Spatial Distribution of Eukaryotic Communities Using High-Throughput Sequencing Along a Pollution Gradient in the Arsenic-Rich Creek Sediments of Carnoulès Mine, France

Saline mine water influences eukaryote life in shallow groundwater of a tropical sandy stream

Eukaryotic communities in groundwater may be particularly sensitive to disturbance because they are adapted to stable environmental conditions and often have narrow spatial distributions. Traditional methods for characterising these communities, focussing on groundwater-inhabiting macro- and meiofauna (stygofauna), are challenging because of limited taxonomic knowledge and expertise (particularly in less-explored regions), and the time and expense of morphological identification. The primary objective of this study was to evaluate the vulnerability of eukaryote communities in shallow groundwater to mine water discharge containing elevated concentrations of magnesium (Mg) and sulfate (SO4). The study was undertaken in a shallow sand bed aquifer within a wet-dry tropical setting. The aquifer, featuring a saline mine water gradient primarily composed of elevated Mg and SO4, was sampled from piezometers in the creek channel upstream and downstream of the mine water influence during the dry season when only subsurface water flow was present. Groundwater communities were characterised using both morphological assessments of stygofauna from net samples and environmental DNA (eDNA) targeting the 18S rDNA and COI mtDNA genes. eDNA data revealed significant shifts in community composition in response to mine waters, contrasting with findings from traditional morphological composition data. Changes in communities determined using eDNA data were notably associated with concentrations of SO42-, Mg2+ and Na+, and water levels in the piezometers. This underscores the importance of incorporating molecular approaches in impact assessments, as relying solely on traditional stygofauna sampling methods in similar environments may lead to inaccurate conclusions about the responses of the assemblage to studied impacts.

Metataxonomy of acid mine drainage microbiomes from the Santa Catarina Carboniferous Basin (Southern Brazil)

Mining activities generate large quantities of wastes that significantly alter the biogeochemistry and ecological structure of entire river basins. Microbial communities that develop in these areas present a variety of survival and adaptation mechanisms. Knowing this diversity at the molecular level is strategic both for understanding adaptive processes and for identifying genomes with potential use in bioremediation and bioprospecting. In this work, prokaryotic and eukaryotic communities were evaluated by meta-taxonomics (16S and 18S amplicons) in sediments and water bodies impacted by acid mine drainage in an important coal mining area in southern Brazil. Five sampling stations were defined on a gradient of impacts (pH 2.7-4.25). Taxon diversity was directly proportional to pH, being greater in sediments than in water. The dominant prokaryotic phyla in the samples were Proteobacteria, Actinobacteria, Acidobacteria, OD1, Nitrospirae, and Euryarchaeota, and among the eukaryotes, algae (Ochrophyta, Chlorophyta, Cryptophyceae), fungi (Basidiomycota, Ascomycota, and Cryptomycota), and protists (Ciliophora, Heterolobosea, Cercozoa). The prokaryotic genera Leptospirillum, Acidithiobacillus, Acidiphilium, Thiomonas, Thermogymnomonas, and Acidobacterium, and the eukaryotic genera Pterocystis and Poteriospumella were associated with more acidic conditions and higher metal concentrations, while the prokaryotic genera Sediminibacterium, Gallionella Geothrix, and Geobacter were more abundant in transitional environments.

High diversity and isolated distribution of aquatic heterotrophic protists in salars of the Atacama Desert at different salinities

The species richness of eukaryotes in the hypersaline environment is generally thought to be low. However, recent studies showed a high degree of phylogenetic novelty at these extreme conditions with variable chemical parameters. These findings call for a more thorough look into the species richness of hypersaline environments. In this study, various hypersaline lakes (salars, 1-348 PSU) as well as further aquatic ecosystems of northern Chile were investigated regarding diversity of heterotrophic protists by metabarcoding studies of surface water samples. Investigations of genotypes of 18S rRNA genes showed a unique community composition in nearly each salar and even among different microhabitats within one salar. The genotype distribution showed no clear connection to the composition of main ions at the sampling sites, but protist communities from similar salinity ranges (either hypersaline, hyposaline or mesosaline) clustered together regarding their OTU composition. Salars appeared to be fairly isolated systems with only little exchange of protist communities where evolutionary lineages could separately evolve.

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.

Changes in Microeukaryotic Communities in the Grand Canal of China in Response to Floods

Floods are frequent natural disasters and could have serious impacts on aquatic environments. Eukaryotic communities in artificial canals influenced by floods remain largely unexplored. This study investigated the spatiotemporal variabilities among eukaryotes in response to floods in the Grand Canal, China. Generally, 781,078 sequence reads were obtained from 18S rRNA gene sequencing, with 304,721 and 476,357 sequence reads detected before and after flooding, respectively. Sediment samples collected after the floods exhibited a higher degree of richness and biodiversity but lower evenness than those before the floods. The eukaryotic communities changed from Fungi-dominated before floods to Stramenopile-dominated after floods. The spatial turnover of various species was the main contributor to the longitudinal construction of eukaryotes both before the floods (β_SIM = 0.7054) and after the floods (β_SIM = 0.6858). Some eukaryotic groups responded strongly to floods and might pose unpredictable risks to human health and environmental health. For example, Pezizomycetes, Catenulida, Glomeromycetes, Ellipura, etc. disappeared after the floods. Conversely, Lepocinclis, Synurale, Hibberdiales, Acineta, Diptera, and Rhinosporidium were all frequently detected after the floods, but not prior to the floods. Functional analyses revealed amino acid metabolism, carbohydrate metabolism, translation, and energy metabolism as the main metabolic pathways, predicting great potential for these processes in the Grand Canal.

Metatranscriptomic outlook on green and brown food webs in acid mine drainage

Acid mine drainages (AMDs), metal-rich acidic effluents generated by mining activities, are colonized by prokaryotic and eukaryotic microorganisms widely distributed among different phyla. We compared metatranscriptomic data from two sampling stations in the Carnoulès AMD and from a third station in the nearby Amous River, focussing on processes involved in primary production and litter decomposition. A synergistic relationship between the green and brown food webs was favoured in the AMD sediments by the low carbon content and the availability of mineral nutrients: primary production of organic matter would benefit C-limited decomposers whose activity of organic matter mineralization would in turn profit primary producers. This balance could be locally disturbed by heterogeneous factors such as an input of plant debris from the riparian vegetation, strongly boosting the growth of Tremellales which would then outcompete primary producers. In the unpolluted Amous River on the contrary, the competition for limited mineral nutrients was dominated by the green food web, fish and bacterivorous protists having a positive effect on phytoplankton. These results suggest that in addition to direct effects of low pH and metal contamination, trophic conditions like carbon or mineral nutrient limitations also have a strong impact on assembly and activities of AMDs' microbial communities.

Microbiome of highly polluted coal mine drainage from Onyeama, Nigeria, and its potential for sequestrating toxic heavy metals

Drains from coal mines remain a worrisome point-source of toxic metal/metalloid pollutions to the surface- and ground-waters worldwide, requiring sustainable remediation strategies. Understanding the microbial community subtleties through microbiome and geochemical data can provide valuable information on the problem. Furthermore, the autochthonous microorganisms offer a potential means to remediate such contamination. The drains from Onyeama coal mine in Nigeria contained characteristic sulphates (313.0 ± 15.9 mg l⁻¹), carbonate (253.0 ± 22.4 mg l⁻¹), and nitrate (86.6 ± 41.0 mg l⁻¹), having extreme tendencies to enrich receiving environments with extremely high pollution load index (3110 ± 942) for toxic metals/metalloid. The drains exerted severe degree of toxic metals/metalloid contamination (Degree of contamination: 3,400,000 ± 240,000) and consequent astronomically high ecological risks in the order: Lead > Cadmium > Arsenic > Nickel > Cobalt > Iron > Chromium. The microbiome of the drains revealed the dominance of Proteobacteria (50.8%) and Bacteroidetes (18.9%) among the bacterial community, whereas Ascomycota (60.8%) and Ciliophora (12.6%) dominated the eukaryotic community. A consortium of 7 autochthonous bacterial taxa exhibited excellent urease activities (≥ 253 µmol urea min⁻¹) with subsequent stemming of acidic pH to > 8.2 and sequestration of toxic metals (approx. 100% efficiency) as precipitates (15.6 ± 0.92 mg ml⁻¹). The drain is a point source for metals/metalloid pollution, and its bioremediation is achievable with the bacteria consortium.

Biofilm and planktonic microbial communities in highly acidic soil (pH < 3) in the Soos National Nature Reserve, Czech Republic

Biofilm formation is a typical life strategy used by microorganisms populating acidic water systems. The same strategy might be used by microbes in highly acidic soils that are, however, neglected in this regard. In the present study, the microbial community in such highly acidic soil in the Soos National Nature Reserve (Czech Republic) has been investigated using high-throughput DNA sequencing and the organisms associated with biofilm life mode and those preferring planktonic life were distinguished using the biofilm trap technique. Our data show the differences between biofilm and planktonic microbiota fraction, although the majority of the organisms were capable of using both life modes. The by far most abundant prokaryotic genus was Acidiphilium and fungi were identified among the most abundant eukaryotic elements in biofilm formations. On the other hand, small flagellates from diverse taxonomical groups predominated in plankton. The application of cellulose amendment as well as the depth of sampling significantly influenced the composition of the detected microbial community.

A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology

Current technologies could identify the abundance and functions of specific microbes, and evaluate their individual effects on microbial ecology. However, these microbes interact with each other, as well as environmental factors, in the form of complex network. Determination of their combined ecological influences remains a challenge. In this study, we developed a tripartite microbial-environment network (TMEN) analysis method that integrates microbial abundance, metabolic function, and environmental data as a tripartite network to investigate the combined ecological effects of microbes. Applying TMEN to analyzing the microbial-environment community structure in the sediments of Hangzhou Bay, one of the most seriously polluted coastal areas in China, we found that microbes were well-organized into 4 bacterial communities and 9 archaeal communities. The total organic carbon, sulfate, chemical oxygen demand, salinity, and nitrogen-related indexes were detected as crucial environmental factors in the microbial-environmental network. With close interactions with these environmental factors, Nitrospirales and Methanimicrococcu were identified as hub microbes with connection advantage. Our TMEN method could close the gap between lack of efficient statistical and computational approaches and the booming of large-scale microbial genomic and environmental data. Based on TMEN, we discovered a potential microbial ecological mechanism that crucial species with significant influence on the microbial community ecology would possess one or two of the community advantages for enhancing their ecological status and essentiality, including abundance advantage and connection advantage.

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.

Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China

The effects of environmental and species structure on soil eukaryotic microbes inhabiting semi-arid mountains remain unclear. Furthermore, whether community assembly differs in a variety of soil habitat types, for example, artificial forest, artificial bush, farmland, and natural grassland, is not well understood. Here, we explored species diversity and composition of soil eukaryotic microbes south of the Taihang Mountains (mid-western region of China) using Illumina sequencing of the 18S rRNA gene (V4) region on the MiSeq platform. The results suggest that the forest soil habitat type improved the diversity and abundance of soil eukaryotic microbes that will benefit the restoration of degraded soil. The SAR (Stramenopiles, Alveolates, Rhizaria) supergroup and Metazoa were the dominant soil eukaryotic microbial groups at the phylum level. About 26% of all operational taxonomic units were common among the different soil habitat types. The O-elements, water content, soil organic matter, and elevation significantly influenced the abundance of soil eukaryote communities (P < 0.05). Our findings provide some reference for the effectiveness of local ecological restoration and the establishment of a soil eukaryotic microbe resource databases in a semi-arid area.

Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing

Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2 cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18 S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2 g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes.

Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage

Acid mine drainages are characterized by their low pH and the presence of dissolved toxic metallic species. Microorganisms survive in different microhabitats within the ecosystem, namely water, sediments, and biofilms. In this report, we surveyed the microbial diversity within all domains of life in the different microhabitats at Los Rueldos abandoned mercury underground mine (NW Spain), and predicted bacterial function based on community composition. Sediment samples contained higher proportions of soil bacteria (AD3, Acidobacteria), as well as Crenarchaeota and Methanomassiliicoccaceae archaea. Oxic and hypoxic biofilm samples were enriched in bacterial iron oxidizers from the genus Leptospirillum, order Acidithiobacillales, class Betaproteobacteria, and archaea from the class Thermoplasmata. Water samples were enriched in Cyanobacteria and Thermoplasmata archaea at a 3–98% of the sunlight influence, whilst Betaproteobacteria, Thermoplasmata archaea, and Micrarchaea dominated in acid water collected in total darkness. Stalactites hanging from the Fe-rich mine ceiling were dominated by the neutrophilic iron oxidizer Gallionella and other lineages that were absent in the rest of the microhabitats (e.g., Chlorobi, Chloroflexi). Eukaryotes were detected in biofilms and open-air water samples, and belonged mainly to clades SAR (Alveolata and Stramenopiles), and Opisthokonta (Fungi). Oxic and hypoxic biofilms displayed higher proportions of ciliates (Gonostomum, Oxytricha), whereas water samples were enriched in fungi (Paramicrosporidium and unknown microbial Helotiales). Predicted function through bacterial community composition suggested adaptive evolutive convergence of function in heterogeneous communities. Our study showcases a broad description of the microbial diversity across different microhabitats in the same environment and expands the knowledge on the diversity of microbial eukaryotes in AMD habitats.