Eukaryotic Community Structure Research Articles

Microbial community structure and diversity attached to the periphyton in different urban aquatic habitats.

Periphyton is a complex community composed of diverse prokaryotes and eukaryotes; understanding the characteristics of microbial communities within periphyton becomes crucial for biogeochemical cycles and energy dynamics of aquatic ecosystems. To further elucidate the community characteristics of periphyton across varied aquatic habitats, including unpolluted ecologically restored lakes, aquaculture ponds, and areas adjacent to domestic and industrial wastewater treatment plant outfalls, we explored the composition and diversity of prokaryotic and eukaryotic communities in periphyton by employing Illumina MiSeq sequencing. Our findings indicated that the prokaryotic communities were predominantly composed of Proteobacteria (40.92%), Bacteroidota (21.01%), and Cyanobacteria (10.12%), whereas the eukaryotic communities were primarily characterized by the dominance of Bacillariophyta (24.09%), Chlorophyta (20.83%), and Annelida (15.31%). Notably, Flavobacterium emerged as a widely distributed genus among the prokaryotic community. Unclassified_Tobrilidae exhibited higher abundance in unpolluted ecologically restored lakes. Chaetogaster and Nais were enriched in aquaculture ponds and domestic wastewater treatment plant outfall area, respectively, while Surirella and Gomphonema dominated industrial sewage treatment plant outfall area. The alpha diversity of eukaryotes was higher in unpolluted ecologically restored lakes. pH and nitrogen content ( , , and TN) significantly explained the variations for prokaryotic and eukaryotic community structures, respectively. Eukaryotic communities exhibited a more pronounced response to habitat variations compared to prokaryotic communities. Moreover, the association networks revealed an intensive positive correlation between dominant Bacillariophyta and Bacteroidota. This study provided useful data for identifying keystone species and understanding their ecological functions.

New sensitive tools to characterize meta-metabolome response to short- and long-term cobalt exposure in dynamic river biofilm communities

Untargeted metabolomics is a non-a priori analysis of biomolecules that characterizes the metabolome variations induced by short- and long-term exposures to stressors. Even if the metabolite annotation remains lacunar due to database gaps, the global metabolomic fingerprint allows for trend analyses of dose-response curves for hundreds of cellular metabolites. Analysis of dose/time-response curve trends (biphasic or monotonic) of untargeted metabolomic features would thus allow the use of all the chemical signals obtained in order to determine stress levels (defense or damage) in organisms. To develop this approach in a context of time-dependent microbial community changes, mature river biofilms were exposed for 1 month to four cobalt (Co) concentrations (from background concentration to 1 × 10−6 M) in an open system of artificial streams. The meta-metabolomic response of biofilms was compared against a multitude of biological parameters (including bioaccumulation, biomass, chlorophyll a content, composition and structure of prokaryotic and eukaryotic communities) monitored at set exposure times (from 1 h to 28 d). Cobalt exposure induced extremely rapid responses of the meta-metabolome, with time range inducing defense responses (TRIDeR) of around 10 s, and time range inducing damage responses (TRIDaR) of several hours. Even in biofilms whose structure had been altered by Co bioaccumulation (reduced biomass, chlorophyll a contents and changes in the composition and diversity of prokaryotic and eukaryotic communities), concentration range inducing defense responses (CRIDeR) with similar initiation thresholds (1.41 ± 0.77 × 10−10 M Co2+ added in the exposure medium) were set up at the meta-metabolome level at every time point. In contrast, the concentration range inducing damage responses (CRIDaR) initiation thresholds increased by 10 times in long-term Co exposed biofilms. The present study demonstrates that defense and damage responses of biofilm meta-metabolome exposed to Co are rapidly and sustainably impacted, even within tolerant and resistant microbial communities.

Diversity and distribution analysis of eukaryotic communities in the Xiangshan Bay, East China sea by metabarcoding approach

Eukaryotic communities play an important role in the coastal ecosystem of Xiangshan Bay, a narrow semi-closed bay famous for fisheries and marine farming. However, information on the diversity and composition of eukaryotic communities in Xiangshan Bay remains unclear. In this study, the metabarcoding approach was utilized to comprehensively investigate the eukaryotic plankton community structure and dominant taxa, particularly eukaryotic microalgae, in the Xiangshan Bay over a period of four months in 2018. The results showed that the three major phyla were Arthropoda, Chlorophyta, and Bacillariophyta. The richness indices revealed that species richness peaked in February and was at its lowest in May. Diversity indices showed that the samples collected in May had the lowest diversity. Centropages was detected in the samples of all months, however, its highest dominance was observed in the samples collected in February. In addition, compared to other months, a greater proportion of eukaryotic microalgae was witnessed in March. The three eukaryotic algae with highest abundances in March were Cyclotella, Prorocentrum, and Thalassiosira. Moreover, high diversity of pico-sized (0.2–2.0 μm) phytoplankton (which are often easily missed by microscopy) was discovered in this study by using metabarcoding approach. This study highlights the strength and significance of the metabarcoding approach to uncover a large number of eukaryotic species which remains undetectable during application of conventional approaches. The findings of this study reveals that the eukaryotic community structure varies noticeably in both time and space throughout sampling period, with temperature being the most important environmental factor influencing these changes. This study lays a solid foundation to understand eukaryotic plankton composition, temporal and spatial dynamics and the distribution mechanism of eukaryotic plankton community in Xiangshan Bay, providing theoretical reference for further studies related to marine ecology.

Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints.

The use of novel high-throughput sequencing (HTS) technologies to examine the responses of natural multidomain microbial communities to scrubber effluent discharges to the marine environment is still limited. Thus, we applied metabarcoding sequencing targeting the planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, and protozooplankton) in mesocosm experiments with natural microbial communities from a polluted and an unpolluted site. Furthermore, metagenomic analysis revealed changes in the taxonomic and functional dominance of multidomain marine microbial communities after scrubber effluent additions. The results indicated a clear shift in the microbial communities after such additions, which favored bacterial taxa with known oil and polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness with planktonic unicellular eukaryotes employing variable trophic strategies, suggesting that environmentally relevant bacteria can influence eukaryotic community structure. Furthermore, Clusters of Orthologous Genes associated with pathways of PAHs and monocyclic hydrocarbon degradation increased in numbers at treatments with high scrubber effluent additions acutely. These genes are known to express enzymes acting at various substrates including PAHs. These indications, in combination with the abrupt decrease in the most abundant PAHs in the scrubber effluent below the limit of detection-much faster than their known half-lives-could point toward a bacterioplankton-initiated rapid ultimate biodegradation of the most abundant toxic contaminants of the scrubber effluent. The implementation of HTS could be a valuable tool to develop multilevel biodiversity indicators of the scrubber effluent impacts on the marine environment, which could lead to improved impact assessment. Environ Toxicol Chem 2024;43:1012-1029. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

The effect of type and combination of fertilizers on eukaryotic microbiome of date palm rhizosphere

The date palm (Phoenix dactylifera) is an important cultivated crop in arid areas. Here, we studied the effect of plant genotype and type of fertilizers on the eukaryotic community structures of the date palm rhizosphere. Samples were collected from one wild population, five cultivars from two farms, and a factorial fertilizer experiment (organic, chemical, and biofertilizer) in Qatar. The eukaryotic communities were sequenced using a next-generation sequencing method. A total of 2422 Operational Taxonomic Units (OTUs) were identified as belonging to 15 phyla, Chlorophyta, Streptophyta, Imbricatea, Chytridiomycota, Ascomycota, Olpidiomycota, being dominant. The wild-type date palms showed a low number of OTUs compared to cultivated date palms, potentially due to the strong influence of soil salinity and low moisture level. However, the wild-type date palm hosted the highest number of unique OTUs. PCA revealed that the eukaryotic microbiome of the wild date palms was separated from the cultivated date palms and that the eukaryotic microbial diversity varied between date palm cultivars in similar environments. Using the highest amounts of biofertilizer and chemical fertilizer decreased the species diversity within the samples. However, a high concentration of biofertilizer combined with a low concentration of chemical fertilizers enhanced the eukaryotic diversity within the samples. We conclude that cultivar type (biotic factor), type of fertilizer, and dosage (abiotic factor) play significant roles in determining the microbiome diversity of the rhizosphere. The wild date palm population could potentially host salt and drought-tolerating eukaryotes that should be further investigated for future development of biofertilizers suitable for drylands.

Microbial eukaryote community succession over hundreds of years in Chinese lakes

Microbial eukaryotes play critical roles in maintaining the health and stability of lake ecosystems. Consequently, investigating the spatial and temporal evolution of microbial eukaryotic community structures and associated environmental drivers can inform water ecology studies and water environmental protection efforts. In this study, sediment core samples were collected from Lakes Chaohu, Erhai, Lugu and Fuxian in China to reconstruct lake microbial eukaryotic community succession using sediment DNA profiling methods. Mantel tests were used to identify the key factors influencing community succession and explore the mechanisms underlying ecological network changes. Statistical analyses revealed that community structures and diversity in Lakes Chaohu and Erhai shifted in the 2000s and 1980s, respectively, while the communities of Lakes Fuxian and Lugu did not exhibit significant changes during the study period, which may be due to the oligotrophic state of these two lakes. Ciliophora and Chlorophyta were the primary eukaryotic microbial taxa in the four lakes during the study period, with overall relative abundances of 27.2 % and 22.3 %, respectively. The diversities of microbial eukaryotic communities in the lakes were significantly correlated with nutrient enrichment and meteorological factors. Lastly, the ecological niche gap of microbial eukaryotes gradually overlapped after community shifts in Lake Chaohu, while biased interactions strengthened. Overall, this study reveals the impacts of long-term human activities and climate change on lake ecosystems from multiple perspectives of microbial eukaryotic community structure, diversity and ecological network, these findings will contribute to integrate microbial indicators in freshwater environmental monitoring in the future.

Linking Groundwater to Surface Discharge Ecosystems: Archaeal, Bacterial, and Eukaryotic Community Diversity and Structure in Quebec (Canada).

Aquifer systems are composed of water flowing from surface recharge areas, to the subsurface and back to the surface in discharge regions. Groundwater habitats harbor a large microbial biomass and diversity, potentially contributing to surface aquatic ecosystems. Although this contribution has been widely studied in marine environments, very little is known about the connection between underground and surface microbial communities in freshwater settings. Therefore, in this study, we used amplicon sequencing to analyze the archaeal, bacterial, and eukaryotic community diversity and structure in groundwater and surface water samples, spanning the vast regions of the Laurentides and Lanaudières in the Quebec province (Canada). Our results show significant differences between subsurface and surface taxa; with more fungi, Amoebozoa, and chemolithoautotrophic prokaryotes involved in nitrogen-, sulfur-, and iron-cycling dominating the underground samples; while algae, ciliates, methanogens, and Actinobacteria dominate the surface discharge waters. Microbial source tracking suggested that only a small portion of the microbial communities in the groundwater contributed to the surface discharge communities. However, many taxa were shared between both habitats, with a large range of functional diversity, likely explaining their survival in both subsurface and surface water ecosystems.

Evolution of fungal and non-fungal eukaryotic communities in response to thermophilic co-composting of various nitrogen-rich green feedstocks.

Thermophilic composting is a promising soil and waste management approach involving diverse micro and macro-organisms, including eukaryotes. Due to sub-optimal amounts of nutrients in manure, supplemental feedstock materials such as Lantana camara, and Tithonia diversifolia twigs are used in composting. These materials have, however, been reported to have antimicrobial activity in in-vitro experiments. Furthermore, the phytochemical analysis has shown differences in their complexities, thus possibly requiring various periods to break down. Therefore, it is necessary to understand these materials' influence on the biological and physical-chemical stability of compost. Most compost microbiome studies have been bacterial-centric, leaving out eukaryotes despite their critical role in the environment. Here, the influence of different green feedstock on the fungal and non-fungal eukaryotic community structure in a thermophilic compost environment was examined. Total community fungal and non-fungal eukaryotic DNA was recovered from triplicate compost samples of four experimental regimes. Sequencing for fungal ITS and non-fungal eukaryotes; 18S rDNA was done under the Illumina Miseq platform, and bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 workflow in R version 4.1. Samples of mixed compost and composting day 84 recorded significantly (P<0.05) higher overall fungal populations, while Lantana-based compost and composting day 84 revealed the highest fungal community diversity. Non-fungal eukaryotic richness was significantly (P< 0.05) more abundant in Tithonia-based compost and composting day 21. The most diverse non-fungal eukaryotic biome was in the Tithonia-based compost and composting day 84. Sordariomycetes and Holozoa were the most contributors to the fungal and non-fungal community interactions in the compost environment, respectively. The findings of this study unravel the inherent influence of diverse composting materials and days on the eukaryotic community structure and compost's biological and chemical stability.

Eukaryotic Community Structure and Interspecific Interactions in a Stratified Acidic Pit Lake Water in Anhui Province.

The stratified acidic pit lake formed by the confluence of acid mine drainage has a unique ecological niche and is a model system for extreme microbial studies. Eukaryotes are a component of the AMD community, with the main members including microalgae, fungi, and a small number of protozoa. In this study, we analyzed the structural traits and interactions of eukaryotes (primarily fungi and microalgae) in acidic pit lakes subjected to environmental gradients. Based on the findings, microalgae and fungi were found to dominate different water layers. Specifically, Chlorophyta showed dominance in the well-lit aerobic surface layer, whereas Basidiomycota was more abundant in the dark anoxic lower layer. Co-occurrence network analysis showed that reciprocal relationships between fungi and microalgae were prevalent in extremely acidic environments. Highly connected taxa within this network were Chlamydomonadaceae, Sporidiobolaceae, Filobasidiaceae, and unclassified Eukaryotes. Redundancy analysis (RDA) and random forest models revealed that Chlorophyta and Basidiomycota responded strongly to environmental gradients. Further analysis indicated that eukaryotic community structure was mainly determined by nutrient and metal concentrations. This study investigates the potential symbiosis between fungi and microalgae in the acidic pit lake, providing valuable insights for future eukaryotic biodiversity studies on AMD remediation.

Field investigation on the change process of microbial community structure in large-deep reservoir during the initial impoundment

During the initial impoundment of large-deep reservoir, the aquatic environment changed dramatically in various aspects such as water level, hydrological regime, and pollutants, which could alter microorganisms’ community structure, break the balance of the aquatic ecosystem and even endanger the aquatic ecosystem. However, the interaction of microbial communities and water environment during the initial impoundment process of a large-deep reservoir remained unclear. To this end, in-situ monitoring and sampling analysis on water quality and microbial communities during the initial impoundment process of a typical large-deep reservoir named Baihetan were conducted so as to explore the response of microbial community structure to the changes of water environmental factors during the initial impoundment of large deep reservoir and reveal the key driving factors affecting microbial community structure. The spatio-temporal variation in water quality was analyzed, and the microbial community structure in the reservoir was investigated based on high-throughput sequencing. The results showed that the COD of each section increased slightly, and the water quality after impoundment was slightly poorer than that before the impoundment. Water temperature and pH were proved to be the key factors affecting the structure of bacterial and eukaryotic communities respectively during the initial impoundment. The research results revealed the role of microorganisms and their interaction with biogeochemical processes in the large-deep reservoir ecosystem, which was crucial for later operation and management of the reservoir and the protection of the reservoir water environment.

Response of microbial community of surface and deep chlorophyll maximum to nutrients and light in South China Sea

In oligotrophic seas such as South China Sea, the subsurface or deep chlorophyll maximum (DCM) is always present. The surface planktonic community receives sufficient light, but is short of nutrients. The DCM layer is under light limitation, but frequent supply of nutrients. Therefore, vertical mixing becomes critical in determining their community composition and drives their changes by responding to light and nutrients. In this study, we conducted an onboard experiment by collecting seawater samples at surface and the DCM layer and adding nutrients, and incubated them under full sunlight and 10% light, and examined the diversity of bacterial and eukaryotic communities and their cell abundance using 16/18S high throughput sequencing and FCM approaches. Our study found large differences in bacterial and eukaryotic community structure and cell abundance between the surface and DCM. After 72 hours of culture, taxonomically the incubated surface water was dominated by pico-eukaryotic phytoplankton, while the incubated DCM layer water is dominated by diatoms, which suggests diatoms are the main functional group of phytoplankton bloom after a vertical mixing event. These findings indicate that phytoplankton at the DCM respond to enhanced light and frequent supplied nutrients due to vertical mixing and thus maintain primary productivity in the otherwise oligotrophic oceans.

Differentiation strategies for planktonic bacteria and eukaryotes in response to aggravated algal blooms in urban lakes.

Aggravated algal blooms potentially decreased environmental heterogeneity. Different strategies of planktonic bacteria and eukaryotes in response to aggravated algal blooms. Environmental constraints of plankton showed different patterns over time.

THE UTILITY OF METAGENOMIC DATA FOR THE BLACK SEA ECOLOGICAL STATUS ASSESSMENT

According to Marine Strategy Framework Directive the assessment of marine ecosystems’ environmental status is performed with 11 Descriptors, which are based on biological, physical and chemical parameters. The biological indexes are calculated based on taxonomic structure and distribution of eukaryotic communities. Meanwhile, bacterioplankton is sensitive to anthropogenic impact and is thus a promising indicator of aquatic environment status. We have tested the utility of ecological pressure index (Pi) calculated with chemical data and bacterial community-based index (microgAMBI) for the assessment of Black sea waters ecological status. According to our estimations Pi varied depending on the chemical data used for its calculation, which indicates the necessity of using a wide range of xenobiotics in complex ecological status assessment. MicrogAMBI indicated that the Black sea surface waters can be characterized by “good” environmental status. “Moderate”, “poor” and “bad” ecological status was shown for 3 stations, yet there were no significant region-specific differences between the shelf zone and the open water. Actinomycetales, Halomonadaceae and Shewanella relative abundance was associated with higher microgAMBI estimations and respectively with worse ecological status. Meanwhile, positive correlation was found between Synechococcus, Acidimicrobiaceae, Pelagibacteraceae, Rhodobacteraceae, Microbacteriaceae, Polaribacter, Rhodothermaceae and Chloroflexi abundance and “good” ecological status. Microbial metagenomic data is promising for the complex assessmnet of Black sea waters ecological status, however, more research is needed to validate this approach. The development of metagenomic databases will contribite to increase in precision of microgAMBI calculation and subsequent ecological status analysis.

Physiochemical and biological characteristics of fouling on landfill leachate treatment systems surface

Fouling of landfill leachate, a biofilm formation process on the surface of the collection system, migration pipeline and treatment system causes low efficiency of leachate transportation and treatment and increases cost for maintenance of those facilities. In addition, landfill leachate fouling might accumulate pathogens and antibiotic resistance genes (ARGs), posing threats to the environment. Characterization of the landfill leachate fouling and its associated environmental behavior is essential for the management of fouling. In this study, physicochemical and biological properties of landfill leachate fouling and the possible accumulation capacity of pathogens and ARGs were investigated in nitrification (aerobic condition) and denitrification (anaerobic condition) process during landfill leachate biological treatment, respectively. Results show that microbial (bacterial, archaeal, eukaryotic, and viral) community structure and function (carbon fixation, methanogenesis, nitrification and denitrification) differed in fouling under aerobic and anaerobic conditions, driven by the supplemental leachate water quality. Aerobic fouling had a higher abundance of nitrification and denitrification functional genes, while anaerobic fouling harbored a higher abundance of carbon fixation and methanogenesis genes. Both forms of leachate fouling had a higher abundance of pathogens and ARGs than the associated leachate, suggesting the accumulation capacity of fouling on biotic pollutants. Specifically, aerobic fouling harbored three orders of magnitude higher multidrug resistance genes mexD than its associated leachate. This finding provides fundamental knowledge on the biological properties of leachate fouling and suggests that leachate fouling might harbor significant pathogens and ARGs.

Effects of Returning Different Organic Materials in Combination with Inorganic Fertilizers on the Diversity of Eukaryotic Microorganisms in Semi-Arid Northern China

Soil eukaryotic microorganisms are important to biodiversity, and returning different kinds of organic materials to the field could improve the biodiversity of soil eukaryotic microorganisms. However, no detailed research has been conducted in the northern China semi-arid area in returning the different organic materials to the field and determining the status of eukaryotic microorganisms. Therefore, we explored the effects of various organic materials returning to the soil in combination with inorganic fertilizer on the diversity and community structure of eukaryotic microorganisms in Shanxi province, China. Soil samples were collected from five different fertilization treatments: chemical fertilizer (F), chemical fertilizer + cattle manure (FM), chemical fertilizer + straw (FS), chemical fertilizer + pig manure (FC) and control without fertilizers (CK). High-throughput sequencing was applied to analyze the eukaryotic diversity and community structure. Results showed that the dominant eukaryotic microorganisms among soil samples were Fungi, Viridiplantae, Metazoa and Protist. Although α-diversity was not significantly different among the five treatments, principal coordinate analysis and permutational multivariate analysis of variance illustrated significant differences (p &lt; 0.001) in β-diversity of eukaryotic microorganism under treatments with different organic materials. Redundancy analysis showed that the soil properties, including total potassium, available nitrogen, available potassium and organic matter were the main factors attributed to eukaryotic microorganisms’ community structure in this region.

Impacts of sea ice melting procedures on measurements of microbial community structure

Microorganisms play critical roles in sea ice biogeochemical processes. However, microbes living within sea ice can be challenging to sample for scientific study. Because most techniques for microbial analysis are optimized for liquid samples, sea ice samples are typically melted first, often applying a buffering method to mitigate osmotic lysis. Here, we tested commonly used melting procedures on three different ice horizons of springtime, first year, land-fast Arctic sea ice to investigate potential methodological impacts on resulting measurements of cell abundance, photophysiology, and microbial community structure as determined by 16S and 18S rRNA gene amplicon sequencing. Specifically, we compared two buffering methods using NaCl solutions (“seawater,” melting the ice in an equal volume of 35-ppt solution, and “isohaline,” melting with a small volume of 250-ppt solution calculated to yield meltwater at estimated in situ brine salinity) to direct ice melting (no buffer addition) on both mechanically “shaved” and “non-shaved” samples. Shaving the ice shortened the melting process, with no significant impacts on the resulting measurements. The seawater buffer was best at minimizing cell lysis for this ice type, retaining the highest number of cells and chlorophyll a concentration. Comparative measurements of bacterial (16S) community structure highlighted ecologically relevant subsets of the community that were significantly more abundant in the buffered samples. The results for eukaryotic (18S) community structure were less conclusive. Taken together, our results suggest that an equivalent-volume seawater-salinity buffered melt is best at minimizing cell loss due to osmotic stress for springtime Arctic sea ice, but that either buffer will reduce bias in community composition when compared to direct melting. Overall, these findings indicate potential methodological biases that should be considered before developing a sea ice melting protocol for microbiological studies and afterwards, when interpreting biogeochemical or ecological meaning of the results.

Characteristics of Eukaryotic Phytoplankton Community Structure and Its Relationship with Environmental Factors in Danjiangkou Reservoir

Eukaryotic phytoplankton play crucial roles in ecosystem processes, and understanding their community composition and abundance is of great importance to protect the balance of aquatic ecosystems. Danjiangkou Reservoir is a canyon lake in central China that acts as the water source of the Mid-route of South-to-North Water Diversion Project. In this study, the composition of planktonic microeukaryotes from water samples with a depth ranging from 0.5 to 20 m in Danjiangkou Reservoir were investigated using high-throughput 18S rDNA gene sequencing. The environmental factors including pH, water temperature (WT), nitrate (NO3--N), ammonia (NH4+-N), total nitrogen (TN), conductivity (Cond.), water depth, and dissolved oxygen (DO) in the reservoir areas were measured, and their correlations with the abundance and diversity of eukaryotic phytoplankton were analyzed. The results of high-throughput sequencing showed that a total of 68 genera of phytoplankton belonging to 12 phyla were detected, and the phytoplankton communities were mainly composed of Dinophyceae, Bacillariophyta, and Chlorophyta. In particular, significant differences in the diversity of phytoplankton communities on a vertical distribution were found. The diversity and abundance of the phytoplankton communities in Songgang (SG), Tumen (TM), and Dangzikou (DZK) decreased with the increase in water depth, and the relationship between phytoplankton and water depth in other sampling sites was not obvious. The results of RDA showed that NO3--N, water depth, DO, pH, and WT could influence the vertical distribution of the phytoplankton community in the Danjiangkou Reservoir. Among these phytoplankton types, Dinophyceae was negatively correlated with NO3--N and water depth and positively correlated with other environmental factors. Meanwhile, Bacillariophyta was positively correlated with NO3--N and water depth and negatively correlated with other environmental factors. In addition, Chlorophyta was negatively correlated with WT, pH, and DO and not significantly correlated with water depth.

Metagenomic analysis of heavy metal-contaminated soils reveals distinct clades with adaptive features

Heavy metal pollution poses a serious threat to soil, water, and the atmospheric environment. Many microbes sustain and respond to the metal stress, and the mechanisms involved in these processes remain unclear. The metagenomics and metatranscriptomics approaches were applied to study the structure and function of eukaryotic microbial communities in heavy metal-contaminated soils of two geographic locations situated in different climatic regions. To achieve this, amplicons of the hypervariable V4 region of 18S rDNA and cDNA synthesized from 18S rRNA extracted from these soils were generated and sequenced through paired-end sequencing chemistry on the Illumina-MiSeq platform. The NGS dataset processed by the Mothur pipeline and analyzed by Parallel-Meta 3 pipeline illustrated the presence of all the major eukaryotic phyla. Taxa diversity and community structure of micro-eukaryotes within and between the samples from two locations were compared. Clustering, heatmap, and PCA analysis supported the variation in taxonomic diversity and community structure in the datasets of these two sites. Analysis of taxa abundance in both sites identified marker organisms for the further characterization of such types of environments. A functional metatranscriptomics study revealed the identification of various expressed eukaryotic genes, which are involved in metal tolerance. These metal-tolerant gene families were phylogenetically related to the different eukaryotic lineages reported in the metagenomic analysis. Hence, this approach could be widely applied in microbial ecology to understand the role of active microbes in such specific environmental conditions.

Eukaryotic diversity of marine biofouling from coastal to offshore areas

Marine biofouling communities, including biofilms, are composed of many eukaryotes with high taxonomic and functional diversities. However, molecular characterization of eukaryotic diversity of marine biofouling has been barely developed due to the only recent interest in research areas such as marine renewable energies, antifouling technologies, or plastic pollution. The aim of this study was to compare the diversity and taxonomic composition of biofouling through different metabarcoding approaches used to detect the widest range of taxa from samples collected in several contrasted marine environments (French Atlantic and Mediterranean coasts). Thus, we assessed four DNA extraction methods and six primers pairs targeting the 18S rDNA gene (including the V1-V2, V4TAR, V4UNI, V7 and V9 regions) and the COI gene, the latter with two databases (BOLD and MIDORI). In addition the influence of primers selection was analyzed at three sites to compare geographic variations in eukaryotic diversity. Although none of the extraction methods greatly altered the community diversity or composition. we have observed that eukaryotic biofouling community diversity and structure varied depending on primers pairs, reference databases and sites. 18S rDNA regions allowed the detection of more taxa at the species level, including microeukaryotes, while the COI recovered more ASVs, but with a large proportion that remained taxonomically unassigned probably because BOLD and MIDORI specifically targeted metazoans. Interestingly, the spatial pattern obtained with both COI and 18S rDNA markers were similar showing that spatial selection occurred throughout a wide diversity of eukaryotic taxa. These results encouraged the use of these two complementary markers for future metabarcoding investigations but also highlighted the relevance of completing databases to enhance the identification of biofouling eukaryotes.

Fine-scale differences in eukaryotic communities inside and outside salmon aquaculture cages revealed by eDNA metabarcoding.

Aquaculture impacts on marine benthic ecosystems are widely recognized and monitored. However, little is known about the community changes occurring in the water masses surrounding aquaculture sites. In the present study, we studied the eukaryotic communities inside and outside salmonid aquaculture cages through time to assess the community changes in the neighbouring waters of the farm. Water samples were taken biweekly over five months during the production phase from inside the cages and from nearby points located North and South of the salmon farm. Eukaryotic communities were analyzed by eDNA metabarcoding of the partial COI Leray-XT fragment. The results showed that eukaryotic communities inside the cages were significantly different from those in the outside environment, with communities inside the cages having higher diversity values and more indicator species associated with them. This is likely explained by the appearance of fouling species that colonize the artificial structures, but also by other species that are attracted to the cages by other means. Moreover, these effects were highly localized inside the cages, as the communities identified outside the cages, both North and South, had very similar eukaryotic composition at each point in time. Overall, the eukaryotic communities, both inside and outside the cages, showed similar temporal fluctuations through the summer months, with diversity peaks occurring at the end of July, beginning of September, and in the beginning of November, with the latter showing the highest Shannon diversity and richness values. Hence, our study suggests that seasonality, together with salmonid aquaculture, are the main drivers of eukaryotic community structure in surface waters surrounding the farm.