Genetic diversity of picoeukaryotes in eight lakes differing in trophic status

Microbial Communities Are Shaped by Different Ecological Processes in Subtropical Reservoirs of Different Trophic States

Understanding microbial community structure and the underlying control mechanisms are fundamental purposes of aquatic ecology. However, little is known about the seasonality and how trophic conditions regulate plankton community in subtropical reservoirs. In this study, we study the prokaryotic and picoeukaryotic communities and their interactions during wet and dry seasons in two subtropical reservoirs: one at oligotrophic state and another at mesotrophic state. Distinct microbial community compositions (prokaryotes and picoeukaryotes) and seasonal variation pattern were detected in the oligotrophic and mesotrophic reservoirs. The interactions between prokaryotic and picoeukaryotic communities were more prevalent in the oligotrophic reservoir, suggesting enhanced top-down control of small eukaryotic grazers on the prokaryotic communities. On the other hand, the microbial community in the mesotrophic reservoir was more influenced by physico-chemical parameters and showed a stronger seasonal variation, which may be the result of distinct nutrient levels in wet and dry seasons, indicating the importance of bottom-up control. Our study contributes to new understandings of the environmental and biological processes that shape the structure and dynamics of the planktonic microbial communities in reservoirs of different trophic states.

Trophic State Drives the Diversity of Protists in a Tropical River (New River, Belize)

Land use disrupts the ecosystem functioning of freshwater systems and significantly affects trophic state. Consequently, biodiversity is severely affected by changes to the ecosystem. Microbial eukaryotes (i.e., protists) play an essential role in ecosystem functioning, contributing to biogeochemical processes, nutrient cycling, and food webs. Protist composition is a useful biological quality parameter for monitoring aquatic ecosystems and determining aquatic system health. In this study, we investigated the effects of land usage and trophic state on the communities of microbial eukaryotes in the New River (Belize, C.A.). Land use and trophic state both significantly affected protist community compositions, with impacted and mesotrophic sampled sites having higher biodiversity when compared to other sites. Autotrophic organisms dominated indirectly impacted and eutrophic sites, while impacted and mesotrophic sites had proportional ratios of autotrophic and heterotrophic organisms. Our study highlights the significant effects of trophic gradients on protistan community composition, even at the local scales.

Annual Protist Community Dynamics in a Freshwater Ecosystem Undergoing Contrasted Climatic Conditions: The Saint-Charles River (Canada)

Protists are key stone components of aquatic ecosystems, sustaining primary productivity and aquatic food webs. However, their diversity, ecology and structuring factors shaping their temporal distribution remain strongly misunderstood in freshwaters. Using high-throughput sequencing on water samples collected over 16 different months (including two summer and two winter periods), combined with geochemical measurements and climate monitoring, we comprehensively determined the pico- and nanoeukaryotic community composition and dynamics in a Canadian river undergoing prolonged ice-cover winters. Our analysis revealed a large protist diversity in this fluctuating ecosystem and clear seasonal patterns demonstrating a direct and/or indirect selective role of abiotic factors, such as water temperature or nitrogen concentrations, in structuring the eukaryotic microbial community. Nonetheless, our results also revealed that primary productivity, predatory as well as parasitism lifestyles, inferred from fine phylogenetic placements, remained potentially present over the annual cycle, despite the large seasonal fluctuations and the remodeling of the community composition under ice. In addition, potential interplays with the bacterial community composition were identified supporting a possible contribution of the bacterial community to the temporal dynamics of the protist community structure. Our results illustrate the complexity of the eukaryotic microbial community and provide a substantive and useful dataset to better understand the global freshwater ecosystem 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.

Microbial Diversity of Hypersaline Sediments from Lake Lucero Playa in White Sands National Monument, New Mexico, USA

Lake Lucero is a gypsum-rich, hypersaline, ephemeral playa located on the southern part of the Alkali Flat at the White Sands National Monument (WSNM), New Mexico, USA. This modern playa setting provides a dynamic extreme environment that changes from a freshwater lake to a hypersaline dry desert during the year. We investigated the microbial diversity (bacteria, archaea, and microbial eukaryotes) of the Lake Lucero sediments using 16S- and 18S-based amplicon sequencing approach and explored the diversity patterns in different geochemical microenvironments. Our results indicated that similar microbial communities, in particular bacterial communities colonized, were remarkably consistent across our depth profiles. Therefore, these communities show a first-order relevance on the environmental conditions (moisture content, oxygen content, and mineral composition). We found that Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Gemmatimonadetes were the major bacterial phyla, while Cyanobacteria were present in relatively low abundances and appeared only at the surface. Genus level assessment reflected that Truepera, Delftia, and Pseudomonas were the predominant bacterial genera across all samples. Euryarchaeota was the major archaeal phylum in all the samples, while Candidatus Halobonum and Candidatus Nitrososphaera were the main genera. Diatoms were the dominant eukaryotic group in surface samples and Fungi, Ciliophora, Metazoa, and Nematodes were the other major groups. As expected, metabolic inference indicated that aerobic microbial communities were near surface colonizers, with anaerobic communities dominating with increasing depth. We demonstrated that these microbial communities could be used to characterize unique geochemical microenvironments enabling us to extrapolate these results into other terrestrial and possibly extraterrestrial environments with comparable geochemical characteristics.

Marked seasonality and high spatial variability of protist communities in shallow freshwater systems

Small eukaryotes have key roles in aquatic ecosystems, influencing their local environment, global biogeochemical cycles and climate. Their impact depends on community structure, which varies along time. However, very few studies take into account temporal variation. This is especially true for small, shallow freshwater systems, which remain largely understudied despite their wide variety, global surface and intense microbial activity. We have monthly followed changes in the community structure of small microbial eukaryotes (0.2-5 μm cell diameter) for 2 years in four ponds and one brook located in North-Western France based on massive 18S rDNA amplicon 454 pyrosequencing. We detected a total of 3742 stringently defined operational taxonomic units (OTUs) encompassing all recognized eukaryotic supergroups and lineages of uncertain affiliation. Although geographically close, protist communities in the five ecosystems were contrasting, with very few shared OTUs, suggesting that environmental selection mainly drives community structure. The temporal dynamics of different high-rank taxa appeared complex and rapid at monthly scales. Despite this, a clear and reproducible seasonality was observed. As expected, low-abundance OTUs dominated the community. Although some of them appeared sporadically or remained at low frequencies during the survey, others occasionally reached relatively high abundances, sometimes recurrently. This shows that at least a fraction of low-abundance eukaryotes constitutes a seed bank. The annual proportion of primary producers, free-living heterotrophs and parasites appeared remarkably constant among the different ecosystems, suggesting underlying trends of ecosystem carrying capacity for these functional groups.

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.

A novel investigation of a blister-like syndrome in aquarium Echinopora lamellosa

This study investigates potential causes of a novel blister-like syndrome in the plating coral Echinopora lamellosa. Visual inspections of this novel coral syndrome showed no obvious signs of macroparasites and the blisters themselves manifested as fluid-filled sacs on the surface of the coral, which rose from the coenosarc between the coral polyps. Histological analysis of the blisters showed that there was no associated necrosis with the epidermal or gastrodermal tissues. The only difference between blistered areas and apparently healthy tissues was the presence of proliferated growth (possible mucosal cell hyperplasia) directly at the blister interface (area between where the edge of the blister joined apparently healthy tissue). No bacterial aggregates were identified in any histological samples, nor any sign of tissue necrosis identified. We conclude, that the blister formations are not apparently caused by a specific microbial infection, but instead may be the result of irritation following growth anomalies of the epidermis. However, future work should be conducted to search for other potential casual agents, including viruses.