| 1. |
- Lin, Qi, et al.
(författare)
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Transient social-ecological dynamics reveal signals of decoupling in a highly disturbed Anthropocene landscape
- 2024
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences (PNAS). - 0027-8424 .- 1091-6490. ; 121:17
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the transient dynamics of interlinked social-ecological systems (SES) is imperative for assessing sustainability in the Anthropocene. However, how to identify critical transitions in real-world SES remains a formidable challenge. In this study, we present an evolutionary framework to characterize these dynamics over an extended historical timeline. Our approach leverages multidecadal rates of change in socioeconomic data, paleoenvironmental, and cutting-edge sedimentary ancient DNA records from China's Yangtze River Delta, one of the most densely populated and intensively modified landscapes on Earth. Our analysis reveals two significant social-ecological transitions characterized by contrasting interactions and feedback spanning several centuries. Initially, the regional SES exhibited a loosely connected and ecologically sustainable regime. Nevertheless, starting in the 1950s, an increasingly interconnected regime emerged, ultimately resulting in the crossing of tipping points and an unprecedented acceleration in soil erosion, water eutrophication, and ecosystem degradation. Remarkably, the second transition occurring around the 2000s, featured a notable decoupling of socioeconomic development from ecoenvironmental degradation. This decoupling phenomenon signifies a more desirable reconfiguration of the regional SES, furnishing essential insights not only for the Yangtze River Basin but also for regions worldwide grappling with similar sustainability challenges. Our extensive multidecadal empirical investigation underscores the value of coevolutionary approaches in understanding and addressing social-ecological system dynamics.
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| 2. |
- Olajos, Fredrik, 1987-
(författare)
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Using environmental DNA to unravel aquatic ecosystem dynamics
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Human-induced climate change has led to unprecedented declines in Earth's biodiversity and significant habitat loss. Aquatic ecosystems areespecially at risk, facing pollution, overexploitation, and destruction. Consequently, monitoring biodiversity is critical. Traditional monitoring methods are often low in detection rates, time-consuming, invasive, and harmful to species, which hampers comprehensive biodiversity assessments. Environmental DNA (eDNA) offers a rapid alternative fortaxonomic identification, extracting genetic material from soil, sediments, or water without capturing living organisms, proving useful where traditional methods fall short. However, its integration into aquatic ecology is hampered by unresolved methodological issues.This thesis demonstrates how eDNA can help reconstruct fish colonization histories in lakes post-glacial retreat. I employed species-specific primers with digital droplet PCR and metagenomic shotgun sequencing on ancient DNA from Holocene lake sediments. My findings show the detectability of DNA from ancient fish populations. However, each method exhibited technical limitations that led to varying degrees offalse negatives and false positive results. Additionally, I examined how Northern pike (Esox Lucius) affects ecological speciation in Europeanwhitefish (Coregonus lavaretus), promoting a shift from insectivorous to piscivorous states, enhancing predator biodiversity and biomass. Dietan alyses of piscivorous birds through digital droplet PCR revealed that smaller whitefish support a larger, more diverse bird community. Finally, I compared two molecular techniques for quantifying bird diets from fecal DNA, finding that metabarcoding with a universal fish primer and digital droplet PCR yielded similar results. This research enhances ourunderstanding of the potential and limitations of molecular tools forspecies identification and aids the integration of eDNA into aquatic ecology.
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| 3. |
- Rincón-Tomás, Blanca, et al.
(författare)
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Revisiting the mercury cycle in marine sediments : A potential multifaceted role for Desulfobacterota
- 2024
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Ingår i: Journal of Hazardous Materials. - : Elsevier. - 0304-3894 .- 1873-3336. ; 465
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Tidskriftsartikel (refereegranskat)abstract
- Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used culture-independent (metagenomics, metabarcoding) and culture-dependent approaches in anoxic marine sediments to identify microbial indicators of mercury pollution and analyze the distribution of genes involved in mercury reduction (merA) and demethylation (merB). While none of the isolates featured merB genes, 52 isolates, predominantly affiliated with Gammaproteobacteria, were merA positive. In contrast, merA genes detected in metagenomes were assigned to different phyla, including Desulfobacterota, Actinomycetota, Gemmatimonadota, Nitrospirota, and Pseudomonadota. This indicates a widespread capacity for mercury reduction in anoxic sediment microbiomes. Notably, merA genes were predominately identified in Desulfobacterota, a phylum previously associated only with mercury methylation. Marker genes involved in the latter process (hgcAB) were also mainly assigned to Desulfobacterota, implying a potential central and multifaceted role of this phylum in the mercury cycle. Network analysis revealed that Desulfobacterota were associated with anaerobic fermenters, methanogens and sulfur-oxidizers, indicating potential interactions between key players of the carbon, sulfur and mercury cycling in anoxic marine sediments.
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| 4. |
- Von Eggers, Jordan M., et al.
(författare)
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Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes
- 2024
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Ingår i: Environmental Microbiology. - : John Wiley & Sons. - 1462-2912 .- 1462-2920. ; 26:3
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Tidskriftsartikel (refereegranskat)abstract
- Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We sequenced the 16S rRNA gene of bacteria and archaea from 48 sediment cores across 36 lakes in four disconnected mountain ranges in Wyoming, USA and used null models to infer assembly processes across depth, spatial isolation, and varying environments. Although we expected strong dispersal limitations across these isolated settings, community composition was primarily shaped by environmental selection. Communities consistently shifted from domination by organisms that degrade organic matter at the surface to methanogenic, low-energy adapted taxa in deeper zones. Stochastic processes—like dispersal limitation—contributed to differences among lakes, but because these effects weakened with depth, selection processes ultimately governed subsurface microbial biogeography.
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| 5. |
- Yan, Dongna, et al.
(författare)
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Anthropogenic drivers accelerate the changes of lake microbial eukaryotic communities over the past 160 years
- 2024
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Ingår i: Quaternary Science Reviews. - : Elsevier. - 0277-3791 .- 1873-457X. ; 327
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Tidskriftsartikel (refereegranskat)abstract
- Human impacts on Earth's atmosphere, hydrosphere, litosphere and biosphere are so significant as to naming a new geological epoch, the Anthropocene. Lakes and their biota are highly sensitive to environmental changes. Among aquatic organisms, microbial eukaryotes play fundamental roles associated with lake ecosystem functioning, food webs, nutrient cycling, and pollutant degradation. However, the response of lake microbial eukaryotic community during the Anthropocene to changes in environmental conditions remain poorly understood. Here, we applied a 18S metabarcoding approach to sedimentary DNA to reconstruct the temporal dynamics of microbial eukaryotic community over the past 160 years. We investigated the influence of environmental conditions and of biotic interactions on the microbial eukaryotes in Sihailongwan Maar Lake, one of the candidate sites of Global boundary Stratotype Section and Point (GSSP) for demarcation of the Anthropocene. Microbial eukaryotes were dominated by dinoflagellates, chlorophytes, ciliates, pirsoniales, rotifers, ochrophytes, apicomplexans and cercozoans that were divided into four functional groups that are photoautotrophs, mixotrophs, consumers and parasites. The predominance of phototrophs and their strong associations with organisms from other trophic levels, confirmed their crucial roles in nutrient cycling, energy flows and ecosystem services in freshwater ecosystems. Abrupt changes in the 1950s in microbial eukaryotic diversity and composition were consistent with changes observed in the pollutants emissions i.e., heavy metals, combustion indices (spheroidal carbonaceous particles, polycyclic aromatic hydrocarbon, Soot F14C), radioactivity indicators (239,240Pu, 129I/127I), nutrients (total organic carbon, total nitrogen, phosphorus), and temperature. Statistical analysis revealed that anthropogenic drivers controlled the temporal dynamic of microbial eukaryotic community. Our findings provide additional biostratigraphy evidence of the impact of environmental change on this lake biota, which further supports the value of this system to characterize the Anthropocene.
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| 6. |
- Yan, Dongna, et al.
(författare)
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Historical trajectories of antibiotics resistance genes assessed through sedimentary DNA analysis of a subtropical eutrophic lake
- 2024
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Ingår i: Environment International. - : Elsevier. - 0160-4120 .- 1873-6750. ; 186
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Tidskriftsartikel (refereegranskat)abstract
- Investigating the occurrence of antibiotic-resistance genes (ARGs) in sedimentary archives provides opportunities for reconstructing the distribution and dissemination of historical (i.e., non-anthropogenic origin) ARGs. Although ARGs in freshwater environments have attracted great attention, historical variations in the diversity and abundance of ARGs over centuries to millennia remain largely unknown. In this study, we investigated the vertical change patterns of bacterial communities, ARGs and mobile genetic elements (MGEs) found in sediments of Lake Chenghai spanning the past 600 years. Within resistome preserved in sediments, 177 ARGs subtypes were found with aminoglycosides and multidrug resistance being the most abundant. The ARG abundance in the upper sediment layers (equivalent to the post-antibiotic era since the 1940s) was lower than those during the pre-antibiotic era, whereas the ARG diversity was higher during the post-antibiotic era, possibly because human-induced lake eutrophication over the recent decades facilitated the spread and proliferation of drug-resistant bacteria. Statistical analysis suggested that MGEs abundance and the bacterial community structure were significantly correlated with the abundance and diversity of ARGs, suggesting that the occurrence and distribution of ARGs may be transferred between different bacteria by MGEs. Our results provide new perspectives on the natural history of ARGs in freshwater environments and are essential for understanding the temporal dynamics and dissemination of ARGs.
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| 7. |
- Yan, Dongna, et al.
(författare)
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Organic matter content and source is associated with the depth-dependent distribution of prokaryotes in lake sediments
- 2024
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Ingår i: Freshwater Biology. - : John Wiley & Sons. - 0046-5070 .- 1365-2427. ; 69, s. 496-508
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Tidskriftsartikel (refereegranskat)abstract
- Aquatic sediments harbour a diverse array of microorganisms that drive organic matter recycling, carbon sequestration and greenhouse gases (e.g., CO2, CH4, N2O) emissions. Although largely studied in water columns, vertical profiles of the diversity and composition of prokaryotic communities (i.e., Bacteria and Archaea) in aquatic sediments are still rare. More specifically, much remains to be learnt about their vertical distribution in lake sediments and how environmental conditions at the time of burial have impacted their diversity and composition.We investigated the vertical distribution of prokaryotic community with 16S rRNA gene quantitative (q)PCR and metabarcoding approaches applied to 93 sediment layers collected in a 2-m-long sediment core from the eutrophic alkaline Lake Chenghai in subtropical China. We aimed to study the diversity, composition and structure distribution of the prokaryotic community as well as environmental factors influencing it.Bacterial abundance was found to decrease with sediment depth although the richness of both bacterial and archaeal assemblages slightly increased with sediment depth. In terms of composition, a strongly stratified sediment–depth pattern was observed in which Proteobacteria, Desulfobacterota, Bacteroidota and Verrucomicrobiota dominated the inventories in the surface sediment layers, whereas Chloroflexi, Spirochaetota, Planctomycetota, Crenarchaeota were more abundant in the deep sediment layers. Organic matter contents and sources were identified as major factors shaping the structure of the prokaryotic community.Overall, our study provides new evidence about how lake sediment's prokaryotic community are linked to external sources of energy. This complement existing data from other lake systems towards a better understanding of sediment prokaryotic community's contribution to biogeochemical cycle in lakes.
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| 8. |
- Yan, Dongna, et al.
(författare)
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Sedimentary DNA reveals phytoplankton diversity loss in a deep maar lake during the Anthropocene
- 2024
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Ingår i: Limnology and Oceanography. - : John Wiley & Sons. - 0024-3590 .- 1939-5590.
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Tidskriftsartikel (refereegranskat)abstract
- Anthropogenic-driven environmental change, including current climate warming, has influenced lake ecosystems globally during the Anthropocene. Phytoplankton are important indicators of environmental changes in lakes and play a fundamental role in maintaining the functioning and stability of these ecosystems. However, the extent to which lake phytoplankton were affected by anthropogenic or climatic forces during the Anthropocene remains unclear. Here, we investigated the 160-yr-long dynamics of the phytoplankton community (cyanobacteria and eukaryotic microalgae) in response to anthropogenic forcing in Sihailongwan Maar Lake—a candidate for a Global boundary Stratotype Section and Point for demarcation of the Anthropocene—using DNA metabarcoding and traditional paleolimnological approaches. Our results show a significant decline in phytoplankton diversity and an abrupt shift in community composition around the 1950s, corresponding to the beginning of the “Great Acceleration” period. Specifically, phytoplankton taxa coexistence patterns, niche differentiation, and assembly mechanisms changed significantly after the 1950s. Overall, increases in air temperature and anthropogenic forcing appear to be the dominant controls for community reorganization and diversity decline of the phytoplankton from this deep maar lake. A neutral community model suggests that phytoplankton community composition was mainly controlled by stochastic processes before the 1950s; however, as time progressed, deterministic effects driven by anthropogenic global warming increased. The results of this study imply that anthropogenic perturbations have led to a loss of phytoplankton diversity and a further decline in ecological resilience in deep lakes, with likely knock-on effects on the productivity and function of lake ecosystems.
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