The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy

Sludge retention time in anaerobic digestion affects Archaea by a cascade through microeukaryotes

Anaerobic digestion is a crucial process for treating organic waste, such as wastewater sludge, agricultural residues and food waste. While the influence of physicochemical parameters on the prokaryotic community composition in anaerobic digesters has been extensively characterized, the role of biotic interactions in shaping the prokaryotic communities remains poorly understood. This study addresses this knowledge gap by analyzing the complete active microbiome of nine full-scale anaerobic digesters. Our findings reveal that eukaryotes, consisting primarily of protists and fungi, account for approximately 40 % of RNA sequence reads alongside dominant Archaea, indicating their substantial role in the digestion process. Our results suggest that the chosen sludge retention time during anaerobic digestion indirectly affects the archaeal community composition and thus treatment efficacy by cascading through eukaryotes, highlighting their integral role in the system. This study highlights the critical role of eukaryotes in regulating prokaryotic communities and their indirect contribution to the optimization of anaerobic digestion efficiency.

Molecular diversity and potential ecological risks of toxic HAB species in the coastal waters off Qinhuangdao, China

Harmful algal blooms (HABs) have occurred frequently in the coastal waters off Qinhuangdao (CWQ) of the Bohai Sea during the past two decades, with paralytic shellfish toxins frequently exceeding safe levels in recent years. However, the biodiversity of toxic HAB species remain poorly understood. Cruise observations in the CWQ of the Bohai Sea from August to November 2021 were used, to investigate the biodiversity, geographical and temporal distributions of toxic HAB species, and associated environmental factors. Through amplicon sequence variants (ASVs)-based metabarcoding analysis, 4261 ASVs of five microalgae phyla were identified in this study, of which Dinoflagellata was the most dominant phylum in most sampling sites. Consequently, 257 microalgae species were annotated in this study, in which 70 were identified as HAB species, including 33 toxic HAB species have been reported to produce toxins or potentially toxic substances. Notably, most HAB species were widely distributed in the CWQ in August to November, especially the toxic species Karlodinium veneficum. Moreover, some toxic HAB species may be distributed in the CWQ all year round, with a high risk of toxic HAB outbreak. Eight environmental factors were evaluated, and the temperature was found to be the key environmental factor influencing the distribution and seasonal variation of dominant HAB species. This research highlights the necessity for monitoring toxic HAB species for accurate prevention and mitigation of HABs.

A Long-Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS-MBON 2018-2020

Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio-temporal scales. We established an international Marine Biodiversity Observation Network (ARMS-MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard-bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018-2019 and retrieved in 2018-2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open-access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to ~5500 amplicon sequence variants and ~1800 operational taxonomic units, and up to ~250 and ~50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non-indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3-6 months during the main growth season to use resources as efficiently as possible and that post-sequencing curation is applied to enable statistical comparison of spatio-temporal entities. We suggest that ARMS should be used in biological monitoring programs and long-term ecological research and encourage the adoption of our ARMS-MBON protocols.

Is the Composition of Communities in Bromeliad Water and Adjacent Soil Similar?

Soil and bromeliads are important habitats contributing to the biodiversity of the Atlantic Forest in Brazil. However, knowledge of unicellular eukaryotes and bacteria in these environments remains limited. This study compared the diversity and community structure of unicellular eukaryotes, fungi, metazoan, and bacteria in bromeliad water tanks (BWT) and adjacent soil using 16S and 18S rRNA gene metabarcoding. Communities differed significantly between habitats but shared some taxa, suggesting habitat connectivity. Ciliates dominated unicellular eukaryotes in BWT, while Cercozoa prevailed in soil. Bacterial communities were dominated by Pseudomonadota, while fungal composition was more uniform, with Ascomycota as the dominant phylum across samples. Metazoan communities varied among abundant phyla, and their presence in BWT suggests the use of this water resource within the forest. This study provides essential baseline data on eukaryotic and bacterial diversity in this unique ecosystem, highlighting how distinct habitats within the Atlantic Forest support different communities.

Temporal dynamics of communities on plastic debris in a polluted marine habitat

This study investigated the succession of prokaryotic and eukaryotic communities on polystyrene panels deployed for 25 weeks in a harbour environment influenced by anthropogenic activities. These activities resulted in an excess of nutrients from sewage and agricultural discharges, as well as the release of hydrocarbons and other pollutants. An eDNA metabarcoding approach targeting the 16S and 18S rRNA genes was used. This innovative methodology allowed a detailed analysis of the community development and succession, providing an in-depth view of biodiversity and ecological dynamics associated with plastic substrates. The microbial biofilm community remained stable throughout the experiment enriched in Rhodobacteraceae (16.97 %) and Flavobacteriaceae (17.99 %). Only minor differences observed between the early and late stages, consistent with their identification as key components of the biofilm. For the eukaryotic community, the early colonization stages were dominated by Alveolata (63.39 %) and Stramenopiles (23.53 %). Later stages showed changes in the community with Chlorophyta (20.14 %) and Opisthokonta (94.32 %) being the most abundant phyla. Richness, as alpha diversity index based on retrieved ASVs, varied from 1875 to 2481 and from 159 to 405 for prokaryotes and eukaryotes, respectively. This indicated an adaptive succession of plastic-associated communities in aquatic ecosystems. Potential plastic-degrading groups found in the prokaryotic community showed a dynamic distribution across colonization stages. Trophic dynamics on plastic debris showed that heterotrophs dominated the eukaryotic community. Our results confirmed the role of plastics as vectors in marine ecosystems, for complex communities composed of bacteria, algae, and invertebrates. This highlighted potential risks to the health of marine ecosystems.

Is the Gelatinous Matrix of Nassellaria (Radiolaria) a Strategy for Coping With Oligotrophy?

Radiolaria are heterotrophic protists abundant in the world's oceans, playing important roles in biogeochemical cycles. Some host photosynthetic algae, contributing to primary production. Such mixotrophic behaviour is believed to explain their success in oligotrophic waters, notably Collodaria, exclusively mixotrophic radiolarians within a gelatinous matrix. Yet, understanding of Radiolaria ecology is limited to direct observations, as they have so far withstood reproduction in culture and lack genome data. Sampling oligotrophic California Current revealed abundant, rarely observed Nassellaria of the genus Phlebarachnium, characterised to live within a gelatinous matrix. Phylogenetic reconstruction of ribosomal DNA suggests that distantly related Nassellaria lineages independently developed the ability to produce a gelatinous matrix ~150 million years ago. By matching physical samples with genetic data, we identified these rarely observed organisms in global datasets, revealing their affinity for oligotrophic conditions. Co-occurrence networks showed distinct biogeography patterns for gelatinous matrix-forming Radiolaria compared to those without. Results suggest the matrix might be an adaptation to oligotrophic waters, increasing the effective volume, favouring prey capture, and creating a larger microenvironment for symbionts, thus promoting ecological success in nutrient-depleted waters. This study advances our understanding of the adaptation of poorly known eukaryotic groups, specifically when evolution occurs independently across lineages.

Rhizosphere-colonizing bacteria persist in the protist microbiome

Soils contain diverse predatory protists that affect the abundance and behavior of rhizosphere bacteria, including bacteria that may benefit plant health. Protists harbor their own bacterial microbiomes, and we previously observed that plants inoculated with protists harbored rhizosphere bacteria similar to those in the protist inoculum. To determine how protist microbiomes affect the rhizosphere, we profiled the bacteria of eight diverse rhizosphere protist isolates after 2 years of laboratory culture. We then compared the protist culture microbiomes to maize rhizosphere communities 6 weeks after protist inoculation. Introduction of protists enriched 13 protist-associated bacterial amplicon sequence variants (ASVs) in the rhizosphere, which comprised ~10% of the rhizosphere bacterial community. Additional bacterial ASVs ranked highly in abundance in both rhizosphere (top 100) and protist (top 20) microbiomes; together, a median 47% of the protist microbiome was enriched or in high rank abundance in the rhizosphere. Inoculation with three out of eight protist cultures positively affected root biomass traits, but a protist mixture had no effect, indicating that the impact of protist-associated bacteria on plant growth is context dependent. Isolates of protist-associated bacteria had both positive and negative effects on protist growth in culture, suggesting that the bacteria use multiple strategies to survive in proximity to predators. This study demonstrates that even after long-term laboratory culture, rhizosphere protist cultures host bacteria that can colonize the rhizosphere of maize. The findings also identify diverse groups of rhizosphere-colonizing bacteria that persist among protist predators, which suggests that these bacteria could associate with or benefit from protists in the soil.

IMPORTANCE

Understanding the impact of predatory protists on the plant microbiome will be essential to deploy protists in sustainable agriculture. This study shows that eight rhizosphere protist isolates hosted diverse and distinct bacterial communities and that a large proportion of these bacteria could be found colonizing the maize root environment 6 weeks after protists were inoculated onto seedlings. This study demonstrates that certain bacteria from the maize rhizosphere can persist for years in protist cultures and retain the ability to colonize rhizosphere soil, suggesting that protists might support the survival of these rhizosphere bacteria in the absence of the plant.

EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes

The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss a standardised approach to functionally classify the soil eukaryome in a holistic way. Here we compiled EukFunc, the first functional reference database that characterises the most abundant and functionally important soil eukaryotic groups: fungi, nematodes and protists. We classified the 14,060 species in the database based on their mode of nutrient acquisition into the main functional classes of symbiotroph (40%), saprotroph (26%), phototroph (17%), predator (16%) and unknown (2%). EukFunc provides further detailed information about nutrition mode, including a secondary functional class (i.e., for organisms with multiple nutrition modes), and preyed or associated organisms for predatory or symbiotic taxa, respectively. EukFunc is available in multiple formats for user-friendly functional analyses of specific taxa or annotations of metabarcoding datasets, both embedded in the R package EukFunc. Using a soil dataset from alpine and subalpine meadows, we highlighted the extended ecological insights obtained from combining functional information across the entire soil eukaryome as compared to focusing on fungi, protists or nematodes individually. EukFunc streamlines the annotation process, enhances efficiency and accuracy, and facilitates the investigation of the functional roles of soil eukaryotes-a prerequisite to better understanding soil systems.

Conventional and organic farms with more intensive management have lower soil functionality

Organic farming is often considered to be more sustainable than conventional farming. However, both farming systems comprise highly variable management practices. In this study, we show that in organic and conventional arable fields, the multifunctionality of soils decreases with increasing agricultural management intensity. Soil organic carbon content and bacterial biomass, respectively, were the strongest abiotic and biotic predictors of soil multifunctionality. Greater soil multifunctionality was associated with less-frequent inversion tillage and higher frequency of grass-legume cover cropping, and organic farming did not outperform conventional farming. Our results suggest that reducing management intensity will enhance soil multifunctionality in both conventional and organic farming. This implies that, in contexts where high-yielding, high-intensity agriculture prevails, the paradigm of sustainable intensification should be replaced by "productive deintensification."

Temporal and spatial dynamics of harmful algal bloom-associated microbial communities in eutrophic Clear Lake, California

Clear Lake is a large, natural eutrophic lake located in northern California, United States. Persistent, toxic cyanobacterial blooms have been reported in the lake since 2011. However, our understanding of the spatiotemporal distribution of toxin-producing genera and their interaction with the biotic and abiotic environment is limited. Moreover, few studies have addressed how the co-occurring microbial communities respond to these toxic cyanobacterial blooms. Using multi-domain 16S/18S rRNA gene amplicon sequencing, a strong seasonal succession within the cyanobacterial and co-occurring eukaryotic assemblage was identified, which was primarily explained by variation in total phosphorus (~30%, P < 0.001) and temperature (~15%, P < 0.01). Cyanobacterial seasonal succession was often initiated by proliferation of diazotrophs (Dolichospermum and Nodularia) with concomitant increases in total nitrogen, followed by blooms of non-diazotrophs, such as Microcystis, Limnothrix, and Planktothrix. The picocyanobacterium Cyanobium, previously undocumented in the lake, was a dominant summer taxon in the western part of Clear Lake, accounting for ~45%-80% relative abundance of the cyanobacterial reads. Seasonal succession within the eukaryotic assemblage was influenced by photosynthetic chlorophytes and diatoms, as well as mixotrophic ciliates and cryptophytes. Among all toxin-producing cyanobacterial genera, Microcystis abundance was most strongly correlated with microcystin concentrations (P < 0.001), both of which appeared to influence co-occurring eukaryotes. Finally, using putative relationships based on correlation of sequence abundance and environmental variables, several potential grazers of Microcystis were identified, including cyclopoid copepods and Cryptomonas. These correlations need further confirmation and experimental work to validate the nature of the relationships.IMPORTANCEClear Lake is an important habitat for fish and wildlife, which also provides a myriad of human benefits, such as recreation, irrigation, and drinking water. Moreover, the lake is vital for tribal tradition and cultural practices. However, since the last decade, the lake has experienced recurring harmful algal blooms with toxin levels that frequently exceed California voluntary guidance levels. These high toxin concentrations pose a substantial threat to the residents, visitors, and tribal sustenance fishing and beneficial uses. However, significant gaps remain in our understanding of these toxic algal bloom dynamics and their interaction with the abiotic and biotic environments. This study characterized the seasonal and spatial patterns in the distribution of bloom-causing cyanobacteria and identified Microcystis as the major toxin producer in Clear Lake. Additionally, the co-occurring bacterial and eukaryotic microbial communities were also characterized, and their potential interactions with the cyanobacterial assemblage were identified and discussed.

Identity and timing of protist inoculation affect plant performance largely irrespective of changes in the rhizosphere microbial community

Bacterivorous soil protists can have positive impacts on plant performance, making them attractive targets for novel strategies to improve crop production. However, we generally lack the knowledge required to make informed choices regarding the protist species to be used or the optimal conditions for such amendments. Here, we examined how identity, diversity, and timing of inoculation of well-described protists impacted plant development and rhizosphere microbiome assembly. We first studied the impact of individual inoculation of six well-characterized protists on lettuce growth, with Cercomonas sp. S24D2 emerging as the strain with the largest impact on plant growth. In a second step, we created a three-protist species mixture inoculant by adding two protist species (Acanthamoeba sp. C13D2 and a heterolobosean isolate S18D10), based on differences in their feeding patterns. We then inoculated Cercomonas sp. either individually or in the protist mixture to lettuce plants 1 week before, simultaneously with, or 1 week after seedling transfer. We monitored plant growth and nutrient content, as well as impacts on the resident soil and rhizosphere microbiome composition. We found that early protist inoculation provided the greatest increase in aboveground biomass compared to the non-inoculated control. Single- and mixed-species inoculations had similar impacts on plant development and only minor impacts on prokaryotic community composition. While early inoculation seems to be the most promising timing for eliciting the positive effects of protist amendments, further, more systematic studies will be necessary to determine the conditions and ecological interactions that yield consistent and predictable improvements in plant performance.

IMPORTANCE

The application of microorganisms, including bacterivorous soil protists, has been increasingly suggested as a sustainable agricultural approach. While positive impacts of the presence of predatory protists have been generally reported, the effects of the selected species and amendment conditions are largely unknown. Here, we examined how identity, diversity, and timing of inoculation of well-described protists impacted plant development and rhizosphere microbiome assembly. One species emerged as the one having the strongest impact in our specific system. This result highlights the importance of species selection for optimal outcome, but also suggests a huge potential in the barely investigated protist diversity for targeted application. Furthermore, the application of the inoculants before plant transfer showed the strongest effects on plants, providing some useful and new insights on the optimal time for such amendments.

Unraveling the relationships between midge abundance and incidence, microbial communities, and soil and water properties in a protected natural tallgrass prairie

BACKGROUND

Biting midges (Culicoides spp.) are small blood-feeding flies (Diptera: Ceratopogonidae) that transmit numerous pathogens that impact animal and human health. The larvae of several Culicoides spp., including vectors, are often found in organically enriched, moist soil habitats. However, the influence of biotic (e.g., cohabiting fauna, potential prey taxa) and abiotic factors (e.g., soil or water properties, time) on abundance and incidence of larval Culicoides in natural habitats is not well understood. This study evaluated the relationships between bacterial and protistan communities, soil and water physicochemical properties, and the abundance and incidence of Culicoides species in larval habitats at the Konza Prairie Biological Station in Kansas.

METHODS

Soil and water samples were collected monthly from March 2021 to February 2022 from four midge larval habitat sites, including three grazed (low-production cattle-grazed (LPCG), high-production cattle-grazed (HPCG), and bison-grazed sites) and one formally ungrazed (i.e., no managed large mammals) site. Midge incidence and abundance were evaluated using emergence assays, which assessed the number of adults emerging from collected soil samples, and bacterial and protistan communities in these samples were characterized through amplicon sequencing of the 16S and 18S rRNA genes. Physicochemical properties of water and soil were also analyzed.

RESULTS

Irrespective of site, the highest midge abundance was reported in warmer months between March and September, except June. Moreover, the greatest midge abundance, incidence, and prevalence occurred at the HPCG and bison-grazed sites, which had a persistent water source. Specific lineages of bacterial and protistan communities, soil texture, organic matter, and total dissolved solids in water samples were directly associated with the abundance of Culicoides spp. that emerged from soil samples.

CONCLUSIONS

Both biotic (bacterial and protistan communities, presence of host animals), and abiotic (soil and water properties, season) factors affected the abundance and incidence of Culicoides spp. in natural habitats. The results presented in this study expand our understanding of the ecological and environmental factors influencing larval ecology of biting midges in natural developmental substrates. These insights have important implications for identifying potential developmental sites, which can be used for targeted management of Culicoides.

Assessment of ship hull-attached marine diatoms: species composition and reattachment

Ship biofouling is a primary pathway for the introduction and global spread of non-indigenous species, posing significant risks to marine ecosystems. However, the extent to which ship hull-attached diatoms survive and disperse following in-water hull cleaning (IwHC) remains poorly understood. Here, we analyzed the attached diatoms compositions in the in-water hull cleaning water (IwHCW) from three international ships entering Korea as well as benthic diatoms at nearby stations, using both morphological and molecular methods. In addition, we assessed the survival of ship hull-attached diatoms using reattachment analysis. Water temperature and salinity varied during sampling of the IwHCW of the ships, while the conditions at the four nearby stations were more consistent. The diatom Halamphora spp. was most abundant in the IwHCW of the ships, whereas Achnanthes species dominated at the nearby stations. Non-metric Multidimensional Scaling (NMDS) revealed significant variation in species composition between the IwHCW and the stations, suggesting limited dispersal of ship-associated diatoms or spatiotemporal influences. Survival and reattachment analyses revealed that Halamphora oceanica survived for over 21 days in unfiltered IwHCW, with no attached diatoms observed in IwHCW filtered through 5 and 32 μm filters. These findings indicate that diatoms in an unfiltered IwHCW may survive and reattach to substrates, highlighting the need for IwHC risk assessment and biofouling management in coastal waters.

Patterns and drivers of diatom diversity and abundance in the global ocean

Diatoms constitute one of the most diverse and ecologically important phytoplankton groups, yet their large-scale diversity patterns and drivers of abundance are unclear due to limited observations. Here, we utilize Tara Oceans molecular and morphological data, spanning pole to pole, to describe marine diatom diversity, abundance, and environmental adaptation and acclimation strategies. The dominance of diatoms among phytoplankton in terms of relative abundance and diversity is confirmed, and the most prevalent genera are Chaetoceros, Thalassiosira, Actinocyclus and Pseudo-nitzschia. We define 25 distinct diatom communities with varying environmental preferences illustrative of different life strategies. The Arctic Ocean stands out as a diatom hotspot with 6 of the diatom communities being exclusive to it. Light harvesting and photoprotection are among the cellular functions in which natural diatom populations invest the bulk of their transcriptional efforts. This comprehensive study sheds light on marine diatom distributions, offering insights to assess impacts of global change and oceanic anthropogenic impacts.

Cryptic infection of a giant virus in a unicellular green alga

Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown. Here we describe a 617 kbp integrated giant viral element in the model green alga Chlamydomonas reinhardtii. We resolve the integrated viral genome using long-read sequencing, identify a putative polinton-like integrase, and show that viral particles accumulate primarily during the stationary growth phase. A diverse array of viral-encoded selfish genetic elements is expressed during viral activity, including several Fanzor nuclease-encoding transposable elements. In addition, we show that field isolates of Chlamydomonas sp. harbor signatures of endogenous giant viruses related to the C. reinhardtii virus that exhibit similar infection dynamics, suggesting that giant virus latency is prevalent in natural host communities. Our work describes an unusually large temperate virus of a unicellular eukaryote, substantially expanding the scope of cryptic viral infections in the virosphere.

Altered precipitation and nighttime warming reshape the vertical distribution of soil microbial communities

Soil depth determines microbial community composition. Yet, it remains largely unexplored how climate changes affect the vertical distribution of soil microbial communities. Here, we investigated the effects of altered precipitation and nighttime warming on microbial communities in the topsoils (0-20 cm) and subsoils (20-50 cm) of a temperate grassland in Inner Mongolia, China. As commonly observed under nutrient scarcity conditions, bacterial and fungal α-diversity and network complexity decreased with soil depth. However, protistan α-diversity and network complexity increased, which was attributed to less niche overlap and smaller body size. Strikingly, the slopes of linear regressions of microbial α-diversity/network complexity and soil depth were all reduced by altered precipitation. Microbial community composition was significantly influenced by both depth and reduced precipitation, and to a lesser extent by nighttime warming and elevated precipitation. The ribosomal RNA gene operon (rrn) copy number, a genomic proxy of bacterial nutrient demand, decreased with soil depth, and the percentages of positive network links were higher in the subsoil, supporting the "hunger game" hypothesis. Both reduced precipitation and nighttime warming decreased the rrn copy number in the subsoils while increasing the percentages of positive links, enhancing potential niche sharing among bacterial species. The stochasticity level of bacterial and fungal community assemblies decreased with soil depth, showing that depth acted as a selection force. Altered precipitation increased stochasticity, attenuating the depth's filtering effect and diminishing its linear relationship with microbial diversity. Collectively, we unveiled the predominant influence of altered precipitation in affecting the vertical distribution of soil microbial communities.IMPORTANCEUnderstanding how climate change impacts the vertical distribution of soil microbial communities is critical for predicting ecosystem responses to global environmental shifts. Soil microbial communities exhibit strong depth-related stratification, yet the effects of climate change variables, such as altered precipitation and nighttime warming, on these vertical patterns have been inadequately studied. Our research uncovers that altered precipitation disrupts the previously observed relationships between soil depth and microbial diversity, a finding that challenges traditional models of soil microbial ecology. Furthermore, our study provides experimental support for the hunger game hypothesis, highlighting that oligotrophic microbes, characterized by lower ribosomal RNA gene operon (rrn) copy numbers, are selectively favored in nutrient-poor subsoils, fostering increased microbial cooperation for resource exchange. By unraveling these complexities in soil microbial communities, our findings offer crucial insights for predicting ecosystem responses to climate change and for developing strategies to mitigate its adverse impacts.

Parasite sedimentary DNA reveals fish introduction into a European high-mountain lake by the seventh century

High-mountain lakes were historically fishless due to natural barriers, but human introductions have led to widespread fish presence. Although particularly intensive during the last decades, historical documents indicate introductions in European high mountains already during the 14th and 15th centuries, but they could have occurred before, provided the intensive land use of the high mountain had started earlier. We used ancient environmental DNA from lake sediments (sedDNA) to investigate this hypothesis. Fish ectoparasites from various clades were identified using the 18S rRNA gene in the sediment record of a deep, high-mountain Pyrenean lake, with Ichthyobodo (Kinetoplastea) being of particular interest due to its consistent occurrence. The study shows a continued presence of fish parasites in the lake since the 7th century, which coincides with the Late-Roman and Visigothic extensive mountain use for sheep pasturing as supported by nearby archeological remains and increased lake primary production evidenced by photosynthetic pigments.

Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot

The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00300-025-03380-y.

Impacts of forest expansion on microbial diversity and community assembly in fragmented mountain ecosystems

Under the influence of global climate change and human activities, forest expansion has become increasingly significant in shaping ecosystems. However, its effects on soil microbial communities remain poorly understood. This study investigates the impacts of forest expansion on soil bacteria, fungi, and protists within mountaintop forest ecosystems. Soil samples were collected from three forest habitats: non-forest expansion mountaintops (NFE-Top), forest expansion mountaintops (FE-Top) and mountain bottoms (FE-Bottom). This study revealed that forest expansion promoted microbial sharing between mountaintop and bottom forests, resulting in greater community similarity between FE-Top and FE-Bottom compared to NFE-Top and FE-Bottom. Notably, forest expansion significantly reduced microbial diversity and altered community composition, particularly within bacterial communities. Microbial network analyses indicated that forest expansion mountaintops were more stable, with higher robustness, and lower vulnerability than non-forest expansion mountaintops. Stochastic assembly processes dominated the microbial communities across all forest habitats, with their relative importance increasing after forest expansion. Furthermore, forest expansion decreased the community-level habitat niche breadth of microbial communities. Distinct environmental factors were the primary indicators of microbial community dissimilarities across different habitats, with TP, pH, and moisture acting as key indicators of these differences in NFE-Top, FE-Top, and FE-Bottom, respectively. These findings highlight the important role of forest expansion in shaping microbial community dynamics and emphasize the potential of microbial communities as indicators of ecosystem changes.

Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers

Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.

Seasonal dynamics and factors shaping microbiomes in freshwater finfish earthen aquaculture ponds in Bangladesh

BACKGROUND

The pondwater microbiome is believed to play a key role in fish health, including shaping mucosal surface microbiomes that help to protect against disease. How different physiochemical features relating to season, geographical locations, as well as crop species shape the pond water microbiome in the finfish aquaculture system, is not well established. Pangasius (Pangasianodon hypophthalmus) and tilapia (Oreochromis niloticus) are two of the most widely farmed fish species and disease is a major impediment to the expansion of their production. We applied 16S and 18S rRNA metabarcoding to assess how pond physicochemistry and geographical location shape water microbiomes in pangasius and tilapia aquaculture earthen ponds in Bangladesh.

RESULTS

Planctomycetota, Pseudomonadota and Actinomycetota were the dominant bacterial phyla while Stramenopiles and Alveolata were the dominant microeukaryotes (divisions) in the pangasius and tilapia ponds water. The relative abundance of Planctomycetota was higher in the pangasius ponds compared with tilapia ponds, and Actinomycetota, and Pseudomonadota were relatively higher in tilapia ponds. Tilapia pond water also exhibited a higher microbial diversity compared to that in pangasius ponds. The pondwater microbial diversity was at its lowest in winter (and/or in monsoon) and highest in the pre-monsoon period. The microbial community structures differed across the different seasons, geographical locations, culture systems, and crop species, with season and geographical locations showing the strongest effects. Of the water physicochemistry features assessed, temperature and pH were found to have a weak but significant effect on the water microbiome content for both pangasius and tilapia ponds. Pangasius and tilapia ponds shared over 46% of ASVs, and around 30% of ASVs were shared across the different study geographical locations.

CONCLUSION

Our findings demonstrate that microbial communities in pangasius and tilapia aquaculture systems in Bangladesh are shaped by season, geographical location, crop species, as well as effects from water physicochemistry. Our results provide insights into the dynamic nature and environmental influences on water microbiomes that may be applied for use in pond management for improving aquaculture productivity and enhancement of overall fish health.

Light-Mediated Population Dynamics of Picocyanobacteria Shaping the Diurnal Patterns of Microbial Communities in an Atoll Lagoon

The diurnal cycle of light significantly impacts microbes, making diurnal investigations crucial for understanding microbial communities. Zhubi Reef is known to harbor exceptionally rich biodiversity, with both zooplankton and seawater properties demonstrating diurnal patterns. However, microbial community structures and their potential diurnal dynamics remain largely unexplored. This study is the first to utilize flow cytometry and high-throughput sequencing to investigate prokaryotic and microeukaryotic communities in the Zhubi lagoon, focusing on diurnal variations under different light intensities. The picophytoplankton cell abundance and the microbial community structures both exhibit clear diurnal variations. Light is identified as the primary driver of diurnal variations in the picophytoplankton cell abundance. The diurnal variation in microbial community diversity is driven by changes in the cell abundance of two dominant picocyanobacterial groups. Our findings reveal the diurnal variation in microbial community structures is mediated by the light-driven fluctuation of dominant cyanobacterial populations, and the diurnal variation patterns of specific populations may vary with habitats and sampling timepoints. This research provides valuable insights into the microbial community structure within the Zhubi lagoon.

Traits determine dispersal and colonization abilities of microbes

Many microbes disperse through the air, yet the phenotypic traits that enhance or constrain aerial dispersal or allow successful colonization of new habitats are poorly understood. We used a metabarcoding bacterial and eukaryotic data set to explore the trait structures of the aquatic, terrestrial, and airborne microbial communities near the Salton Sea, California, as well as those colonizing a series of experimental aquatic mesocosms. We assigned taxonomic identities to amplicon sequence variants (ASVs) and matched them to functional trait values through published papers and databases that infer phenotypic and/or metabolic traits information from taxonomy. We asked what traits distinguish successful microbial dispersers and/or colonizers from terrestrial and aquatic source communities. Our study found broad differences in taxonomic and trait composition between dispersers and colonizers compared to the source soil and water communities. Dispersers were characterized by larger cell diameters, colony formation, and fermentation abilities, while colonizers tended to be phototrophs that form mucilage and have siliceous coverings. Shorter population doubling times, spore-, and/or cyst-forming organisms were more abundant among the dispersers and colonizers than the sources. These results show that the capacity for aerial dispersal and colonization varies among microbial functional groups and taxa and is related to traits that affect other functions like resource acquisition, predator avoidance, and reproduction. The ability to disperse and colonize new habitats may therefore distinguish microbial guilds based on tradeoffs among alternate ecological strategies.IMPORTANCEMicrobes have long been thought to disperse rapidly across biogeographic barriers; however, whether dispersal or colonization vary among taxa or groups or is related to cellular traits remains unknown. We use a novel approach to understand how microorganisms disperse and establish themselves in different environments by looking at their traits (physiology, morphology, life history, and behavior characteristics). By collecting samples from habitats including water, soil, and the air and colonizing experimental tanks, we found dispersal and invasion vary among microorganisms. Some taxa and functional groups are found more often in the air or colonizing aquatic environments, while others that are commonly found in the soil or water rarely disperse or invade new habitat. Interestingly, the traits that help microorganisms survive and thrive also play a role in their ability to disperse and colonize. These findings have significant implications for understanding microorganisms' success and adaptation to new environments.

Eukaryotic phytoplankton drive a decrease in primary production in response to elevated CO2 in the tropical and subtropical oceans

Ocean acidification caused by increasing anthropogenic CO2 is expected to impact marine phytoplankton productivity, yet the extent and even direction of these changes are not well constrained. Here, we investigate the responses of phytoplankton community composition and productivity to acidification across the western North Pacific. Consistent reductions in primary production were observed under acidified conditions in the North Pacific Subtropical Gyre and the northern South China Sea, whereas no significant changes were found at the northern boundary of the subtropical gyre. While prokaryotic phytoplankton showed little or positive responses to high CO2, small (<20 µm) eukaryotic phytoplankton which are primarily limited by low ambient nitrogen drove the observed decrease in community primary production. Extrapolating these results to global tropical and subtropical oceans predicts a potential decrease of about 5 Pg C y-1 in primary production in low Chl-a oligotrophic regions, which are anticipated to experience both acidification and stratification in the future.

Assessment of the short-term salinity effect on algal biofilm through field transfer in the Drâa river (Southeastern Morocco) using metabarcoding and morphological analyses

As a result of human activities and climate change, salinity levels have risen considerably in many of the world's rivers, particularly in arid and semi-arid areas. This freshwater salinization primarily affects microalgal biofilms, the primary producers in aquatic ecosystems. This study is aimed at assessing short-term salinity effects on benthic algal communities in the Drâa river, Morocco, using biofilm field-transfer experiments. Artificial substrates were initially positioned in three sites of the Drâa river with different salinity levels. After 4 weeks, the biofilm-colonized substrates were transferred from one site to another in both directions. After a further 4 weeks, the algal biofilms were sampled to assess their community composition, alpha and beta diversity, and biomass in response to salinity changes using molecular and morphological analyses. Transferring biofilms from low-salt to saline sites significantly reduced biomass but increased it in the reverse transfer. Eliminating certain sensitive microalgae taxa decreased alpha diversity in all biofilm transfers from low-salt sites to the most saline one. Biofilm diversity increased significantly in the opposite transfer. Significant changes were observed in biofilm composition when transferred into saltwater showing an increase in halophilic and euryhaline diatom taxa. In contrast, transfers from saltwater sites to low-salt sites increased oligohaline diatom species. As a result, increasing salinity reduced algal biomass and diversity, while decreasing salinity caused the opposite effect. These results can help predict the salinity variations effects on benthic algae, highlight the potential dangers of increased river salinization, and promote salinity reduction in aquatic ecosystems subject to secondary salinization.

Amoeba community dynamics and assembly mechanisms in full-scale drinking water distribution networks under various disinfectant regimens

Free-living amoebae (FLA) are prevalent in drinking water distribution networks (DWDNs), yet our understanding of FLA community dynamics and assembly mechanisms in DWDNs remains limited. This study characterized the occurrence patterns of amoeba communities and identified key factors influencing their assembly across four full-scale DWDNs in three Chinese cities, each utilizing different disinfectants (chlorine, chloramine, and chlorine dioxide). High-throughput sequencing of full-length 18S rRNA genes revealed highly diverse FLA communities and an array of rare FLA species in DWDNs. Unique FLA community structures and higher gene copy numbers of three amoeba taxa of concern (Vermamoeba vermiformis, Acanthamoeba, and Naegleria fowleri) were observed in the chloraminated DWDN, highlighting the distinct impact of chloramine on shaping the amoeba community. The FLA communities in DWDNs were primarily driven by deterministic processes, with disinfectant and nitrogen compounds (nitrate, nitrite, and ammonia) identified as the main influencing factors. Machine learning models revealed high SHapley Additive exPlanations (SHAP) values of dominant amoeba genera (e.g., Vannella and Vermamoeba), indicating their critical ecological roles in shaping broader bacterial and eukaryotic communities. Correlation analyses between amoeba genera and bacterial taxa revealed that 82 % of the bacterial taxa exhibiting a negative correlation with amoebae were gram-negative, suggesting the preferred predation of amoebae toward gram-negative bacteria. Network analysis revealed the presence of only one to two amoebae in distinct modules, suggesting that individual amoebae might be selective in grazing. These findings provide insight into the amoeba community dynamics, assembly mechanisms and ecological roles of amoebae in drinking water, which can aid in risk assessments and mitigation strategies within DWDNs.

Comparison of Relative and Absolute Abundance and Biomass of Freshwater Phytoplankton Taxa Using Metabarcoding and Microscopy

Phytoplankton is the basis of the food web and an indicator of environmental change in aquatic ecosystems. Phytoplankton assessment uses microscopy, which estimates the composition, absolute abundance and biomass of taxa, and metabarcoding, which estimates the composition, high richness and diversity, and relative abundance of taxa. Problems remain with the consistency of results from these two methods and the quantification of metabarcoding. Using 18S rRNA metabarcoding and microscopy we compared the relative or absolute abundance and biomass of phytoplankton taxa (class or genus/species) in the south basin of Lake Baikal in spring over 3 years. Absolute abundance/biomass of phytoplankton taxa estimated by metabarcoding was obtained by combining relative abundances of amplicon sequence variants (ASV produced by error-correcting method) derived from the V8-V9 region of 18S rRNA gene amplicon sequencing (primers were used that accurately represented the mean relative abundance of different microalgae) with total or class-specific abundance/biomass of phytoplankton estimated by light microscopy. Many Spearman correlations were found between relative (non- or clr-transformed) or absolute abundances/biomasses of the same phytoplankton classes or genus/species. Correlation coefficients were higher between absolute values than between relative values. Correlations were found between relative or absolute abundance/biomass, estimated by both methods, of the classes Bacillariophyceae, Coscinodiscophyceae, Mediophyceae, Chrysophyceae, Cryptophyceae, and Chlorophyceae, but not Dinophyceae and Trebouxiophyceae. Correlations were found between relative or absolute abundance/biomass of dominant species and ASVs of diatoms (Ulnaria, Aulacoseira, Stephanodiscus), Chrysophyceae (Dinobryon), and Cryptophyceae (Cryptomonas). Thus, the consistency of the dynamics of the relative or absolute abundance/biomass of phytoplankton taxa estimated by the two methods was revealed. Absolute abundances/biomasses of taxa estimated by metabarcoding in combination with microscopy improve the accuracy of metabarcoding-based ecological assessment.

Macroalgal Biofilm Harbours a Wide Diversity of Parasitic Protists With Distinct Temporal Dynamics

Marine macroalgae surfaces create a nutrient-rich environment that promotes the formation of epiphyte biofilms. Biofilms are complex systems that facilitate ecological interactions within the community, yet parasitism remains largely unexplored. This study describes the diversity and temporal dynamics of the microeukaryotic community in the biofilm of Mediterranean macroalgae during summer, focusing on parasitic groups. Protist diversity was assessed using metabarcoding sequencing of the V4 region of the 18S rDNA gene using primers biased against metazoans. The macroalgal biofilm exhibited dynamic shifts in the microeukaryotic community structure associated to three phases of biofilm formation. Each phase was characterised by the dominance of specific eukaryotic and parasitic groups with clear successions between them. Our study revealed a high diversity of parasitic protists from different lineages in the macroalgal biofilm. These parasites can infect a wide variety of hosts, including the basibiont, species within the biofilm (micro- and macrocolonizers), nearby marine hosts and terrestrial organisms. The highest diversity and abundance of parasites were found in the mature phase of the biofilm, where the complexity and stability of the system seem to favour parasitism. The parasite assemblage was dominated by Apicomplexa, with many corresponding to unknown diversity, demonstrating that biofilms are a hotspot of unknown parasitic interactions. These parasites could potentially affect the dynamics of these communities and facilitate ecological interactions between the biofilm and surrounding organisms, suggesting that parasitism play a key, but still unexplored role, in shaping complex marine biofilms network.

The relationship between protist consumers and soil functional genes under long-term fertilization

Protists play a crucial role in terrestrial ecosystems by participating in biogeochemical cycles and contributing to ecological balance and stability. However, much remains to be understood about the intricate interactions between soil protists and biogeochemical processes. Here, we collected rhizosphere soil samples from seven distinct fertilization treatments to investigate the responses of bacteria, protists and functional genes to these varying fertilization practices during sorghum's maturity season. The community composition of both protists and bacteria were significantly affected by different fertilization treatments, with organic fertilization increasing protist diversity but not affecting bacterial diversity. There were noticeable variations in the compositions of functional genes across different fertilization treatments, with organic fertilization enhancing the relative abundance of carbon and phosphorus cycling genes. While fertilization generally increased the relative abundance of protistan consumers, it was observed that organic fertilizers decreased the relative abundance of phototrophs. A substantial number of bacterial taxa, including Acidibacter, Steroidobacter, Lysobacter and Agromyces, which correlated positively with functional genes, were found to be prey for protistan consumers, indicating their crucial role in predicting soil functional genes. Altogether, this study highlights the significant impact of fertilization treatments, especially organic fertilization, on the diversity and functional dynamics of protist and bacterial communities, emphasizing the key role of protistan consumers in regulating the soil microbial community and modulating soil biogeochemical cycles.

The Rise of Algae promoted eukaryote predation in the Neoproterozoic benthos

The proliferation of marine algae in the Neoproterozoic Era is thought to have stimulated the ecology of predatory microbial eukaryotes. To test this proposal, we introduced algal particulate matter (APM) to marine sediments underlying a modern marine oxygen minimum zone with bottom-water oxygen concentrations approximating those of the late Neoproterozoic water column. We found that under anoxia, APM significantly stimulated microbial eukaryote gene expression, particularly genes involved in anaerobic energy metabolism and phagocytosis, and increased the relative abundance of 18S rRNA from known predatory clades. We additionally confirmed that APM promoted the reproduction of benthic foraminifera under anoxia with higher-than-expected net growth efficiencies. Overall, our findings suggest that algal biomass exported to the Neoproterozoic benthos stimulated the ecology of benthic predatory protists under anoxia, thereby creating more modern food webs by enhancing the transfer of fixed carbon and energy to eukaryotes occupying higher trophic levels, including the earliest benthic metazoans.

Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA

The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.

With a little help from my friends: importance of protist-protist interactions in structuring marine protistan communities in the San Pedro Channel

Marine protists form complex communities that are shaped by environmental and biological ecosystem properties, as well as ecological interactions between organisms. While all of these factors play a role in shaping protistan communities, the specific ways in which these properties and interactions influence protistan communities remain poorly understood. Fourteen years and 9 months of eukaryotic amplicon (18S-V4 rRNA gene) data collected monthly at the San Pedro Ocean Time-series (SPOT) station were used to evaluate the impacts that environmental and biological factors, and protist-protist interactions had on protistan community composition. Statistical analysis of the amplicon data revealed that seasonal patterns in protistan community composition were apparent, but that the environmental data collected through routine time-series sampling efforts could not explain most of the variability that was evident in the communities. To identify some of the protist-protist interactions that may have played a role in shaping protistan communities, ecological networks were constructed using the amplicon data and the network predictions were compared against a database of confirmed protist-protist interactions. The database comparisons revealed hundreds of established parasitic, predator-prey, photosymbiotic, and mutualistic relationships in the networks. Although many interactions were confirmed using the database, these confirmed interactions constituted only 2% of the interactions identified at the SPOT station, highlighting the need to better characterize protist-protist interactions in marine environments. Finally, the network-predicted interactions that were not found in the database were used to identify putative, novel protist-protist interactions that may have played a role in structuring the protistan communities at the SPOT station.

IMPORTANCE

Network analyses are commonly used to identify some of the ecological interactions that may be occurring between protists in the ocean; however, evaluating predictions obtained from these analyses remains difficult due to the large number of interactions that may be recovered and the limited amount of information available on protist-protist interactions in nature. In this study, ecological network analyses were conducted using data collected at the San Pedro Ocean Time-series (SPOT) station and the network predictions were compared against a database of established protist-protist interactions. These database comparisons revealed hundreds of confirmed protist-protist interactions, and thousands of putative, novel interactions that may be occurring at the SPOT station. The database comparisons carried out in this study provide a new way of evaluating network predictions and highlight the complex, yet critical role that ecological interactions play in shaping protistan community composition in marine ecosystems.

Temporal succession of marine microbes drives plastisphere community convergence in subtropical coastal waters

Marine plastic pollution is a pervasive environmental issue, with microplastics serving as novel substrates for microbial colonization in aquatic ecosystems. This study investigates the succession of plastisphere communities on four common plastic types (polyethylene, polypropylene, polyethylene terephthalate, and polystyrene) in subtropical coastal waters of Hong Kong SAR. Over a 42-day period, we analysed the temporal development of microbial communities using a three-domain universal metabarcoding method. Our results reveal that temporal succession is a stronger driver of community structure than plastic type, with prokaryotic communities converging across different plastics as biofilms mature. Despite this convergence, plastisphere communities remain distinct from planktonic communities throughout the experiment, suggesting that plastics create unique ecological niches in marine environments. We observed differences in diversity patterns and community composition among prokaryotic, eukaryotic, and chloroplastic communities, highlighting the importance of multi-domain analyses in plastisphere research. Functional predictions suggest potential roles of prokaryotic communities in biogeochemical cycling and possible pathogenicity, highlighting the ecological and public health implications of plastisphere formation. This study provides valuable insights into the dynamics of microbial colonization across domains on marine plastics and enhances our understanding of how these anthropogenic substrates influence microbial ecology in marine ecosystems.

Dynamics of wheat rhizosphere microbiome and its impact on grain production across growth stages

Crop plant microbiomes are increasingly seen as important in plant nutrition and health, and a key to maintaining food productivity. Currently, little is known of the temporal changes that occur in the wheat rhizosphere microbiome as the plant develops, and how this varies among different sites. We used a pot-based mesocosm experiment with the same modern wheat cultivar grown in eight soils from across the North China Plain, a major wheat producing area. DNA from rhizosphere soil was taken from wheat plants, from seedling up to grain harvesting stage, and amplicon sequenced for prokaryotes and microeukaryotes, followed by community analysis. Our results showed that rhizosphere diversity of prokaryotes and microeukaryotes increased over time in most sites. While there was turnover between earlier- and later-arriving species, the predominant successional model was accumulation, with early arrivals remaining in place as others colonized the rhizosphere. Rhizosphere community network modularity and stability increased during the development and maturation of the wheat plant. The abundances of certain stage-specific keystone species were correlated with eventual grain yield - suggesting a potentially important role in wheat production. Some keystone species belonged to groups previously implicated in various functions. This study provides a basis for further experimental investigation of the wheat rhizosphere microbiome, its role in determining crop yields, and the potential for microbiome engineering to promote yields. The sequential arrival and accumulation of microbiota suggests that deliberate inoculation might accelerate this process.

Spatial and temporal variation of Antarctic microbial interactions: a study around the west Antarctic Peninsula

BACKGROUND

The west Antarctic Peninsula (WAP) is a region of rapid environmental changes, with regional differences in climate warming along the north-south axis of the peninsula. Along the WAP, Palmer corresponds to a warmer region with lesser sea ice extent in the north compared to Rothera ~ 400 km to the south. Comprehensive and comparative, year-round assessments of the WAP microbial community dynamics in coastal surface waters at these two locations are imperative to understand the effects of regional climate warming variations on microbial community dynamics, but this is still lacking.

RESULTS

We report on the seasonal diversity, taxonomic overview, as well as predicted inter-and intra-domain causal effects (interactions) of the bacterial and microbial eukaryotic communities close to the Palmer station and at the Rothera time-series site between July 2013 and April 2014. Our 16S- and 18S-rRNA gene amplicon sequencing data showed that across all seasons, both bacteria and microbial eukaryotic communities were considerably different between the two sites which could be attributed to seawater temperature, and sea ice coverage in combination with sea ice type differences. Overall, in terms of biotic drivers, causal-effect modelling suggests that bacteria were stronger drivers of ecosystem dynamics at Palmer, while microbial eukaryotes played a stronger role at Rothera. The parasitic taxa Syndiniales persevered at both sites across the seasons, with Palmer and Rothera harbouring different key groups. Up to 62.3% of the negative causal effects were driven by Syndiniales at Rothera compared to only 13.5% at Palmer, suggesting that parasitism drives community dynamics at Rothera more strongly than at Palmer. Conversely, SAR11 Clade II, which was less abundant but persistent year-round at both sites, was the dominant driver at Palmer, evidenced by many (28.2% and 37.4% of positive and negative effects respectively) strong causal effects. Article note: Kindly check first page article notes are correct.

CONCLUSIONS

Our research has shed light on the dynamics of microbial community composition and correlative interactions at two sampling locations that represent different climate regimes along the WAP.

Enhancing microbial predator-prey detection with network and trait-based analyses

BACKGROUND

Network analyses are often applied to microbial communities using sequencing survey datasets. However, associations in such networks do not necessarily indicate actual biotic interactions, and even if they do, the nature of the interactions commonly remains unclear. While network analyses are valuable for generating hypotheses, the inferred hypotheses are rarely experimentally confirmed.

RESULTS

We employed cross-kingdom network analyses, applied trait-based functions to the microorganisms, and subsequently experimentally investigated the found putative predator-prey interactions to evaluate whether, and to what extent, correlations indicate actual predator-prey relationships. For this, we investigated algae and their protistan predators in biocrusts of three distinct polar regions, i.e., Svalbard, the Antarctic Peninsula, and Continental Antarctica. Network analyses using FlashWeave indicated that 89, 138, and 51 correlations occurred between predatory protists and algae, respectively. However, trait assignment revealed that only 4.7-9.3% of said correlations link predators to actually suitable prey. We further confirmed these results with HMSC modeling, which resulted in similar numbers of 7.5% and 4.8% linking predators to suitable prey for full co-occurrence and abundance models, respectively. The combination of network analyses and trait assignment increased confidence in the prediction of predator-prey interactions, as we show that 82% of all experimentally investigated correlations could be verified. Furthermore, we found that more vicious predators, i.e., predators with the highest growth rate in co-culture with their prey, exhibit higher stress and betweenness centrality - giving rise to the future possibility of determining important predators from their network statistics.

CONCLUSIONS

Our results support the idea of using network analyses for inferring predator-prey interactions, but at the same time call for cautionary consideration of the results, by combining them with trait-based approaches to increase confidence in the prediction of biological interactions. Video Abstract.

Terroir and farming practices drive arbuscular mycorrhizal fungal communities in French vineyards

Background

Nature-based management of vineyards is at the heart of a sustainable development for the next decades. Although much is known about grapevine benefits from Arbuscular Mycorrhizal Fungi (AMF), little is known about the influence of vineyard terroir and farming practices on AMF communities.

Methods

We examined the relative effect of wine terroir and agricultural practices (organic, conversion, and conventional) on AMF abundance and diversity across 75 vineyards distributed over 14 wine terroirs in 6 winegrowing regions in France. We estimate AMF abundance by measuring spore density and root mycorrhization rates, and characterize AMF communities composition using metabarcoding by sampling both root and spore compartments for each vineyard.

Results

Organic farming slightly increases AMF abundance (spore density and mycorrhization rate). Vineyards under conversion and using organic practices display a higher AMF diversity than conventional ones. Terroirs vary widely in terms of AMF abundance and diversity, with the median of OTUs count per sample ranging from 9 (Côte des Blancs) to 35 (Gigondas). The composition of AMF communities is structured mainly by terroir and in a lesser extent by practice. The effect of terroir on AMF communities is partially explained by distance decay and soil properties, but the majority of variation is still explained only by the terroir identity. Organic practices improve both abundance and diversity of AMF in vineyards, possibly leading to more productivity and resilience of grapevines.

Conclusion

This large-scale study highlights the importance of terroir in our understanding of vineyard microbiome and paves the way to incorporation of AMF in microbial terroir studies and applications.

Shallow Hydrothermal Fluids Shape Microbial Dynamics at the Tagoro Submarine Volcano (Canary Islands, Spain)

Shallow underwater hydrothermal systems are often overlooked despite their potential contribution to marine diversity and biogeochemistry. Over a decade after its eruption, the Tagoro submarine volcano continues to emit heat, reduced compounds, and nutrients into shallow waters, serving as a model system for studying the effects of diffuse hydrothermal fluids on surface microbial communities. The impact on both phytoplankton and bacterial communities was examined through experimental manipulations mimicking dilution levels up to ~100 m from the primary crater of Tagoro. Chlorophyll a concentration doubled in the presence of hydrothermal products, with peak levels detected about a day earlier than in controls. Picoeukaryotes and Synechococcus cell abundances moderately increased, yet small eukaryotic phytoplankton (≤ 5 μm) predominated in the hydrothermally enriched bottles. Dinoflagellates, diatoms, small green algae and radiolarians particularly benefited from the hydrothermal inputs, along with phototrophic and chemoautotrophic bacteria. Our results indicate that hydrothermal products in shallow waters enhance primary production driven by phototrophic microbes, potentially triggering a secondary response associated with increased organic matter availability. Additionally, protistan grazing and parasitism emerged as key factors modulating local planktonic communities. Our findings highlight the role of shallow submarine hydrothermal systems in enhancing local primary production and element cycling.

Indications of a benthic foraminifer Cribrononion gnythosuturatum to salinities revealed by eDNA metabarcoding and morphological methods

Cribrononion gnythosuturatum is a widely distributed benthic foraminifer. However, its adaptability to salinity changes is still poorly understood. To investigate the response of C. gnythosuturatum to salinity changes, sediment samples were collected from an intertidal zone of the Yellow Sea and cultured at 13 salinity gradients from 0 to 60 psu for 10 weeks. The results of the culture experiments were analyzed using morphological and eDNA methods. The results showed that extremely high tests broken rate at low salinities (<15 psu). Under high salinities (>50 psu), the stained protoplasm was concentrated in the center of the chambers. Meanwhile, both morphological and eDNA metabarcoding results showed that under abnormal salinity conditions (15-25 psu or 40-50 psu), the abundance, relative abundance and growth rate of C. gnythosuturatum reached the maximum value, while the tests were well preserved. This study reveals the mechanism by which C. gnythosuturatum is used as a salinity indicator for paleoenvironments.

Contribution of environmental and biological factors to bacterial community structure and stability in a subalpine lake

Bacterial community play an essential role in regulating water quality and the global biogeochemical cycle in aquatic ecosystems. However, how trophic interactions (i.e., biotic factors) regulate the diversity and composition of bacterial community in lake ecosystems remains unknown. Here, we employed DNA meta-barcoding of water samples to explore the impact of bacterivorous protozoans on the bacterial community. The results showed significant seasonal variations in the diversity and composition of both bacterial and protist communities. The composition of bacterivorous protozoans was identified as the primary predictor for the bacterial community alpha diversity in spring and summer, and for beta diversity in spring and autumn, indicating that biotic interactions play a greater role in driving the diversity of bacterial community across different seasons. Biological factors were more important than environmental factors for explaining the variations in the relative abundance of several bacterial genera (i.e., Pseudoxanthomonas, hgcI_clade, and Pseudorhodobacter). Network analyses showed that bacterial networks differed among seasons, and the autumn network exhibited the highest stability. Our findings indicated that the bacterial community stability was significantly affected by environmental factors, specifically SO4 2-and PO4 3-, rather than bacterivorous protozoans. Overall, our findings provide new perspectives on the role of trophic interactions in maintaining the structure of bacterial community in different seasons, and enhance our understanding of the bacterial community assembly in lake ecosystems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00256-8.

Sequential decline in cyanobacterial, total prokaryotic, and eukaryotic responses to backward flow in a river connected to Lake Taihu

River ecosystems face escalating challenges due to altered flow regimes from human activities, such as urbanization with hydrological modifications. Understanding the role of microbial communities for ecosystems with changing flow regimes is still incomplete and remains at the frontier of aquatic microbial ecology. In particular, influences of riverine backward flow on the aquatic biota remain largely unknown. Therefore, we examined the impact of backward flow on the cyanobacterial, total prokaryotic, and eukaryotic communities in the Changdougang River, which naturally flows into Lake Taihu, through environmental DNA metabarcoding. We analyzed the differences in community diversity, assembly, and ecological network stability among groups under backward, weak, and forward flow direction conditions. Non-metric multidimensional scaling showed higher variations in communities of groups across flow direction conditions than seasonal groups. Variations in alpha and beta diversity showed that cyanobacterial and total prokaryotic communities experienced strong homogenization under backward flow conditions, whereas the ecological uniqueness of the eukaryotic community decreased. Assembly of the three flow-related communities was primarily governed by drift and dispersal limitation in stochastic processes. However, in the cyanobacterial community, homogeneous selection in deterministic processes increased from 22.79 % to 42.86 % under backward flow, aligning with trends observed in the checkerboard score (C-score). More importantly, the topological properties of ecological networks and the degree of average variation revealed higher stability in the cyanobacterial community compared to total prokaryotic and eukaryotic communities. Considering the variations in cohesion, the network stability in the cyanobacterial community decreased under backward flow. Our findings emphasize the distinct and sequentially diminishing responses of cyanobacterial, total prokaryotic, and eukaryotic communities to backward flowing rivers. This knowledge is crucial for maintaining ecological health of rivers, assessing the complex ecological impacts on hydrological engineering, and formulating sustainable water management strategies.

Pitfalls in gut single-cell eukaryote research

Gut single-celled eukaryotes (GSCEs) are found in billions of people worldwide, but we still know little about their functions and relationships in human gut ecology. Lately, retrospective analysis of bacterial data obtained by next-generation sequencing (NGS) methods has been used to identify links between GSCEs, gut bacteria, host metabolism, and host phenotypical traits, suggesting possible direct or indirect associations to favorable gut microbiome features and other health parameters. Here, we highlight some of the pitfalls related to the research strategy typically used so far and propose action points that could pave the way for a more accurate understanding of GSCEs in human health and disease.

The protist community of the oligotrophic waters of the Gulf of Mexico is distinctly shaped by depth-specific physicochemical conditions during the warm season

Marine protists are key components of biogeochemical cycles and microbial food webs, which respond quickly to environmental factors. In the Gulf of Mexico (GoM), the Loop Current intensifies in summer and supplies the gulf with warm and oligotrophic waters. However, the cyclonic eddies within the GoM create favorable conditions for biological productivity by bringing nutrient-rich water to the subsurface layer. In this study, we investigated the response of the protist community to the regional physicochemical conditions, its spatial and temporal variability, the influence of mesoscale structures, and its ecological roles in the mixed layer (ML) and deep chlorophyll maximum (DCM). This is the first study to conduct a V9-18S rRNA gene survey for this community in the Mexican Exclusive Economic Zone of the GoM. The regional distribution, temporal changes, and mesoscale structures significantly affected the structure of the protist community in the ML. In contrast, only mesoscale structures significantly affected the protist community in the DCM. Different protist assemblages were also present between the ML and DCM, with the Alveolata representing ∼60% of the community in both layers, followed by haptophytes and MAST (Marine Stramenopiles) in the ML; pelagophytes and radiolarians were the more prevalent taxa in the DCM. Finally, co-occurrence analyses revealed that competition, parasitism, and predation were the potential interactions shaping these communities at both depths.

Together throughout the year: seasonal patterns of bacterial and eukaryotic microbial communities in a macrotidal estuary

BACKGROUND

Estuaries are complex ecosystems linking river and marine environments, where microorganisms play a key role in maintaining ecosystem functions. In the present study, we investigated monthly 8 sites at two depth layers and over a one-year period the bacterial and eukaryotic community dynamics along the Seine macrotidal estuary (Normandy, France). To date, the taxonomy of the microbial diversity present in this anthropized estuary remains elusive and the drivers of the microbial community structure are still unknown.

RESULTS

The metabarcoding analysis of 147 samples revealed both a high bacterial and eukaryotic diversity, dominated by Proteobacteria, Bacteriodota, Actinobacteriota and Bacillariophyta, Spirotrichea, Dinophyceae, respectively. Along the estuary we only detected significant spatial patterns in the bacterial and eukaryotic community compositions for three and two months out of twelve, respectively. However, we found a clear seasonal effect on the diversity of both microbial communities driven by physical and chemical variables that were fluctuating over the year (temperature, irradiance, river flow). Biotic associations were also significant drivers of both alpha and beta diversity. Throughout the year, we identified a diverse and abundant core microbiota composed of 74 bacterial and 41 eukaryotic OTUs. These regionally abundant species include habitat generalists encompassing heterotrophs, phototrophs and consumers. Yet, many of these core OTUs remain taxonomically and functionally poorly assigned.

CONCLUSIONS

This molecular survey represents a milestone in the understanding of macrotidal estuary dynamics and the Seine ecosystem, through the identification of putative markers of ecosystem functioning. It also identifies seasons and biotic associations as main drivers of the Seine estuary microbiota and reveals the importance of a core microbiota throughout the year.

Differences in Biogeographic Patterns and Mechanisms of Assembly in Estuarine Bacterial and Protist Communities

As transitional ecosystems between land and sea, estuaries are characterized by a unique environment that supports complex and diverse microbial communities. A comprehensive analysis of microbial diversity and ecological processes at different trophic levels is crucial for understanding the ecological functions of estuarine ecosystems. In this study, we systematically analyzed the diversity patterns, community assembly, and environmental adaptability of bacterial and protist communities using high-throughput sequencing techniques. The results revealed a higher alpha diversity for the bacteria than for protists, and the beta diversity pattern was dominated by species turnover in both communities. In addition, the two community assemblages were shown to be dominated by deterministic and stochastic processes, respectively. Furthermore, our results emphasized the influence of the local species pool on microbial communities and the fact that, at larger scales, geographic factors played a more significant role than environmental factors in driving microbial community variation. The study also revealed differences in environmental adaptability among different microbial types. Bacteria exhibited strong adaptability to salinity, while protists demonstrated greater resilience to variations in dissolved oxygen, nitrate, and ammonium concentrations. These results suggested differences in environmental adaptation strategies among microorganisms at different trophic levels, with bacteria demonstrating a more pronounced environmental filtering effect.

Soil nutrient limitation controls trophic cascade effects of micro-food web-derived ecological functions in degraded agroecosystems

INTRODUCTION

Soil nutrient supply drives the ecological functions of soil micro-food webs through bottom-up and top-down mechanisms in degraded agroecosystems. Nutrient limitation responds sensitively to variations in degraded agroecosystems through restoration practices, such as legume intercropping.

OBJECTIVES

This study examined the effects of legume intercropping on trophic cascade dynamics through resource supply in degraded purple soil ecosystems.

METHODS

A field experiment was conducted with three plantation types: Camellia oleifera monoculture (CK), C. oleifera-Arachis hypogaea (peanut) intercropping (CP), and C. oleifera-Senna tora intercropping (CS). Using soil nutrient limitation as a premise, modified by legume intercropping, we assessed the biodiversity of soil biotic taxa, analysed their community composition, and applied partial least squares path modelling (PLS-PM) to link trophic cascade with ecological functions.

RESULTS

Legume intercropping altered the abundance of biotic taxa, leading to changes in biotic diversity and microbial life strategies. The PLS-PM results indicated that legume intercropping enhanced bacterial diversity by aggravating soil P limitation, which subsequently increased protist consumer diversity and omnivore-predator nematode abundance through a bottom-up effect. Omnivore-predator nematodes and protist consumers indirectly influenced soil P metabolism, down-regulated through bacteria in the top-down effect. We observed high consistency between the untargeted metabolomic analysis and soil nutrient limitations. These findings indicate that soil micro-food web structure and function responded sensitively to legume intercropping in degraded ecosystems.

CONCLUSION

The results highlight the role of soil nutrient limitation in shaping micro-food webs and suggest that soil P limitation controls the down-regulation of soil P-related ecological functions through bottom-up and top-down effects.

Novel High-Quality Amoeba Genomes Reveal Widespread Codon Usage Mismatch Between Giant Viruses and Their Hosts

The need for high-quality protist genomes has prevented in-depth computational and experimental studies of giant virus-host interactions. In addition, our current knowledge of host range is highly biased due to the few hosts used to isolate novel giant viruses. This study presents 6 high-quality amoeba genomes from known and potential giant virus hosts belonging to 2 distinct eukaryotic clades: Amoebozoa and Discoba. We employ their genomic data to investigate the predictability of giant virus host range. Using a combination of long- and short-read sequencing, we obtained highly contiguous and complete genomes of Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba terricola, Naegleria clarki, Vermamoeba vermiformis, and Willaertia magna, contributing to the collection of sequences for the eukaryotic tree of life. We found that the 6 amoebae have distinct codon usage patterns and that, contrary to other virus groups, giant viruses often have different and even opposite codon usage with their known hosts. Conversely, giant viruses with matching codon usage are frequently not known to infect or replicate in these hosts. Interestingly, analyses of integrated viral sequences in the amoeba host genomes reveal potential novel virus-host associations. Matching of codon usage preferences is often used to predict virus-host pairs. However, with the broad-scale analyses performed in this study, we demonstrate that codon usage alone appears to be a poor predictor of host range for giant viruses infecting amoeba. We discuss the potential strategies that giant viruses employ to ensure high viral fitness in nonmatching hosts. Moreover, this study emphasizes the need for more high-quality protist genomes. Finally, the amoeba genomes presented in this study set the stage for future experimental studies to better understand how giant viruses interact with different host species.

Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate

Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as downregulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free, and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.

Urbanization enhances consumer protist-driven ARGs dissemination in riverine ecosystems

Despite the emergence of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARBs), how biological inter-trophic interactions, modulated by watershed urbanization, shape the resistome remains unexplored. We collected water samples from the highly urbanized (western: 65 % built land, sewage-affected) and lesser-urbanized (northern: 25 % built land, drinking water source) downstream tributaries of the Jiulong River in southeast China over dry and wet seasons. We utilized metagenomic and amplicon (16S and 18S rDNA) sequencing to investigate the relationships among microeukaryotic algae, consumer protists, bacterial communities, and the resistome. Metagenomic results showed that ARG-MGE-carrying contigs (mobile ARGs), rather than ARG-carrying contigs (non-mobile ARGs), exhibited more pronounced discrepancies between tributaries. A higher total abundance of ARGs and a greater number of co-shared ARGs between pathogen and non-pathogen bacteria were observed in the more urbanized western tributary. Structural equation modeling revealed that consumer protist-bacteria and algae-bacteria cohesions predominantly influenced the resistome in the western and northern tributaries, respectively. Additionally, consumer protists had more significant associations (511 out of 634) with bacteria carrying mobile ARGs in western tributary, while algae had more significant associations (73 out of 105) in northern tributary. These results highlight the distinct inter-trophic driving factors of the resistome modulated by watershed urbanization.

Comparative Analysis of Protist Communities in Oilsands Tailings Using Amplicon Sequencing and Metagenomics

The Canadian province of Alberta contains substantial oilsands reservoirs, consisting of bitumen, clay and sand. Extracting oil involves separating bitumen from inorganic particles using hot water and chemical diluents, resulting in liquid tailings waste with ecotoxicologically significant compounds. Ongoing efforts aim to reclaim tailings-affected areas, with protist colonisation serving as one assessment method of reclamation progress. Oilsands-associated protist communities have mainly been evaluated using amplicon sequencing of the 18S rRNA V4 region; however, this barcode may overlook important protist groups. This study examined how community assessment methods between the V4 and V9 regions differ in representing protist diversity across four oilsands-associated environments. The V9 barcode identified more operational taxonomical units (OTUs) for Discoba, Metamonada and Amoebozoa compared with the V4. A comparative shotgun metagenomics approach revealed few eukaryotic contigs but did recover a complete Paramicrosporidia mitochondrial genome, only the second publicly available from microsporidians. Both V4 and V9 markers were informative for assessing community diversity in oilsands-associated environments and are most effective when combined for a comprehensive taxonomic estimate, particularly in anoxic environments.