Eukaryotic plankton species diversity and community structure in the Xiao Jiang River (the primary tributary of Upper Yangtze River), Yunnan.

The Xiao Jiang River, as a crucial element of ecological restoration in the upper reaches of the Yangtze River, plays an indispensable role in agricultural water utilization and water ecology within its watersheds. The water quality status of the Xiao Jiang River not only impacts local water-ecological equilibrium and economic benefits but also holds paramount importance for sustaining ecosystem health in the Yangtze River basin. Plankton surveys and environmental physicochemical detection were conducted in the major channel region of the Xiao Jiang River in dry and wet periods in 2022 to better understand the diversity of eukaryotic plankton and its community structure characteristics. Environmental DNA is an emerging method that combines traditional ecology with second-generation sequencing technology. It can detect species from a single sample that are difficult to find by traditional microscopy, making the results of plankton diversity studies more comprehensive. For the first time, environmental DNA was used to investigate eukaryotic plankton in the Xiao Jiang River . The results showed that a total of 881 species of plankton from 592 genera in 17 phyla were observed. During the dry period, 480 species belonging to 384 genera within17 phyla were detected, while, during the wet period, a total of 805 species belonging to 463 genera within 17 phyla were recorded. The phylum Ciliophora dominated the zooplankton, while the phylum Chlorophyta and Bacillariophyta dominated the phytoplankton. The presence of these dominant species indicate that the water quality conditions in the study area are oligotrophic and mesotrophic. Principal coordinate analysis and difference test showed that the number of plankton ASVs, abundance, species richness, dominating species, and diversity indices differed between the dry and wet periods. Spearman correlation analysis and redundancy analysis (RDA) of relative abundance data with environmental physicochemical factors revealed that water temperature (WT), dissolved oxygen (DO), potential of hydrogenacidity (pH), ammonia nitrogen (NH3-N), total nitrogen (TN), electrical conductivity (EC) and the determination of redox potential (ORP) were the main environmental physicochemical factors impacting the plankton community structure. The results of this study can serve as a provide data reference at the plankton level for water pollution management in the Xiao Jiang River, and they are extremely important for river ecological restoration and biodiversity recovery in the Yangtze River basin.

Climate influences the gut eukaryome of wild rodents in the Great Rift Valley of Jordan.

BACKGROUND: The mammalian gut microbiome includes a community of eukaryotes with significant taxonomic and functional diversity termed the eukaryome. The molecular analysis of eukaryotic diversity in microbiomes of wild mammals is still in its early stages due to the recent emergence of interest in this field. This study aimed to fill this knowledge gap by collecting data on eukaryotic species found in the intestines of wild rodents. Because little is known about the influence of climate on the gut eukaryome, we compared the composition of the gut eukaryotes in two rodent species, Mus musculus domesticus and Acomys cahirinus, which inhabit a transect crossing a temperate and tropical zone on the Jordanian side of the Great Rift Valley (GRV). METHODS: We used high-throughput amplicon sequencing targeting the 18S rRNA gene in fecal samples from rodents to identify eukaryotic organisms, their relative abundance, and their potential for pathogenicity. RESULTS: Nematodes and protozoa were the most prevalent species in the eukaryome communities, whereas fungi made up 6.5% of the total. Sixty percent of the eukaryotic ASVs belonged to taxa that included known pathogens. Eighty percent of the rodents were infected with pinworms, specifically Syphacia obvelata. Eukaryotic species diversity differed significantly between bioclimatic zones (p = 0.001). Nippostrongylus brasiliensis and Aspiculuris tetraptera were found to be present exclusively in the Sudanian zone rodents. This area has not reported any cases of Trichuris infections. Yet, Capillaria infestations were unique to the Mediterranean region, while Trichuris vulpis infestations were also prevalent in the Mediterranean and Irano-Turanian regions. CONCLUSIONS: This study highlights the importance of considering host species diversity and environmental factors when studying eukaryome composition in wild mammals. These data will be valuable as a reference to eukaryome study.

Three-domain microbial communities in the gut of Pachnoda marginata larvae: A comparative study revealing opposing trends in gut compartments.

This study aimed to examine the bacterial, methanogenic archaeal, and eukaryotic community structure in both the midgut and hindgut of Pachnoda marginata larvae using an amplicon sequencing approach. The goal was to investigate how various diets and the soil affect the composition of these three-domain microbial communities within the gut of insect larvae. The results indicated a notable variation in the microbial community composition among the gut compartments. The majority of the bacterial community in the hindgut was composed of Ruminococcaceae and Christensenellaceae. Nocardiaceae, Microbacteriaceae, and Lachnospiraceae were detected in midgut samples from larvae feeding on the leaf diet, whereas Sphingomonadaceae, Rhodobacteraceae, and Promicromonasporaceae dominated the bacterial community of midgut of larvae feeding on the straw diet. The diet was a significant factor that influenced the methanogenic archaeal and eukaryotic community patterns. The methanogenic communities in the two gut compartments significantly differed from each other, with the midgut communities being more similar to those in the soil. A higher diversity of methanogens was observed in the midgut samples of both diets compared to the hindgut. Overall, the microbiota of the hindgut was more host-specific, while the assembly of the midgut was more influenced by the environmental microorganisms.

Temporal variations of bacterial and eukaryotic community in coastal waters-implications for aquaculture.

Despite increased attention to the aquaculture environment, there is still a lack of understanding regarding the significance of water quality. To address this knowledge gap, this study utilized high-throughput sequencing of 16S rRNA and 18S rRNA to examine microbial communities (bacteria and eukaryotes) in coastal water over different months through long-term observations. The goal was to explore interaction patterns in the microbial community and identify potential pathogenic bacteria and red tide organisms. The results revealed significant differences in composition, diversity, and richness of bacterial and eukaryotic operational taxonomic units (OTUs) across various months. Principal coordinate analysis (PCoA) demonstrated distinct temporal variations in bacterial and eukaryotic communities, with significant differences (P = 0.001) among four groups: F (January-April), M (May), S (June-September), and T (October-December). Moreover, a strong association was observed between microbial communities and months, with most OTUs showing a distinct temporal preference. The Kruskal-Wallis test (P < 0.05) indicated significant differences in dominant bacterial and eukaryotic taxa among months, with each group exhibiting unique dominant taxa, including potential pathogenic bacteria and red tide organisms. These findings emphasize the importance of monitoring changes in potentially harmful microorganisms in aquaculture. Network analysis highlighted positive correlations between bacteria and eukaryotes, with bacteria playing a key role in network interactions. The key bacterial genera associated with other microorganisms varied significantly (P < 0.05) across different groups. In summary, this study deepens the understanding of aquaculture water quality and offers valuable insights for maintaining healthy aquaculture practices. KEY POINTS: • Bacterial and eukaryotic communities displayed distinct temporal variations. • Different months exhibited unique potential pathogenic bacteria and red tide organisms. • Bacteria are key taxonomic taxa involved in microbial network interactions.

Contrasting Community Assembly Mechanisms Underlie Similar Biogeographic Patterns of Surface Microbiota in the Tropical North Pacific Ocean.

Marine microbiota are critical components of global biogeochemical cycles. However, the biogeographic patterns and ecological processes that structure them remain poorly understood, especially in the oligotrophic ocean. In this study, we used high-throughput sequencing of 16S and 18S rRNA genes to investigate the distribution patterns of bacterial and microeukaryotic communities and their assembly mechanisms in the surface waters of the tropical North Pacific Ocean. The fact that both the bacterial and the microeukaryotic communities showed similar distribution patterns (i.e., similar distance-decay patterns) and were clustered according to their geographic origin (i.e., the western tropical North Pacific and central tropical North Pacific) suggested that there was a significant biogeographic pattern of microbiota in the North Pacific Ocean. Indices of alpha diversity such as species richness, phylogenetic diversity, and the Shannon diversity index also differed significantly between regions. The correlations were generally similar between spatial and environmental variables and the alpha and beta diversities of bacteria and microeukaryotes across the entire region. The relative importance of ecological processes differed between bacteria and microeukaryotes: ecological drift was the principal mechanism that accounted for the structure of bacterial communities; heterogeneous selection, dispersal limitation, and ecological drift collectively explained much of the turnover of the microeukaryote communities. IMPORTANCE Bacteria and microeukaryotes are extremely diverse groups in the ocean, where they regulate elemental cycling and energy flow. Studies of marine microbial ecology have benefited greatly from the rapid progress that has been made in genomic sequencing and theoretical microbial ecology. However, the spatial distribution of marine bacteria and microeukaryotes and the nature of the assembly mechanisms that determine their distribution patterns in oligotrophic marine waters are poorly understood. In this study, we used high-throughput sequencing methods to identify the distribution patterns and ecological processes of bacteria and microeukaryotes in an oligotrophic, tropical ocean. Our study showed that contrasting community assembly mechanisms underlaid similar biogeographic patterns of surface bacterial and microeukaryotic communities in the tropical North Pacific Ocean.

House fly larval grazing alters dairy cattle manure microbial communities.

BACKGROUND: House fly larvae (Musca domestica L.) require a live microbial community to successfully develop. Cattle manure is rich in organic matter and microorganisms, comprising a suitable substrate for larvae who feed on both the decomposing manure and the prokaryotic and eukaryotic microbes therein. Microbial communities change as manure ages, and when fly larvae are present changes attributable to larval grazing also occur. Here, we used high throughput sequencing of 16S and 18S rRNA genes to characterize microbial communities in dairy cattle manure and evaluated the changes in those communities over time by comparing the communities in fresh manure to aged manure with or without house fly larvae. RESULTS: Bacteria, archaea and protist community compositions significantly differed across manure types (e.g. fresh, aged, larval-grazed). Irrespective of manure type, microbial communities were dominated by the following phyla: Euryarchaeota (Archaea); Proteobacteria, Firmicutes and Bacteroidetes (Bacteria); Ciliophora, Metamonanda, Ochrophyta, Apicomplexa, Discoba, Lobosa and Cercozoa (Protists). Larval grazing significantly reduced the abundances of Bacteroidetes, Ciliophora, Cercozoa and increased the abundances of Apicomplexa and Discoba. Manure aging alone significantly altered the abundance bacteria (Acinetobacter, Clostridium, Petrimonas, Succinovibro), protists (Buxtonella, Enteromonas) and archaea (Methanosphaera and Methanomassiliicoccus). Larval grazing also altered the abundance of several bacterial genera (Pseudomonas, Bacteroides, Flavobacterium, Taibaiella, Sphingopyxis, Sphingobacterium), protists (Oxytricha, Cercomonas, Colpodella, Parabodo) and archaea (Methanobrevibacter and Methanocorpusculum). Overall, larval grazing significantly reduced bacterial and archaeal diversities but increased protist diversity. Moreover, total carbon (TC) and nitrogen (TN) decreased in larval grazed manure, and both TC and TN were highly correlated with several of bacterial, archaeal and protist communities. CONCLUSIONS: House fly larval grazing altered the abundance and diversity of bacterial, archaeal and protist communities differently than manure aging alone. Fly larvae likely alter community composition by directly feeding on and eliminating microbes and by competing with predatory microbes for available nutrients and microbial prey. Our results lend insight into the role house fly larvae play in shaping manure microbial communities and help identify microbes that house fly larvae utilize as food sources in manure. Information extrapolated from this study can be used to develop manure management strategies to interfere with house fly development and reduce house fly populations.

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar.

Pe poke is a naturally fermented sticky soybean food of Myanmar. The present study was aimed to profile the whole microbial community structure and their predictive gene functionality of pe poke samples prepared in different fermentation periods viz. 3 day (3ds), 4 days (4ds), 5 days (5ds) and sun-dried sample (Sds). The pH of samples was 7.6 to 8.7, microbial load was 2.1-3.9 x 108 cfu/g with dynamic viscosity of 4.0±1.0 to 8.0±1.0cP. Metataxonomic profile of pe poke samples showed different domains viz. bacteria (99.08%), viruses (0.65%), eukaryota (0.08%), archaea (0.03%) and unclassified sequences (0.16%). Firmicutes (63.78%) was the most abundant phylum followed by Proteobacteria (29.54%) and Bacteroidetes (5.44%). Bacillus thermoamylovorans was significantly abundant in 3ds and 4ds (p<0.05); Ignatzschineria larvae was significantly abundant in 5ds (p<0.05), whereas, Bacillus subtilis was significantly abundant in Sds (p <0.05). A total of 172 species of Bacillus was detected. In minor abundance, the existence of bacteriophages, archaea, and eukaryotes were also detected. Alpha diversity analysis showed the highest Simpson's diversity index in Sds comparable to other samples. Similarly, a non-parametric Shannon's diversity index was also highest in Sds. Good's coverage of 0.99 was observed in all samples. Beta diversity analysis using PCoA showed no significant clustering. Several species were shared between samples and many species were unique to each sample. In KEGG database, a total number of 33 super-pathways and 173 metabolic sub-pathways were annotated from the metagenomic Open Reading Frames. Predictive functional features of pe poke metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including various essential amino acids, different vitamins, and enzymes. Spearman's correlation was inferred between the abundant species and functional features.

Spatial Variability in Streambed Microbial Community Structure across Two Watersheds.

Both spatial and temporal variability are key attributes of sedimentary microbial communities, and while spatial effects on beta-diversity appear to dominate at larger distances, the character of spatial variability at finer scales remains poorly understood, especially for headwater stream communities. We investigated patterns of microbial community structure (MCS) in biofilms attached to streambed sediments from two watersheds across spatial scales spanning <1 m within a single stream to several hundred kilometers between watersheds. Analyses of phospholipid fatty acid (PLFA) profiles indicated that the variations in MCS were driven by increases in the relative abundance of microeukaryotic photoautotrophs and their contribution to total microbial biomass. Furthermore, streams within watersheds had similar MCS, underscoring watershed-level controls of microbial communities. Moreover, bacterial community structure assayed as either PCR-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints or PLFA profiles edited to remove microeukaryotes indicated a distinct watershed-level biogeography. No distinct stream order-level distributions were identified, although DGGE analyses clearly indicated that there was greater variability in community structure among 1st-order streams than among 2nd- and 3rd-order streams. Longitudinal gradients in microbial biomass and structure showed that the greatest variations were associated with 1st-order streams within a watershed, and 68% of the variation in total microbial biomass was explained by sediment atomic carbon-to-nitrogen ratio (C:N ratio), percent carbon, sediment surface area, and percent water content. This study confirms a distinct microbial biogeography for headwater stream communities driven by environmental heterogeneity across distant watersheds and suggests that eukaryotic photoautotrophs play a key role in structuring bacterial communities on streambed sediments. IMPORTANCE Microorganisms in streams drive many biogeochemical reactions of global significance, including nutrient cycling and energy flow; yet, the mechanisms responsible for the distribution and composition of streambed microbial communities are not well known. We sampled sediments from multiple streams in two watersheds (Neversink River [New York] and White Clay Creek [WCC; Pennsylvania] watersheds) and measured microbial biomass and total microbial and bacterial community structures using phospholipid and molecular methods. Microbial and bacterial community structures displayed a distinct watershed-level biogeography. The smallest headwater streams within a watershed showed the greatest variation in microbial biomass, and 68% of that variation was explained by the atomic carbon-to-nitrogen ratio (C:N ratio), percent carbon, sediment surface area, and percent water content. Our study revealed a nonrandom distribution of microbial communities in streambeds, and showed that microeukaryotic photoautotrophs, environmental heterogeneity, and geographical distance influence microbial composition and spatial distribution.

General decline in the diversity of the airborne microbiota under future climatic scenarios.

Microorganisms attached to aerosols can travel intercontinental distances, survive, and further colonize remote environments. Airborne microbes are influenced by environmental and climatic patterns that are predicted to change in the near future, with unknown consequences. We developed a new predictive method that dynamically addressed the temporal evolution of biodiversity in response to environmental covariates, linked to future climatic scenarios of the IPCC (AR5). We fitted these models against a 7-year monitoring of airborne microbes, collected in wet depositions. We found that Bacteria were more influenced by climatic variables than by aerosols sources, while the opposite was detected for Eukarya. Also, model simulations showed a general decline in bacterial richness, idiosyncratic responses of Eukarya, and changes in seasonality, with higher intensity within the worst-case climatic scenario (RCP 8.5). Additionally, the model predicted lower richness for airborne potential eukaryotic (fungi) pathogens of plants and humans. Our work pioneers on the potential effects of environmental variability on the airborne microbiome under the uncertain context of climate change.

Updating changes in human gut microbial communities associated with Clostridioides difficile infection.

Clostridioides difficile is the causative agent of antibiotic-associated diarrhea, a worldwide public health problem. Different factors can promote the progression of C. difficile infection (CDI), mainly altered intestinal microbiota composition. Microbial species belonging to different domains (i.e., bacteria, archaea, eukaryotes, and even viruses) are synergistically and antagonistically associated with CDI. This review was aimed at updating changes regarding CDI-related human microbiota composition using recent data and an integral approach that included the different microorganism domains. The three domains of life contribute to intestinal microbiota homeostasis at different levels in which relationships among microorganisms could explain the wide range of clinical manifestations. A holistic understanding of intestinal ecosystem functioning will facilitate identifying new predictive factors for infection and developing better treatment and new diagnostic tools, thereby reducing this disease's morbidity and mortality.

Seasonal Variability of the Airborne Eukaryotic Community Structure at a Coastal Site of the Central Mediterranean.

The atmosphere represents an underexplored temporary habitat for airborne microbial communities such as eukaryotes, whose taxonomic structure changes across different locations and/or regions as a function of both survival conditions and sources. A preliminary dataset on the seasonal dependence of the airborne eukaryotic community biodiversity, detected in PM10 samples collected from July 2018 to June 2019 at a coastal site representative of the Central Mediterranean, is provided in this study. Viridiplantae and Fungi were the most abundant eukaryotic kingdoms. Streptophyta was the prevailing Viridiplantae phylum, whilst Ascomycota and Basidiomycota were the prevailing Fungi phyla. Brassica and Panicum were the most abundant Streptophyta genera in winter and summer, respectively, whereas Olea was the most abundant genus in spring and autumn. With regards to Fungi, Botrytis and Colletotrichum were the most abundant Ascomycota genera, reaching the highest abundance in spring and summer, respectively, while Cryptococcus and Ustilago were the most abundant Basidiomycota genera, and reached the highest abundance in winter and spring, respectively. The genus community structure in the PM10 samples varied day-by-day, and mainly along with the seasons. The impact of long-range transported air masses on the same structure was also proven. Nevertheless, rather few genera were significantly correlated with meteorological parameters and PM10 mass concentrations. The PCoA plots and non-parametric Spearman's rank-order correlation coefficients showed that the strongest correlations generally occurred between parameters reaching high abundances/values in the same season or PM10 sample. Moreover, the screening of potential pathogenic fungi allowed us to detect seven potential pathogenic genera in our PM10 samples. We also found that, with the exception of Panicum and Physcomitrella, all of the most abundant and pervasive identified Streptophyta genera could serve as potential sources of aeroallergens in the studied area.

Protistan grazing impacts microbial communities and carbon cycling at deep-sea hydrothermal vents.

Microbial eukaryotes (or protists) in marine ecosystems are a link between primary producers and all higher trophic levels, and the rate at which heterotrophic protistan grazers consume microbial prey is a key mechanism for carbon transport and recycling in microbial food webs. At deep-sea hydrothermal vents, chemosynthetic bacteria and archaea form the base of a food web that functions in the absence of sunlight, but the role of protistan grazers in these highly productive ecosystems is largely unexplored. Here, we pair grazing experiments with a molecular survey to quantify protistan grazing and to characterize the composition of vent-associated protists in low-temperature diffuse venting fluids from Gorda Ridge in the northeast Pacific Ocean. Results reveal protists exert higher predation pressure at vents compared to the surrounding deep seawater environment and may account for consuming 28 to 62% of the daily stock of prokaryotic biomass within discharging hydrothermal vent fluids. The vent-associated protistan community was more species rich relative to the background deep sea, and patterns in the distribution and co-occurrence of vent microbes provide additional insights into potential predator-prey interactions. Ciliates, followed by dinoflagellates, Syndiniales, rhizaria, and stramenopiles, dominated the vent protistan community and included bacterivorous species, species known to host symbionts, and parasites. Our findings provide an estimate of protistan grazing pressure within hydrothermal vent food webs, highlighting the important role that diverse protistan communities play in deep-sea carbon cycling.

What's under the Christmas Tree? A Soil Sulfur Amendment Lowers Soil pH and Alters Fir Tree Rhizosphere Bacterial and Eukaryotic Communities, Their Interactions, and Functional Traits.

In this study, we describe the legacy effects of a soil sulfur amendment experiment performed 6 years prior and the resulting alterations to the rhizosphere communities of fir trees on a Christmas tree plantation. The pH of bulk soil was ∼1.4 pH units lower than that of untreated soils and was associated with reduced Ca, Mg, and organic matter contents. Similarly, root chemistry differed due to the treatment, with roots in sulfur-amended soils showing significantly higher Al, Mn, and Zn contents and reduced levels of B and Ca. 16S rRNA and 18S rRNA gene sequencing was pursued to characterize the bacterial/archaeal and eukaryotic communities in the rhizosphere soils. The treatment induced dramatic and significant changes in the microbial populations, with thousands of 16S rRNA gene sequence variants and hundreds of 18S rRNA gene variants being significantly different in relative abundances between the treatments. Additionally, co-occurrence networks showed that bacterial and eukaryotic interactions, network topology, and hub taxa were significantly different when constructed from the control and treated soil 16S and 18S rRNA gene amplicon libraries. Metagenome sequencing identified several genes related to transport proteins that differentiated the functional potentials of the communities between treatments, pointing to physiological adaptations in the microbial communities for living at altered pH. These data show that a legacy of soil acidification increased the heterogeneity of the soil communities as well as decreasing taxon connections, pointing to a state of ecosystem instability that has potentially persisted for 6 years. IMPORTANCE We used sulfur incorporation to investigate the legacy effects of lowered soil pH on the bacterial and eukaryotic populations in the rhizosphere of Christmas trees. Acidification of the soils drove alterations of fir tree root chemistry and large shifts in the taxonomic and functional compositions of the communities. These data demonstrate that soil pH influences are manifest across all organisms inhabiting the soil, from the host plant to the microorganisms inhabiting the rhizosphere soils. Thus, this study highlights the long-lasting influence of altering soil pH on soil and plant health as well as the status of the microbiome.

High-throughput detection of eukaryotic parasites and arboviruses in mosquitoes.

Vector-borne pathogens cause many human infectious diseases and are responsible for high mortality and morbidity throughout the world. They can also cause livestock epidemics with dramatic social and economic consequences. Due to its high costs, vector-borne disease surveillance is often limited to current threats, and the investigation of emerging pathogens typically occurs after the reports of clinical cases. Here, we use high-throughput sequencing to detect and identify a wide range of parasites and viruses carried by mosquitoes from Cambodia, Guinea, Mali and the USA. We apply this approach to individual Anopheles mosquitoes as well as pools of mosquitoes captured in traps; and compare the outcomes of this assay when applied to DNA or RNA. We identified known human and animal pathogens and mosquito parasites belonging to a wide range of taxa, as well as DNA sequences from previously uncharacterized organisms. Our results also revealed that analysis of the content of an entire trap could be an efficient approach to monitor and identify rare vector-borne pathogens in large surveillance studies. Overall, we describe a high-throughput and easy-to-customize assay to screen for a wide range of pathogens and efficiently complement current vector-borne disease surveillance approaches.

Gut microbiota composition in health-care facility-and community-onset diarrheic patients with Clostridioides difficile infection.

The role of gut microbiota in the establishment and development of Clostridioides difficile infection (CDI) has been widely discussed. Studies showed the impact of CDI on bacterial communities and the importance of some genera and species in recovering from and preventing infection. However, most studies have overlooked important components of the intestinal ecosystem, such as eukaryotes and archaea. We investigated the bacterial, archaea, and eukaryotic intestinal microbiota of patients with health-care-facility- or community-onset (HCFO and CO, respectively) diarrhea who were positive or negative for CDI. The CDI-positive groups (CO/+, HCFO/+) showed an increase in microorganisms belonging to Bacteroidetes, Firmicutes, Proteobacteria, Ascomycota, and Opalinata compared with the CDI-negative groups (CO/-, HCFO/-). Patients with intrahospital-acquired diarrhea (HCFO/+, HCFO/-) showed a marked decrease in bacteria beneficial to the intestine, and there was evidence of increased Archaea and Candida and Malassezia species compared with the CO groups (CO/+, CO/-). Characteristic microbiota biomarkers were established for each group. Finally, correlations between bacteria and eukaryotes indicated interactions among the different kingdoms making up the intestinal ecosystem. We showed the impact of CDI on microbiota and how it varies with where the infection is acquired, being intrahospital-acquired diarrhea one of the most influential factors in the modulation of bacterial, archaea, and eukaryotic populations. We also highlight interactions between the different kingdoms of the intestinal ecosystem, which need to be evaluated to improve our understanding of CDI pathophysiology.

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing.

BACKGROUND: Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While microbial eukaryotes are critical to these communities, they are challenging to study with shotgun sequencing techniques and are therefore often excluded. RESULTS: Here, we present EukDetect, a bioinformatics method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of 521,824 universal marker genes from 241 conserved gene families, which we curated from 3713 fungal, protist, non-vertebrate metazoan, and non-streptophyte archaeplastida genomes and transcriptomes. EukDetect has a broad taxonomic coverage of microbial eukaryotes, performs well on low-abundance and closely related species, and is resilient against bacterial contamination in eukaryotic genomes. Using EukDetect, we describe the spatial distribution of eukaryotes along the human gastrointestinal tract, showing that fungi and protists are present in the lumen and mucosa throughout the large intestine. We discover that there is a succession of eukaryotes that colonize the human gut during the first years of life, mirroring patterns of developmental succession observed in gut bacteria. By comparing DNA and RNA sequencing of paired samples from human stool, we find that many eukaryotes continue active transcription after passage through the gut, though some do not, suggesting they are dormant or nonviable. We analyze metagenomic data from the Baltic Sea and find that eukaryotes differ across locations and salinity gradients. Finally, we observe eukaryotes in Arabidopsis leaf samples, many of which are not identifiable from public protein databases. CONCLUSIONS: EukDetect provides an automated and reliable way to characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes. We demonstrate that it enables discoveries that would be missed or clouded by false positives with standard shotgun sequence analysis. EukDetect will greatly advance our understanding of how microbial eukaryotes contribute to microbiomes. Video abstract.

Protistology and Cell Biology at the Marine Arago Laboratory of Banyuls-sur-Mer (1961-2000): Personal Recollections.

The history of protistology and the introduction of modern methods of unicell observations is described in a large maritime laboratory over a period of forty years by the initiator of this new team. The development of this team and the doctoral theses developed there are described as well as the major discoveries made. The Arago Laboratory, which was then in 1960 a field laboratory mainly devoted to the collection of biological material, becomes a research laboratory specializing in the study of the major fundamental problems which govern life: the organization and expression of the genome, mitotic processes and their nuclear and cytoplasmic components, cell cycle and its regulation as well as molecular phylogeny. The biological models chosen were essentially the dinoflagellate protists in their great variety: autotrophs, heterotrophs, myxotrophs and able of proliferating at sea, thus disrupting their cell cycle. Coupled with the techniques of biochemistry and molecular biology which it was in its infancy, the most advanced observation methods used electron and confocal microscopy often after use of ultra-cold cryopreparations, necessary to preserve the antigenic sites and allow the highlighting new proteins. The dinoflagellate model was then abandoned in favor of unicellular micro-eukaryotes allowing the development of environmental genomics.

Biogeographical patterns and mechanisms of microbial community assembly that underlie successional biocrusts across northern China.

Biocrusts play critical eco-functions in many drylands, however it is challenging to explore their community assembly, particularly within patched successional types and across climate zones. Here, different successional biocrusts (alga, lichen, and moss-dominated biocrusts) were collected across the northern China, and assembly of biocrust microbial communities was investigated by high-throughput sequencing combined with measurements of soil properties and microclimate environments. Bacterial and eukaryotic communities showed that the maximum and minimum community variation occurred across longitude and latitude, respectively. In the regions where all three stages of biocrusts were involved, the highest community difference existed between successional stages, and decreased with distance. The community assembly was generally driven by dispersal limitation, although neutral processes have controlled the eukaryotic community assembly in hyperarid areas. Along the succession, bacterial community had no obvious patterns, but eukaryotic community showed increasing homogeneity, with increased species sorting and decreased dispersal limitation for community assembly. Compared to early successional biocrusts, there were higher microbial mutual exclusions and more complex networks at later stages, with distinct topological features. Correlation analysis further indicated that the balance between deterministic and stochastic processes might be mediated by aridity, salinity, and total phosphorus, although the mediations were opposite for bacteria and eukaryotes.

Biogeographic patterns of abundant and rare bacterial and microeukaryotic subcommunities in connected freshwater lake zones subjected to different levels of nutrient loading.

AIMS: To reveal whether the patterns of abundant and rare subcommunity composition of both bacteria and microeukaryotes vary between connected regions with different levels of nutrient loading in freshwater lakes. METHODS AND RESULTS: We investigated the abundant and rare subcommunity composition of both bacteria and microeukaryotes in two connected zones (Meiliang Bay (MLB) and Xukou Bay (XKB)) of a large shallow freshwater Lake Taihu via the high-throughput sequencing of bacterial 16S rRNA and microeukaryotic 18S rRNA genes. Even though these two lake zones are connected and share a species bank, they diverge in community composition. Significantly higher alpha diversity was observed for the abundant bacterial subcommunity in the MLB. However, no significant difference in alpha diversity between the rare bacterial subcommunities, as well as both rare and abundant microeukaryotic subcommunities were observed between MLB and XKB. It is demonstrated that both environmental factors and geographic distance play central roles in controlling the rare and abundant microbial subcommunities in the two connected lake zones. CONCLUSIONS: The abundant subcommunity composition of bacteria and microeukaryotes vary between connected regions with different levels of nutrient loading. Dispersal limitation plays a vital role in shaping microbial communities even in connected zones of freshwater lakes. SIGNIFICANCE AND IMPACT OF THE STUDY: Leading to a comprehensive understanding of the characteristics of microbial community in connected lake regions with different levels of nutrient loading.