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Publications (10 of 30) Show all publications
Yan, D., Han, Y., An, Z., Lei, D., Zhao, X., Zhao, H., . . . Capo, E. (2024). Anthropogenic drivers accelerate the changes of lake microbial eukaryotic communities over the past 160 years. Quaternary Science Reviews, 327, Article ID 108535.
Open this publication in new window or tab >>Anthropogenic drivers accelerate the changes of lake microbial eukaryotic communities over the past 160 years
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2024 (English)In: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 327, article id 108535Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Elsevier, 2024
Keywords
Anthropocene, Global changes, Human activities, Microbial eukaryotes ecology, sedDNA
National Category
Geology Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-221018 (URN)10.1016/j.quascirev.2024.108535 (DOI)2-s2.0-85184145411 (Scopus ID)
Funder
Swedish Research Council, 2023-03504
Available from: 2024-03-06 Created: 2024-03-06 Last updated: 2024-03-06Bibliographically approved
Von Eggers, J. M., Wisnoski, N. I., Calder, J. W., Capo, E., Groff, D. V., Krist, A. C. & Shuman, B. (2024). Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes. Environmental Microbiology, 26(3), Article ID e16607.
Open this publication in new window or tab >>Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes
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2024 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 26, no 3, article id e16607Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
John Wiley & Sons, 2024
National Category
Ecology Microbiology
Identifiers
urn:nbn:se:umu:diva-222667 (URN)10.1111/1462-2920.16607 (DOI)001183722700001 ()38477387 (PubMedID)2-s2.0-85187784759 (Scopus ID)
Available from: 2024-04-19 Created: 2024-04-19 Last updated: 2024-04-19Bibliographically approved
Yan, D., Han, Y., Zhong, M., Wen, H., An, Z. & Capo, E. (2024). Historical trajectories of antibiotics resistance genes assessed through sedimentary DNA analysis of a subtropical eutrophic lake. Environment International, 186, Article ID 108654.
Open this publication in new window or tab >>Historical trajectories of antibiotics resistance genes assessed through sedimentary DNA analysis of a subtropical eutrophic lake
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2024 (English)In: Environment International, ISSN 0160-4120, E-ISSN 1873-6750, Vol. 186, article id 108654Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Elsevier, 2024
Keywords
ARGs, Bacterial community, HT-qPCR, MGEs, Sedimentary DNA
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-223614 (URN)10.1016/j.envint.2024.108654 (DOI)38621322 (PubMedID)2-s2.0-85190308164 (Scopus ID)
Funder
Swedish Research Council, 2023-03504
Available from: 2024-04-30 Created: 2024-04-30 Last updated: 2024-04-30Bibliographically approved
Yan, D., An, Z. & Capo, E. (2024). Organic matter content and source is associated with the depth-dependent distribution of prokaryotes in lake sediments. Freshwater Biology, 69, 496-508
Open this publication in new window or tab >>Organic matter content and source is associated with the depth-dependent distribution of prokaryotes in lake sediments
2024 (English)In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 69, p. 496-508Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
John Wiley & Sons, 2024
Keywords
16S metabarcoding, 16S rRNA gene qPCR, prokaryotes, sedimentary DNA, subsurface biosphere
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-221030 (URN)10.1111/fwb.14223 (DOI)001157770700001 ()2-s2.0-85183831510 (Scopus ID)
Available from: 2024-03-06 Created: 2024-03-06 Last updated: 2024-05-07Bibliographically approved
Rincón-Tomás, B., Lanzén, A., Sánchez, P., Estupiñán, M., Sanz-Sáez, I., Bilbao, M. E., . . . Alonso-Sáez, L. (2024). Revisiting the mercury cycle in marine sediments: A potential multifaceted role for Desulfobacterota. Journal of Hazardous Materials, 465, Article ID 133120.
Open this publication in new window or tab >>Revisiting the mercury cycle in marine sediments: A potential multifaceted role for Desulfobacterota
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2024 (English)In: Journal of Hazardous Materials, ISSN 0304-3894, E-ISSN 1873-3336, Vol. 465, article id 133120Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
Elsevier, 2024
Keywords
Desulfobacterota, Marine sediment, Mercury cycle, Mercury pollution
National Category
Environmental Sciences Ecology
Identifiers
urn:nbn:se:umu:diva-218871 (URN)10.1016/j.jhazmat.2023.133120 (DOI)38101011 (PubMedID)2-s2.0-85180454165 (Scopus ID)
Available from: 2024-01-05 Created: 2024-01-05 Last updated: 2024-02-13Bibliographically approved
Yan, D., Picard, M., Han, Y., An, Z., Lei, D., Zhao, X., . . . Capo, E. (2024). Sedimentary DNA reveals phytoplankton diversity loss in a deep maar lake during the Anthropocene. Limnology and Oceanography
Open this publication in new window or tab >>Sedimentary DNA reveals phytoplankton diversity loss in a deep maar lake during the Anthropocene
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2024 (English)In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590Article in journal (Refereed) Epub ahead of print
Abstract [en]

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.

Place, publisher, year, edition, pages
John Wiley & Sons, 2024
National Category
Environmental Sciences Ecology
Identifiers
urn:nbn:se:umu:diva-223508 (URN)10.1002/lno.12562 (DOI)001197768100001 ()2-s2.0-85189963523 (Scopus ID)
Funder
Swedish Research Council, 2023-03504
Available from: 2024-04-29 Created: 2024-04-29 Last updated: 2024-04-29
Capo, E., Cosio, C., Gascón Díez, E., Loizeau, J.-L., Mendes, E., Adatte, T., . . . Bravo, A. G. (2023). Anaerobic mercury methylators inhabit sinking particles of oxic water columns. Water Research, 229, Article ID 119368.
Open this publication in new window or tab >>Anaerobic mercury methylators inhabit sinking particles of oxic water columns
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2023 (English)In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 229, article id 119368Article in journal (Refereed) Published
Abstract [en]

Increased concentration of mercury, particularly methylmercury, in the environment is a worldwide concern because of its toxicity in severely exposed humans. Although the formation of methylmercury in oxic water columns has been previously suggested, there is no evidence of the presence of microorganisms able to perform this process, using the hgcAB gene pair (hgc+ microorganisms), in such environments. Here we show the prevalence of hgc+ microorganisms in sinking particles of the oxic water column of Lake Geneva (Switzerland and France) and its anoxic bottom sediments. Compared to anoxic sediments, sinking particles found in oxic waters exhibited relatively high proportion of hgc+genes taxonomically assigned to Firmicutes. In contrast hgc+members from Nitrospirae, Chloroflexota and PVC superphylum were prevalent in anoxic sediment while hgc+ Desulfobacterota were found in both environments. Altogether, the description of the diversity of putative mercury methylators in the oxic water column expand our understanding on MeHg formation in aquatic environments and at a global scale.

Place, publisher, year, edition, pages
Elsevier, 2023
Keywords
Anaerobic process, Lake Geneva, Mercury methylation, Sinking particles, hgcAB genes
National Category
Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-220771 (URN)10.1016/j.watres.2022.119368 (DOI)000904448500002 ()36459894 (PubMedID)2-s2.0-85145492169 (Scopus ID)
Available from: 2024-02-12 Created: 2024-02-12 Last updated: 2024-02-13Bibliographically approved
Lin, Q., Zhang, K., McGowan, S., Huang, S., Xue, Q., Capo, E., . . . Shen, J. (2023). Characterization of lacustrine harmful algal blooms using multiple biomarkers: historical processes, driving synergy, and ecological shifts. Water Research, 235, Article ID 119916.
Open this publication in new window or tab >>Characterization of lacustrine harmful algal blooms using multiple biomarkers: historical processes, driving synergy, and ecological shifts
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2023 (English)In: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 235, article id 119916Article in journal (Refereed) Published
Abstract [en]

Harmful algal blooms (HABs) producing toxic metabolites are increasingly threatening environmental and human health worldwide. Unfortunately, long-term process and mechanism triggering HABs remain largely unclear due to the scarcity of temporal monitoring. Retrospective analysis of sedimentary biomarkers using up-to-date chromatography and mass spectrometry techniques provide a potential means to reconstruct the past occurrence of HABs. By combining aliphatic hydrocarbons, photosynthetic pigments, and cyanotoxins, we quantified herein century-long changes in abundance, composition, and variability of phototrophs, particularly toxigenic algal blooms, in China's third largest freshwater Lake Taihu. Our multi-proxy limnological reconstruction revealed an abrupt ecological shift in the 1980s characterized by elevated primary production, Microcystis-dominated cyanobacterial blooms, and exponential microcystin production, in response to nutrient enrichment, climate change, and trophic cascades. The empirical results from ordination analysis and generalized additive models support climate warming and eutrophication synergy through nutrient recycling and their feedback through buoyant cyanobacterial proliferation, which sustain bloom-forming potential and further promote the occurrence of increasingly-toxic cyanotoxins (e.g., microcystin-LR) in Lake Taihu. Moreover, temporal variability of the lake ecosystem quantified using variance and rate of change metrics rose continuously after state change, indicating increased ecological vulnerability and declined resilience following blooms and warming. With the persistent legacy effects of lake eutrophication, nutrient reduction efforts mitigating toxic HABs probably be overwhelmed by climate change effects, emphasizing the need for more aggressive and integrated environmental strategies.

Place, publisher, year, edition, pages
Elsevier, 2023
Keywords
Climate warming, Critical transition, Cyanotoxin, Harmful cyanobacterial bloom, Lake paleoecology, Variability
National Category
Ecology Environmental Sciences
Identifiers
urn:nbn:se:umu:diva-220773 (URN)10.1016/j.watres.2023.119916 (DOI)000973328100001 ()37003114 (PubMedID)2-s2.0-85151456070 (Scopus ID)
Available from: 2024-02-12 Created: 2024-02-12 Last updated: 2024-02-13Bibliographically approved
Huston, G. P., Lopez, M. L., Cheng, Y., King, L., Duxbury, L. C., Picard, M., . . . Capo, E. (2023). Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities. Environmental DNA, 5(6), 1449-1472
Open this publication in new window or tab >>Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities
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2023 (English)In: Environmental DNA, E-ISSN 2637-4943, Vol. 5, no 6, p. 1449-1472Article in journal (Refereed) Published
Abstract [en]

Environmental DNA studies have proliferated over the last decade, with promising data describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short- and long-term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro-organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics.

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
environmental DNA, fish monitoring, lake sediment, marine sediment, paleolimnology, sedimentary DNA
National Category
Ecology
Identifiers
urn:nbn:se:umu:diva-214046 (URN)10.1002/edn3.467 (DOI)2-s2.0-85168895893 (Scopus ID)
Available from: 2023-09-06 Created: 2023-09-06 Last updated: 2024-04-26Bibliographically approved
Zhong, M., Capo, E., Zhang, H., Hu, H., Wang, Z., Tian, W., . . . Bertilsson, S. (2023). Homogenisation of water and sediment bacterial communities in a shallow lake (lake Balihe, China). Freshwater Biology, 68(1), 155-171
Open this publication in new window or tab >>Homogenisation of water and sediment bacterial communities in a shallow lake (lake Balihe, China)
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2023 (English)In: Freshwater Biology, ISSN 0046-5070, E-ISSN 1365-2427, Vol. 68, no 1, p. 155-171Article in journal (Refereed) Published
Abstract [en]

Planktonic and benthic bacterial communities hold central roles in the functioning of freshwater ecosystems and mediate key ecosystem services such as primary production and nutrient remineralisation. Although it is clear that such communities vary in composition both within and between lakes, the environmental factors and processes shaping the diversity and composition of freshwater bacteria are still not fully understood. In order to assess seasonal and spatial variability in lake bacterial communities and identify environmental factors underpinning biogeographical patterns, we performed a large-scale sampling campaign with paired water and sediment sample collection at 18 locations during four seasons in Lake Balihe, a subtropical shallow fish-farming lake in mid-eastern China. Pelagic and benthic bacterial communities were distinctly different in terms of diversity, taxonomic composition and community structure, with Actinobacteria, Bacteroidetes, Cyanobacteria and Alphaproteobacteria dominating lake water, and Acidobacteria, Bacteroidetes, Chloroflexi, Gammaproteobacteria and Deltaproteobacteria dominating sediment. Nevertheless, these two communities had stronger spatial concordance and overlap in taxa during spring and autumn seasons. Together, the main drivers of both the spatial and temporal variations in Lake Balihe bacterial communities were identified as water temperature, turbidity, nitrogen and phosphorus availability, and thermal stratification controlled by wind-mixing and activity of the dense farmed fish populations. Notably, populations affiliated with Firmicutes, known to be abundant in fish gut microbiome, were especially abundant in the summer season and locations where high fish biomass was found, suggesting a potential link between fish gut microbiome and the pelagic bacterial communities. Our findings demonstrated seasonal homogenisation of pelagic and benthic bacterial communities linked to marked shifts in a set of seasonally-driven environmental variables including water temperature and nutrient availability. 

Place, publisher, year, edition, pages
John Wiley & Sons, 2023
Keywords
16 S rRNA gene, environmental factors, fish farming, shallow lakes, subtropical zone
National Category
Ecology Microbiology
Identifiers
urn:nbn:se:umu:diva-220775 (URN)10.1111/fwb.14016 (DOI)000883063800001 ()2-s2.0-85142147780 (Scopus ID)
Available from: 2024-02-12 Created: 2024-02-12 Last updated: 2024-02-13Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0001-9143-7061

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