Sedimentary DNA tracks decadal-centennial changes in fish abundance

The Micropaleoecology Framework: Evaluating Biotic Responses to Global Change Through Paleoproxy, Microfossil, and Ecological Data Integration

The microfossil record contains abundant, diverse, and well-preserved fossils spanning multiple trophic levels from primary producers to apex predators. In addition, microfossils often constitute and are preserved in high abundances alongside continuous high-resolution geochemical proxy records. These characteristics mean that microfossils can provide valuable context for understanding the modern climate and biodiversity crises by allowing for the interrogation of spatiotemporal scales well beyond what is available in neo-ecological research. Here, we formalize a research framework of "micropaleoecology," which builds on a holistic understanding of global change from the environment to ecosystem level. Location: Global. Time period: Neoproterozoic-Phanerozoic. Taxa studied: Fossilizing organisms/molecules. Our framework seeks to integrate geochemical proxy records with microfossil records and metrics, and draws on mechanistic models and systems-level statistical analyses to integrate disparate records. Using multiple proxies and mechanistic mathematical frameworks extends analysis beyond traditional correlation-based studies of paleoecological associations and builds a greater understanding of past ecosystem dynamics. The goal of micropaleoecology is to investigate how environmental changes impact the component and emergent properties of ecosystems through the integration of multi-trophic level body fossil records (primarily using microfossils, and incorporating additional macrofossil data where possible) with contemporaneous environmental (biogeochemical, geochemical, and sedimentological) records. Micropaleoecology, with its focus on integrating ecological metrics within the context of paleontological records, facilitates a deeper understanding of the response of ecosystems across time and space to better prepare for a future Earth under threat from anthropogenic climate change.

Unlocking Antarctic molecular time-capsules - Recovering historical environmental DNA from museum-preserved sponges

Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA, trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, we define the term 'heDNA' to denote the historical environmental DNA that can be obtained from the recent past with high spatial and temporal accuracy. Using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method, will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century.

RelQ-mediated alarmone signaling regulates growth, sporulation, and stress-induced biofilm formation in Clostridioides difficile

The bacterial stringent response (SR) is a conserved transcriptional reprogramming pathway mediated by the nucleotide signaling alarmones, (pp)pGpp. The SR has been implicated in antibiotic survival in Clostridioides difficile, a biofilm- and spore-forming pathogen that causes resilient, highly recurrent C. difficile infections. The role of the SR in other processes and the effectors by which it regulates C. difficile physiology are unknown. C. difficile RelQ is a clostridial alarmone synthetase. Deletion of relQ dysregulates C. difficile growth in unstressed conditions, affects susceptibility to antibiotic and oxidative stressors, and drastically reduces biofilm formation. While wild-type C. difficile displays increased biofilm formation in the presence of sub-lethal stress, the ΔrelQ strain cannot upregulate biofilm production in response to stress. Deletion of relQ slows spore accumulation in planktonic cultures but accelerates it in biofilms. This work establishes biofilm formation and sporulation as alarmone-mediated processes in C. difficile and reveals the importance of RelQ in stress-induced biofilm regulation.

Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing

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.

Sedimentary DNA for tracking the long-term changes in biodiversity

Understanding long-term dynamics is vitally important for explaining current biodiversity patterns and setting conservation goals in a changing world. However, the changes in biodiversity in time and space, particularly the dynamics at the centuries or even longer time scales, are poorly documented because of a lack of continuous monitoring data. The sedimentary DNA (sedDNA) has a great potential for paleo-community reconstruction, and it has recently been used as a powerful tool to characterize past dynamics in terms of biodiversity over geological timescales. In particular, it is useful for prokaryotes and eukaryotes that do not fossilize; hence, it is revolutionizing the scope of paleoecological research. Here, a "Research Weaving" method was performed with systematic maps and bibliometric webs based on the Web of Science for Science Citation Index Expanded, presenting a comprehensive landscape of the sedDNA that traces biological dynamics. We identified that most sedDNA-based studies have focused on microbial dynamics and on using samples from multitypes of sediments. This review summarized the advantages and common applications of sedDNA, focused on the biodiversity in microbial communities, and provided an outlook for the future of sedDNA research.

A 75-year history of microplastic fragment accumulation rates in a semi-enclosed hypoxic basin

Plastic budgets in the marine environment and their long-term trends are yet to be fully understood. Measuring the accumulation rates in bottom sediments is crucial to solving the riddle of missing ocean plastics. Previous studies based on coastal sediment cores have found that accumulation rates have increased with increases in plastic production and/or regional populations. However, the correlations between the rates and bioactivities or ocean dynamics, which are crucial for modeling the microplastic sinking process, have not been examined. We revealed a 75-year microplastic fragment (0.3-5.0 mm) accumulation rate history in a hypoxic basin, Beppu Bay, Japan, based on multi-core analysis and 210Pb dating of the sediment which was cross-checked by time control with 137Cs radioactivity peaks. We found that a long-term linear increasing trend with an approximately 20-year variation overlapped with significant peaks around 1990 and 2014 with the first polypropylene microplastic fragment detected from a 1958.8-1961.0 CE sediment layer. The maximum rate was 203 pieces m-2 y-1 with an abundance of 86 pieces kg-1-dry in 2014. Smaller fragments in the size range of 0.3-2.0 mm have been consistently dominant in terms of the accumulation rate throughout the 1955-2015 period, accounting for 85.3 % of the total accumulation rate. The three major polymers (polyethylene, polypropylene, and polystyrene) accounted for 96.6 % of the total rate. The rate was highly and positively correlated with the chlorophyll-a accumulation rate and concentration in the sediment. Based on the microplastic accumulation rates and concentration in the seawater, the mean sinking velocity of microplastics was estimated to be in the order of 101 m d-1. Our results will contribute to significant progress in modeling the microplastic sinking process by offering the first field measurement-based mean sinking velocity and significant correlations between the rate and bioactivity-related signals.

Quantitative environmental DNA metabarcoding shows high potential as a novel approach to quantitatively assess fish community

The simultaneous conservation of species richness and evenness is important to effectively reduce biodiversity loss and keep ecosystem health. Environmental DNA (eDNA) metabarcoding has been used as a powerful tool for identifying community composition, but it does not necessarily provide quantitative information due to several methodological limitations. Thus, the quantification of eDNA through metabarcoding is an important frontier of eDNA-based biomonitoring. Particularly, the qMiSeq approach has recently been developed as a quantitative metabarcoding method and has attracted much attention due to its usefulness. The aim here was to evaluate the performance of the qMiSeq approach as a quantitative monitoring tool for fish communities by comparing the quantified eDNA concentrations with the results of fish capture surveys. The eDNA water sampling and the capture surveys using the electrical shocker were conducted at a total of 21 sites in four rivers in Japan. As a result, we found significant positive relationships between the eDNA concentrations of each species quantified by qMiSeq and both the abundance and biomass of each captured taxon at each site. Furthermore, for seven out of eleven taxa, a significant positive relationship was observed between quantified DNA concentrations by sample and the abundance and/or biomass. In total, our results demonstrated that eDNA metabarcoding with the qMiSeq approach is a suitable and useful tool for quantitative monitoring of fish communities. Due to the simplicity of the eDNA analysis, the eDNA metabarcoding with qMiSeq approach would promote further growth of quantitative monitoring of biodiversity.

Contrasting life-history responses to climate variability in eastern and western North Pacific sardine populations

Massive populations of sardines inhabit both the western and eastern boundaries of the world’s subtropical ocean basins, supporting both commercial fisheries and populations of marine predators. Sardine populations in western and eastern boundary current systems have responded oppositely to decadal scale anomalies in ocean temperature, but the mechanism for differing variability has remained unclear. Here, based on otolith microstructure and high-resolution stable isotope analyses, we show that habitat temperature, early life growth rates, energy expenditure, metabolically optimal temperature, and, most importantly, the relationship between growth rate and temperature are remarkably different between the two subpopulations in the western and eastern North Pacific. Varying metabolic responses to environmental changes partly explain the contrasting growth responses. Consistent differences in the life-history traits are observed between subpopulations in the western and eastern boundary current systems around South Africa. These growth and survival characteristics can facilitate the contrasting responses of sardine populations to climate change.

Using high-resolution stable isotope and microstructure analyses of otoliths, this study reveals that sardine populations in the western and eastern North Pacific have different early life metabolic and growth rates that respond contrastingly to temperature variations. These findings could explain observations of different responses in these populations to decadal-scale temperature anomalies.

Plutonium isotopes in the North Western Pacific sediments coupled with radiocarbon in corals recording precise timing of the Anthropocene

Plutonium (Pu) has been used as a mid-twentieth century time-marker in various geological archives as a result of atmospheric nuclear tests mainly conducted in 1950s. Advancement of analytical techniques allows us to measure ²³⁹Pu and ²⁴⁰Pu more accurately and can thereby reconstruct the Pacific Pu signal that originated from the former Pacific Proving Grounds (PPG) in the Marshall Islands. Here, we propose a novel method that couples annual banded reef building corals and nearshore anoxic marine sediments to provide a marker to precisely determine the start of the nuclear era which is known as a part of the Anthropocene. We demonstrate the efficacy of the methods using sediment obtained from Beppu Bay, Japan, and a coral from Ishigaki Island, Japan. The sedimentary records show a clear Pu increase from 1950, peaking during the 1960s, and then showing a sharp decline during the 1970s. However, a constantly higher isotope ratio between ²³⁹Pu and ²⁴⁰Pu suggest an additional contribution other than global fallout via ocean currents. Furthermore, single elevations in ²⁴⁰Pu/²³⁹Pu provide supportive evidence of close-in-fallout similar to previous studies. Coral skeletal radiocarbon displays a clear timing with the signatures supporting the reliability of the Beppu Bay sediments as archives and demonstrates the strength of this method to capture potential Anthropocene signatures.

Environmental DNA analysis for macro-organisms: species distribution and more

In an era of severe biodiversity loss, biological monitoring is becoming increasingly essential. The analysis of environmental DNA (eDNA) has emerged as a new approach that could revolutionize the biological monitoring of aquatic ecosystems. Over the past decade, macro-organismal eDNA analysis has undergone significant developments and is rapidly becoming established as the golden standard for non-destructive and non-invasive biological monitoring. In this review, I summarize the development of macro-organismal eDNA analysis to date and the techniques used in this field. I also discuss the future perspective of these analytical methods in combination with sophisticated analytical techniques for DNA research developed in the fields of molecular biology and molecular genetics, including genomics, epigenomics, and single-cell technologies. eDNA analysis, which to date has been used primarily for determining the distribution of organisms, is expected to develop into a tool for elucidating the physiological state and behaviour of organisms. The fusion of microbiology and macrobiology through an amalgamation of these technologies is anticipated to lead to the future development of an integrated biology.

The Italian Alpine and Subalpine trouts: Taxonomy, Evolution, and Conservation

Simple Summary

In a great part of the world, trout fishing has long inspired human spiritual ideals of immersion into nature and recreation, far removed from the fast-encroaching urbanization. Concurrently, these values and emotions fueled a white-hot business, establishing a florid market of outdoor recreation. Since the 20th century, the trout-culture industry strived to provide anglers with fishing entertainment by stocking massive amounts of non-native trouts in dozens of countries, irrespective of the lakes’ and rivers’ carrying capacity. This had dire consequences on the structural and functional diversity of these ecosystems. “Trout wars” sparked throughout the world between the promoters of stocking activities and the promoters of “wild trout management” and ethics. The “Italian trout war” has been fought on the harsh battleground of trout taxonomy, ecology, distribution, and native vs. non-native interfertile species. Northern Italy, home to the Italian Alpine and subalpine trouts and economic center of the national trout-culture and stocking industry, was particularly affected by this clash. We review here the state of art of this ongoing debate, outlining our scientific view of the taxonomy, evolution, distribution, and sustainable management of the native Italian trouts of northern Italy.

Abstract

During the last 150 years, the trout-culture industry focused on enhancing trout populations by stocking, in response to the growing anglers’ demand and the habitat degradation associated to the rapid urbanization and hydropower development. The industrialized north of Italy, home to the Italian Alpine and subalpine trout populations, is the source of most of the revenues of the national trout-culture industry. Its rapid growth, and the massive introduction of non-native interfertile trouts eroded the genetic diversity of native lineages, leading to harsh confrontations between scientists, institutions, and sportfishing associations. We review here the state of the art of the taxonomy and distribution of the northern Italian native trouts, presenting both scientific results and historical documentation. We think the only native trouts in this region are Salmo marmoratus, widespread in this region, plus small and fragmented populations of S. ghigii, present only in the South-western Alps. We strongly recommend the interruption of stocking of domesticated interfertile non-native trouts in this area, and recommend the adoption of Evolutionary Significant Units for salmonid fishery management. We further propose future research directions for a sustainable approach to the conservation and ecosystem management of the fishery resources and inland waters of northern Italy.

Reconstruction of 100-year dynamics in Daphnia spawning activity revealed by sedimentary DNA

Environmental DNA (eDNA) is currently developing as a powerful tool for assessing aquatic species dynamics. However, its utility as an assessment tool for quantification remain under debate as the sources of eDNA for different species is not always known. Therefore, accumulating information about eDNA sources from different species is urgently required. The objective of our study was to evaluate whether sedimentary DNA targeting two Daphnia species, D. galeata and D. pulicaria, could track Daphnia population dynamics and resting egg production. Applying a quantitative PCR targeting the mitochondrial 12S rRNA gene on sediment cores collected in Lake Biwa, Japan, we compared sedimentary DNA concentration of Daphnia with the abundance of remains and ephippia, reflecting their abundance and resting egg production, respectively. We found that the sedimentary DNA concentrations of Daphnia for the past century were inconsistent with their population abundance. However, the concentration was highly correlated with the resting egg production. Our results provide evidence that ephippia with resting eggs, released during spawning activities, was a significant source of Daphnia DNA archived in sediments. Our work provides critical insights for using sedimentary DNA as a monitoring tool for egg production dating back 100 years.

Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies

Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cores are often refrigerated (4 °C) for weeks or months before subsampling. We investigated the impact of storage time on changes in DNA (purified or as cell lysate) concentrations and shifts in biological communities following storage of lake surface sediment at 4 °C for up to 24 weeks. Sediment samples (~ 0.22 g, in triplicate per time point) were spiked with purified DNA (100 or 200 ng) or lysate from a brackish water cyanobacterium that produces the cyanotoxin nodularin or non-spiked. Samples were analysed every 1–4 weeks over a 24-week period. Droplet digital PCR showed no significant decrease in the target gene (nodularin synthetase – subunit F; ndaF) over the 24-week period for samples spiked with purified DNA, while copy number decreased by more than half in cell lysate-spiked samples. There was significant change over time in bacteria and eukaryotic community composition assessed using metabarcoding. Amongst bacteria, the cyanobacterial signal became negligible after 5 weeks while Proteobacteria increased. In the eukaryotic community, Cercozoa became dominant after 6 weeks. These data demonstrate that DNA yields and community composition data shift significantly when sediments are stored chilled for more than 5 weeks. This highlights the need for rapid subsampling and appropriate storage of sediment core samples for paleogenomic studies.

Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean

Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009–2012) specimens with archival (1911–1926) and archaeological (2nd century BCE–15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these.

Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami

Environmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks. Water and sediment samples from the tanks were collected after the removal of fish. In the field trial, sediment cores were collected in Moune Bay, northeast Japan, where unusual blooms of jellyfish (Aurelia sp.) occurred after a tsunami. The samples were analyzed by layers to detect the eDNA of jellyfish. The tank experiment revealed that after fish were removed, eDNA was not present in the water the next day, or subsequently, whereas eDNA was detectable in the sediment for 12 months. In the sediment core samples, jellyfish eDNA was detected at high concentrations above the layer with the highest content of polycyclic aromatic hydrocarbons, reflecting tsunami-induced oil spills. Thus, marine sediment eDNA preserves a record of target species for at least one year and can be used to reconstruct past faunal occurrence.

On the Way to the Fluvial Anthroposphere—Current Limitations and Perspectives of Multidisciplinary Research

Floodplains represent a global hotspot of sensitive socioenvironmental changes and early human forcing mechanisms. In this review, we focus on the environmental conditions of preindustrial floodplains in Central Europe and the fluvial societies that operated there. Due to their high land-use capacity and the simultaneous necessity of land reclamation and risk minimisation, societies have radically restructured the Central European floodplains. According to the current scientific consensus, up to 95% of Central European floodplains have been extensively restructured or destroyed. Therefore, question arises as to whether or when it is justified to understand Central European floodplains as a ‘Fluvial Anthroposphere’. The case studies available to date show that human-induced impacts on floodplain morphologies and environments and the formation of specific fluvial societies reveal fundamental changes in the medieval and preindustrial modern periods. We aim to contribute to disentangling the questions of when and why humans became a significant controlling factor in Central European floodplain formation, and how humans in interaction with natural processes and other chains of effects have modified floodplains. As a conclusion, we superimpose emerging fields of research concerning the onset of the Fluvial Anthroposphere and provide 10 specific thematic objectives for future multidisciplinary work.

Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations

The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.