Resilience of Freshwater Communities of Small Microbial Eukaryotes Undergoing Severe Drought Events

Integrating depth-dependent protist dynamics and microbial interactions in spring succession of a freshwater reservoir

BACKGROUND

Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating protists into the well-described spring dynamics of Římov reservoir, Czech Republic. Over a 2-month period covering transition from mixing to established stratification, we collected water samples from three reservoir depths (0.5, 10 and 30 m) with a frequency of up to three times per week. Microbial eukaryotic and prokaryotic communities were analysed using SSU rRNA gene amplicon sequencing and dominant protistan groups were enumerated by Catalysed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). Additionally, we collected samples for water chemistry, phyto- and zooplankton composition analyses.

RESULTS

Following the rapid changes in environmental and biotic parameters during spring, protistan and bacterial communities displayed swift transitions from a homogeneous community to distinct strata-specific communities. A prevalence of auto- and mixotrophic protists dominated by cryptophytes was associated with spring algal bloom-specialized bacteria in the epilimnion. In contrast, the meta- and hypolimnion showcased a development of a protist community dominated by putative parasitic Perkinsozoa, detritus or particle-associated ciliates, cercozoans, telonemids and excavate protists (Kinetoplastida), co-occurring with bacteria associated with lake snow.

CONCLUSIONS

Our high-resolution sampling matching the typical doubling time of microbes along with the combined microscopic and molecular approach and inclusion of all main components of the microbial food web allowed us to unveil depth-specific populations' successions and interactions in a deep lentic ecosystem.

Foundation species stabilize an alternative eutrophic state in nutrient-disturbed ponds via selection on microbial community

Eutrophication due to nutrient addition can result in major alterations in aquatic ecosystem productivity. Foundation species, individually and interactively, whether present as invasive species or as instruments of ecosystem management and restoration, can have unwanted effects like stabilizing turbid eutrophic states. In this study, we used whole-pond experimental manipulations to investigate the impacts of disturbance by nutrient additions in the presence and absence of two foundation species: Dreissena polymorpha (a freshwater mussel) and Myriophyllum spicatum (a macrophyte). We tracked how nutrient additions to ponds changed the prokaryotic and eukaryotic communities, using 16S, 18S, and COI amplicon sequencing. The nutrient disturbance and foundation species imposed strong selection on the prokaryotic communities, but not on the microbial eukaryotic communities. The prokaryotic communities changed increasingly over time as the nutrient disturbance intensified. Post-disturbance, the foundation species stabilized the prokaryotic communities as observed by the reduced rate of change in community composition. Our analysis suggests that prokaryotic community change contributed both directly and indirectly to major changes in ecosystem properties, including pH and dissolved oxygen. Our work shows that nutrient disturbance and foundation species strongly affect the prokaryotic community composition and stability, and that the presence of foundation species can, in some cases, promote the emergence and persistence of a turbid eutrophic ecosystem state.

Transformation of Biofilm to Carbon Sinks after Prolonged Droughts Linked with Algal Biodiversity Change

Global climate change significantly increased the duration of droughts in intermittent rivers, impacting benthic microbial-mediated biogeochemical processes. However, the impact of prolonged droughts on the carbon contribution of intermittent rivers remains poorly understood. In this study, we investigated the potential effects of varying drought gradients (ranging from 20 to 130 days) on benthic biofilms community structure (algae, bacteria, and fungi) and their carbon metabolism functions (ecosystem metabolism and carbon dioxide (CO2) emission fluxes) using mesocosm experiments. Our findings indicate that longer drought durations lead to reduced alpha diversity and community heterogeneity, tighter interdomain networks, and an increased role of stochastic processes in community assembly, with a discernible threshold at around 60 days. Concurrently, the biofilm transforms into a carbon sink following a drought period of 60 days, as evidenced by the transformation of CO2 emission fluxes from 633.25 ± 194.69 to -349.61 ± 277.79 mg m-2 h-1. Additionally, the partial least-squares path model revealed that the resilience of algal communities and network stability may drive biofilm's transformation into a carbon sink, primarily through the heightened resilience of autotrophic metabolism. This study underscores the significance of the carbon contribution from intermittent rivers, as the shift in carbon metabolism functions with increasing droughts could lead to skewed estimations of current riverine carbon fluxes.

Eukaryotes contribute more than bacteria to the recovery of freshwater ecosystem functions under different drought durations

Global climate change mostly impacts river ecosystems by affecting microbial biodiversity and ecological functions. Considering the high functional redundancy of microorganisms, the unknown relationship between biodiversity and ecosystem functions obstructs river ecological research, especially under the influence of increasing weather extremes, such as in intermittent rivers and ephemeral streams (IRES). Herein, dry-wet alternation experiments were conducted in artificial stream channels for 25 and 90 days of drought, both followed by 20 days of rewetting. The dynamic recovery of microbial biodiversity and ecosystem functions (represented by ecosystem metabolism and denitrification rate) were determined to analyse biodiversity-ecosystem-function (BEF) relationships after different drought durations. There was a significant difference between bacterial and eukaryotic biodiversity recovery after drought. Eukaryotic biodiversity was more sensitive to drought duration than bacterial, and the eukaryotic network was more stable under dry-wet alternations. Based on the establishment of partial least squares path models, we found that eukaryotic biodiversity has a stronger effect on ecosystem functions than bacteria after long-term drought. Indeed, this work represents a significant step forward for further research on the ecosystem functions of IRES, especially emphasizing the importance of eukaryotic biodiversity in the BEF relationship.

Taxonomic dependency of beta diversity for bacteria, archaea, and fungi in a semi-arid lake

Microbial beta diversity has been recently studied along the water depth in aquatic ecosystems, however its turnover and nestedness components remain elusive especially for multiple taxonomic groups. Based on the beta diversity partitioning developed by Baselga and Local Contributions to Beta Diversity (LCBD) partitioning by Legendre, we examined the water-depth variations in beta diversity components of bacteria, archaea and fungi in surface sediments of Hulun Lake, a semi-arid lake in northern China, and further explored the relative importance of environmental drivers underlying their patterns. We found that the relative abundances of Proteobacteria, Chloroflexi, Euryarchaeota, and Rozellomycota increased toward deep water, while Acidobacteria, Parvarchaeota, and Chytridiomycota decreased. For bacteria and archaea, there were significant (p < 0.05) decreasing water-depth patterns for LCBD and LCBDRepl (i.e., species replacement), while increasing patterns for total beta diversity and turnover, implying that total beta diversity and LCBD were dominated by species turnover or LCBDRepl. Further, bacteria showed a strong correlation with archaea regarding LCBD, total beta diversity and turnover. Such parallel patterns among bacteria and archaea were underpinned by similar ecological processes like environmental selection. Total beta diversity and turnover were largely affected by sediment total nitrogen, while LCBD and LCBDRepl were mainly constrained by water NO2 --N and NO3 --N. For fungal community variation, no significant patterns were observed, which may be due to different drivers like water nitrogen or phosphorus. Taken together, our findings provide compelling evidences for disentangling the underlying mechanisms of community variation in multiple aquatic microbial taxonomic groups.

Microbial eukaryotes assemblages and potential novel diversity in four tropical East-African Great Lakes

East-African Great Lakes are old and unique natural resources heavily utilized by their bordering countries. In those lakes, ecosystem functioning is dominated by pelagic processes, where microorganisms are key components, however protistan diversity is barely known. We investigated the community composition of small eukaryotes (< 10 µm) in surface waters of four African Lakes (Kivu, Edward, Albert and Victoria) by sequencing the 18S rRNA gene. Moreover, in the meromictic Lake Kivu, two stations were vertically studied. We found high protistan diversity distributed in 779 operational taxonomic units (OTUs), spanning in eleven high-rank lineages, being Alveolata (31%), Opisthokonta (20%) and Stramenopiles (17%) the most represented supergroups. Surface protistan assemblage were associated to conductivity and productivity gradients; whereas depth, had a strong effect on protistan community in Kivu, with higher contribution of heterotrophic organisms. Approximately 40% of OTUs had low similarity (< 90%) with reported sequences in public databases, these were mostly coming from deep anoxic waters of Kivu, suggesting a high extent of novel diversity. We also detected several taxa so far considered exclusive of marine ecosystems. Our results unveiled a complex and largely undescribed protistan community, in which several lineages have adapted to different niches after crossing the salinity boundary.

Microbial Community Resilience across Ecosystems and Multiple Disturbances

The ability of ecosystems to withstand disturbances and maintain their functions is being increasingly tested as rates of change intensify due to climate change and other human activities. Microorganisms are crucial players underpinning ecosystem functions, and the recovery of microbial communities from disturbances is therefore a key part of the complex processes determining the fate of ecosystem functioning. However, despite global environmental change consisting of numerous pressures, it is unclear and controversial how multiple disturbances affect microbial community stability and what consequences this has for ecosystem functions. This is particularly the case for those multiple or compounded disturbances that occur more frequently than the normal recovery time. The aim of this review is to provide an overview of the mechanisms that can govern the responses of microbes to multiple disturbances across aquatic and terrestrial ecosystems. We first summarize and discuss properties and mechanisms that influence resilience in aquatic and soil biomes to determine whether there are generally applicable principles. Following, we focus on interactions resulting from inherent characteristics of compounded disturbances, such as the nature of the disturbance, timing, and chronology that can lead to complex and nonadditive effects that are modulating the response of microorganisms.

Evaluation of V2 18S rDNA barcode marker and assessment of sample collection and DNA extraction methods for metabarcoding of autotrophic euglenids

Even though the interest in metabarcoding in environmental studies is growing, euglenids are still underrepresented in both sea and freshwater bodies researches. The reason for this situation could be the unsuitability of universal eukaryotic DNA barcodes and primers as well as the lack of a verified protocol, suitable to assess euglenid diversity. In this study, using specific primers for the V2 hypervariable region of 18S rDNA for metabarcoding resulted in obtaining a high fraction (85%) of euglenid reads and species‐level identification of almost 90% of them. Fifty species were detected by the metabarcoding method, including almost all species observed using a light microscope. We investigated three biomass harvesting methods (filtering, centrifugation and scraping the side of a collection vessel) and determined that centrifugation and filtration outperformed scrapes, but the choice between them is not crucial for the reliability of the analysis. In addition, eight DNA extraction methods were evaluated. We compared five commercially available DNA isolation kits, two CTAB‐based protocols and a chelating resin. For this purpose, the efficiency of extraction, quality of obtained DNA, preparation time and generated costs were taken into consideration. After examination of the aforementioned criteria, we chose the GeneMATRIX Soil DNA Purification Kit as the most suitable for DNA isolation.

Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns

Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.

Metatranscriptomics From a Small Aquatic System: Microeukaryotic Community Functions Through the Diurnal Cycle

Light is an important factor for the growth of planktonic organisms, and many of them depend on the diurnal light/dark cycle to regulate key metabolic processes. So far, most of the diel responses were only studied in single species or marine and large lake communities. Yet, we lack information on whether these processes are regulated similarly in small aquatic systems such as ponds. Here, we investigated the activity of a microeukaryotic community from a temperate, small freshwater pond in response to the diurnal cycle. For this, we took samples at midday and night during the Central European summer. We extracted pigments and RNA from samples and the sequencing of eukaryotic transcripts allowed us to obtain day and night metatranscriptomes. Differentially expressed transcripts primarily corresponded to photosynthesis-related and translational processes, and were found to be upregulated at midday with high light conditions compared to darkness. Unique gene ontology classes were found at each respective condition. During the day, ontology classes including photoreception for photosynthesis, defense, and stress mechanisms dominated, while motility, ribosomal assembly and other large, energy-consuming processes were restricted to the night. Euglenophyta and Chlorophyta dominated the active phototrophic community, as shown by the pigment composition analysis. Regarding the gene expression patterns, we could confirm that the pond community appears to follow similar diurnal dynamics as those described for larger aquatic ecosystems. Overall, combining pigment analyses, metatranscriptomics, and data on physicochemical factors yielded considerably more insight into the metabolic processes performed by the microeukaryotic community of a small freshwater ecosystem.

Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes

Rain fed granite rock basins are ancient geological landforms of worldwide distribution and structural simplicity. They support habitats that can switch quickly from terrestrial to aquatic along the year. Diversity of animals and plants, and the connexion between communities in different basins have been widely explored in these habitats, but hardly any research has been carried out on microorganisms. The aim of this study is to provide the first insights on the diversity of eukaryotic microbial communities from these environments. Due to the ephemeral nature of these aquatic environments, we predict that the granitic basins should host a high proportion of dormant microeukaryotes. Based on an environmental DNA diversity survey, we reveal diverse communities with representatives of all major eukaryotic taxonomic supergroups, mainly composed of a diverse pool of low abundance OTUs. Basin communities were very distinctive, with alpha and beta diversity patterns non-related to basin size or spatial distance respectively. Dissimilarity between basins was mainly characterised by turnover of OTUs. The strong microbial eukaryotic heterogeneity observed among the basins may be explained by a complex combination of deterministic factors (diverging environment in the basins), spatial constraints, and randomness including founder effects. Most interestingly, communities contain organisms that cannot coexist at the same time because of incompatible metabolic requirements, thus suggesting the existence of a pool of dormant organisms whose activity varies along with the changing environment. These organisms accumulate in the pools, which turns granitic rock into high biodiversity microbial islands whose conservation and study deserve further attention.

Hydrological variations shape diversity and functional responses of streambed microbes

Microbiota inhabiting the intermittent streambeds mediates several in-stream processes that are essential for ecosystem function. Reduced stream discharge caused by the strengthened intermittency and increased duration of the dry phase is a spreading global response to changes in climate. Here, the impacts of a 5-month desiccation, one-week rewetting and punctual storms, which interrupted the dry period, were examined. The genomic composition of total (DNA) and active (RNA) diversity, and the community level physiological profiles (CLPP) were considered as proxies for functional diversity to describe both prokaryotes and eukaryotes inhabiting the surface and hyporheic streambeds. Comparisons between the genomic and potential functional responses helped to understand how and whether the microbial diversity was sensitive to the environmental conditions and resource acquisition, such as water stress and extracellular enzyme activities, respectively. RNA expression showed the strongest relationship with the environmental conditions and resource acquisition, being more responsive to changing conditions compared to DNA diversity, especially in the case of prokaryotes. The DNA results presumably reflected the legacy of the treatments because inactive, dormant, or dead cells were included, suggesting a slow microbial biomass turnover or responses of the microbial communities to changes mainly through physiological acclimation. On the other hand, microbial functional diversity was largely explained by resources acquisition, such as metrics of extracellular enzymes, and appeared vulnerable to the hydrological changes and duration of desiccation. The data highlight the need to improve the functional assessment of stream ecosystems with the application of complementary metrics to better describe the streambed microbial dynamics under dry-rewet stress.

Coupled effects of land use pattern and hydrological regime on composition and diversity of riverine eukaryotic community in a coastal watershed of Southeast China

The coupled effects of land use pattern and hydrological regime on composition and diversity of riverine eukaryotic community are needed for understanding riverine ecosystem health and algal blooming mechanism. In-situ monitoring and 18S rRNA gene sequencing were used to investigate spatiotemporal variations of eukaryotic community in three types of watershed with different dominant land use type (i.e. urban, forest, and natural) during three seasons (i.e. dry, transition, and wet seasons) in a coastal watershed of Southeast China. Results showed that agricultural and urban watersheds had significantly higher diversity in dry and transition seasons, and higher richness in transition and wet seasons than those in forest watershed. The non-metric multidimensional scaling analysis further verified great spatiotemporal variations of eukaryotic community. Stramenopiles, Alveolata, Animalia, and Eukaryota, dominated the sequences reads for all sampling sites in three seasons. Agricultural watershed had the highest relative abundant of Animalia, whereas Eukaryota was the most abundant in urban watershed and forest watershed had the highest relative abundance of Stramenopiles and Alveolata. The RDA ordination showed that Builtup and streamflow were two most important factors for moderate taxa and abundant taxa, respectively. Variation partitioning revealed that land use pattern and hydrological regime together explained 54.4%, 61% and 67.2% variances of the composition of eukaryotic community. Among three sampling seasons, the relative contribution of land use pattern was higher than that of hydrological regime. The results of this investigation demonstrated how land use pattern and hydrological regime affected the composition and diversity of riverine eukaryotic community. The findings can provide a useful insight into the riverine eukaryotic communities and their underlying ecological mechanisms in coastal China watersheds.

Grazers superimpose humidity effect on stream biofilm resistance and resilience to dry-rewet stress

Temperate low order streams increasingly experience intermittency and drying due to climate change. In comparison to well-studied Mediterranean streams, drying events in canopied temperate streams occur under higher ambient humidity which probably affects the metabolic response to drying. Previous work on drying sediments (in temperate streams) did not consider the interactions of trophic levels. We hypothesized that preservation of sediment moisture due to high humidity increases resistance to drying in temperate streambed biofilms and fast resilience of biofilm activity after flow resumption. We also expected the presence of macroinvertebrate grazers to modulate the biofilm response to dry-rewet stress. Following a two-level factorial design in 24 microcosms, we tested the effect of drying intensity (moderate and intense) and grazer presence and absence (P. antipodarum) on the activity of biofilm colonizing shallow hyporheic sediment. We measured the community respiration over a drying period of 27 days, a single rewetting event and a follow-up of three days. Grazer presence stimulated biofilm community respiration (CR_mic) in the permanently wet control, but decreased biofilm resistance to desiccation (<0.2% of pre-disturbed activity), regardless of drying intensity. In the absence of grazers, higher atmospheric humidity in moderately drying microcosms resulted in maintaining a film of adhesive water and low CR_mic (29% of pre-disturbed respiration) until the end of the drying period. After flow resumption, the CR_mic increased within 8 h, achieving 79-83% of pre-disturbed respiration (no grazers) and 15-41% (with grazers), respectively. Results show that short dry periods in temperate streams, even under high humidity, impact the streambed biofilm community negatively. The complex response and strong effect of grazer presence indicates that experiments including interactions of trophic levels and settings mimicking environmental factors during dry-rewet stress are needed.

A meta-barcoding census of freshwater planktonic protists in Appalachia – Natural Tunnel State Park, Virginia, USA

The purpose of our study was to survey the freshwater planktonic protists within an inland natural preserve in the Ridge and Valley physiographic province of the Appalachian Region using metabarcoding. Microbial eukaryotes are essential primary producers and predators in small freshwater ecosystems, yet they are often overlooked due to the difficulty of identification. This has been remedied, in part, by the cost reduction of high throughput DNA sequencing and the growth of barcode databases, making the identification and analysis of microorganisms by way of metabarcoding surveys in complex ecosystems increasingly feasible. Water samples were collected from five sites at the Natural Tunnel State Park in Scott County, VA (USA), representing three common bodies of water found in this region. Samples were initially collected during a Bioblitz event in April 2016 and then seven and fourteen weeks afterwards. Metabarcode analysis of the 23S and 18S genes identified 3663 OTUs representing 213 family level and 332 genus level taxa. This study provides an initial barcode census within a region that has a reputation as a temperate biodiversity “hotspot”. The overall protist diversity was comparably high to other temperate systems, but not unusually high; the microalgal diversity, however, was higher than that reported for other temperate regions. The three types of water bodies had their own distinctive protist biomes despite close proximity.

EukRef-Ciliophora: a manually curated, phylogeny-based database of small subunit rRNA gene sequences of ciliates

High-throughput sequencing (HTS) surveys, among the most common approaches currently used in environmental microbiology, require reliable reference databases to be correctly interpreted. The EukRef Initiative (eukref.org) is a community effort to manually screen available small subunit (SSU) rRNA gene sequences and produce a public, high-quality and informative framework of phylogeny-based taxonomic annotations. In the context of EukRef, we present a database for the monophyletic phylum Ciliophora, one of the most complex, diverse and ubiquitous protist groups. We retrieved more than 11 500 sequences of ciliates present in GenBank (28% from identified isolates and 72% from environmental surveys). Our approach included the inference of phylogenetic trees for every ciliate lineage and produced the largest SSU rRNA tree of the phylum Ciliophora to date. We flagged approximately 750 chimeric or low-quality sequences, improved the classification of 70% of GenBank entries and enriched environmental and literature metadata by 30%. The performance of EukRef-Ciliophora is superior to the current SILVA database in classifying HTS reads from a global marine survey. Comprehensive outputs are publicly available to make the new tool a useful guide for non-specialists and a quick reference for experts.

Cryptophyta as major bacterivores in freshwater summer plankton

Small bacterivorous eukaryotes play a cardinal role in aquatic food webs and their taxonomic classification is currently a hot topic in aquatic microbial ecology. Despite increasing interest in their diversity, core questions regarding predator–prey specificity remain largely unanswered, e.g., which heterotrophic nanoflagellates (HNFs) are the main bacterivores in freshwaters and which prokaryotes support the growth of small HNFs. To answer these questions, we fed natural communities of HNFs from Římov reservoir (Czech Republic) with five different bacterial strains of the ubiquitous betaproteobacterial genera Polynucleobacter and Limnohabitans. We combined amplicon sequencing and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) targeting eukaryotic 18 S rRNA genes to track specific responses of the natural HNF community to prey amendments. While amplicon sequencing provided valuable qualitative data and a basis for designing specific probes, the number of reads was insufficient to accurately quantify certain eukaryotic groups. We also applied a double-hybridization technique that allows simultaneous phylogenetic identification of both predator and prey. Our results show that community composition of HNFs is strongly dependent upon prey type. Surprisingly, Cryptophyta were the most abundant bacterivores, although this phylum has been so far assumed to be mainly autotrophic. Moreover, the growth of a small lineage of Cryptophyta (CRY1 clade) was strongly stimulated by one Limnohabitans strain in our experiment. Thus, our study is the first report that colorless Cryptophyta are major bacterivores in summer plankton samples and can play a key role in the carbon transfer from prokaryotes to higher trophic levels.