The molecular ecology of microbial eukaryotes unveils a hidden world

Gazing into the abyss: A glimpse into the diversity, distribution, and behaviour of heterotrophic protists from the deep-sea floor

The benthic biome of the deep-sea floor, one of the largest biomes on Earth, is dominated by diverse and highly productive heterotrophic protists, second only to prokaryotes in terms of biomass. Recent evidence suggests that these protists play a significant role in ocean biogeochemistry, representing an untapped source of knowledge. DNA metabarcoding and environmental sample sequencing have revealed that deep-sea abyssal protists exhibit high levels of specificity and diversity across local regions. This review aims to provide a comprehensive summary of the known heterotrophic protists from the deep-sea floor, their geographic distribution, and their interactions in terms of parasitism and predation. We offer an overview of the most abundant groups and discuss their potential ecological roles. We argue that the exploration of the biodiversity and species-specific features of these protists should be integrated into broader deep-sea research and assessments of how benthic biomes may respond to future environmental changes.

Correlation between Antimicrobial Activity Values and Total Phenolic Content/Antioxidant Activity in Rubus idaeus L

Plant by-products, which are discarded into the environment, are rich in valuable compounds. The aim of this research was to determine the antibacterial activity of Rubus idaeus L. morphological parts and its correlation with total phenolic content and antioxidant activity. The authors also aimed to evaluate the plant's potential as added-value products. New aspects were revealed for further use and for making novel and natural products. The study's results indicated that raspberry leaves, inflorescences, and fruits could effectively combat three Gram-positive bacteria. According to the findings, among the various plant parts, root and seed extracts had the lowest antibacterial activity. Data revealed moderate, weak, or very weak correlation between the antimicrobial activity and phenolic content parameters. These findings underscore the viability of substituting synthetic antimicrobials with natural alternatives. The present study is significant for preparing novel products as antibacterials by appropriate and optimized processing using all raspberry morphological parts, and the research results show promising prospects for future purposeful utilisation of nature-based products. Raspberry plant parts can find applications in emerging fields that generate economic and environmental value.

Taxonomic Diversity of Pico-/Nanoeukaryotes Is Related to Dissolved Oxygen and Productivity, but Functional Composition Is Shaped by Limiting Nutrients in Eutrophic Coastal Oceans

Pico-/nanoeukaryotes (P/NEs) comprise both primary producers and bacterial predators, playing important biogeochemical and ecological roles in the marine microbial loop. Besides the difference in size, these small-sized fractions can be distinguished from microplankton by certain functional and ecological traits. Nevertheless, little information is available regarding patterns of their taxonomic and functional diversity and community composition along environmental gradients in coastal marine ecosystems. In this study, we applied high-throughput sequencing of 18S rRNA gene to assess the taxonomic species richness and community composition of P/NEs in surface waters of Bohai Sea and North Yellow Sea, northern China spanning a 600-km distance during summer and winter of 2011. The richness of operational taxonomic units (OTUs) formed a U-shaped relationship with concentration of chlorophyll a (Chl-a, a proxy of primary productivity), but a stronger, negative relationship with concentration of dissolved oxygen (DO). These two factors also significantly co-varied with the OTU-based community composition of P/NEs. The effect of geographic distance on community composition of P/NEs was negligible. Among the three functional groups defined by trophic traits, heterotrophs had the highest OTU richness, which exhibited a U-shaped relationship with both DO and Chl-a. The community of P/NEs was dominated by heterotrophs and mixotrophs in terms of read numbers, which showed a trade-off along the gradient of phosphate, but no significant changes along DO and Chl-a gradients, indicating functional redundancy. Similarly, the proportion of phototrophs was significantly and positively correlated with the concentration of silicate. Our results indicate that taxonomic and functional composition of P/NEs are decoupled on a regional scale, and limiting nutrients are important factors in modulating functional composition of these microorganisms in the studied area. These findings contribute toward gaining a better understanding of how diversity of small eukaryotes and their functions are structured in coastal oceans and the effect of environmental changes on the structuring process.

Protist diversity and function in the dark ocean - Challenging the paradigms of deep-sea ecology with special emphasis on foraminiferans and naked protists

The dark ocean and the underlying deep seafloor together represent the largest environment on this planet, comprising about 80% of the oceanic volume and covering more than two-thirds of the Earth's surface, as well as hosting a major part of the total biosphere. Emerging evidence suggests that these vast pelagic and benthic habitats play a major role in ocean biogeochemistry and represent an "untapped reservoir" of high genetic and metabolic microbial diversity. Due to its huge volume, the water column of the dark ocean is the largest reservoir of organic carbon in the biosphere and likely plays a major role in the global carbon budget. The dark ocean and the seafloor beneath it are also home to a largely enigmatic food web comprising little-known and sometimes spectacular organisms, mainly prokaryotes and protists. This review considers the globally important role of pelagic and benthic protists across all protistan size classes in the deep-sea realm, with a focus on their taxonomy, diversity, and physiological properties, including their role in deep microbial food webs. We argue that, given the important contribution that protists must make to deep-sea biodiversity and ecosystem processes, they should not be overlooked in biological studies of the deep ocean.

Time series are critical to understand microbial plankton diversity and ecology

How diverse are marine planktonic protist communities? How much seasonality do they exhibit? For a very long time, these two old and challenging questions in the field of plankton ecology could be addressed only for large-size protist species, based on cell counting under the microscope. The recent application of molecular techniques, notably massive marker-gene amplicon sequencing approaches (metabarcoding), has allowed investigating with unprecedented level of resolution the small-sized (<20 µm) planktonic eukaryotes too. An amazing diversity of these tiny organisms has been unveiled but details about their temporal dynamics remain much more elusive. In a From the Cover article in this issue of Molecular Ecology, Giner et al. (2019) introduce a new Recurrence Index (RI) to specifically look for seasonality in time-series metabarcoding data. They inspected the temporal dynamics of all operational taxonomic units (OTUs) in a rich sequence data set of pico- and nanoplanktonic eukaryotes in samples collected monthly during 10 years. Although most OTUs did not show seasonality, some abundant ones did, which explains why some averaging methods can find seasonality at the less detailed level of whole planktonic communities. Not surprisingly, the very complex small-sized eukaryotic plankton communities are composed of organisms with miscellaneous temporal dynamics.

Widespread Dominance of Kinetoplastids and Unexpected Presence of Diplonemids in Deep Freshwater Lakes

Kinetoplastid flagellates are generally abundant in the deep sea and recently they were even found to be dominant in the hypolimnion of a deep freshwater lake. Therefore, to understand the distribution of kinetoplastids in deep freshwater lakes, we have collected vertical samples from five lakes in Japan. The abundance of kinetoplastids was enumerated by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization, and the diversity was determined by 18S amplicon sequencing using universal eukaryote and kinetoplastid-specific primers. Kinetoplastids were abundant in the deep waters of all the lakes, contributing up to 53.6% of total nanoeukaryotes. Despite this significant contribution, kinetoplastids remain undetected by amplicon sequencing using universal primers that are widely used in eukaryotic diversity studies. However, they were detected with specific primers, and the communities were characterized by both ubiquitous and lake-specific unique OTUs. Oligotyping of a ubiquitous and dominant OTU revealed the presence of lake-specific sequence types (oligotypes). Remarkably, we also detected diplonemids (a sister group of kinetoplastids and considered to be specific in the marine habitat) using kinetoplastid-specific primers, showing their presence in freshwaters. Underestimation of kinetoplastids and diplonemids using universal primers indicates that euglenozoan flagellates are overlooked in diversity studies worldwide. The present study highlighted the importance of kinetoplastids in the hypolimnion of deep lakes, thereby indicating their role in material cycling in deep waters.

Combining morphology, behaviour and genomics to understand the evolution and ecology of microbial eukaryotes

Microbial eukaryotes (protists) are structurally, developmentally and behaviourally more complex than their prokaryotic cousins. This complexity makes it more difficult to translate genomic and metagenomic data into accurate functional inferences about systems ranging all the way from molecular and cellular levels to global ecological networks. This problem can be traced back to the advent of the cytoskeleton and endomembrane systems at the origin of eukaryotes, which endowed them with a range of complex structures and behaviours that still largely dominate how they evolve and interact within microbial communities. But unlike the diverse metabolic properties that evolved within prokaryotes, the structural and behavioural characteristics that strongly define how protists function in the environment cannot readily be inferred from genomic data, since there is generally no simple correlation between a gene and a discrete activity or function. A deeper understanding of protists at both cellular and ecological levels, therefore, requires not only high-throughput genomics but also linking such data to direct observations of natural history and cell biology. This is challenging since these observations typically require cultivation, which is lacking for most protists. Potential remedies with current technology include developing a more phylogenetically diverse range of model systems to better represent the diversity, as well as combining high-throughput, single-cell genomics with microscopic documentation of the subject cells to link sequence with structure and behaviour. This article is part of a discussion meeting issue 'Single cell ecology'.

Challenges in evidencing the earliest traces of life

Earth has been habitable for 4.3 billion years, and the earliest rock record indicates the presence of a microbial biosphere by at least 3.4 billion years ago-and disputably earlier. Possible traces of life can be morphological or chemical but abiotic processes that mimic or alter them, or subsequent contamination, may challenge their interpretation. Advances in micro- and nanoscale analyses, as well as experimental approaches, are improving the characterization of these biosignatures and constraining abiotic processes, when combined with the geological context. Reassessing the evidence of early life is challenging, but essential and timely in the quest to understand the origin and evolution of life, both on Earth and beyond.

Silver stress differentially affects growth of phototrophic and heterotrophic chrysomonad flagellate populations

Silver ions are among the predominant anthropogenic introduced pollutants in aquatic systems. As silver has effects on species at all trophic levels the community composition in aquatic habitats can be changed as a result of silver stress. The response of planktonic protists to environmental stressors is particularly important as they act both as producers and consumers in complex planktonic communities. Chrysomonad flagellates are of major interest, since this group includes heterotrophic, mixotrophic and phototrophic taxa, and therefore allows analysis of silver stress in organisms with contrasting nutritional strategies independent of a potential taxonomic bias. In a series of lab experiments, we compared the response of different trophic chrysophyte strains to low (5 μg L^-1), medium (10 μg L^-1) and high (20 μg L^-1) nominal Ag concentrations in combination with changes in temperature and light intensity (phototrophs), temperature and food concentration (heterotrophs), or a combination of the above settings (mixotrophs). All tested strains were negatively affected by silver in their growth rates. The phototrophic strains reacted strongly to silver stress, whereas light intensity and temperature had only minor effects on growth rates. For heterotrophic strains, high food concentration toned down the effect of silver, whereas temperatures outside the growth optimum had a combined stress effect. The mixotrophic strains reacted differently depending on whether their nutritional mode was dominated by heterotrophy or by phototrophy. The precise response pattern across all variables was uniquely different for every single species we tested. The present work contributes to a deeper understanding of the effects of environmental stressors on complex planktonic communities. It indicates that silver will negatively impact planktonic communities and may create shifts in their composition and functioning.

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: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is an ongoing community-driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the eukaryotic tree of life and microbial ecologists, who use environmental sequence data to develop reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous mining and annotation of sequence data by providing protocols, guidelines, and tools. The EukRef pipeline and tools allow users interested in a particular group of microbial eukaryotes to retrieve all sequences belonging to that group from International Nucleotide Sequence Database Collaboration (INSDC) (GenBank, the European Nucleotide Archive [ENA], or the DNA DataBank of Japan [DDBJ]), to place those sequences in a phylogenetic tree, and to curate taxonomic and environmental information for the group. We provide guidelines to facilitate the process and to standardize taxonomic annotations. The final outputs of this process are (1) a reference tree and alignment, (2) a reference sequence database, including taxonomic and environmental information, and (3) a list of putative chimeras and other artifactual sequences. These products will be useful for the broad community as they become publicly available (at eukref.org) and are shared with existing reference databases.

Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes

Freshwater systems are characterized by an enormous diversity of eukaryotic protists and prokaryotic taxa. The community structures in different lakes are thereby influenced by factors such as habitat size, lake chemistry, biotic interactions, and seasonality. In our study, we used high throughput 454 sequencing to study the diversity and temporal changes of prokaryotic and eukaryotic planktonic communities in three Austrian lakes during the ice-free season. In the following year, one lake was sampled again with a reduced set of sampling dates to observe reoccurring patterns. Cluster analyses (based on SSU V9 (eukaryotic) and V4 (prokaryotic) OTU composition) grouped samples according to their origin followed by separation into seasonal clusters, indicating that each lake has a unique signature based on OTU composition. These results suggest a strong habitat-specificity of microbial communities and in particular of community patterns at the OTU level. A comparison of the prokaryotic and eukaryotic datasets via co-inertia analysis (CIA) showed a consistent clustering of prokaryotic and eukaryotic samples, probably reacting to the same environmental forces (e.g., pH, conductivity). In addition, the shifts in eukaryotic and bacterioplanktonic communities generally occurred at the same time and on the same scale. Regression analyses revealed a linear relationship between an increase in Bray-Curtis dissimilarities and elapsed time. Our study shows a pronounced coupling between bacteria and eukaryotes in seasonal samplings of the three analyzed lakes. However, our temporal resolution (biweekly sampling) and data on abiotic factors were insufficient to determine if this was caused by direct biotic interactions or by reacting to the same seasonally changing environmental forces.

What Defines the "Kingdom" Fungi?

The application of environmental DNA techniques and increased genome sequencing of microbial diversity, combined with detailed study of cellular characters, has consistently led to the reexamination of our understanding of the tree of life. This has challenged many of the definitions of taxonomic groups, especially higher taxonomic ranks such as eukaryotic kingdoms. The Fungi is an example of a kingdom which, together with the features that define it and the taxa that are grouped within it, has been in a continual state of flux. In this article we aim to summarize multiple lines of data pertinent to understanding the early evolution and definition of the Fungi. These include ongoing cellular and genomic comparisons that, we will argue, have generally undermined all attempts to identify a synapomorphic trait that defines the Fungi. This article will also summarize ongoing work focusing on taxon discovery, combined with phylogenomic analysis, which has identified novel groups that lie proximate/adjacent to the fungal clade-wherever the boundary that defines the Fungi may be. Our hope is that, by summarizing these data in the form of a discussion, we can illustrate the ongoing efforts to understand what drove the evolutionary diversification of fungi.

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.

Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error

Small subunit ribosomal DNA (SSU rDNA) is widely used for phylogenetic inference, barcoding and other taxonomy-based analyses. Recent studies indicate that SSU rDNA of ciliates may have a high level of sequence variation within a single cell, which impacts the interpretation of rDNA-based surveys. However, sequence variation can come from a variety of sources including experimental errors, especially the mutations generated by DNA polymerase in PCR. In the present study, we explore the impact of four DNA polymerases on sequence variation and find that low-fidelity polymerases exaggerate the estimates of single-cell sequence variation. Therefore, using a polymerase with high fidelity is essential for surveys of sequence variation. Another source of variation results from errors during amplification of SSU rDNA within the polyploidy somatic macronuclei of ciliates. To investigate further the impact of SSU rDNA copy number variation, we use a high-fidelity polymerase to examine the intra-individual SSU rDNA polymorphism in ciliates with varying levels of macronuclear amplification: Halteria grandinella, Blepharisma americanum and Strombidium stylifer We estimate the rDNA copy numbers of these three species by single-cell quantitative PCR. The results indicate that: (i) sequence variation of SSU rDNA within a single cell is authentic in ciliates, but the level of intra-individual SSU rDNA polymorphism varies greatly among species; (ii) rDNA copy numbers vary greatly among species, even those within the same class; (iii) the average rDNA copy number of Halteria grandinella is about 567 893 (s.d. = 165 481), which is the highest record of rDNA copy number in ciliates to date; and (iv) based on our data and the records from previous studies, it is not always true in ciliates that rDNA copy numbers are positively correlated with cell or genome size.

Symbiosis in eukaryotic evolution

Fifty years ago, Lynn Margulis, inspiring in early twentieth-century ideas that put forward a symbiotic origin for some eukaryotic organelles, proposed a unified theory for the origin of the eukaryotic cell based on symbiosis as evolutionary mechanism. Margulis was profoundly aware of the importance of symbiosis in the natural microbial world and anticipated the evolutionary significance that integrated cooperative interactions might have as mechanism to increase cellular complexity. Today, we have started fully appreciating the vast extent of microbial diversity and the importance of syntrophic metabolic cooperation in natural ecosystems, especially in sediments and microbial mats. Also, not only the symbiogenetic origin of mitochondria and chloroplasts has been clearly demonstrated, but improvement in phylogenomic methods combined with recent discoveries of archaeal lineages more closely related to eukaryotes further support the symbiogenetic origin of the eukaryotic cell. Margulis left us in legacy the idea of 'eukaryogenesis by symbiogenesis'. Although this has been largely verified, when, where, and specifically how eukaryotic cells evolved are yet unclear. Here, we shortly review current knowledge about symbiotic interactions in the microbial world and their evolutionary impact, the status of eukaryogenetic models and the current challenges and perspectives ahead to reconstruct the evolutionary path to eukaryotes.

Ecological and evolutionary significance of novel protist lineages

Environmental molecular surveys targeting protist diversity have unveiled novel and uncultured lineages in a variety of ecosystems, ranging from completely new high-rank lineages, to new taxa moderately related to previously described organisms. The ecological roles of some of these novel taxa have been studied, showing that in certain habitats they may be responsible for critical environmental processes. Moreover, from an evolutionary perspective they still need to be included in a more accurate and wider understanding of the eukaryotic tree of life. These seminal discoveries promoted the development and use of a wide range of more in-depth culture-independent approaches to access this diversity, from metabarcoding and metagenomics to single cell genomics and FISH. Nonetheless, culturing using classical or innovative approaches is also essential to better characterize this new diversity. Ecologists and evolutionary biologists now face the challenge of apprehending the significance of this new diversity within the eukaryotic tree of life.

Protistan community analysis: key findings of a large-scale molecular sampling

Protists are perhaps the most lineage-rich of microbial lifeforms, but remain largely unknown. High-throughput sequencing technologies provide opportunities to screen whole habitats in depth and enable detailed comparisons of different habitats to measure, compare and map protistan diversity. Such comparisons are often limited by low sample numbers within single studies and a lack of standardisation between studies. Here, we analysed 232 samples from 10 sampling campaigns using a standardised PCR protocol and bioinformatics pipeline. We show that protistan community patterns are highly consistent within habitat types and geographic regions, provided that sample processing is standardised. Community profiles are only weakly affected by fluctuations of the abundances of the most abundant taxa and, therefore, provide a sound basis for habitat comparison beyond random short-term fluctuations in the community composition. Further, we provide evidence that distribution patterns are not solely resulting from random processes. Distinct habitat types and distinct taxonomic groups are dominated by taxa with distinct distribution patterns that reflect their ecology with respect to dispersal and habitat colonisation. However, there is no systematic shift of the distribution pattern with taxon abundance.

Cumulative effect of zinc oxide and titanium oxide nanoparticles on growth and chlorophyll a content of Picochlorum sp

The use of nanoparticles (NPs) is of increasing significance due to their large potential for various applications. Great attention should be paid on the possible impacts of nanoparticles on the environment as large amounts of them may reach the environment by accident or voluntarily. Marine algae are potential organisms for usage in nanopollution bioremediation in aquatic system, because of their ability to adapt to long exposure to NPs. Thus, it is of prime importance to study the possible interactions of different NPs with microalgae in assessing their potential environmental risks. Most studies on potential environmental effects of ZnO and TiO2 NPs have been performed independently and following the widely accepted, standardized test systems, which had been developed for the characterization of chemicals. In this study, we have examined the cumulative effect of ZnO and TiO2 NPs on Picochlorum sp. in addition to the individual effects of these NPs over 32 days. Our results indicate that the toxicity and availability of NPs to marine algae are reduced by their aggregation and sedimentation. NPs are found to have a negative effect on algal growth and chlorophyll a concentration during the early growth stages. In contrast, the case is reversed during the late growth stages. There is no significant difference between the effect of the NPs when they are used separately and when both ZnO and TiO2 are used together in the test (P > 0.05).

Functional Metagenomics: Construction and High-Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes

Activity-based metagenomics is one of the most efficient approaches to boost the discovery of novel biocatalysts from the huge reservoir of uncultivated bacteria. In this chapter, we describe a highly generic procedure of metagenomic library construction and high-throughput screening for carbohydrate-active enzymes. Applicable to any bacterial ecosystem, it enables the swift identification of functional enzymes that are highly efficient, alone or acting in synergy, to break down polysaccharides and oligosaccharides.

Effect of magnetic iron oxide (Fe₃O₄) nanoparticles on the growth and photosynthetic pigment content of Picochlorum sp

Magnetite iron oxide (Fe3O4) nanoparticles (NPs) are key materials applied in many different fields of modern technology. The potential environmental impact of these NPs is of great concern. In this study, initially the effect of Fe3O4 NPs size (20 and 40 nm) as well as bulk (>100 nm) at 200 mg L(-1) on Picochlorum sp. (Trebouxiophyceae, Chlorophyta) is investigated during the different growth phases. The most inhibitory NPs were then chosen to assess their effects at different concentrations. The 20 nm NPs at 200 mg L(-1) were found to significantly reduce the viable cell concentration and chlorophyll a content during the exponential growth phase compared to the other particle sizes. However, the 20 nm NPs at different concentrations were found to promote algal growth during the late growth stages (stationary and decline phases) compared to the control. Additionally, algae were found to accelerate the aggregation and sedimentation of nanoparticles into the medium and therefore can be considered as potential organisms for bioremediation of nano-pollution.

Response of the microbial community to seasonal groundwater level fluctuations in petroleum hydrocarbon-contaminated groundwater

The effects of seasonal groundwater level fluctuations on the contamination characteristics of total petroleum hydrocarbons (TPH) in soils, groundwater, and the microbial community were investigated at a typical petrochemical site in northern China. The measurements of groundwater and soil at different depths showed that significant TPH residue was present in the soil in this study area, especially in the vicinity of the pollution source, where TPH concentrations were up to 2600 mg kg(-1). The TPH concentration in the groundwater fluctuated seasonally, and the maximum variation was 0.8 mg L(-1). The highest TPH concentrations were detected in the silty clay layer and lied in the groundwater level fluctuation zones. The groundwater could reach previously contaminated areas in the soil, leading to higher groundwater TPH concentrations as TPH leaches into the groundwater. The coincident variation of the electron acceptors and TPH concentration with groundwater-table fluctuations affected the microbial communities in groundwater. The microbial community structure was significantly different between the wet and dry seasons. The canonical correspondence analysis (CCA) results showed that in the wet season, TPH, NO3(-), Fe(2+), TMn, S(2-), and HCO3(-) were the major factors correlating the microbial community. A significant increase in abundance of operational taxonomic unit J1 (97% similar to Dechloromonas aromatica sp.) was also observed in wet season conditions, indicating an intense denitrifying activity in the wet season environment. In the dry season, due to weak groundwater level fluctuations and low temperature of groundwater, the microbial activity was weak. But iron and sulfate-reducing were also detected in dry season at this site. As a whole, groundwater-table fluctuations would affect the distribution, transport, and biodegradation of the contaminants. These results may be valuable for the control and remediation of soil and groundwater pollution at this site and in other petrochemical-contaminated areas. Furthermore, they are probably helpful for reducing health risks to the general public from contaminated groundwater.

Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities

Amplicon read sequencing has revolutionized the field of microbial diversity studies. The technique has been developed for bacterial assemblages and has undergone rigorous testing with mock communities. However, due to the great complexity of eukaryotes and the numbers of different rDNA copies, analyzing eukaryotic diversity is more demanding than analyzing bacterial or mock communities, so studies are needed that test the methods of analyses on taxonomically diverse natural communities. In this study, we used 20 samples collected from the Baltic Sea ice, slush and under-ice water to investigate three program packages (UPARSE, mothur and QIIME) and 18 different bioinformatic strategies implemented in them. Our aim was to assess the impact of the initial steps of bioinformatic strategies on the results when analyzing natural eukaryotic communities. We found significant differences among the strategies in resulting read length, number of OTUs and estimates of diversity as well as clear differences in the taxonomic composition of communities. The differences arose mainly because of the variable number of chimeric reads that passed the pre-processing steps. Singleton removal and denoising substantially lowered the number of errors. Our study showed that the initial steps of the bioinformatic amplicon read processing strategies require careful consideration before applying them to eukaryotic communities.

Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems

Although inland water bodies are more heterogeneous and sensitive to environmental variation than oceans, the diversity of small protists in these ecosystems is much less well known. Some molecular surveys of lakes exist, but little information is available from smaller, shallower and often ephemeral freshwater systems, despite their global distribution and ecological importance. We carried out a comparative study based on massive pyrosequencing of amplified 18S rRNA gene fragments of protists in the 0.2-5 μm size range in one brook and four shallow ponds located in the Natural Regional Park of the Chevreuse Valley, France. Our study revealed a wide diversity of small protists, with 812 stringently defined operational taxonomic units (OTUs) belonging to the recognized eukaryotic supergroups (SAR--Stramenopiles, Alveolata, Rhizaria--Archaeplastida, Excavata, Amoebozoa, Opisthokonta) and to groups of unresolved phylogenetic position (Cryptophyta, Haptophyta, Centrohelida, Katablepharida, Telonemida, Apusozoa). Some OTUs represented deep-branching lineages (Cryptomycota, Aphelida, Colpodellida, Tremulida, clade-10 Cercozoa, HAP-1 Haptophyta). We identified several lineages previously thought to be marine including, in addition to MAST-2 and MAST-12, already detected in freshwater, MAST-3 and possibly MAST-6. Protist community structures were different in the five ecosystems. These differences did not correlate with geographical distances, but seemed to be influenced by environmental parameters.

Phytoplankton diversity and community composition along the estuarine gradient of a temperate macrotidal ecosystem: combined morphological and molecular approaches

Microscopical and molecular analyses were used to investigate the diversity and spatial community structure of spring phytoplankton all along the estuarine gradient in a macrotidal ecosystem, the Baie des Veys (eastern English Channel). Taxa distribution at high tide in the water column appeared to be mainly driven by the tidal force which superimposed on the natural salinity gradient, resulting in a two-layer flow within the channel. Lowest taxa richness and abundance were found in the bay where Teleaulax-like cryptophytes dominated. A shift in species composition occurred towards the mouth of the river, with the diatom Asterionellopsis glacialis dramatically accumulating in the bottom waters of the upstream brackish reach. Small thalassiosiroid diatoms dominated the upper layer river community, where taxa richness was higher. Through the construction of partial 18S rDNA clone libraries, the microeukaryotic diversity was further explored for three samples selected along the surface salinity gradient (freshwater - brackish - marine). Clone libraries revealed a high diversity among heterotrophic and/or small-sized protists which were undetected by microscopy. Among them, a rich variety of Chrysophyceae and other lineages (e.g. novel marine stramenopiles) are reported here for the first time in this transition area. However, conventional microscopy remains more efficient in revealing the high diversity of phototrophic taxa, low in abundances but morphologically distinct, that is overlooked by the molecular approach. The differences between microscopical and molecular analyses and their limitations are discussed here, pointing out the complementarities of both approaches, for a thorough phytoplankton community description.

Primer pairs for the specific environmental detection and T-RFLP analysis of the ubiquitous flagellate taxa Chrysophyceae and Kinetoplastea

Bacterivorous protists play a key role in microbial soil food webs, however due to the lack of specific PCR protocols targeting selected protist taxa, knowledge on the diversity and dynamics of these groups is scarce. We developed specific PCR primers in combination with a T-RFLP protocol for the cultivation-independent analysis of two important taxa of bacterivorous flagellates, the Chrysophyceae and Kinetoplastea, in soil samples. Sequence analysis of clone libraries originating from two soils in temperate regions demonstrated the specificity of the respective primer pairs. Clone sequences affiliating to the Chrysophyceae mainly clustered within the clade C2, which has been known so far for its presence mainly in cold climatic regions, whereas Kinetoplastea sequences were mainly related to the Neobodonid clade. Based on an in silico restriction analysis of database sequence entries, suitable restriction enzymes for a T-RFLP approach were selected. This in silico approach revealed the necessity to use a combination of two restriction enzymes for T-RFLP analysis of the Chrysophyceae. Soil T-RFLP profiles reflected all T-RFs of the clone library sequences obtained from the same soils and allowed to distinguish flagellate communities from different sites. We propose to use these primer pairs for PCR detection and rapid fingerprint screening in environmental samples and envisage their use also for quantitative PCR or next generation sequencing approaches.

Picoplankton dynamics and picoeukaryote diversity in a hyper-eutrophic subtropical lagoon

Picoplankton (cells with a diameter of 0.2-3.0 μm) is the dominant contributor to both primary production and biomass in the ocean. Most of the previous studies on picoplankton have been conducted in the oligotrophic open sea with few in the eutrophic area. In this study, we investigated the dynamics of different groups of picoplankton and the diversity of picoeukaryote (based on 18S rDNA) in a hyper-eutrophic marine coastal lagoon. The results indicated that temperature and phosphate concentration were most responsible for the dynamics of different picoplankton groups. Examination of 135 clones revealed 27 different Denaturing Gradient Gel Electrophoresis (DGGE) patterns. At least 7 high-level taxonomic groups of picoeukaryote were recorded. The picoeukaryotic diversities included Alveolates, Stramenopiles, Haptophyceae, and Viridiplantae, with Stramenopiles being the most diverse group. Overall the results of this study indicated that picoplankton diversity was low relative to studies conducted in more oligotrophic waters.

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks

SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.

Monthly to interannual variability of microbial eukaryote assemblages at four depths in the eastern North Pacific

The monthly, seasonal and interannual variability of microbial eukaryote assemblages were examined at 5 m, the deep chlorophyll maximum, 150 m and 500 m at the San Pedro Ocean Time-series station (eastern North Pacific). The depths spanned transitions in temperature, light, nutrients and oxygen, and included a persistently hypoxic environment at 500 m. Terminal restriction fragment length polymorphism was used for the analysis of 237 samples that were collected between September 2000 and December 2010. Spatiotemporal variability patterns of microeukaryote assemblages indicated the presence of distinct shallow and deep communities at the SPOT station, presumably reflecting taxa that were specifically adapted for the conditions in those environments. Community similarity values between assemblages collected 1 month apart at each depth ranged between ∼20% and ∼84% (averages were ∼50-59%). The assemblage at 5 m was temporally more dynamic than deeper assemblages and also displayed substantial interannual variability during the first ∼3 years of the study. Evidence of seasonality was detected for the microbial eukaryote assemblage at 5 m between January 2008 and December 2010 and at 150 m between September 2000 and December 2003. Seasonality was not detected for assemblages at the deep chlorophyll a maximum, which varied in depth seasonally, or at 500 m. Microbial eukaryote assemblages exhibited cyclical patterns in at least 1 year at each depth, implying an annual resetting of communities. Substantial interannual variability was detected for assemblages at all depths and represented the largest source of temporal variability in this temperate coastal ecosystem.

Lineage-specific molecular probing reveals novel diversity and ecological partitioning of haplosporidians

Haplosporidians are rhizarian parasites of mostly marine invertebrates. They include the causative agents of diseases of commercially important molluscs, including MSX disease in oysters. Despite their importance for food security, their diversity and distributions are poorly known. We used a combination of group-specific PCR primers to probe environmental DNA samples from planktonic and benthic environments in Europe, South Africa and Panama. This revealed several highly distinct novel clades, novel lineages within known clades and seasonal (spring vs autumn) and habitat-related (brackish vs littoral) variation in assemblage composition. High frequencies of haplosporidian lineages in the water column provide the first evidence for life cycles involving planktonic hosts, host-free stages or both. The general absence of haplosporidian lineages from all large online sequence data sets emphasises the importance of lineage-specific approaches for studying these highly divergent and diverse lineages. Combined with host-based field surveys, environmental sampling for pathogens will enhance future detection of known and novel pathogens and the assessment of disease risk.

Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection

BACKGROUND

Deep hypersaline anoxic basins (DHABs) are isolated habitats at the bottom of the eastern Mediterranean Sea, which originate from the ancient dissolution of Messinian evaporites. The different basins have recruited their original biota from the same source, but their geological evolution eventually constituted sharp environmental barriers, restricting genetic exchange between the individual basins. Therefore, DHABs are unique model systems to assess the effect of geological events and environmental conditions on the evolution and diversification of protistan plankton. Here, we examine evidence for isolated evolution of unicellular eukaryote protistan plankton communities driven by geological separation and environmental selection. We specifically focused on ciliated protists as a major component of protistan DHAB plankton by pyrosequencing the hypervariable V4 fragment of the small subunit ribosomal RNA. Geospatial distributions and responses of marine ciliates to differential hydrochemistries suggest strong physical and chemical barriers to dispersal that influence the evolution of this plankton group.

RESULTS

Ciliate communities in the brines of four investigated DHABs are distinctively different from ciliate communities in the interfaces (haloclines) immediately above the brines. While the interface ciliate communities from different sites are relatively similar to each other, the brine ciliate communities are significantly different between sites. We found no distance-decay relationship, and canonical correspondence analyses identified oxygen and sodium as most important hydrochemical parameters explaining the partitioning of diversity between interface and brine ciliate communities. However, none of the analyzed hydrochemical parameters explained the significant differences between brine ciliate communities in different basins.

CONCLUSIONS

Our data indicate a frequent genetic exchange in the deep-sea water above the brines. The "isolated island character" of the different brines, that resulted from geological events and contemporary environmental conditions, create selective pressures driving evolutionary processes, and with time, lead to speciation and shape protistan community composition. We conclude that community assembly in DHABs is a mixture of isolated evolution (as evidenced by small changes in V4 primary structure in some taxa) and species sorting (as indicated by the regional absence/presence of individual taxon groups on high levels in taxonomic hierarchy).

Evidence for isolated evolution of deep-sea ciliate communities through geological separation and environmental selection

Background

Deep hypersaline anoxic basins (DHABs) are isolated habitats at the bottom of the eastern Mediterranean Sea, which originate from the ancient dissolution of Messinian evaporites. The different basins have recruited their original biota from the same source, but their geological evolution eventually constituted sharp environmental barriers, restricting genetic exchange between the individual basins. Therefore, DHABs are unique model systems to assess the effect of geological events and environmental conditions on the evolution and diversification of protistan plankton. Here, we examine evidence for isolated evolution of unicellular eukaryote protistan plankton communities driven by geological separation and environmental selection. We specifically focused on ciliated protists as a major component of protistan DHAB plankton by pyrosequencing the hypervariable V4 fragment of the small subunit ribosomal RNA. Geospatial distributions and responses of marine ciliates to differential hydrochemistries suggest strong physical and chemical barriers to dispersal that influence the evolution of this plankton group.

Results

Ciliate communities in the brines of four investigated DHABs are distinctively different from ciliate communities in the interfaces (haloclines) immediately above the brines. While the interface ciliate communities from different sites are relatively similar to each other, the brine ciliate communities are significantly different between sites. We found no distance-decay relationship, and canonical correspondence analyses identified oxygen and sodium as most important hydrochemical parameters explaining the partitioning of diversity between interface and brine ciliate communities. However, none of the analyzed hydrochemical parameters explained the significant differences between brine ciliate communities in different basins.

Conclusions

Our data indicate a frequent genetic exchange in the deep-sea water above the brines. The “isolated island character” of the different brines, that resulted from geological events and contemporary environmental conditions, create selective pressures driving evolutionary processes, and with time, lead to speciation and shape protistan community composition. We conclude that community assembly in DHABs is a mixture of isolated evolution (as evidenced by small changes in V4 primary structure in some taxa) and species sorting (as indicated by the regional absence/presence of individual taxon groups on high levels in taxonomic hierarchy).

Phylogenetic composition and distribution of picoeukaryotes in the hypoxic northwestern coast of the Gulf of Mexico

Coastal marine hypoxic, or low-oxygen, episodes are an increasing worldwide phenomenon, but its effect on the microbial community is virtually unknown by far. In this study, the community structure and phylogeny of picoeukaryotes in the Gulf of Mexico, which are exposed to severe hypoxia in these areas was explored through a clone library approach. Both oxic surface waters and suboxic bottom waters were collected in August 2010 from three representative stations on the inner Louisiana shelf near the Atchafalaya and Mississippi River plumes. The bottom waters of the two more western stations were much more hypoxic in comparison to those of the station closest to the Mississippi River plume, which were only moderately hypoxic. A phylogenetic analysis of a total 175 sequences, generated from six 18S rDNA clone libraries, demonstrated a clear dominance of parasitic dinoflagellates from Marine alveolate clades I and II in all hypoxic waters as well as in the surface layer at the more western station closest to the Atchafalaya River plume. Species diversity was significantly higher at the most hypoxic sites, and many novel species were present among the dinoflagellate and stramenopile clades. We concluded that hypoxia in the Gulf of Mexico causes a significant shift in picoeukaryote communities, and that hypoxia may cause a shift in microbial food webs from grazing to parasitism.

Short-term responses of unicellular planktonic eukaryotes to increases in temperature and UVB radiation

Background

Small size eukaryotes play a fundamental role in the functioning of coastal ecosystems, however, the way in which these micro-organisms respond to combined effects of water temperature, UVB radiations (UVBR) and nutrient availability is still poorly investigated.

Results

We coupled molecular tools (18S rRNA gene sequencing and fingerprinting) with microscope-based identification and counting to experimentally investigate the short-term responses of small eukaryotes (<6 μm; from a coastal Mediterranean lagoon) to a warming treatment (+3°C) and UVB radiation increases (+20%) at two different nutrient levels. Interestingly, the increase in temperature resulted in higher pigmented eukaryotes abundances and in community structure changes clearly illustrated by molecular analyses. For most of the phylogenetic groups, some rearrangements occurred at the OTUs level even when their relative proportion (microscope counting) did not change significantly. Temperature explained almost 20% of the total variance of the small eukaryote community structure (while UVB explained only 8.4%). However, complex cumulative effects were detected. Some antagonistic or non additive effects were detected between temperature and nutrients, especially for Dinophyceae and Cryptophyceae.

Conclusions

This multifactorial experiment highlights the potential impacts, over short time scales, of changing environmental factors on the structure of various functional groups like small primary producers, parasites and saprotrophs which, in response, can modify energy flow in the planktonic food webs.

Eukaryotic life in biofilms formed in a uranium mine

The underground uranium mine Königstein (Saxony, Germany), currently in the process of remediation, represents an underground acid mine drainage (AMD) environment, that is, low pH conditions and high concentrations of heavy metals including uranium, in which eye-catching biofilm formations were observed. During active uranium mining from 1984 to 1990, technical leaching with sulphuric acid was applied underground on-site resulting in a change of the underground mine environment and initiated the formation of AMD and also the growth of AMD-related copious biofilms. Biofilms grow underground in the mine galleries in a depth of 250 m (50 m above sea level) either as stalactite-like slime communities or as acid streamers in the drainage channels. The eukaryotic diversity of these biofilms was analyzed by microscopic investigations and by molecular methods, that is, 18S rDNA PCR, cloning, and sequencing. The biofilm communities of the Königstein environment showed a low eukaryotic biodiversity and consisted of a variety of groups belonging to nine major taxa: ciliates, flagellates, amoebae, heterolobosea, fungi, apicomplexa, stramenopiles, rotifers and arthropoda, and a large number of uncultured eukaryotes, denoted as acidotolerant eukaryotic cluster (AEC). In Königstein, the flagellates Bodo saltans, the stramenopiles Diplophrys archeri, and the phylum of rotifers, class Bdelloidea, were detected for the first time in an AMD environment characterized by high concentrations of uranium. This study shows that not only bacteria and archaea may live in radioactive contaminated environments, but also species of eukaryotes, clearly indicating their potential influence on carbon cycling and metal immobilization within AMD-affected environment.

Pitfalls of establishing DNA barcoding systems in protists: the cryptophyceae as a test case

A DNA barcode is a preferrably short and highly variable region of DNA supposed to facilitate a rapid identification of species. In many protistan lineages, a lack of species-specific morphological characters hampers an identification of species by light or electron microscopy, and difficulties to perform mating experiments in laboratory cultures also do not allow for an identification of biological species. Thus, testing candidate barcode markers as well as establishment of accurately working species identification systems are more challenging than in multicellular organisms. In cryptic species complexes the performance of a potential barcode marker can not be monitored using morphological characters as a feedback, but an inappropriate choice of DNA region may result in artifactual species trees for several reasons. Therefore a priori knowledge of the systematics of a group is required. In addition to identification of known species, methods for an automatic delimitation of species with DNA barcodes have been proposed. The Cryptophyceae provide a mixture of systematically well characterized as well as badly characterized groups and are used in this study to test the suitability of some of the methods for protists. As species identification method the performance of blast in searches against badly to well-sampled reference databases has been tested with COI-5P and 5'-partial LSU rDNA (domains A to D of the nuclear LSU rRNA gene). In addition the performance of two different methods for automatic species delimitation, fixed thresholds of genetic divergence and the general mixed Yule-coalescent model (GMYC), have been examined. The study demonstrates some pitfalls of barcoding methods that have to be taken care of. Also a best-practice approach towards establishing a DNA barcode system in protists is proposed.

Unveiling trophic functions of uncultured protist taxa by incubation experiments in the brackish Baltic Sea

BACKGROUND

Our knowledge of the phylogeny and diversity of aquatic protists is rapidly increasing due to molecular surveys and next-generation sequencing approaches. This has led to a considerable discrepancy between the taxa known from cultures and those known from environmental 18S rRNA gene sequences. Hence, it is generally difficult to assign ecological functions to new taxa detected by culture-independent molecular approaches.

METHODOLOGY/PRINCIPAL FINDINGS

A combination of unamended dark incubations and 18S rRNA sequencing was chosen to link molecular diversity data of uncultured protists with heterotrophic, presumably bacterivorous, growth. The incubations, conducted with Baltic Sea brackish water, resulted in a consistent shift from a protistan community dominated by phototrophs to one in which heterotrophs predominated. This was determined on the basis of cell abundance and 18S rRNA sequences derived from fingerprint analysis and clone libraries. The bulk of enriched phylotypes after incubation were related to hitherto uncultured marine taxa within chrysophytes, ochrophytes, choanoflagellates, cercozoans, and picobiliphytes, mostly represented in recently established or here defined environmental clades. Their growth in the dark, together with coinciding results from studies with a similar objective, provides evidence that these uncultured taxa represent heterotrophic or mixotrophic species.

CONCLUSIONS/SIGNIFICANCE

These findings shed some light into the trophic role of diverse uncultured protists especially within functionally heterogeneous groups (e.g., chrysophytes, ochrophytes) and groups that appear to be puzzling with regard to their nutrition (picobiliphytes). Additionally, our results indicate that the heterotrophic flagellate community in the southwestern Baltic Sea is dominated by species of marine origin. The combination of unamended incubations with molecular diversity analysis is thus confirmed as a promising approach to explore the trophic mode of environmentally relevant protist taxa for which only sequence data are currently available.