARs; mean 176.1×109 valves m2 a1), organic carbon accumulation rates (OCARs; mean 4.6 g m−2 a−1), and mercury accumulation rates (HgARs; mean 63.4 µg m−2 a−1). We discuss the environmental forcings behind shifts in diatom species and find moderate responses of key taxa to the cold glacial period, postglacial warming, the Younger Dryas, and the Holocene Thermal Maximum. The short-core data likely suggest recent change of the diatom community at the beginning of the 20th century related to human-induced warming but only little evidence of atmospheric deposition of contaminants. Significant correlation between DAR and OCAR in the Holocene interglacial indicates within-lake bioproduction represents bulk organic carbon deposited in the lake sediment. During both glacial and interglacial episodes HgAR is mainly bound to organic matter in the lake associated with biochemical substrate conditions. There were only ambiguous signs of increased HgAR during the industrialization period. We conclude that if increased short-term emissions are neglected