| 1. |
- Cabrol, Léa, et al.
(författare)
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Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea
- 2023
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Ingår i: mSystems. - : American Society for Microbiology. - 2379-5077. ; 8:4
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Tidskriftsartikel (refereegranskat)abstract
- In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc+) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc+ microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc+ microorganisms belonged to a unique assemblage of diverse—previously underappreciated—anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc+) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc+ microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.
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| 2. |
- Capo, Eric, et al.
(författare)
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A consensus protocol for the recovery of mercury methylation genes from metagenomes
- 2023
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 23:1, s. 190-204
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Tidskriftsartikel (refereegranskat)abstract
- Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.
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| 3. |
- Williams, John W., et al.
(författare)
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Strengthening global-change science by integrating aeDNA with paleoecoinformatics
- 2023
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Ingår i: Trends in Ecology & Evolution. - : Elsevier. - 0169-5347 .- 1872-8383. ; 38:10, s. 946-960
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 4. |
- Capo, Eric, et al.
(författare)
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Anaerobic mercury methylators inhabit sinking particles of oxic water columns
- 2023
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Ingår i: Water Research. - : Elsevier. - 0043-1354 .- 1879-2448. ; 229
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 5. |
- Huston, Grayson P., et al.
(författare)
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Detection of fish sedimentary DNA in aquatic systems : A review of methodological challenges and future opportunities
- 2023
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Ingår i: Environmental DNA. - : John Wiley & Sons. - 2637-4943. ; 5:6, s. 1449-1472
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 6. |
- Lin, Qi, et al.
(författare)
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Characterization of lacustrine harmful algal blooms using multiple biomarkers : historical processes, driving synergy, and ecological shifts
- 2023
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Ingår i: Water Research. - : Elsevier. - 0043-1354 .- 1879-2448. ; 235
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 7. |
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Tracking environmental change using lake sediments : volume 6: sedimentary DNA
- 2023. - 1
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Samlingsverk (redaktörskap) (refereegranskat)abstract
- This book, entitled Tracking Environmental Change Using Lake Sediments: Volume 6 – Sedimentary DNA, provides an overview of the applications of sedimentary DNA-based approaches to paleolimnological studies. These approaches have shown considerable potential in providing information about the long-term changes of overall biodiversity in lakes and their watersheds in response to natural and anthropogenic changes, as well as tracking human migrations over the last thousands of years.Although the first studies investigating the preservation of these molecular proxies in sediments originate from the late-1990s, the number of scientific publications on this topic has increased greatly over the last five years. Alongside numerous ecological findings, several sedimentary DNA studies have been dedicated to understanding the reliability of this approach to reconstruct past ecosystem changes. Despite the major surge of interest, a comprehensive compilation of sedimentary DNA approaches and applications has yet to be attempted. The overall aim of this DPER volume is to fill this knowledge gap.
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| 8. |
- Zhong, Meifang, et al.
(författare)
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Homogenisation of water and sediment bacterial communities in a shallow lake (lake Balihe, China)
- 2023
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Ingår i: Freshwater Biology. - : John Wiley & Sons. - 0046-5070 .- 1365-2427. ; 68:1, s. 155-171
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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