Abstract
Long-term time series have provided evidence that anthropogenic pressures can threaten lakes. Yet it remains unclear how and the extent to which lake biodiversity has changed during the ...Anthropocene, in particular for microbes. Here, we used DNA preserved in sediments to compare modern micro-eukaryotic communities with those from the end of the 19th century, i.e., before acceleration of the human imprint on ecosystems. Our results obtained for 48 lakes indicate drastic changes in the composition of microbial communities, coupled with a homogenization of their diversity between lakes. Remote high elevation lakes were globally less impacted than lowland lakes affected by local human activity. All functional groups (micro-algae, parasites, saprotrophs and consumers) underwent significant changes in diversity. However, we show that the effects of anthropogenic changes have benefited in particular phototrophic and mixotrophic species, which is consistent with the hypothesis of a global increase of primary productivity in lakes.
Studies on the active rare biosphere at the RNA level are mainly focused on Bacteria and Archaea and fail to include the protists, which are involved in the main biogeochemical cycles of the earth. ...In this study, the richness, composition and activity of the rare protistan biosphere were determined from a temporal survey of two lakes by pyrosequencing. In these ecosystems, the always rare OTUs represented 77.2% of the total OTUs and 76.6% of the phylogenetic diversity. From the various phylogenetic indices computed, the phylogenetic units (PUs) constituted exclusively by always rare OTUs were discriminated from the other PUs. Therefore, the rare biosphere included mainly taxa that are distant from the reference databases compared to the dominant ones. In addition, the rarest OTUs represented 59.8% of the active biosphere depicted by rRNA and the activity (rRNA:rDNA ratio) increased with the rarity. The high rRNA:rDNA ratio determined in the rare fraction highlights that some protists were active at low abundances and contribute to ecosystem functioning. Interestingly, the always rare and active OTUs were characterized by seasonal changes in relation with the main environmental parameters measured. In conclusion, the rare eukaryotes represent an active, dynamic and overlooked fraction in the lacustrine ecosystems.
•We compared the diversity of protists in freshwater, marine plankton and soil.•Soil hosts the highest protist γ diversity, followed by oceans and freshwater.•Phagocytosis seems to be the dominant ...process in eukaryotic nutrient acquisition.•Relative abundance of phototrophs in soils is comparable to marine systems.
Protists dominate eukaryotic diversity and play key functional roles in all ecosystems, particularly by catalyzing carbon and nutrient cycling. To date, however, a comparative analysis of their taxonomic and functional diversity that compares the major ecosystems on Earth (soil, freshwater and marine systems) is missing. Here, we present a comparison of protist diversity based on standardized high throughput 18S rRNA gene sequencing of soil, freshwater and marine environmental DNA. Soil and freshwater protist communities were more similar to each other than to marine protist communities, with virtually no overlap of Operational Taxonomic Units (OTUs) between terrestrial and marine habitats. Soil protists showed higher γ diversity than aquatic samples. Differences in taxonomic composition of the communities led to changes in a functional diversity among ecosystems, as expressed in relative abundance of consumers, phototrophs and parasites. Phototrophs (eukaryotic algae) dominated freshwater systems (49% of the sequences) and consumers soil and marine ecosystems (59% and 48%, respectively). The individual functional groups were composed of ecosystem- specific taxonomic groups. Parasites were equally common in all ecosystems, yet, terrestrial systems hosted more OTUs assigned to parasites of macro-organisms while aquatic systems contained mostly microbial parasitoids. Together, we show biogeographic patterns of protist diversity across major ecosystems on Earth, preparing the way for more focused studies that will help understanding the multiple roles of protists in the biosphere.
The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These ...conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs.
Display omitted
•Current biomonitoring approaches are widely used but have some limitations.•DNA metabarcoding provides a new complementary tool for biomonitoring.•Metabarcoding allows extending the range of taxa used as bioindicators.•Metabarcoding data could be used to establish molecular metrics and indices.•Future work should standardise procedures and improve data analysis.
The emergence of DNA analyses of lake sediments has opened up many new areas of inquiry, including the study of taxa that were traditionally not considered in paleolimnology because they do not leave ...distinct morphological fossils. Here, we discuss the potential and challenges associated with the study of DNA in paleolimnology to address critical research questions in lacustrine ecology. We examine some recent applications by highlighting studies that have quantified centennial to millennial-scale dynamics, and that considered a diversity of planktonic groups, including bacteria, phytoplankton and zooplankton. We also summarize the main methodological precautions to be taken into account for implementing these types of DNA analyses. Based on our review of the literature focused on the analysis of DNA preserved in lake sediments, the emerging topics we have identified include: (1) the spread, establishment and effect of invasive species, (2) past fish population dynamics, (3) interactions within lacustrine communities, identified through network analyses, (4) potential application of metabarcoding for transfer functions. There are many new and exciting questions that could be addressed using DNA preserved in lake sediment and this will no doubt be an area of continued expansion in the field of paleolimnology for many years to come.
Marine Archaea are important players among microbial plankton and significantly contribute to biogeochemical cycles, but details regarding their community structure and long-term seasonal activity ...and dynamics remain largely unexplored. In this study, we monitored the interannual archaeal community composition of abundant and rare biospheres in northwestern Mediterranean Sea surface waters by pyrosequencing 16S rDNA and rRNA. A detailed analysis of the rare biosphere structure showed that the rare archaeal community was composed of three distinct fractions. One contained the rare Archaea that became abundant at different times within the same ecosystem; these cells were typically not dormant, and we hypothesize that they represent a local seed bank that is specific and essential for ecosystem functioning through cycling seasonal environmental conditions. The second fraction contained cells that were uncommon in public databases and not active, consisting of aliens to the studied ecosystem and representing a nonlocal seed bank of potential colonizers. The third fraction contained Archaea that were always rare but actively growing; their affiliation and seasonal dynamics were similar to the abundant microbes and could not be considered a seed bank. We also showed that the major archaeal groups, Thaumarchaeota marine group I and Euryarchaeota group II.B in winter and Euryarchaeota group II.A in summer, contained different ecotypes with varying activities. Our findings suggest that archaeal diversity could be associated with distinct metabolisms or life strategies, and that the rare archaeal biosphere is composed of a complex assortment of organisms with distinct histories that affect their potential for growth.
The reconstruction of human-driven, Earth-shaping dynamics is important for understanding past human/environment interactions and for helping human societies that currently face global changes. ...However, it is often challenging to distinguish the effects of the climate from human activities on environmental changes. Here we evaluate an approach based on DNA metabarcoding used on lake sediments to provide the first high-resolution reconstruction of plant cover and livestock farming history since the Neolithic Period. By comparing these data with a previous reconstruction of erosive event frequency, we show that the most intense erosion period was caused by deforestation and overgrazing by sheep and cowherds during the Late Iron Age and Roman Period. Tracking plants and domestic mammals using lake sediment DNA (lake sedDNA) is a new, promising method for tracing past human practices, and it provides a new outlook of the effects of anthropogenic factors on landscape-scale changes.
Ciliates are unicellular heterotrophic organisms that play a key role in aquatic planktonic and benthic food webs. Advances in sedimentary DNA (sed-DNA) analysis offer the possibility to integrate ...these bioindicators in paleoenvironmental reconstructions. In this study, we used the top-bottom paleolimnological approach and metabarcoding techniques applied to sed-DNA to compare the recent and past (i.e. prior to major anthropogenic impacts) ciliate communities of 48 lakes located along an elevation gradient. Our results show an overall decline in the β-diversity in recent time, especially in lowland lakes, which are more strongly exposed to local human pressures. Analyses of the functional groups indicate important restructuration of the food web, including the recent increase in mixotrophs. Moreover, changes in the benthic ciliates were consistent with the widespread increase in deep water anoxia. Our results provided evidence that sed-DNA can uncover information about past ciliate communities on a wide variety of lakes. Overall, our study demonstrates the potential of using ciliates as new paleoindicators, integrating information from the pelagic to the benthic zones, and providing valuable insights into ecosystem functioning through a trait-based functional community approach. As paleoindicator, they thus offer a more holistic view on the long-term changes of aquatic ecosystems.
Human impacts on biodiversity are well recognized, but uncertainties remain regarding patterns of diversity change at different spatial and temporal scales. Changes in microbial assemblages are, in ...particular, not well understood, partly due to the lack of community composition data over relevant scales of space and time. Here, we investigate biodiversity patterns in cyanobacterial assemblages over one century of eutrophication and climate change by sequencing DNA preserved in the sediments of ten European peri-Alpine lakes. We found species losses and gains at the lake scale, while species richness increased at the regional scale over approximately the past 100 years. Our data show a clear signal for beta diversity loss, with the composition and phylogenetic structure of assemblages becoming more similar across sites in the most recent decades, as have the general environmental conditions in and around the lakes. We attribute patterns of change in community composition to raised temperatures affecting the strength of the thermal stratification and, as a consequence, nutrient fluctuations, which favoured cyanobacterial taxa able to regulate buoyancy. Our results reinforce previous reports of human-induced homogenization of natural communities and reveal how potentially toxic and bloom-forming cyanobacteria have widened their geographic distribution in the European temperate region.
Increases in atmospheric temperature and nutrients from land are thought to be promoting the expansion of harmful cyanobacteria in lakes worldwide, yet to date there has been no quantitative ...synthesis of long‐term trends. To test whether cyanobacteria have increased in abundance over the past ~ 200 years and evaluate the relative influence of potential causal mechanisms, we synthesised 108 highly resolved sedimentary time series and 18 decadal‐scale monitoring records from north temperate‐subarctic lakes. We demonstrate that: (1) cyanobacteria have increased significantly since c. 1800 ce, (2) they have increased disproportionately relative to other phytoplankton, and (3) cyanobacteria increased more rapidly post c. 1945 ce. Variation among lakes in the rates of increase was explained best by nutrient concentration (phosphorus and nitrogen), and temperature was of secondary importance. Although cyanobacterial biomass has declined in some managed lakes with reduced nutrient influx, the larger spatio‐temporal scale of sedimentary records show continued increases in cyanobacteria throughout the north temperate‐subarctic regions.
PDF
