Microeukaryotic Communities Research Articles

Exploring the diversity of microeukaryotic communities in New England tide pools

Though historically understudied, due in large part to most species being uncultivable, microbial eukaryotes (i.e. protists) are abundant and widespread across diverse habitats. Recent advances in molecular techniques, including metabarcoding, allow for the characterization of poorly known protist lineages. This study surveys the diversity of SAR (Stramenopila, Alveolata, and Rhizaria), a major eukaryotic clade that is estimated to represent about half of all eukaryotic diversity. SAR lineages use varied metabolic strategies like mixotrophy in dinoflagellates (Alveolata), parasitism in apicomplexans (Alveolata) and labyrinthulids (Stramenopila), and life cycle stages that include encystment and attachment (e.g. in ciliates, Alveolata) to survive in highly dynamic habitats. Using metabarcoding primers designed specifically to target a portion of the 18S small subunit ribosomal RNA (SSU-rRNA) gene of SAR lineages, we compare protist community composition from tide pools in Acadia National Park, Maine, USA. We characterize over 500 lineages, here operational taxonomic units (OTUs), many of which are found abundant in the tide pool environment. We also find that communities vary by month sampled and exhibit patterns by size (i.e. macro-, micro-, and nano-sized). Taken together, these data allow us to further catalog protist diversity in extreme environments (e.g. those subject to extreme fluctuations in temperature and salinity during tidal cycles). Such data are critical in the explorations of biodiversity patterns among microorganisms on our rapidly changing planet.

Satellite taxa regulated the response of constructed wetlands microeukaryotic community to changing hydraulic loading rate

Revealing how species interaction and assembly processes structure the core and satellite microeukaryotic subcommunities in an engineering environment is crucial for understanding how biodiversity influences system function. By investigating the core and satellite microeukaryotic subcommunities in constructed wetlands (CWs), we depicted an integrated distribution pattern of microeukaryotic communities in the CWs with different hydraulic loading rates (HLRs). Surprisingly, our results suggested that high HLR reduced the diversity and network stability of the microeukaryote community in CW. The stochastic process becomes more important with the increased HLR. In addition, satellite and core taxa varied inconsistently under different HLRs except for niche breadth. And the changes in all taxa were consistent with those in satellite taxa. Satellite taxa, but not core taxa, was an important driver in shaping the dynamics of microeukaryotic communities and played an important role in maintaining the stability of the microeukaryotic community. Overall, our results not only fill a gap in understanding the microeukaryotic community dynamics and its basic drivers of CWs under different HLRs but also highlights the particular importance of satellite microeukaryotes in mediating biogeochemical cycles in CWs ecosystems.

Trophic interactions regulate microbial responses to environmental conditions and partially counteract nitrogen transformation potential in urban river bends

River bends are distinguished by high biodiversity and elevated rates of biogeochemical activities due to complex hydromorphological processes that form diverse geomorphic units, making it challenging to elucidate the impact of trophic interactions on community assembly and biogeochemical processes. Here, we clarify the effect of trophic interactions in determining the assembly of multi-trophic microbial communities and the impact on nitrogen transformation potential by distinguishing the direct and cascading effects of environmental conditions based on 32 samples collected from a typical urban river bends. It was found that both bacterial and micro-eukaryotic communities were determined by homogeneous selection (indicated by β-nearest taxon index, accounted for 85% and 48.3%, respectively), whereas the dominant environmental factors were different, being sediment particle size (P < 0.05) and nitrogen (P < 0.05), respectively. Both the microbial co-occurrence network and the significant association (P < 0.05) between β-nearest taxon index and trophic transfer efficiency changes showed that the trophic interactions strongly shaped microbial communities in the urban river bends. The path modeling suggested that environmental conditions resulted in an increase in abundance of multi-trophic microbial communities via direct effects (mean standardized effects = 0.21), but reductions in abundance of bacteria via cascading effects, i.e., trophic interaction (mean standardized effects = −0.1). When considering direct and cascading effects together, environmental conditions in urban river bends were found to enhance the abundance of microbial communities, with decreasing magnitude at the higher trophic level. Analogously, the path modeling also indicated the nitrogen transformation potential enhanced by environmental conditions via direct effects, but partly counteracted by trophic interactions via cascading effects. The obtained results could provide a theoretical basis for the regulation and restoration of urban rivers.

Shifts in soil prokaryotic and microeukaryotic communities following a translocation of wet meadows to derelict land

AbstractHuman exploitation of natural resources dictates the need for the sustainable use of lands already in use. To combine the conservation of meadows with land recycling, 13,000 m2 of turf were translocated from a built‐up area to an abandoned quarry. Three Molinion meadows were monitored for three seasons—before the translocation and for two years afterwards. The composition of the main groups of microorganisms—bacteria, archaea, fungi, microfauna, and unicellular algae—was examined to check the stability of soil ecosystem. After observing changes in the ratio of ammonia to nitrate in the translocated turf, the bacterial and archaeal ammonia monooxygenase gene (amoA) copy numbers were quantified. Following the translocation, the α‐diversity of prokaryotes and eukaryotes remained usually similar. The structure of the microbial communities has changed: relative abundance of Acidobacteria (Acidobacteriota) and Mortierellomycota increased, along with fungal saprotrophs, while several other phyla decreased. The number of bacterial amoA gene copies has risen 7‐fold in two years. The slight acidification of the soil had an influence; however, the presumed turf aeration and moisture drop initially impacted the soil communities. In conclusion, turf block translocation preserves diversity. However, cutting turf for transportation followed by dryer conditions at the receptor location lead to a functional switch in microbial communities. Increased activities of ammonia oxidisers and saprotrophs proceeded to nitrification and humus degradation, which may indicate degradation of soil. When translocating wet meadows, it is crucial to ensure the hydrological regime at receptor sites to support long‐term success.

Microbial community shifts induced by plastic and zinc as substitutes of tire abrasion

Aquatic environments serve as a sink for anthropogenic discharges. A significant part of the discharge is tire wear, which is increasingly being released into the environment, causing environmental disasters due to their longevity and the large number of pollutants they contain. Main components of tires are plastic and zinc, which therefore can be used as substitutes for tire abrasion to study the effect on microbial life. We investigate environmentally realistic concentrations of plastic and zinc on a freshwater microeukaryotic community using high-throughput sequencing of the 18S V9 region over a 14-day exposure period. Apart from a generally unchanged diversity upon exposure to zinc and nanoplastics, a change in community structure due to zinc is evident, but not due to nanoplastics. Evidently, nanoplastic particles hardly affect the community, but zinc exposure results in drastic functional abundance shifts concerning the trophic mode. Phototrophic microorganisms were almost completely diminished initially, but photosynthesis recovered. However, the dominant taxa performing photosynthesis changed from bacillariophytes to chlorophytes. While phototrophic organisms are decreasing in the presence of zinc, the mixotrophic fraction initially benefitted and the heterotrophic fraction were benefitting throughout the exposure period. In contrast to lasting changes in taxon composition, the functional community composition is initially strongly imbalanced after application of zinc but returns to the original state.

Early warning of red tides using bacterial and eukaryotic communities in nearshore waters

Anthropogenic discharge activities have increased nutrient pollution in coastal areas, leading to algal blooms and microbial community changes. Particularly, microbial communities could easily be affected with variation in nutrient pollution, and thus offered a promising strategy to predict early red tides warning via microbial community-levels variation and their keystone taxa hysteretic responses to nutrient pollution. Herein high-throughput sequencing technology from 52 samples were used to explore the variation of microbial communities and find the significant tipping points with aggravating nutrient conditions in Xiaoping Island coastal area. Results indicated that bacterial and microeukaryote communities were generally spatial and seasonal heterogeneity and were influenced by the different nutrient conditions. Procrustes test results showed that the comprehensive index of organics polluting (OPI), total nitrogen (TN), inorganic nitrogen (DIN), and total phosphorus (TP) were significantly correlated with the composition of bacteria and microeukaryotes. A SEGMENTED analysis revealed that the threshold of TN, DIN, and NH4–N for bacterial community were 0.23 ± 0.091 mg/L, 0.21 ± 0.084 mg/L, 0.09 ± 0.057 mg/L, respectively. Tipping points for TN, DIN, and NH4–N agreed with the concentration during Ceratium tripos and Skeletonema costatum blooms. Co-occurrence network results found that Planktomarina, Acinetobacter, and Verrucomicrobiaceae were keystone and OPI-discriminatory taxa. The abundant changes of Planktomarina at station A1 were significantly correlated with the development of C. tripos blooms (r = 0.55, p < 0.05), and also significantly correlated with TN, DIN, and NO3–N (r≥|0.55|, p < 0.05). The abundant changes of Acinetobacter and Verrucomicrobiaceae at station C1 were significantly correlated with the development of C. tripos blooms (r ≥ 0.77, p < 0.05), and also significantly correlated with PO4–P (r ≥ 0.64, p < 0.05). The dynamic abundance of keystone taxa showed that the trend of rapid changes could be monitored 1.5 months before the occurrence of red tide. Therefore, this study provides an assessment method for early warning of red tide occurrence and factors that trigger red tide.

Apparent biogeographical trends in Alexandrium blooms for northern Europe: identifying links to climate change and effective adaptive actions

The marine dinoflagellate Alexandrium Halim represents perhaps the most significant and intensively studied genus with respect to species diversity, life history strategies, toxigenicity, biogeographical distribution, and global magnitude and consequences harmful algal blooms (HABs). The socioeconomic impacts, environmental and human health risks, and mitigation strategies for toxigenic Alexandrium blooms have also been explored in recent years. Human adaptive actions based on future scenarios of bloom dynamics and shifts in biogeographical distribution under climate-change parameters remain under development and not yet implemented on a regional scale. In the CoCliME (Co-development of climate services for adaptation to changing marine ecosystems) project these issues were addressed with respect to past, current and anticipated future status of key HAB genera and expected benefits of enhanced monitoring. Data on the distribution and frequency of Alexandrium blooms related to paralytic shellfish toxin (PST) events from key CoCliME Case Study areas, comprising the North Sea and adjacent Kattegat-Skagerrak, Norwegian Sea, and Baltic Sea, and eastern North Atlantic marginal seas, were evaluated in a contemporary and historical context over the past several decades. The first evidence of possible biogeographical expansion of Alexandrium taxa into eastern Arctic gateways was provided from DNA barcoding signatures. Various key climate change indicators, such as salinity, temperature, and water-column stratification, relevant to Alexandrium bloom initiation and development were identified. The possible influence of changing variables on bloom dynamics, magnitude, frequency and spatial and temporal distribution were interpreted in the context of regional ocean climate models. These climate change impact indicators may play key roles in selecting for the occurrence and diversity of Alexandrium species within the broader microeukaryote communities. For example, shifts to higher temperature and lower salinity regimes predicted for the southern North Sea indicate the potential for increased Alexandrium blooms, currently absent from this area. Ecological and socioeconomic impacts of Alexandrium blooms and effects on fisheries and aquaculture resources and coastal ecosystem function are evaluated, and, where feasible, effective adaptation strategies are proposed herein as emerging climate services.

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

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

Assessing the core microbial symbionts of jellyfish in Indonesian and Vietnamese marine lakes

AbstractJellyfish are a well-known component of marine ecosystems. Here, we aimed to assess whether populations of the jellyfish species Mastigias cf. papua and Cassiopea ornata inhabiting different marine lakes and jellyfish species from open water habitat host ‘core’ symbionts and if there is evidence of species-specific host-microbial associations. Compositionally, jellyfishes hosted prokaryotic communities distinct from those found in water samples. All jellyfish samples across habitats and species exhibited a core OTU, assigned to the genus Endozoicomonas. This OTU was particularly abundant (&gt;90% of all sequences) in C. ornata from one Papuan marine lake. Additionally, an OTU assigned to the Entomoplasmatales order was found in all but two jellyfish specimens, and was particularly abundant in marine lake specimens from Berau and Papua, Indonesia. Given the well-known relationship between Endozoicomonas and Symbiodinium spp., we tested for Symbiodinium presence in pooled specimens of M. papua from Berau. Our results showed that OTUs assigned to the genus Symbiodinium accounted for &gt;99% of all sequences in jellyfish-associated microeukaryotic communities; these were closely related to organisms from Symbiodinium clade C. These results suggest the existence of a widespread and abundant jellyfish core symbiont, which may interact with symbiotic Symbiodinium populations to influence host fitness.

Illuminating protist diversity in pitcher plants and bromeliad tanks.

Many species of plants have evolved structures called phytotelmata that store water and trap detritus and prey. These structures house diverse communities of organisms, the inquiline microbiome, that aids breakdown of litter and prey. The invertebrate and bacterial food webs in these systems are well characterized, but less is known about microbial eukaryotic community dynamics. In this study we focus on microbes in the SAR clade (Stramenopila, Alveolata, Rhizaria) inhabiting phytotelmata. Using small subunit rDNA amplicon sequencing from repeated temporal and geographic samples of wild and cultivated plants across the Northeast U.S.A., we demonstrate that communities are variable within and between host plant type. Across habitats, communities from tropical bromeliads grown in a single room of a greenhouse were nearly as heterogeneous as wild pitcher plants spread across hundreds of kilometers. At the scale of pitcher plants in a single bog, analyses of samples from three time points suggest that seasonality is a major driver of protist community structure, with variable spring communities transitioning to more homogeneous communities that resemble the surrounding habitat. Our results indicate that protist communities in phytotelmata are variable, likely due to stochastic founder events and colonization/competition dynamics, leading to tremendous heterogeneity in inquiline microeukaryotic communities.

Soil pH Determines the Spatial Distribution, Assembly Processes, and Co-existence Networks of Microeukaryotic Community in Wheat Fields of the North China Plain.

Soil microeukaryotes play a pivotal role in soil nutrient cycling and crop growth in agroecosystems. However, knowledge of microeukaryotic community distribution patterns, assembly processes, and co-existence networks is greatly limited. Here, microbial eukaryotes in bulk and rhizosphere soils of the North China Plain were investigated. The results showed that soil pH was the driving factor for the microeukaryotic community composition in the bulk and rhizosphere soils. The soil microeukaryotic community could significantly differ between alkaline and acidic soils. The results indicated that the soil pH had a stronger effect than niche differences on community composition. Partial Mantel tests showed that soil pH and spatial distance had similar effects on the microeukaryotic community composition in the bulk soil. However, in the rhizosphere soil, spatial distance had a stronger effect than soil pH. Infer Community Assembly Mechanisms by Phylogenetic bin-based null model (iCAMP) analysis revealed that drift was the most important process driving microeukaryotic community assembly, with an average relative importance of 37.4–71.1%. Dispersal limitation displayed slightly greater importance in alkaline rhizosphere than in alkaline bulk soils. Meanwhile, the opposite trend was observed in acidic soils. In addition, the contribution of each assembly process to each iCAMP lineage “bin” varied according to the acidic or alkaline conditions of the soil and the niche environment. High proportions of positive links were found within the four ecological networks. Alkaline soil networks, especially the alkaline bulk soil network, showed greater complexity than the acidic soil networks. Natural connectivity analysis revealed that the rhizosphere community had a greater stability than the bulk soil community in alkaline soil. This study provides a foundation for understanding the potential roles of microbial eukaryotes in agricultural soil ecosystem functioning.

Depth induced assembly discrepancy of multitrophic microbial communities affect microbial nitrogen transformation processes in river cross-sections

Understanding how the structures and functions of bacterial and microeukaryotic communities vary within cross-sections will improve managements aimed at restoring river ecological functions. However, no comprehensive investigation has examined how microbial community characteristics vary within cross-sections, which makes the accurate calculation and prediction of microbial metabolic processing of substances in rivers difficult. Here, the distributions, co-occurrence networks, and assemblies of bacterial and microeukaryotic communities and their feedback to nitrogen transformation in cross-sections of the Yangtze River were studied by coupling ecological theory, biogeochemistry, and DNA meta-barcoding methods. The study found that depth in cross-sections was the primary driving factor regulating the composition of sediment bacterial and microeukaryotic communities. Co-occurrence network analysis indicated that the effect of bacteria on the co-occurrence network decreased and the network become more simplified and instability with depth in river cross-sections. Quantified using the β-nearest taxon index, the H2 layer sediment (depth 10–20 m) displayed the largest variation in selection processes for microbial assemblies, while homogeneous selection and homogenizing dispersal contributed most to the bacterial and microeukaryotic assemblies in the H3 layer (depth >20 m). Cross-sectional depth and denitrification genes had a significant quadratic correlation, with the highest microbial nitrogen-removal potential occurring in the H2 layer sediment. Structural equation models showed that the sediment nitrogen distributions were regulated by distinct environmental pathways at different depths, and that the H2 layer sediment was primary driven by bacterial community. In this layer, river cross-sectional depth influenced nitrogen transformation by regulating the distribution of sediment particle sizes, which then influenced the assembly of the multitrophic microbial communities. This study will improve river management by clarifying the importance of cross-sectional depth to the ecological function of rivers.

Exploring the taxonomic and functional diversity of marine benthic micro-Eukaryotes along the Red Sea coast of Jeddah city

BackgroundsDiverse marine habitats along Jeddah's Red Sea coast support rich biodiversity. Few studies have been done on its diverse communities, especially its microbial counterparts. Metagenomic analysis of marine benthic micro-eukaryotic communities was performed for the first time on the Red Sea coast of Jeddah. This research looks into their community structure and metabolic potential. MethodsNext-generation sequencing was used to examine the micro-eukaryotic communities of seven sedimentary soil samples from four Jeddah coast locations. After isolating DNA from seven benthic sedimentary soil samples, the 18S rDNA V4 regions were amplified and sequenced on the Illumina MiSeq. It was also verified using an Agilent Technologies 2100 Bioanalyzer with a DNA 1000 chip (Agilent Technologies, Fisher Scientific). A standard curve of fluorescence readings generated by qPCR quantification using the Illumina library was achieved using the GS FLX library. Metagenomic data analysis was used to evaluate the microbial communities' biochemical and enzymatic allocations in studied samples. ResultsBlast analysis showed that the top ten phyla were Annelida, Eukaryota, Diatomea, Porifera, Phragmoplastophyta, Arthropoda, Dinoflagellata, Xenacoelomorpha Nematoda, and uncultured. Annelida was also found in the highest percentage (93%), in the sample M followed by Porifera (64%), the most abundant in the control sample then Eukaryotes (61%), Phragmatoplastophyta (55%), Arthropoda, and Diatomea (the least common) (32%). community diversity analysis: using Shannon and inverse Simpson indices showed sediment composition to be effective. Also, PICRUST2 indicated that the most abundant pathways were pyruvate fermentation to isobutanol, pyrimidine deoxyribonucleotide phosphorylation, adenosine ribonucleotide de novo biosynthesis, guanosine ribonucleotide de novo biosynthesis, NAD salvage pathway I, the super pathway of glyoxylate bypass and aerobic respiration I (cytochrome c). ConclusionResults showed that high throughput metagenomics could reveal species diversity and estimate gene profiles. Environmental factors appear to be more important than geographic variation in determining the structure of these microbial communities. This study provides the first report of marine benthic micro-eukaryotic communities found on the Red Sea coast of Jeddah and will serve as a good platform for future research.

The Effects of DNA Extraction Kits and Primers on Prokaryotic and Eukaryotic Microbial Community in Freshwater Sediments.

DNA based sequencing technology has revolutionized the field of microbial ecology and environmental studies. However, biases can be introduced at all experimental steps and, thus, affect the interpretation of microbial community. So far, previous studies on the biases introduced from the key steps of DNA extraction and primer sets mainly focused on the bacterial communities in soil or sediment samples, while little is known about the effect on the eukaryotic microbial communities. Here, we studied the effects of three different DNA extraction kits on both prokaryotic and micro-eukaryotic communities by 16S and 18S rRNA gene amplicon sequencing, and further disentangled the influence of primer choice on the micro-eukaryotic communities. Our results showed that the FastDNA SPIN Kit for Soil and DNeasy PowerSoil Kit produced much higher DNA yield with good reproducibility, and observed more eukaryotic OTUs compared to the MinkaGene DNA extraction kit, but all three kits exhibited comparable ability in recovering bacterial alpha diversity. Of the two primer sets, both targeting the V4 region of the 18S rRNA gene, the TAR primer set detected higher number of unique OTUs than the EK primer set, while the EK primer set resulted in longer amplicons and better reproducibility between replicates. Based on our findings, we recommend using the DNeasy PowerSoil Kit with the EK primer set to capture the abundant micro-eukaryotic taxa from freshwater sediment samples. If a more complete picture of the eukaryotic microbial community is desired, the TAR primer set in combination with the FastDNA SPIN Kit is more efficient in this study.

Community assembly of microbial habitat generalists and specialists in urban aquatic ecosystems explained more by habitat type than pollution gradient

Urban freshwater ecosystems have important ecosystem functions, provide habitats for diverse microbial communities and are susceptible to multiple interconnected factors such as environmental pollution. Despite the ecological significance of bacteria and microeukaryotes, little is known about how their community assembly responds to various environmental factors across water and sediment habitats and ecological processes shaping them. Here, environmental DNA-based approaches were used to investigate the community assembly processes of bacteria and microeukaryotes (including habitat generalists and specialists) in urban water and sediment across an urban-pollution gradient in Wuhan, central China. The diversity, community composition and potential function of bacteria and microeukaryotes showed significantly stronger variation between water and sediment than across an urban pollution gradient. Although, bacterial and microeukaryotic community assemblies were dominated by strong selection processes in both water and sediment habitats, but a contrasting community assembly mechanism was identified between habitat generalists and specialists. Bacterial and microeukaryotic communities showed a greater response to physicochemical variability in water, while a strong distance-decay relationship was found in sediment. Further, cross-kingdom microbial network analysis revealed strong modular associations of bacteria and microeukaryotes, meanwhile, microeukaryotic habitat specialists might be keystone, but generalists have higher proportion of connections in the networks. This study provides significant insights into the response of bacteria and microeukaryotes to different urban pollutions between water and sediment, and the ecological processes structuring microbial community dynamics across habitat types under anthropogenic disturbances.

New Contribution to the Diversity of the Anaerobic Genus Metopus (Ciliophora, Armophorea), With Descriptions of Three New Marine Species

Armophorean ciliates constitute an important component of microeukaryotic community in anaerobic or hypoxic environments. Yet, their diversity remains poorly known due to under-sampling or the scarcity of knowledge. In this study, three metopid ciliates, i.e., Metopus paraes sp. n., Metopus spiculatus sp. n., and Metopus parapellitus sp. n., collected from coastal sediments in Qingdao and Rizhao, China, were investigated using live observation, protargol staining, and molecular phylogenetic methods. M. paraes sp. n. can be distinguished by its long caudal cilia. M. spiculatus sp. n. resembles M. vestitus in many ways, but differs mainly in having a beak-like preoral dome end and a conspicuous tail. The most remarkable features of M. parapellitus sp. n. include an ovate body shape, caudal cilia located at the rear end and right posterior body, and an adoral zone that never extends onto the dorsal surface. Sequence divergences supported the species identification of these three species. Phylogenetic analyses confirmed that the Metopus is not monophyletic, and first revealed that all marine species of Metopus form a well-supported clade. The clustering of these marine forms with M. es (type species) is not rejected by the AU test, which infers that the marine clade represents the genus Metopus together with M. es.

Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi

Intensification of fish farming practices is being driven by the demand for increased food production to support a rapidly growing global human population, particularly in lower-middle income countries. Intensification of production, however, increases the risk of disease outbreaks and thus the likelihood for crop losses. The microbial communities that colonise the skin mucosal surface of fish are poorly understood, but are important in maintaining fish health and resistance against disease. This skin microbial community is susceptible to disruption through stressors associated with transport, handling and the environment of intensive practices, and this risks the propagation of disease-causing pathogens. In this study, we characterised the microbial assemblages found on tilapia skin — the most widely farmed finfish globally — and in the surrounding water of seven earthen aquaculture ponds from two pond systems in distinct geographic regions in Malawi. Metabarcoding approaches were used to sequence the prokaryotic and microeukaryotic communities. We found 92% of prokaryotic amplicon sequence variants were common to both skin and water samples. Differentially enriched and core taxa, however, differed between the skin and water samples. In tilapia skin, Cetobacterium, Paucibacter, Pseudomonas and Comamonadaceae were enriched, whereas, the cyanobacteria Cyanobium, Microcystis and/or Synechocystis, and the diatom Cyclotella, were most prevalent in pond water. Ponds that clustered together according to their water prokaryotic communities also had similar microeukaryotic communities indicating strong environmental influences on prokaryotic and microeukaryotic community structures. While strong site-specific clustering was observed in pond water, the grouping of tilapia skin prokaryotes by pond site was less distinct, suggesting fish microbiota have a greater buffering capacity against environmental influences. The characterised diversity, structure and variance of microbial communities associated with tilapia culture in Malawi provide the baseline for studies on how future intensification practices may lead to microbial dysbiosis and disease onset.

Microbial stowaways: Waterbirds as dispersal vectors of aquatic pro‐ and microeukaryotic communities

AbstractAimWaterbirds are important dispersal vectors of multicellular organisms; however, no study to date has focused on their potential role in dispersing aquatic microbial communities. We explicitly studied endozoochory of prokaryotes and unicellular microeukaryotes by waterbirds using DNA metabarcoding. By directly comparing the dispersed set of organisms to the source pool of a natural metacommunity, we aimed at a realistic estimate of the importance of waterbird zoochory for natural microbial communities.LocationTemporary saline soda pans in Austria and Hungary.TaxonProkaryotes and unicellular microeukaryotes.MethodsIn 2017 and 2018, water samples were collected from a network of 25 temporary ponds along with fresh droppings of five waterbird species including the dominant greylag goose (Anser anser). Prokaryotic and microeukaryotic communities were identified via 16S and 18S rRNA gene amplicon sequencing. After quality filtering of sequence reads, pro‐ and microeukaryotic amplicon sequence variant (ASV) compositions were compared between the aquatic and dropping samples, across years and waterbird species.Results28% of the dominant aquatic prokaryotic and 19% of the microeukaryotic ASVs were transported by A. anser. ASV richness was lower, but compositional variation was higher in A. anser droppings than in aquatic communities, probably resulting from stochastic pick‐up from multiple aquatic habitats. The composition of prokaryotic ASVs in bird droppings differed among the 2 years and reflected the actual aquatic communities. The dispersed set of microbes were largely similar among the waterbird species except for the planktivore filter‐feeder northern shoveler (Spatula clypeata), which dispersed more microeukaryotes than the other waterbirds.Main conclusionsUsing an amplicon sequencing approach to characterize aquatic microorganisms in waterbird droppings and in the associated environment, our study provides strong evidence for endozoochory of natural communities. These results imply that waterbirds may be crucial in maintaining ecological connectivity between aquatic habitats at the level of microbial communities.

Biogeography of Micro-Eukaryotic Communities in Sediment of Thermokarst Lakes Are Jointly Controlled by Spatial, Climatic, and Physicochemical Factors Across the Qinghai-Tibet Plateau

Thermokarst lakes are formed following ice-rich permafrost thaw and widely distribute in the cold regions with high latitude and elevation. However, the micro-eukaryotic communities (MECs) in thermokarst lakes are not well studied. Employing 18S rRNA gene sequencing, we assessed the biogeography of MECs and their driving factors in sediments of thermokarst lakes across the Qinghai-Tibet Plateau (QTP). Results showed that Diatom, Gastrotricha, Nematozoa, Ciliophora, and Cercozoa were dominant lineages in relative abundance and OTU richness. MECs varied substantially across the lakes in terms of diversity and composition. Structural equation modeling and mantel test showed that both OTU richness and community structure of MECs had close relationships with spatial factors, climatic factors, and sediment properties, particularly with latitude, mean annual precipitation, pH, as well as nutrient concentrations and stoichiometric ratios. Moreover, different groups of microbial eukaryotes (taxonomic groups and co-occurrence modules) responded differentially to the measured environmental variables. The results suggested that the biogeography of sediment MECs of thermokarst lakes on the QTP were jointly controlled by spatial and climatic factors as well as sediment properties. This study provides the first view of the composition, diversity, and underlying drivers of MECs dynamic in surface sediments of thermokarst lakes across the QTP.

Microeukaryotic Community Shifting Along a Lentic-Lotic Continuum

As an important regulator of ecosystem functions in river systems, microeukaryotes play an important role in energy and material conversion, yet little is known about the shift along a lentic-lotic continuum. In this study, the 18S rRNA genes sequencing was used to identify the microeukaryotic communities at 82 sites along a lentic-lotic continuum with the aim of understanding the impact of upstream inlet river on microeukaryotic communities in Baiyang Lake (BYD) and its downstream. Our results showed that the upstream inlet river affected the diversity and community composition of microeukaryotes in BYD and downstream rivers, and environmental variables greatly affected the composition of microeukaryotic community. The community composition in BYD had lower variabilities. Co-occurrence network analysis revealed that the network was non-random and clearly parsed into three modules, and different modules were relatively more abundant to a particular area. As keystone taxa, some nodes of the upstream microeukaryotic network played an important role in structuring network and maintaining the stability of the ecosystem. In BYD and downstream, the microeukaryotic network was highly fragmented, and the loss of keystone taxa would have an adverse impact on the integrity and function of the microeukaryotic community. Microeukaryotes had strong tendencies to co-occur, which may contribute to the stability and resilience of microeukaryotic communities. Overall, these findings extend the current understanding of the diversity and community composition of microeukaryotic along a lentic-lotic continuum.