Diversity Of Eukaryotic Communities Research Articles

Tetracycline and quinolone contamination mediate microbial and antibiotic resistant gene composition in epiphytic biofilms of mesocosmic wetlands

The fate and ecological impact of antibiotics on aquatic ecosystems have not been properly elucidated in mesocosm wetlands scale. This study explored how tetracyclines (TCs, including tetracycline TC and oxytetracycline) and fluoroquinolones (QNs, including ciprofloxacin CIP and levofloxacin) affect mesocosm wetlands with vegetated V. spiralis, focusing on their impact on epiphytic biofilm microbial communities and antibiotic resistance genes (ARGs). Results showed that submerged plants absorbed more antibiotics than sediment. Both TCs and QNs disrupted microbial communities in different ways and increased eukaryotic community diversity in a concentration-dependent manner (2-4 mg/L for CIP, 4-8 mg/L for TC). TCs mainly inhibited epiphytic bacteria, while CIP increased bacterial phyla abundance. TC reduced Cyanobacteriota, Acidobacteriota, and Patescibacteria but increased Bacillota, Bacteroidota, and Armatimonadota. In contrast, CIP reduced Bacteroidota, Cyanobacteriota, and Gemmatimonadota but increased Bacillota, Planctomycetota, and Acidobacteriota. Significant differences in ARG profiles were observed between QNs and TCs, with TCs having a more substantial effect on ARGs due to their stronger impact on bacterial communities. Both antibiotics raised ARG levels with higher concentrations, particularly for multidrug resistance, tetracyclines, trimethoprim, sulfonamides, aminoglycosides, and fosfomycin, emphasizing their role in antimicrobial resistance. The study suggests that antibiotics can either stimulate or inhibit ARGs depending on their effects on bacterial communities. This study provides key evidence on the ecological mechanisms underlying the impact of TCs and QNs on epiphytic microbes of mesocosm wetlands.

A comparison of two gene regions for assessing community composition of eukaryotic marine microalgae from coastal ecosystems

Two gene regions commonly used to characterise the diversity of eukaryotic communities using metabarcoding are the 18S ribosomal DNA V4 and V9 gene regions. We assessed the effectiveness of these two regions for characterising diverisity of coastal eukaryotic microalgae communities (EMCs) from tropical and temperate sites. We binned amplicon sequence variants (ASVs) into the high level taxonomic groups: dinoflagellates, pennate diatoms, radial centric diatoms, polar centric diatoms, chlorophytes, haptophytes and ‘other microalgae’. When V4 and V9 generated ASV abundances were compared, the V9 region generated a higher number of raw reads, captured more diversity from all high level taxonomic groups and was more closely aligned with the community composition determined using light microscopy. The V4 region did resolve more ASVs to a deeper taxonomic resolution within the dinoflagellates, but did not effectively resolve other major taxonomic divisions. When characterising these communities via metabarcoding, the use of multiple gene regions is recommended, but the V9 gene region can be used in isolation to provide high-level community biodiversity to reflect relative abundances within groups. This approach reduces the cost of sequencing multiple gene regions whilst still providing important baseline ecosystem function information.

Anticancer drugs drive changes in the performance, abundance, diversity, and composition of eukaryotic communities of an aerobic granular sludge system

Anticancer drugs are emerging contaminants that are being increasingly detected in urban wastewater. However, there is limited knowledge on the use of biological wastewater treatments, such as granular sludge systems (AGSs), to remove these substances and on their impacts on the general performance of the system and the eukaryotic communities in the granules. We investigated the impacts of three anticancer drugs commonly found in wastewater treatment plants and applied at three different concentrations on the removal efficiency of anticancer drugs, physicochemical parameters, and the eukaryotic microbiome of an AGS operated in a sequential batch reactor (SBR). Anticancer drugs applied at medium and high concentrations significantly decreased the removal efficiency of total nitrogen, the granular biomass concentration, and the size and setting velocity of granules. However, these effects disappeared after not adding the drugs for about a month thus showing the plasticity of the system to return to original levels. Regardless of the concentration of anticancer drugs tested, the AGS technology was effective in removing these substances, with removal rates in the range of 68.5%–100%. The presence of anticancer drugs at medium and high concentrations significantly decreased the abundance of total fungi, an effect that was linked to changes in the physicochemical parameters. Anticancer drugs also induced decreases in the diversity of the eukaryotic community, altered the community composition, and reduced the network complexity when applied at medium and high concentrations. Taxa responsive to the presence of anticancer drugs were identified. The diversity and composition of the eukaryotic microbiome returned to original diversity levels after not adding the drugs for about a month. Overall, this study increases our understanding of the impacts of anticancer drugs on the performance and eukaryotic microbiome of an AGS and highlights the need for monitoring these substances.

Comparative analysis of eukaryotic microbial communities associated with Acropora formosa, sediment, and seawater in a coral reef ecosystem of Whale island, Nha Trang bay, Vietnam

In this study, eukaryotic microbial communities associated with coral Acropora formosa and its natural surroundings, sediment and seawater, in a coral reef ecosystem of Whale Island, Nha Trang Bay, Vietnam were investigated. First, genetic material was taken from Acropora formosa’s surface mucus layer (SML) as well as the sediment underneath and seawater above the colonies from four different sampling locations in a coral reef ecosystem. Subsequently, the data were sequenced using 18S rRNA gene amplicon sequencing method. Sequences (reads) were then analyzed in Rstudio version 4.2.0. Bioinfomatic tools such as DADA2 pipeline clustered the sequences into amplicon sequence variants (ASVs), to which the taxonomy was assigned using SILVA 132 database. The majority of the sequences was categorized at the kingdom and phylum levels, but fewer sequences were identified at genus and species level. The visualization of the results revealed changes in abundance and composition of the eukaryotic communities in all samples. The results demonstrated that phylum Dinoflagellata had the highest relative abundance in coral samples. Meanwhile, Ochrophyta was the most prevalent phylum in seawater samples. Notably, after filtering out the sequences with abundance less than 2%, only genus Symbiodinium appeared significantly in coral samples. The composition of samples from coral sampling sites was more consistent. The same was true for samples of seawater, whereas the composition of sediment samples varied more. Alpha and beta diversity indices confirmed that there were significant differences (p < 0.05) in abundance and composition of eukaryotic communities among three different habitats. These findings come as the first effort to explore the diversity of eukaryotic communities in different habitats and could be valuable for further study in functional profiling or metabolic functions of microbial communities in the coral ecosystem.

Gravity-driven membrane system treating heavy metals-containing secondary effluent: Improved removal of heavy metals and mechanism

This study aimed at investigating the removal performance of the gravity-driven membrane (GDM) system in treating the heavy metals-containing secondary effluent, as well as evaluating the respective roles of Fe and Mn addition on the removal of heavy metals. GDM process with the formation of biocake layer exerted effective removals of Cr, Pb and Cd, with an average removal efficiency of 98%, 95% and 40%, respectively, however, after removing the biocake layer, the removal efficiencies of Cr, Pb and Cd reduced to 59%, 85% and 19%, respectively, indicating that the biocake layer played a fundamental role in removing heavy metals. With the assistance of Fe, the removal efficiency of heavy metals increased, and exhibited a positive response to the Fe dosage, due to the adsorption by the freshly generated iron oxides. On the contrary, the Mn involvement would result in the reduction of Cd removal due to the competitive adsorption of residual dissolved Mn2+ and Cd. Furthermore, the addition of a high dosage of Fe increased the diversity of eukaryotic communities and facilitated the elimination of heavy metals, however, the involvement of Mn would lead to a reduction in microbial diversity, resulting in a decrease of heavy metal removal efficiency. These findings are expected to develop new tactics to enhance heavy metal removal and promote widespread application of GDM technology in the fields of deep treatment of heavy metals-containing wastewater and reclamation of secondary effluent.

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.

Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes.

The biogeography of eukaryotes in drinking water systems is poorly understood relative to that of prokaryotes or viruses, limiting the understanding of their role and management. A challenge with studying complex eukaryotic communities is that metagenomic analysis workflows are currently not as mature as those that focus on prokaryotes or viruses. In this study, we benchmarked different strategies to recover eukaryotic sequences and genomes from metagenomic data and applied the best-performing workflow to explore the factors affecting the relative abundance and diversity of eukaryotic communities in drinking water distribution systems (DWDSs). We developed an ensemble approach exploiting k-mer- and reference-based strategies to improve eukaryotic sequence identification and identified MetaBAT2 as the best-performing binning approach for their clustering. Applying this workflow to the DWDS metagenomes showed that eukaryotic sequences typically constituted small proportions (i.e., <1%) of the overall metagenomic data with higher relative abundances in surface water-fed or chlorinated systems with high residuals. The α and β diversities of eukaryotes were correlated with those of prokaryotic and viral communities, highlighting the common role of environmental/management factors. Finally, a co-occurrence analysis highlighted clusters of eukaryotes whose members' presence and abundance in DWDSs were affected by disinfection strategies, climate conditions, and source water types.

Exogenous Microorganisms Promote Moss Biocrust Growth by Regulating the Microbial Metabolic Pathway in Artificial Laboratory Cultivation.

Moss-dominated biocrusts (moss crusts) are a feasible approach for the ecological restoration of drylands, but difficulty obtaining inoculum severely limits the progress of large-scale field applications. Exogenous microorganisms could improve moss growth and be conducive to moss inoculum propagation. In this study, we investigated the growth-promoting effects and potential mechanisms of exogenous microorganism additives on moss crusts. We used an incubator study to examine the effects of inoculation by heterotrophic microorganisms (Streptomyces pactum, Bacillus megaterium) and autotrophic microorganisms (Chlorella vulgaris, Microcoleus vaginatus) combined with Artemisia sphaerocephala gum on the growth of Bryum argenteum, the dominant moss crusts species in sandy deserts. Amplicon sequencing (16S and 18S rRNA) and PICRUSt2 were used to illustrate the microbial community structure and potential function in the optimal treatment at different developmental stages. Our results showed that exogenous microorganisms significantly promoted moss growth and increased aboveground biomass. After 30 days of cultivation, the Streptomyces pactum (1 g kg–1 substrate) + Chlorella vulgaris (3.33 L m–2) treatment presented optimal moss coverage, height, and density of 97.14%, 28.31 mm, and 2.28 g cm–2, respectively. The best-performing treatment had a higher relative abundance of Streptophyta—involved in moss growth—than the control. The control had significantly higher soil organic carbon than the best-performing treatment on day 30. Exogenous microorganisms improved eukaryotic community diversity and richness and may enhance soil microbial functional and metabolic diversity, such as growth and reproduction, carbon fixation, and cellulose and lignin decomposition, based on functional predictions. In summary, we identified the growth-promoting mechanisms of exogenous additives, providing a valuable reference for optimizing propagation technology for moss inoculum.

Temporal variability of microbial communities during the past 600 years in a Tibetan lake sediment core

Over the past decades, the Tibetan Plateau has been experiencing rapid climate change and increasing anthropogenic disturbance. The existing multi-proxy sediment records highlight the complex interplay of physical and ecological changes as a response to past climate changes on the Tibetan Plateau. Yet, it remains an open question of how sedimentary microbial communities respond to past climate changes and anthropogenic interventions. Using high-throughput Illumina sequencing, this study investigated the temporal changes of prokaryotic and eukaryotic communities in a Tibetan lake sediment core spanning the last 600 years. There were obvious temporal distributions of prokaryotic and eukaryotic indicator taxa, and these temporal patterns were mainly influenced by mean annual temperature (MAT), total phosphorus (TP) and nitrogen:phosphorus ratio (N:P). The alpha diversity of eukaryotic communities significantly increased with time ( P < 0.001), while the alpha diversity of prokaryotic communities did not exhibit obvious temporal turnover. Both prokaryotic and eukaryotic communities exhibited significant temporal-decay relationships. However, the turnover rate of the temporal-decay of eukaryotes (0.119) was significantly higher than that of prokaryotes (0.092). The effect of TP and N:P on the prokaryotic and eukaryotic communities were higher than that of MAT. The insights gained from this study can be helpful to understand the effects of past climate change and anthropogenic activities on the temporal distribution patterns of microbial communities, thus providing insights into predicting the succession of microbial communities and underlying mechanisms that drive them under future climate scenarios. • Microbial indicator taxa displayed obvious temporal distribution patterns. • Eukaryotes showed higher temporal turnover rate than bacteria. • MAT, TP and N:P influenced prokaryotic and eukaryotic communities in past 600 years.

Eukaryotes in soil aggregates across conservation managements: Major roles of protists, fungi and taxa linkages in soil structuring and C stock

The stabilization of soil organic carbon (SOC) promoted by conservation agriculture (CA) depends on soil aggregation. Aggregation protects SOC and creates heterogeneous microhabitats hosting diverse soil biota which in turn promote aggregation. A long-term experiment, studying the interaction of tillage with nitrogen (N) fertilization on a soybean-wheat rotation, was used to investigate eukaryotic community diversity, composition, and structure within small macroaggregates (sM) and occluded microaggregates (mM). Using high-throughput Illumina sequencing, we found (i) a different eukaryote diversity response to management intensification across soil aggregates and soil depths; (ii) a conserved core community composition of eukaryotes across CA treatments and aggregates at surface and subsurface layers; (iii) a different effect of tillage on eukaryotic community structure in sM and mM along the soil profile according to N availability; (iv) a positive association of protists, and fungi with the amount of sM and mM, and their SOC content; (v) a stronger complexity of within- and cross-domain networks (eukaryotes and eukaryotes-prokaryotes) in mM than in sM at surface layer. Overall, our findings demonstrate for the first time that protists together with fungi play major roles in soil structuring and C cycling, and that Cercozoa represent hubs in soil biota aggregate networks.

ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy.

SummaryITSoneWB (ITSone WorkBench) is a Galaxy-based bioinformatic environment where comprehensive and high-quality reference data are connected with established pipelines and new tools in an automated and easy-to-use service targeted at global taxonomic analysis of eukaryotic communities based on Internal Transcribed Spacer 1 variants high-throughput sequencing. Availability and implementationITSoneWB has been deployed on the INFN-Bari ReCaS cloud facility and is freely available on the web at http://itsonewb.cloud.ba.infn.it/galaxy.Supplementary information Supplementary data are available at Bioinformatics online.

Eukaryotic community diversity and pathogenic eukaryotes in a full-scale drinking water treatment plant determined by 18S rRNA and metagenomic sequencing.

In this study, 18S rRNA high-throughput sequencing was applied to investigate the eukaryotic community in a full-scale drinking water treatment plant. Eukaryotic species and microbial functions in raw water and filter biofilms were identified by metagenomic sequencing. The eukaryotic species richness and diversity presented declining trends throughout the treatment process. The lowest eukaryotic species richness was observed in disinfected water. Arthropoda, Ciliophora, Ochrophyta, and Rotifera were the dominant eukaryotic phyla and exhibited high variations in relative abundance among the different treatment units. Sedimentation significantly decreased the abundance of all eukaryotes except Arthropoda. Biological activated carbon (BAC) filtration and chlorine disinfection exerted strong effects on community composition. The eukaryotic communities in water were distinct from those in filter biofilms, as were the communities of different filter biofilms from each other. In contrast, communities were functionally similar among different filter biofilms, with the category metabolism being the dominant category represented, within which amino acid transport and metabolism (E) and energy production and conversion (C) dominated among subcategories. Seventy-one eukaryotic species pathogenic to humans were identified in raw water and filter biofilms. Quantitative PCR (qPCR) results showed that Acanthamoeba spp. and Vermamoeba vermiformis were present during some treatment processes, with concentrations of 12-1.2 × 105 copies/mL and 1 copy/mL, respectively. Neither of the two pathogenic amoebae was found in disinfected water. Canonical correspondence analysis (CCA) showed that pH was the most important environmental factor affecting eukaryotic community composition. Overall, the results provide insights into the eukaryotic community diversity in drinking water treatment plants and the potential eukaryotic hazards involved in drinking water production.

Sensitive community responses of microbiota to copper in sediment toxicity test.

Sediment contamination is widespread and can be toxic to aquatic ecosystems and impair human health. Despite their significant ecological function, meio- and microbiota in aquatic ecosystems have been poorly studied in conventional sediment ecotoxicity tests because of the difficulty in sample collecting and identification. In the present study, a novel DNA metabarcoding method was used to assess the effects of spiked copper (Cu) on benthic eukaryotic and prokaryotic communities in laboratory sediment toxicity tests with macroinvertebrates, the chironomid Chironomus tepperi and the amphipod Austrochiltonia subtenuis. In addition to the obvious toxic effects to experimental animals, microbiota (bacteria, protists, algae, and fungi) were significantly altered by spiked Cu in the sediments. The phylogenetic diversity of eukaryotic communities was decreased after spiked-Cu exposure. Even a low-spiked Cu treatment (125 mg/kg) altered structures of eukaryotic and prokaryotic communities in the amphipod experiment. The present study demonstrates that measuring microbiota communities will expand our understanding of the influences of contaminants on aquatic ecosystems. Particularly, the alterations of phylogenetic biodiversity of eukaryotic communities and the structure of sedimentary communities are sensitive indicators for sediment contamination, which can be incorporated in the monitoring and assessment of sediment quality. Environ Toxicol Chem 2018;37:599-608. © 2017 SETAC.

Eukaryotic community diversity and spatial variation during drinking water production (by seawater desalination) and distribution in a full-scale network

Characterization of eukaryotic community dominated by fungi for drinking water distribution network fed by reverse osmosis seawater desalination plant.

Carboxyl-modified multi-walled carbon nanotubes-filled PDMS nanocomposites for anti-biofouling applications

In the current study, six carboxyl-modified multi-walled carbon nanotubes (cMWNTs)-filled PDMS nanocomposites (CPs) were successfully prepared, respectively. The antifouling (AF) properties of the CPs surfaces were evaluated via the long-term field immersion assays. The effects of the CPs surfaces on the attachment and colonization of the pioneer biofilm communities were investigated using the single-strand conformation polymorphism (SSCP) technique via the comparison of the diversity indices. Different CPs surfaces (i.e. the P1–P6 surfaces) have exhibited differential and excellent AF properties in the sea trial test as compared to that of the unfilled PDMS (P0) surface, indicating that the six cMWNT nanoparticles (i.e. the C1–C6 fillers) have demonstrated better AF properties, when used as reinforcing fillers in the PDMS matrix. The only reinforcing cMWNT filler (i.e. the C3 filler, 50 nm diameter, 10–20 μm length) has been identified and determined in the field. In addition, the partially aggregated cMWNT filler in the PDMS matrix was found to contribute to the improved AF properties of the CPs. The CPs surfaces can significantly reduce the adherent pioneer eukaryotic community diversity and richness, which may have dramatically modulating effect on the attachment and colonization of pioneer eukaryotic microbes. In contrast, most CPs (i.e. the P1–P5 surfaces) can only exert slight perturbation effect on the pioneer prokaryotic communities. Only the P6 surface can exert significant perturbation effect on the adherent pioneer prokaryotic and eukaryotic communities at the same time. The functionalized CPs surfaces may have the potential to be used for future maritime applications.

Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the western Antarctic Peninsula

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 73:107-121 (2014) - DOI: https://doi.org/10.3354/ame01703 Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the western Antarctic Peninsula Catherine M. Luria1,2, Hugh W. Ducklow3, Linda A. Amaral-Zettler1,2,4,* 1Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912, USA 2The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA 3Lamont-Doherty Earth Observatory of Columbia University, Palisades, New York 10964, USA 4Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, Rhode Island 02912, USA *Corresponding author: amaral@mbl.edu ABSTRACT: The classic view of polar ocean foodwebs emphasizes large predators sustained by energy and material flow through short, efficient diatom-krill-predator food chains. Bacterial activity is generally low in cold polar waters compared to that at lower latitudes. This view appears to be changing, with new studies of microbial foodwebs in Arctic and Antarctic oceans. We characterized bacterial, archaeal, and eukaryotic community diversity and composition from 2 depths (near surface and below the euphotic zone) at 4 sites, including the inshore and offshore, and north and south corners of a sampling grid along the western coast of the Antarctic Peninsula (WAP). We detected up to 2-fold higher richness in microbial eukaryotes at surface and deep inshore northern stations as compared to southern stations, but offshore northern and southern stations revealed either no trend or higher richness at depth in the south. In contrast, bacterial and archaeal richness showed no significant differences either inshore or offshore at northern versus southern extents, but did vary with depth. Archaea were virtually absent in summer surface waters, but were present in summer deep and winter surface samples. Overall, winter bacterial and archaeal assemblages most closely resembled summer sub-euphotic zone assemblages, reflecting well-established seasonal patterns of water column turnover and stratification that result in an isolated layer of ‘winter water’ below the euphotic zone. Inter-domain heterotroph-phototroph interactions were evident from network analysis. The WAP is among the most rapidly warming regions on earth. Our results provide a baseline against which future change in microbial communities may be assessed. KEY WORDS: Antarctica · MIRADA-LTERS · Palmer LTER · Pyrosequencing · V6 · V9 · Microbial oceanography Full text in pdf format Supplementary material PreviousNextCite this article as: Luria CM, Ducklow HW, Amaral-Zettler LA (2014) Marine bacterial, archaeal and eukaryotic diversity and community structure on the continental shelf of the western Antarctic Peninsula. Aquat Microb Ecol 73:107-121. https://doi.org/10.3354/ame01703 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 73, No. 2. Online publication date: October 02, 2014 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2014 Inter-Research.

Response of spring and summer riverine microbial communities following glyphosate exposure

Seasonal variation in the response of riverine microbial communities to an environmentally relevant exposure to glyphosate (about 10 μg l −1) was assessed on natural communities collected in spring and summer, using two 14-day microcosm studies. The two experiments showed no major effect of glyphosate on algal biomass (chlorophyll a concentrations), bacterial activity ([ 3H]thymidine incorporation), or bacterial community diversity (16S PCR-TTGE detection). Effects on algal community composition (genus-level taxonomic identification) and eukaryotic community diversity (18S PCR-DGGE on <100 μm organisms) were only detected on the samples collected in summer. This work demonstrates that even if the effects of a short pulse of glyphosate (10 μg l −1) on riverine microorganisms seem to be limited, the responses of natural microbial communities to glyphosate exposure (and probably to other pesticide exposures) can clearly vary between the experiments, and can be seasonally dependent.