Eukaryotic 18S rRNA Research Articles

Exploring the Genetic and Morphological Diversity of Argulus Ectoparasite Infecting the Aquaculture and Ornamental Fish in Tripura

Background: The present study screened for isolation of Argulus spp. infecting fishes based on the report of causing substantial economic losses both in aquaculture ponds and ornamental shops across several locations in Tripura, India. Methods: Identification of Argulus spp. was performed based on morphological, and molecular techniques. The molecular identification of Argulus spp. was performed using universal eukaryotic 18S rRNA genetic markers. Prevalence analysis was performed to determine the infestation rate of Argulus spp. in different hosts. Result: Seven A. japonicus, one A. coregoni and one A. foliaceus isolates were identified based on molecular and morphological features. In the present study it was found that A. japonicus infected a wide range of host species, including Goldfish, Milky Koi carp, Mrigal, Rohu, Catla and Subunkin. It was the first instance of A. japonicus infecting milky koi carp both in India and globally. On the other hand, A. foliaceus and A. coregoni infected only tiger oscar and goldfish respectively, indicating a rather narrow range of host diversity.

National-scale distribution of protists associated with sorghum leaves and roots.

Protists, as integral constituents of the plant microbiome, are posited to confer substantial benefits to plant health and performance. Despite their significance, protists have received considerably less attention compared to other constituents of the plant microbiome, such as bacteria and fungi. To investigate the diversity and community structure of protists in sorghum leaves and roots, we employed amplicon sequencing of the eukaryotic 18S rRNA gene in 563 leaf and root samples collected from 57 locations across China. We found significant differences in the diversity and community structure of protists in sorghum leaves and roots. The leaf was taxonomically dominated by Evosea, Cercozoa and Ciliophora, while the root was dominated by Endomyxa, Cercozoa and Oomycota. The functional taxa of protists exhibited notable differences between leaves and roots, with the former being predominantly occupied by consumers and the latter by parasites. The community composition of protists in the leaf was predominantly influenced by mean annual precipitation, whereas soil pH played a more significant role in the root. The present study identified the most abundant and distributed protists in sorghum leaves and roots and elucidated the underlying factors that govern their community structure. The present study offers a novel perspective on the factors that shape plant-associated protist communities and their potential roles in enhancing the functionality of plant ecosystems.

The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins (Pygoscelis papua) in their natural environment

The microbiome is a key factor in the health, well-being, and success of vertebrates, contributing to the adaptive capacity of the host. However, the impact of geographic and biotic factors that may affect the microbiome of wild birds in polar environments is not well defined. To address this, we determined the bacterial 16S rRNA gene sequence profiles in faecal samples from pygoscelid penguin populations in the Scotia Arc, focusing on gentoo penguins. This mesopredatory group breeds in defined colonies across a wide geographic range. Since diet could influence microbiome structure, we extracted dietary profiles from a eukaryotic 18S rRNA gene sequence profile. The bacterial microbiome profiles were considered in the context of a diverse set of environmental and ecological measures. Integrating wide geographic sampling with bacterial 16S and eukaryotic 18S rRNA gene sequencing of over 350 faecal samples identified associations between the microbiome profile and a suite of geographic and ecological factors. Microbiome profiles differed according to host species, colony identity, distance between colonies, and diet. Interestingly there was also a relationship between the proportion of host DNA (in relation to total 18S rRNA gene signal) and the microbiome, which may reflect gut passage time. Colony identity provided the strongest association with differences in microbiome profiles indicating that local factors play a key role in the microbiome structure of these polar seabirds. This may reflect the influence of local transfer of microbes either via faecal-oral routes, during chick feeding or other close contact events. Other factors including diet and host species also associate with variation in microbiome profile, and in at least some locations, the microbiome composition varies considerably between individuals. Given the variation in penguin microbiomes associated with diverse factors there is potential for disruption of microbiome associations at a local scale that could influence host health, productivity, and immunological competence. The microbiome represents a sensitive indicator of changing conditions, and the implications of any changes need to be considered in the wider context of environmental change and other stressors.

Distinct changes in tomato-associated multi-kingdom microbiomes during Meloidogyne incognita parasitism

BackgroundThe interplay between root-knot nematode (RKN) parasitism and the complex web of host-associated microbiota has been recognized as pivotal for effective management of the pest. However, studies assessing this relationship have focussed on the bacterial and fungal communities, neglecting the unicellular eukaryotic members. Here, we employed amplicon sequencing analysis of the bacterial 16S rRNA, fungal ITS and eukaryotic 18S rRNA genes, and comprehensively examined how the microbiome composition, diversity and networking developed with time in the rhizospheres and roots of RKN-inoculated and non-inoculated tomato plants.ResultsAs expected, infection with the RKN Meloidogyne incognita decreased plant growth. At individual timepoints, we found distinct bacterial, fungal and eukaryote community structures in the RKN-inoculated and non-inoculated rhizospheres and roots, and RKN inoculation affected several taxa in the root-associated microbiome differentially. Correlation analysis revealed several bacterial and fungal and few protist taxa that correlated negatively or positively with M. incognita. Moreover, network analysis using bacterial, fungal and eukaryotic data revealed more dynamic networks with higher robustness to disturbances in the RKN-inoculated than in the non-inoculated rhizospheres/roots. Hub taxa displayed a noticeable successional pattern that coincided with different phases of M. incognita parasitism. We found that fungal hubs had strong negative correlations with bacteria and eukaryotes, while positive correlations characterized hub members within individual kingdoms.ConclusionOur results reveal dynamic tomato-associated microbiomes that develop along different trajectories in plants suffering M. incognita infestation and non-infested plants. Overall, the results identify stronger associations between RKN and bacterial and fungal taxa than between eukaryotic taxa and RKN, suggesting that fungal and bacterial communities could play a larger role in the regulation of RKN. The study identifies several putative RKN-antagonistic bacterial and fungal taxa and confirms the antagonistic potential previously identified in other taxa.

Environmental DNA reveals fine‐scale spatial and temporal variation of marine mammals and their prey species in a Scottish marine protected area

AbstractMarine mammal foraging grounds are popular focal points for marine protected area (MPA) implementation, despite being temporally dynamic, requiring continuous monitoring to infer prey availability and abundance. Marine mammal distributions are assumed to be driven by their prey in foraging areas, but limited understanding of prey distributions often prevents us from exploring how shifting prey availability impacts both seasonal and long‐term marine mammal distributions. Environmental DNA (eDNA) metabarcoding could enhance the understanding of marine mammal habitat use in relation to their prey through simultaneous monitoring of both. However, eDNA applications focused on marine mammals or predator–prey dynamics have been limited to date. In this study, we assess spatiotemporal changes in the distribution and abundance of cetaceans, minke whales (Balaenoptera acutorostrata), bottlenose dolphins (Tursiops truncatus) and harbor porpoises (Phocoena phocoena) in relation to key prey species in a newly established MPA, employing eDNA metabarcoding. We recovered 105 molecular operational taxonomic units (OTUs) from marine vertebrates using two primer sets targeting 12S and 16S genes, along with 112 OTUs from a broader eukaryotic primer set targeting 18S rRNA. Overall, key forage fish prey species, sandeels and clupeids, were the most abundant teleost fishes detected, although their availability varied temporally and with distance from shore. We also found clear spatial partitioning between coastal bottlenose dolphins and the more pelagic minke whales and harbor porpoises, paralleling availability of their main prey species. Other species of conservation interest were also detected including the critically endangered European eel (Anguilla anguilla), Atlantic bluefin tuna (Thunnus thynnus), and the invasive pink salmon (Oncorhynchus gorbuscha). This study demonstrates the application of eDNA to detect spatiotemporal trends in the occurrence and abundance of cetacean predators and their prey, furthering our understanding of fine‐scale habitat use within MPAs. Future long‐term monitoring of predator–prey dynamics with eDNA could improve our ability to predict climate‐induced shifts in foraging grounds and enhance rapid responses with appropriate management actions.

Prevalence and Preferred Niche of Small Eukaryotes with Mixotrophic Potentials in the Global Ocean.

Unicellular eukaryotes that are capable of phago-mixotrophy in the ocean compete for inorganic nutrients and light with autotrophs, and for bacterial prey with heterotrophs. In this study, we ask what the overall prevalence of eukaryotic mixotrophs in the vast open ocean is, and how the availability of inorganic nutrients, light, and prey affects their relative success. We utilized the Tara Oceans eukaryotic 18S rRNA gene and environmental context variables dataset to conduct a large-scale field analysis. We also performed isolate-based culture experiments to verify growth and nutritional resource relationships for representative mixotrophic taxa. The field analysis suggested that the overall prevalence of mixotrophs were negatively correlated with nutrient concentrations and positively associated with light availability. Concentrations of heterotrophic bacteria as a single variable also presented a positive correlation with mixotrophic prevalence, but to a lesser extent. On the other hand, the culture experiments demonstrated a taxa-specific relationship between mixotrophic growth and nutrition resources, i.e., the growth of one group was significantly dependent on light availability, while the other group was less affected by light when they received sufficient prey. Both groups were capable of growing efficiently with low inorganic nutrients when receiving sufficient prey and light. Therefore, our field analysis and culture experiments both suggest that phago-mixotrophy for ocean eukaryotes is seemingly an efficient strategy to compensate for nutrient deficiency but unnecessary to compensate for light scarcity. This study collectively revealed a close relationship between abiotic and biotic nutritional resources and the prevalence of trophic strategies, shedding light on the importance of light and nutrients for determining the competitive success of mixotrophs versus autotrophic and heterotrophic eukaryotes in the ocean.

First report of Paracapillaria philippinensis infection in flowerhorn cichlid in India.

The flowerhorn cichlid is a popular ornamental fish in many Asian countries. The present study reports the occurrence of Paracapillaria philippinensis (Chitwood et al., 1968), a parasitic nematode in flowerhorn cichlid (Cichlasoma sp.) from south India. The infected fish demonstrated clinical symptoms viz. dark coloration, poor appetite, lethargy, erratic swimming, and white stringy faeces. Microscopic observation of the intestinal content and faeces revealed the presence of adult worms, larvae, and unembryonated eggs. PCR amplification of eukaryotic 18S rRNA, P. philippinensis-specific SSU rRNA gene, and the subsequent sequence analysis confirmed the species identity as P. philippinensis. The generated sequences were submitted in the GenBank, NCBI, under the accession numbers, MK895507.1, MK895446.1, MW144993.1, and OR685675.1. This is the first scientific report of P. philippinensis in fish from India, and it confirms that the flowerhorn cichlid can act as a definitive host for P. philippinensis. This report alerts fish handlers and enthusiasts to undertake suitable precautionary measures while handling live flowerhorn cichlids to prevent possible transmission of P. Philippinensis, which has the potential to infect humans causing intestinal capillariasis.

Seasonal dynamics of gut microbiome: A study of multi-kingdom microbiota of earthworm gut in an urban park

Earthworms play an important role in maintaining terrestrial ecosystem function. In urban areas, earthworms mainly inhabit parks where they function through feeding and excretion of soil elements and nutrient turnover. Seasonal diet strongly alters the earthworm gut microbiome and thus affects this ecological process, but the seasonal variation of eukaryotes is still poorly described. In this study, we obtained earthworm samples from three seasons: summer, autumn and winter, assessing the gut microbiome of earthworms using bacterial 16S rRNA and eukaryotic 18S rRNA gene amplicon sequencing techniques. We identified biomarkers that significantly change with seasons and analyzed eukaryotic-bacterial interactions under seasonal variation through inter-kingdom networks. The results of this study showed that season significantly influenced the diversity of earthworm gut bacterial community, while the diversity of eukaryotic community was relatively stable. Inter-kingdom molecular ecological network analysis revealed high degree of positive or negative interactions between fungi and bacteria, protists and bacteria, and fungi and protists as keystone taxonomies divided the network into several modules. In summary, the gut eukaryotic community is more stable than the bacterial community throughout the seasons, and it has shown to maintain season-long homeostasis in the earthworm gut.

Filter no more: A modified plankton sampler for rapid in‐water eDNA capture

Abstract The combination of an efficient sampling method and high‐throughput analysis of environmental DNA (eDNA) can be a powerful approach for characterising biodiversity across aquatic ecosystems. Plankton net tows are one of the oldest, simplest, and least expensive methods for seston and eDNA collection, but require laborious filtration steps which often lead to clogging and/or the introduction of contaminants. In this study, we used a cruising speed net (CSN) device enabling the collection of seston‐derived eDNA at 5 knots speed combined with a novel modified cod‐end with 20 μm nylon mesh inserts enabling eDNA capture while towing. We compared the performance of the CSN sampling protocol with the original conventional filtration of water sample versus the modified cod‐end. Samples were collected in parallel horizontal tows along New Zealand's North‐Eastern coastline. Concentrated water was filtered on conventional 5 μm cellulose acetate membranes, while the 20 μm nylon mesh inserts were immediately isolated post‐towing. Metabarcoding of bacterial 16S rRNA, eukaryotic nuclear 18S rRNA and mitochondrial COI genes, revealed no significant difference in alpha diversity between filtration techniques. In terms of community composition, a clear and significant shift could be observed between sampling sites and environments. Significant differences could be detected between filtration methods for 16S and COI markers, likely driven by fine‐scale differences at more turbid sheltered sites. Nonetheless, each technique could detect shifts in communities between sites and environments with similar sensitivity. Our results demonstrate the promising potential of the modified cod‐end to enable practical and cost‐effective isolation of eDNA‐derived biodiversity data from any vessel types (at ≤5 knots) across a large range of aquatic ecosystems and biogeographic scales.

Precipitation seasonality and soil pH drive the large-scale distribution of soil invertebrate communities in agricultural ecosystems.

Soil invertebrates contribute significantly to vital ecosystem functions such as the breakdown of organic matter and cycling of essential nutrients, but our knowledge of their large-scale distribution in agricultural systems is limited, which hinders our ability to robustly predict how they will respond to future global change scenarios. Here, we employed metabarcoding analysis of eukaryotic 18S rRNA genes to examine the diversity and community composition of invertebrates in 528 sorghum rhizosphere and bulk soils, collected from 53 experimental field sites across China. Our results revealed that Nematoda, Arthropoda, and Annelida were the dominant soil invertebrate groups in agroecosystems. Among all climatic and soil parameters we examined, precipitation seasonality (i.e. the irregular distribution of precipitation during a normal year) had the strongest relationship with the richness of soil invertebrates, with an increase in soil invertebrate richness predicted with increasing precipitation seasonality. Mean annual precipitation and soil pH were the most important predictors of soil invertebrate community structure, with numerous invertebrate phylotypes showing either significantly positive or negative relationships with these two variables. Our findings suggest that shifts in precipitation patterns and soil pH, induced by future climate change and agricultural practices, will have important consequences for the distribution of soil invertebrate communities, with implications for agricultural ecosystem sustainability.

Selecting 16S rRNA Primers for Microbiome Analysis in a Host-Microbe System: The Case of the Jellyfish Rhopilema nomadica.

Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remains a major decision when initiating any new microbiome study. Based on a detailed literature survey of studies focusing on cnidarian microbiomes, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfish Rhopilema nomadica as a model. Although all primers exhibit a similar pattern in bacterial community composition, the performance of the V3V4 primer set was superior to V1V2 and V4V5. The V1V2 primers misclassified bacteria from the Bacilli class and exhibited low classification resolution for Rickettsiales, which represent the second most abundant 16S rRNA gene sequence in all the primers. The V4V5 primer set detected almost the same community composition as the V3V4, but the ability of these primers to also amplify the eukaryotic 18S rRNA gene may hinder bacterial community observations. However, after overcoming the challenges possessed by each one of those primers, we found that all three of them show very similar bacterial community dynamics and compositions. Nevertheless, based on our results, we propose that the V3V4 primer set is potentially the most suitable for studying jellyfish-associated bacterial communities. Our results suggest that, at least for jellyfish samples, it may be feasible to directly compare microbial community estimates from different studies, each using different primers but otherwise similar experimental protocols. More generally, we recommend specifically testing different primers for each new organism or system as a prelude to large-scale 16S rRNA gene amplicon analyses, especially of previously unstudied host-microbe associations.

Assessing the Fate of Superparamagnetic Iron Oxide Nanoparticles Carrying Usnic Acid as Chemical Cargo on the Soil Microbial Community.

In the present study we evaluate the effect of superparamagnetic iron oxide nanoparticles (SPIONs) carrying usnic acid (UA) as chemical cargo on the soil microbial community in a dystrophic red latosol (oxysol). Herein, 500 ppm UA or SPIONs-framework carrying UA were diluted in sterile ultrapure deionized water and applied by hand sprayer on the top of the soil. The experiment was conducted in a growth chamber at 25 °C, with a relative humidity of 80% and a 16 h/8 h light-dark cycle (600 lx light intensity) for 30 days. Sterile ultrapure deionized water was used as the negative control; uncapped and oleic acid (OA) capped SPIONs were also tested to assess their potential effects. Magnetic nanostructures were synthesized by a coprecipitation method and characterized by scanning and transmission electron microscopy (SEM and TEM), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), zeta potential, hydrodynamic diameter, magnetic measurements, and release kinetics of chemical cargo. Uncapped and OA-capped SPIONs did not significantly affect soil microbial community. Our results showed an impairment in the soil microbial community exposed to free UA, leading to a general decrease in negative effects on soil-based parameters when bioactive was loaded into the nanoscale magnetic carrier. Besides, compared to control, the free UA caused a significant decrease in microbial biomass C (39%), on the activity of acid protease (59%), and acid phosphatase (23%) enzymes, respectively. Free UA also reduced eukaryotic 18S rRNA gene abundance, suggesting a major impact on fungi. Our findings indicate that SPIONs as bioherbicide nanocarriers can reduce the negative impacts on soil. Therefore, nanoenabled biocides may improve agricultural productivity, which is important for food security due to the need of increasing food production.

Eco-Plastics in the Sea: Succession of Micro- and Macro-Fouling on a Biodegradable Polymer Augmented With Oyster Shell

Impacts of Marine Plastic Debris (MPD) on marine ecosystems are among the most critical environmental concerns of the past three decades. Virgin plastic is often cheaper to manufacture than recycled plastics, increasing rates of plastic released into the environment and thereby impacting ecosystem health and functioning. Along with other environmental effects, MPD can serve as a vector for marine hitchhikers, facilitating unwanted organisms’ transport and subsequent spread. Consequently, there is a growing demand for more eco-friendly replacements of conventional plastic polymers, ideally with fit-for-purpose properties and a well-understood life cycle. We enriched polybutylene succinate (PBS) with three different concentrations of oyster shell to investigate the dynamics of biofouling formation over 18 weeks at the Nelson Marina, Aotearoa/New Zealand. Our study focused on oyster shell concentration as a determinant of fouling assemblages over time. While generally considered as a waste in the aquaculture sector, we used oyster shells as a variable of interest to investigate their potential for both, environmental and economic benefits. Using bacterial 16S and eukaryotic 18S rRNA gene metabarcoding, our results revealed that following immersion in seawater, time played a more critical role than substrate type in driving biofouling community structures over the study period. In total, 33 putative non-indigenous species (NIS) and 41 bacterial families with putative plastic-degrading capability were detected on the different substrates. Our analysis of NIS recruitment revealed a lower contribution of NIS on shell-enriched substrates than unadulterated polymers samples. In contrast, the different concentrations of oyster shells did not affect the specific recruitment of bacterial degraders. Taken together, our results suggest that bio-based polymers and composites with increased potential for biodegradability, recyclability, and aptitude for the selective recruitment of marine invertebrates might offer a sustainable alternative to conventional polymers, assisting to mitigate the numerous impacts associated with MPD.

Phylogenetic diversity and spatiotemporal dynamics of bacterial and microeukaryotic plankton communities in Gwangyang Bay of the Korean Peninsula

Nutrient dynamics function globally, flowing from rivers to the ocean (estuarine–coastal zone), and are vulnerable to climate change. Microbial habitats can be affected by marine nutrient dynamics and may provide a clue to predict microbial responses to environmental heterogeneity in estuarine–coastal zones. We surveyed surface seawater in Gwangyang Bay, a semi-enclosed estuary in Korea, from 2016 to 2018 using a metabarcoding approach with prokaryotic 16S and eukaryotic 18S rRNA genes. Bacterial and microeukaryotic communities in these waters showed distinct local communities in response to environmental heterogeneity and community transition at spatiotemporal scales in the estuarine–coastal zone. The relative abundance of prokaryotic and eukaryotic operational taxonomic units suggested a microbial trophic interaction in the Gwangyang Bay waters. We found that the community assembly process in prokaryotic communities was primarily influenced by biological interaction (immigration–emigration), whereas that in eukaryotic communities was more affected by environmental stress (habitat specificity) rather than by biotic factors. Our findings in the Gwangyang Bay waters may provide information on underlying (biotic or abiotic) factors of the assembly process in microbial communities in the estuarine–coastal zone.

Effects of freshwater salinization on a salt‐naïve planktonic eukaryote community

AbstractFreshwater salinization is a widespread issue, but evidence of ecological effects on aquatic communities remains scarce. We experimentally exposed salt‐naive plankton communities of a north‐temperate, freshwater lake to a gradient of chloride (Cl−) concentration (0.27–1400 mg Cl L−1) with in situ mesocosms. Following 6 weeks, we measured changes in the diversity, composition, and abundance of eukaryotic 18S rRNA gene. Total phytoplankton biomass remained unchanged, but we observed a shift in dominant phytoplankton groups with increasing salt concentration, from Cryptophyta and Chlorophyta at lower chloride concentrations (< 185 mg Cl− L−1) to Ochrophyta at higher chloride concentrations (> 185 mg Cl− L−1). Crustacean zooplankton and rotifers were sensitive to the salinity, and disappeared at low chloride concentrations (< 40 mg Cl− L−1). While ciliates thrived at low chloride concentrations (< 185 mg Cl− L−1), fungal groups dominated at intermediate chloride concentrations (185–640 mg Cl− L−1), and only phytoplankton remained at the highest chloride concentrations (> 640 mg Cl− L−1).

中国东海微型鞭毛虫群落的分布特征及其环境影响因子

PDF HTML阅读 XML下载 导出引用 引用提醒 中国东海微型鞭毛虫群落的分布特征及其环境影响因子 DOI: 10.5846/stxb202103010554 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金项目（41676131，41876155） Distribution of the microbial flagellates' community and the key affecting environmental factors in the East China Sea Author: Affiliation: Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:海洋微型鞭毛虫是海洋原生生物中一类高度异质化的类群，物种多样性高，具有多种营养方式，在全球海洋生态系统中占据广阔的生态位，在生物地球化学循环中发挥着关键作用。然而关于其生物多样性和群落结构的认识十分有限，特别是有关环境因子与其生物地理分布关系的研究更为罕见。为了探究微型鞭毛虫群落多样性、群落结构以及影响其生物地理分布格局的环境因素，将高通量测序技术与传统的显微镜观测方法相结合，全面调查了中国东海春季和秋季微型鞭毛虫的群落特征，并深入探讨了与环境因子之间的关系。结果表明：东海微型鞭毛虫的丰度平均为2.27×103个/mL，表现为近岸处较高、随离岸距离的增加而下降的趋势；Shannon多样性指数呈现表层低于底层、近岸区低于陆架区的特征，反映了生物群落的稳定程度以及对环境条件的适应程度；不同类群的鞭毛虫具有各自独特的营养模式和相对固定的粒级，表现出对温度、盐度、溶解氧等环境因素的不同响应，从而使群落的物种组成和分布模式呈现明显的季节变化和生境差异。研究结果可为深入认识东海海洋微型鞭毛虫的群落结构、分布格局以及环境影响因素提供理论依据。 Abstract:Marine microbial flagellates are a highly heterogeneous group of protists with high biodiversity and multiple trophic modes. They occupy broad niches in global marine ecosystem and play essential roles in the biogeochemical cycles. However, little is known about the distribution of the diversity and community structure of the microbial flagellates in a regional marine area, especially the relationship between their biogeographic distribution and the environmental factors. The East China Sea (ECS) is a marginal sea with sloping topography, leading to a wide coastal area and its adjacent open continental shelf area. The hydrological conditions display gradient changing patterns from the coastal area to the shelf area in the ECS, which could affect the microbial flagellates' communities differently, but is so far understudied. Thus, the ECS region provides a suitable system for the study of the relationship between environmental conditions and microbial flagellates' communities. In order to adequately describe the diversity and community structure of the microbial flagellates, as well as the environmental factors that shape and drive their biogeographic distribution patterns, a comprehensive investigation on the microbial flagellates' communities using combined methods of high-throughput sequencing of eukaryotic 18S rRNA gene V4 region and traditional microscopic observation was conducted in the ECS in spring and autumn, 2019. Intensive exploration also attempted using multiple statistical analyses on interpretation of the relationships between environmental factors and structure of microbial flagellates' communities. The main findings are as follows:Firstly, the average abundance of the nano-sized flagellates in the ECS was 2.27×103 cells/mL, which decreased with increasing distance from the shore. The heterotrophic nano-sized flagellates were dominant at the bottom layer of seawater while the surface seawater was dominated by the pigmented ones. Secondly, the community alpha diversity reflected the community stability and adaptability to environmental conditions, with higher Shannon diversity index both at the bottom seawater and in the shelf area than those at the surface seawater and in the coastal area, respectively. This indicated that the relatively stable environmental characteristics and environmental heterogeneity among different patches in the bottom layer and shelf area might cause sufficient competition and niche differentiation of the community, and thus led to higher biodiversity. Thirdly, different taxa groups of microbial flagellates owned unique nutritional modes and relatively fixed size fractions. The relative richness[numbers of the Operational taxonomic units (OTUs)] and relative abundance (numbers of the sequencing reads) of various taxa were different. Alveolata were the most abundant and diverse taxa in the studied area. Archaeplastida, Hacrobia, and Stramenopiles displayed high relative abundance and richness in the pico-sized flagellates' community, while Rhizaria showed high relative richness mostly in the nano-sized community. Lastly, the potential correlation between the microbial flagellates' communities and environmental factors depended on the degree to which the biological community matched with or adapted to the changing environmental conditions. Different taxa showed different responses to the environmental factors such as temperature, salinity, and dissolved oxygen, etc. This led to the obviously seasonal dynamics and biogeographic distribution patterns of the community composition. Moreover, the geographic distances had an impact on the dispersal limitation of the microbial flagellates' community, which might also result in spatial difference of the community. Specifically, the similarity of the community composition was greatly reduced with the increasing of the environmental heterogeneity and geographical distance. Overall, the findings of this study contribute to improve our understanding of the diversity, community structure, and affecting factors of marine microbial flagellates in the ECS, and to promote the research of marine flagellates from the phenomenon to the process and the mechanism. 参考文献 相似文献 引证文献

Association between Parkinson\u2019s disease and the faecal eukaryotic microbiota

Parkinson’s disease (PD) is one of the most common neurodegenerative disease, and is so far not considered curable. PD patients suffer from several motor and non-motor symptoms, including gastrointestinal dysfunctions and alterations of the enteric nervous system. Constipation and additional intestinal affections can precede the classical motor symptoms by several years. Recently, we reported effects of PD and related medications on the faecal bacterial community of 34 German PD patients and 25 age-matched controls. Here, we used the same collective and analysed the V6 and V7 hypervariable region of PCR-amplified, eukaryotic 18S rRNA genes using an Illumina MiSeq platform. In all, 53% (18) of the PD samples and 72% (18) of the control samples yielded sufficient amplicons for downstream community analyses. The PD samples showed a significantly lower alpha and a different beta eukaryotic diversity than the controls. Most strikingly, we observed a significantly higher relative abundance of sequence affiliated with the Geotrichum genus in the PD samples (39.7%), when compared to the control samples (0.05%). In addition, we observed lower relative abundances of sequences affiliated with Aspergillus/Penicillium, Charophyta/Linum, unidentified Opisthokonta and three genera of minor abundant zooflagellates in the PD samples. Our data add knowledge to the small body of data about the eukaryotic microbiota of PD patients and suggest a potential association of certain gut eukaryotes and PD.

Dataset complexity impacts both MOTU delimitation and biodiversity estimates in eukaryotic 18S rRNA metabarcoding studies

AbstractHow does the evolution of bioinformatics tools impact the biological interpretation of high‐throughput sequencing datasets? For eukaryotic metabarcoding studies, in particular, researchers often rely on tools originally developed for the analysis of 16S ribosomal RNA (rRNA) datasets. Such tools do not adequately account for the complexity of eukaryotic genomes, the ubiquity of intragenomic variation in eukaryotic metabarcoding loci, or the differential evolutionary rates observed across eukaryotic genes and taxa. Recently, metabarcoding workflows have shifted away from the use of operational taxonomic units (OTUs) toward delimitation of amplicon sequence variants (ASVs). We assessed how the choice of bioinformatics algorithm impacts the downstream biological conclusions that are drawn from eukaryotic 18S rRNA metabarcoding studies. We focused on four workflows including UCLUST and VSearch algorithms for OTU clustering, and DADA2 and Deblur algorithms for ASV delimitation. We used two 18S rRNA datasets to further evaluate whether dataset complexity had a major impact on the statistical trends and ecological metrics: a “high complexity” (HC) environmental dataset generated from community DNA in Arctic marine sediments, and a “low complexity” (LC) dataset representing individually barcoded nematodes. Our results indicate that ASV algorithms produce more biologically realistic metabarcoding outputs, with DADA2 being the most consistent and accurate pipeline regardless of dataset complexity. In contrast, OTU clustering algorithms inflate the metabarcoding‐derived estimates of biodiversity, consistently returning a high proportion of “rare” molecular operational taxonomic units (MOTUs) that appear to represent computational artifacts and sequencing errors. However, species‐specific MOTUs with high relative abundance are often recovered regardless of the bioinformatics approach. We also found high concordance across pipelines for downstream ecological analysis based on beta‐diversity and alpha‐diversity comparisons that utilize taxonomic assignment information. Analyses of LC datasets and rare MOTUs are especially sensitive to the choice of algorithms and better software tools may be needed to address these scenarios.

Diet diversity and environment determine the intestinal microbiome and bacterial pathogen load of fire salamanders

Diverse communities of symbiotic microbes inhabit the digestive systems of vertebrates and play a crucial role in animal health, and host diet plays a major role in shaping the composition and diversity of these communities. Here, we characterized diet and gut microbiome of fire salamander populations from three Belgian forests. We carried out DNA metabarcoding on fecal samples, targeting eukaryotic 18S rRNA of potential dietary prey items, and bacterial 16S rRNA of the concomitant gut microbiome. Our results demonstrated an abundance of soft-bodied prey in the diet of fire salamanders, and a significant difference in the diet composition between males and females. This sex-dependent effect on diet was also reflected in the gut microbiome diversity, which is higher in males than female animals. Proximity to human activities was associated with increased intestinal pathogen loads. Collectively, the data supports a relationship between diet, environment and intestinal microbiome in fire salamanders, with potential health implications.

Occurrence of the Freshwater Chrysophyte Poterioochromonas malhamensis in a High Arctic Marine Ecosystem

Kongsfjorden is a small Arctic fjord but with great hydrographic complexity and has changed greatly due to the climate change. Arctic warming has increased melts of sea ice and glaciers that results in higher freshwater content. Microbial community variability and increasing terrestrial input were detected continuously in recent years ITag eukaryotic 18S rRNA V4 metabarcoding, photosynthetic pigments analysis and epifluorescence microscopy were used to reveal the dominant species of small eukaryotic community (<20 μm). Both Spearman correlation and redundant analysis were used to study the correlation between the small eukaryotes and the environmental conditions. In the present study, the surface water with salinity lower than 34 was thicker than in summers of previous years. The freshwater mixotrophic chrysophyte Poterioochromonas malhamensis was found for the first time as the dominant species. No general trends were found for the contributions of P. malhamensis to the total reads of small eukaryotes in water depths; and no obvious differences were found at different stations and water masses. Phagotrophy, which is more common than phototrophy at all times in P. malhamensis, is thought to be the main reason for the prevalence of P. malhamensis in Kongsfjorden. The occurrence of P. malhamensis induced a disorder in the small eukaryotic community, which biodiversity and composition showed weak correlation with the water masses. The dominance of the freshwater-originating phytoplankton may indicate an ecosystem change in the Kongsjforden, which probably might become more remarkable in the future as the climate continues to change.