A metagenomic assessment of microbial eukaryotic diversity in the global ocean

The genomic potential of photosynthesis in piconanoplankton is functionally redundant but taxonomically structured at a global scale

Carbon fixation is a key metabolic function shaping marine life, but the underlying taxonomic and functional diversity involved is only partially understood. Using metagenomic resources targeted at marine piconanoplankton, we provide a reproducible machine learning framework to derive the potential biogeography of genomic functions through the multi-output regression of gene read counts on environmental climatologies. Leveraging the Marine Atlas of Tara Oceans Unigenes, we investigate the genomic potential of primary production in the global ocean. The latter is performed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) and is often associated with carbon concentration mechanisms in piconanoplankton, major marine unicellular photosynthetic organisms. We show that the genomic potential supporting C4 enzymes and RUBISCO exhibits strong functional redundancy and important affinity toward tropical oligotrophic waters. This redundancy is taxonomically structured by the dominance of Mamiellophyceae and Prymnesiophyceae in mid and high latitudes. These findings enhance our understanding of the relationship between functional and taxonomic diversity of microorganisms and environmental drivers of key biogeochemical cycles.

Assessing patterns of metazoans in the global ocean using environmental DNA

Documenting large-scale patterns of animals in the ocean and determining the drivers of these patterns is needed for conservation efforts given the unprecedented rates of change occurring within marine ecosystems. We used existing datasets from two global expeditions, Tara Oceans and Malaspina, that circumnavigated the oceans and sampled down to 4000 m to assess metazoans from environmental DNA (eDNA) extracted from seawater. We describe patterns of taxonomic richness within metazoan phyla and orders based on metabarcoding and infer the relative abundance of phyla using metagenome datasets, and relate these data to environmental variables. Arthropods had the greatest taxonomic richness of metazoan phyla at the surface, while cnidarians had the greatest richness in pelagic zones. Half of the marine metazoan eDNA from metagenome datasets was from arthropods, followed by cnidarians and nematodes. We found that mean surface temperature and primary productivity were positively related to metazoan taxonomic richness. Our findings concur with existing knowledge that temperature and primary productivity are important drivers of taxonomic richness for specific taxa at the ocean's surface, but these correlations are less evident in the deep ocean. Massive sequencing of eDNA can improve understanding of animal distributions, particularly for the deep ocean where sampling is challenging.

Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment

Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2 cm) and bottom depth (250 cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.

Metagenomic 18S rDNA reads revealed zonation of eukaryotic communities in the Yongle blue hole

The Yongle blue hole (YBH), situated in the South China Sea, represents a compelling subject of study in marine microbiology due to its unique redox-layered microbial ecosystems. However, the diversity and ecology of microbial eukaryotes within the YBH remains underexplored. This study endeavors to bridge this gap through the application of the in situ microbial filtration and fixation (ISMIFF) device to collect 0.22-30 μm microbial samples from 21 water layers of YBH. Subsequent extraction of 18S rRNA metagenomic reads of 21 metagenomes and 10 metatranscriptomes facilitated a comprehensive analysis of community structures. Findings revealed a pronounced superiority in the diversity and richness of eukaryotic microorganisms in the oxic zone compared to its suboxic and anoxic counterparts. Notably, Dinophyceae and Maxillopoda emerged as the predominant taxa based on the analysis of the 18S rRNA reads for the V4 and V9 regions, which showed stratification In their relative abundance and suggested their potential role in the thermo-halocline boundaries and oxic-anoxic interface. Specifically, In these eukaryotic microbial communities, Dinophyceae exhibited significant abundance at 20 m (20.01%) and 105 m (26.13%) water depths, while Maxillopoda was prevalent at 40 m (22.84%), 80 m (23.19%), and 100 m (15.42%) depths. A part of these organisms, identified as larvae and protists, were likely attracted by swarming chemosynthetic bacterial prey prevailing at the thermo-halocline boundaries and oxic-anoxic interface. Furthermore, the phylogenetic relationships of the major 18S operational taxonomic units (OTUs) showed a close adjacency to known species, except for three Dinophyceae OTUs. In conclusion, this study provides critical insights into the vertical distribution and transcriptional activity of <30-μm eukaryotic microbes, shedding light on the taxonomic novelty of eukaryotic microorganisms within the semi-enclosed blue holes.

Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes

Two common approaches to study the composition of environmental protist communities are metabarcoding and metagenomics. Raw metabarcoding data are usually processed into Operational Taxonomic Units (OTUs) or amplicon sequence variants (ASVs) through clustering or denoising approaches, respectively. Analogous approaches are used to assemble metagenomic reads into metagenome-assembled genomes (MAGs). Understanding the correspondence between the data produced by these two approaches can help to integrate information between the datasets and to explain how metabarcoding OTUs and MAGs are related with the underlying biological entities they are hypothesised to represent. MAGs do not contain the commonly used barcoding loci, therefore sequence homology approaches cannot be used to match OTUs and MAGs. We made an attempt to match V9 metabarcoding OTUs from the 18S rRNA gene (V9 OTUs) and MAGs from the Tara Oceans expedition based on the correspondence of their relative abundances across the same set of samples. We evaluated several metrics for detecting correspondence between features in these two datasets and developed controls to filter artefacts of data structure and processing. After selecting the best-performing metrics, ranking the V9 OTU/MAG matches by their proportionality/correlation coefficients and applying a set of selection criteria, we identified candidate matches between V9 OTUs and MAGs. In some cases, V9 OTUs and MAGs could be matched with a one-to-one correspondence, implying that they likely represent the same underlying biological entity. More generally, matches we observed could be classified into 4 scenarios: one V9 OTU matches many MAGs; many V9 OTUs match many MAGs; many V9 OTUs match one MAG; one V9 OTU matches one MAG. Notably, we found some instances in which different OTU-MAG matches from the same taxonomic group were not classified in the same scenario, with all four scenarios possible even within the same taxonomic group, illustrating that factors beyond taxonomic lineage influence the relationship between OTUs and MAGs. Overall, each scenario produces a different interpretation of V9 OTUs, MAGs and how they compare in terms of the genomic and ecological diversity they represent.

Unraveling metagenomics through long-read sequencing: a comprehensive review

The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read sequencing (LRS), which offers substantial improvements over its predecessor, short-read sequencing (SRS). LRS produces reads that are several kilobases long, enabling researchers to obtain more complete and contiguous genomic information, characterize structural variations, and study epigenetic modifications. The current leaders in LRS technologies are Pacific Biotechnologies (PacBio) and Oxford Nanopore Technologies (ONT), each offering a distinct set of advantages. This review covers the workflow of long-read metagenomics sequencing, including sample preparation (sample collection, sample extraction, and library preparation), sequencing, processing (quality control, assembly, and binning), and analysis (taxonomic annotation and functional annotation). Each section provides a concise outline of the key concept of the methodology, presenting the original concept as well as how it is challenged or modified in the context of LRS. Additionally, the section introduces a range of tools that are compatible with LRS and can be utilized to execute the LRS process. This review aims to present the workflow of metagenomics, highlight the transformative impact of LRS, and provide researchers with a selection of tools suitable for this task.

Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora

"Kingdom-level" branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down.1,2,3,4 Some are completely new discoveries, whereas others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19th century but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted.2Meteora sporadica5 is a protist with a unique morphology; cells glide over substrates along a long axis of anterior and posterior projections while a pair of lateral "arms" swing back and forth, a motility system without any obvious parallels. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved.6 Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that both the anterior-posterior projections and the arms are supported by microtubules originating from a cluster of subnuclear microtubule organizing centers (MTOCs). Neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be among the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse "supergroup" and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.

VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages

Protocols for characterizing taxonomic assemblages by deep sequencing of short DNA barcode regions (metabarcoding) have revolutionized our understanding of microbial communities and are standardized for bacteria, archaea, and fungi. Unfortunately, comparable methods for host-associated eukaryotes have lagged due to technical challenges. Despite 54 published studies, issues remain with primer complementarity, off-target amplification, and lack of external validation. Here, we present VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis) primers and optimized metabarcoding protocol for host-associated eukaryotic community analysis. Using in silico prediction, panel PCR, engineered mock community standards, and clinical samples, we demonstrate VESPA to be more effective at resolving host-associated eukaryotic assemblages than previously published methods and to minimize off-target amplification. When applied to human and non-human primate samples, VESPA enables reconstruction of host-associated eukaryotic endosymbiont communities more accurately and at finer taxonomic resolution than microscopy. VESPA has the potential to advance basic and translational science on vertebrate eukaryotic endosymbiont communities, similar to achievements made for bacterial, archaeal, and fungal microbiomes.

High amino acid osmotrophic incorporation by marine eukaryotic phytoplankton revealed by click chemistry

The osmotrophic uptake of dissolved organic compounds in the ocean is considered to be dominated by heterotrophic prokaryotes, whereas the role of planktonic eukaryotes is still unclear. We explored the capacity of natural eukaryotic plankton communities to incorporate the synthetic amino acid L-homopropargylglycine (HPG, analogue of methionine) using biorthogonal noncanonical amino acid tagging (BONCAT), and we compared it with prokaryotic HPG use throughout a 9-day survey in the NW Mediterranean. BONCAT allows to fluorescently identify translationally active cells, but it has never been applied to natural eukaryotic communities. We found a large diversity of photosynthetic and heterotrophic eukaryotes incorporating HPG into proteins, with dinoflagellates and diatoms showing the highest percentages of BONCAT-labelled cells (49 ± 25% and 52 ± 15%, respectively). Among them, pennate diatoms exhibited higher HPG incorporation in the afternoon than in the morning, whereas small (≤5 μm) photosynthetic eukaryotes and heterotrophic nanoeukaryotes showed the opposite pattern. Centric diatoms (e.g. Chaetoceros, Thalassiosira, and Lauderia spp.) dominated the eukaryotic HPG incorporation due to their high abundances and large sizes, accounting for up to 86% of the eukaryotic BONCAT signal and strongly correlating with bulk 3H-leucine uptake rates. When including prokaryotes, eukaryotes were estimated to account for 19-31% of the bulk BONCAT signal. Our results evidence a large complexity in the osmotrophic uptake of HPG, which varies over time within and across eukaryotic groups and highlights the potential of BONCAT to quantify osmotrophy and protein synthesis in complex eukaryotic communities.

Mesoscale oceanographic meanders influence protist community function and structure in the southern Indian Ocean

The interface between the nutrient-rich Southern Ocean and oligotrophic Indian Ocean creates unique environmental conditions that can strongly influence biological processes. We investigated protist communities across a mesoscale meander of the Subtropical Front within the Southern Indian Ocean. 18S V9 rDNA metabarcoding suggests a diverse protist community in which the dinoflagellates and parasitic Syndiniales were abundant. Diversity was highest in frontal waters of the mesoscale meander, with differences in community structure inside and outside the meander. While the overall community was dominated by mixotrophic taxa, the frontal boundary of the meander had increased abundances of heterotrophic taxa, with potential implications for net atmospheric CO2 drawdown. Pulse amplitude modulated (PAM) fluorimetry revealed significant differences in the photophysiology of phytoplankton communities inside and outside the meander. By using single-cell PAM microscopy, we identified physiological differences between dinoflagellate and coccolithophore taxa, which may have contributed to changes in photophysiology observed at community level. Overall, our results demonstrate that frontal areas have a strong impact on the composition of protist communities in the Southern Ocean with important implications for understanding biological processes in this region.

Global perspective of environmental distribution and diversity of Perkinsea (Alveolata) explored by a meta-analysis of eDNA surveys

Perkinsea constitutes a lineage within the Alveolata eukaryotic superphylum, mainly composed of parasitic organisms. Some described species represent significant ecological and economic threats due to their invasive ability and pathogenicity, which can lead to mortality events. However, the genetic diversity of these described species is just the tip of the iceberg. Environmental surveys targeting this lineage are still scarce and mainly limited to the Northern Hemisphere. Here, we aim to conduct an in depth exploration of the Perkinsea group, uncovering the diversity across a variety of environments, including those beyond freshwater and marine ecosystems. We seek to identify and describe putative novel organisms based on their genetic signatures. In this study, we conducted an extensive analysis of a metabarcoding dataset, focusing on the V4 region of the 18S rRNA gene (the EukBank dataset), to investigate the diversity, distribution and environmental preferences of the Perkinsea. Our results reveal a remarkable diversity within the Perkinsea, with 1568 Amplicon Sequence Variants (ASVs) identified across thousands of environmental samples. Surprisingly, we showed a substantial diversity of Perkinsea within soil samples (269 ASVs), challenging the previous assumption that this group is confined to marine and freshwater environments. In addition, we revealed that a notable proportion of Perkinsea ASVs (428 ASVs) could correspond to putative new organisms, encompassing the well-established taxonomic group Perkinsidae. Finally, our study shed light on previously unveiled taxonomic groups, including the Xcellidae, and revealed their environmental distribution. These findings demonstrate that Perkinsea exhibits far greater diversity than previously detected and surprisingly extends beyond marine and freshwater environments. The meta-analysis conducted in this study has unveiled the existence of previously unknown clusters within the Perkinsea lineage, solely identified based on their genetic signatures. Considering the ecological and economic importance of described Perkinsea species, these results suggest that Perkinsea may play a significant, yet previously unrecognized, role across a wide range of environments, spanning from soil environments to the abyssal zone of the open ocean with important implications for ecosystem functioning.

Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest

The Brazilian Atlantic Forest and its associated ecosystems are highly biodiverse but still understudied, especially with respect to eukaryotic microbes. Protists represent the largest proportion of eukaryotic diversity and play important roles in nutrient cycling and maintenance of the ecosystems in which they occur. However, much of protist diversity remains unknown, particularly in the Neotropics. Understanding the taxonomic and functional diversity of these organisms is urgently needed, not only to fill this gap in our knowledge, but also to enable the development of public policies for biological conservation. This is the first study to investigate the taxonomic and trophic diversity of the major protist groups in freshwater systems and brackish coastal lagoons located in fragments of the Brazilian Atlantic Forest by DNA metabarcoding, using high-throughput sequencing of the gene coding for the V4 region of the 18S rRNA gene. We compared α and β diversity for all protist communities and assessed the relative abundance of phototrophic, consumer, and parasitic taxa. We found that the protist communities of coastal lagoons are as diverse as the freshwater systems studied in terms of α diversity, although differed significantly in terms of taxonomic composition. Our results still showed a notable functional homogeneity between the trophic groups in freshwater environments. Beta diversity was higher among freshwater samples, suggesting a greater level of heterogeneity within this group of samples concerning the composition and abundance of OTUs.Ciliophora was the most represented group in freshwater, while Diatomea dominated diversity in coastal lagoons.

Distribution Patterns of Benthic Protist Communities Depending on Depth Revealed by Environmental Sequencing-From the Sublittoral to the Deep Sea

Protists are key components of the microbial food web in marine pelagic systems because they link algal and bacterial production to higher trophic levels. However, their functioning and bathymetric distribution in benthic deep-sea ecosystems are still only poorly understood. However, biogeographical patterns of communities can be coupled to the functioning of ecosystems and are therefore important to understand ecological and evolutionary processes. In this study, we investigated the diversity and distribution of benthic protist communities from the sublittoral down to the deep seafloor (50-2000 m) around three islands of the Azores in the North Atlantic Ocean. Using amplicon sequencing of the V9 region (18S rDNA) of 21 samples, we found that protist community compositions from different depths were significantly different. Three assemblages were separated along the following depths: 50 m, 150-500 m and 1000-2000 m, which indicate that deep-sea areas surrounding islands might act as isolating barriers for benthic protist species. A limited gene flow between the communities could favor speciation processes, leading to the unique protist communities found at the different investigated islands.

Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory

BACKGROUND

Marine heterotrophic flagellates (HF) are dominant bacterivores in the ocean, where they represent the trophic link between bacteria and higher trophic levels and participate in the recycling of inorganic nutrients for regenerated primary production. Studying their activity and function in the ecosystem is challenging since most of the HFs in the ocean are still uncultured. In the present work, we investigated gene expression of natural HF communities during bacterivory in four unamended seawater incubations.

RESULTS

The most abundant species growing in our incubations belonged to the taxonomic groups MAST-4, MAST-7, Chrysophyceae, and Telonemia. Gene expression dynamics were similar between incubations and could be divided into three states based on microbial counts, each state displaying distinct expression patterns. The analysis of samples where HF growth was highest revealed some highly expressed genes that could be related to bacterivory. Using available genomic and transcriptomic references, we identified 25 species growing in our incubations and used those to compare the expression levels of these specific genes. Video Abstract CONCLUSIONS: Our results indicate that several peptidases, together with some glycoside hydrolases and glycosyltransferases, are more expressed in phagotrophic than in phototrophic species, and thus could be used to infer the process of bacterivory in natural assemblages.

Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes

BACKGROUND

Diplonemid flagellates are among the most abundant and species-rich of known marine microeukaryotes, colonizing all habitats, depths, and geographic regions of the world ocean. However, little is known about their genomes, biology, and ecological role.

RESULTS

We present the first nuclear genome sequence from a diplonemid, the type species Diplonema papillatum. The ~ 280-Mb genome assembly contains about 32,000 protein-coding genes, likely co-transcribed in groups of up to 100. Gene clusters are separated by long repetitive regions that include numerous transposable elements, which also reside within introns. Analysis of gene-family evolution reveals that the last common diplonemid ancestor underwent considerable metabolic expansion. D. papillatum-specific gains of carbohydrate-degradation capability were apparently acquired via horizontal gene transfer. The predicted breakdown of polysaccharides including pectin and xylan is at odds with reports of peptides being the predominant carbon source of this organism. Secretome analysis together with feeding experiments suggest that D. papillatum is predatory, able to degrade cell walls of live microeukaryotes, macroalgae, and water plants, not only for protoplast feeding but also for metabolizing cell-wall carbohydrates as an energy source. The analysis of environmental barcode samples shows that D. papillatum is confined to temperate coastal waters, presumably acting in bioremediation of eutrophication.

CONCLUSIONS

Nuclear genome information will allow systematic functional and cell-biology studies in D. papillatum. It will also serve as a reference for the highly diverse diplonemids and provide a point of comparison for studying gene complement evolution in the sister group of Kinetoplastida, including human-pathogenic taxa.

Water masses shape pico-nano eukaryotic communities of the Weddell Sea

Polar oceans belong to the most productive and rapidly changing environments, yet our understanding of this fragile ecosystem remains limited. Here we present an analysis of a unique set of DNA metabarcoding samples from the western Weddell Sea sampled throughout the whole water column and across five water masses with different characteristics and different origin. We focus on factors affecting the distribution of planktonic pico-nano eukaryotes and observe an ecological succession of eukaryotic communities as the water masses move away from the surface and as oxygen becomes depleted with time. At the beginning of this succession, in the photic zone, algae, bacteriovores, and predators of small eukaryotes dominate the community, while another community develops as the water sinks deeper, mostly composed of parasitoids (syndinians), mesoplankton predators (radiolarians), and diplonemids. The strongly correlated distribution of syndinians and diplonemids along the depth and oxygen gradients suggests their close ecological link and moves us closer to understanding the biological role of the latter group in the ocean ecosystem.

Discovering marine biodiversity in the 21st century

We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.

Global patterns and rates of habitat transitions across the eukaryotic tree of life

The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine/non-marine transitions but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich phylogenies inferred from a combination of long-read and short-read environmental metabarcoding data spanning the ribosomal DNA operon. Our results show that, overall, marine and non-marine microbial communities are phylogenetically distinct but transitions have occurred in both directions in almost all major eukaryotic lineages, with hundreds of transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has probably been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-marine habitats and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that the salt barrier has played an important role during eukaryote evolution and provide a global perspective on habitat transitions in this domain of life.

Exploring the Taxonomic and Functional Diversity of Marine Benthic Micro-Eukaryotes Along the Red Sea Coast of Jeddah City

Backgrounds

Diverse marine habitats along Jeddah's Red Sea coast support rich biodiversity. Few studies have been done on its diverse communities, especially its microbial counterparts. Metagenomic analysis of marine benthic micro-eukaryotic communities was performed for the first time on the Red Sea coast of Jeddah. This research looks into their community structure and metabolic potential.

Methods

Next-generation sequencing was used to examine the micro-eukaryotic communities of seven sedimentary soil samples from four Jeddah coast locations. After isolating DNA from seven benthic sedimentary soil samples, the 18S rDNA V4 regions were amplified and sequenced on the Illumina MiSeq. It was also verified using an Agilent Technologies 2100 Bioanalyzer with a DNA 1000 chip (Agilent Technologies, Fisher Scientific). A standard curve of fluorescence readings generated by qPCR quantification using the Illumina library was achieved using the GS FLX library. Metagenomic data analysis was used to evaluate the microbial communities' biochemical and enzymatic allocations in studied samples.

Results

Blast analysis showed that the top ten phyla were Annelida, Eukaryota, Diatomea, Porifera, Phragmoplastophyta, Arthropoda, Dinoflagellata, Xenacoelomorpha Nematoda, and uncultured. Annelida was also found in the highest percentage (93%), in the sample M followed by Porifera (64%), the most abundant in the control sample then Eukaryotes (61%), Phragmatoplastophyta (55%), Arthropoda, and Diatomea (the least common) (32%). community diversity analysis: using Shannon and inverse Simpson indices showed sediment composition to be effective. Also, PICRUST2 indicated that the most abundant pathways were pyruvate fermentation to isobutanol, pyrimidine deoxyribonucleotide phosphorylation, adenosine ribonucleotide de novo biosynthesis, guanosine ribonucleotide de novo biosynthesis, NAD salvage pathway I, the super pathway of glyoxylate bypass and aerobic respiration I (cytochrome c).

Conclusion

Results showed that high throughput metagenomics could reveal species diversity and estimate gene profiles. Environmental factors appear to be more important than geographic variation in determining the structure of these microbial communities. This study provides the first report of marine benthic micro-eukaryotic communities found on the Red Sea coast of Jeddah and will serve as a good platform for future research.

Factors influencing the pigment composition and dynamics of photoautotrophic picoplankton in shallow eutrophic lakes

Photoautotrophic picoplankton (0.2–2 μm) can be a major contributor to primary production and play a significant part in the ecosystem carbon flow. However, the understanding about the dynamics of both eukaryotic and prokaryotic components of picoplankton in shallow eutrophic freshwater environments is still poor. Very few studies in these ecosystems reveal the taxonomic composition of picoeukaryotes. The main objective of this study was to investigate the seasonal dynamics of phototrophic picoplankton with the emphasis on the eukaryote community composition in a large shallow, eutrophic lake of the northern temperate zone (Lake Võrtsjärv). Phytoplankton pigments were employed to determine the taxonomic composition of photoautotrophic picoplankton. We found out that photoautotrophic picoplankton constitutes an important part of the phytoplankton community in Lake Võrtsjärv and its contribution can be highly variable (from ~9.3% to ~39%) in different years. The eukaryotic photoautotrophic picoplankton was dominated by diatoms followed by chrysophytes and other minor groups. Picoeukaryotes were prevailing in low-light conditions and low temperatures as their predominance in the picoplankton community was tightly linked to the presence or absence of ice cover. Ice cover strongly suppressed the growth of picocyanobacteria. Total phosphorus, turbidity and metazooplankton abundance had a clear relationship with photoautotrophic picoplankton chlorophyll a.

Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review

Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.

Trophic flexibility of marine diplonemids - switching from osmotrophy to bacterivory

Diplonemids are one of the most abundant groups of heterotrophic planktonic microeukaryotes in the world ocean and, thus, are likely to play an essential role in marine ecosystems. So far, only few species have been introduced into a culture, allowing basic studies of diplonemid genetics, morphology, ultrastructure, metabolism, as well as endosymbionts. However, it remains unclear whether these heterotrophic flagellates are parasitic or free-living and what are their predominant dietary patterns and preferred food items. Here we show that cultured diplonemids, maintained in an organic-rich medium as osmotrophs, can gradually switch to bacterivory as a sole food resource, supporting positive growth of their population, even when fed with a low biovolume of bacteria. We further observed remarkable differences in species-specific feeding patterns, size-selective grazing preferences, and distinct feeding strategies. Diplonemids can discriminate between low-quality food items and inedible particles, such as latex beads, even after their ingestion, by discharging them in the form of large waste vacuoles. We also detected digestion-related endogenous autofluorescence emitted by lysosomes and the activity of a melanin-like material. We present the first evidence that these omnipresent protists possess an opportunistic lifestyle that provides a considerable advantage in the generally food resource-limited marine environments.

Diatoms and Their Microbiomes in Complex and Changing Polar Oceans

Diatoms, a key group of polar marine microbes, support highly productive ocean ecosystems. Like all life on earth, diatoms do not live in isolation, and they are therefore under constant biotic and abiotic pressures which directly influence their evolution through natural selection. Despite their importance in polar ecosystems, polar diatoms are understudied compared to temperate species. The observed rapid change in the polar climate, especially warming, has created increased research interest to discover the underlying causes and potential consequences on single species to entire ecosystems. Next-Generation Sequencing (NGS) technologies have greatly expanded our knowledge by revealing the molecular underpinnings of physiological adaptations to polar environmental conditions. Their genomes, transcriptomes, and proteomes together with the first eukaryotic meta-omics data of surface ocean polar microbiomes reflect the environmental pressures through adaptive responses such as the expansion of protein families over time as a consequence of selection. Polar regions and their microbiomes are inherently connected to climate cycles and their feedback loops. An integrated understanding built on "omics" resources centered around diatoms as key primary producers will enable us to reveal unifying concepts of microbial co-evolution and adaptation in polar oceans. This knowledge, which aims to relate past environmental changes to specific adaptations, will be required to improve climate prediction models for polar ecosystems because it provides a unifying framework of how interacting and co-evolving biological communities might respond to future environmental change.

Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) from abyssal and lower bathyal surficial sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment material. Based on 1685 samples collected throughout the world ocean, we show that DOS diversity is at least threefold that in pelagic realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These benthic communities are spatially structured by ocean basins and particulate organic carbon (POC) flux from the upper ocean. Plankton DNA reaching the DOS originates from abundant species, with maximal deposition at high latitudes. Its seafloor DNA signature predicts variations in POC export from the surface and reveals previously overlooked taxa that may drive the biological carbon pump.

A robust approach to estimate relative phytoplankton cell abundances from metagenomes

Phytoplankton account for >45% of global primary production, and have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found among prokaryotes (cyanobacteria) and multiple eukaryotic lineages containing chloroplasts. Genetic surveys of phytoplankton communities generally consist of PCR amplification of bacterial (16S), nuclear (18S) and/or chloroplastic (16S) rRNA marker genes from DNA extracted from environmental samples. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa, and the fact that rRNA genes do not provide insights into metabolic traits such as photosynthesis. Here, we targeted the photosynthetic gene psbO from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is universally and exclusively present in photosynthetic prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the size-fractionated marine samples collected by Tara Oceans, and showed improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these ecosystems, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine dinoflagellates. To facilitate the incorporation of psbO in molecular-based surveys, we compiled a curated database of >18,000 unique sequences. Overall, psbO appears to be a promising new gene marker for molecular-based evaluations of entire phytoplankton communities.

Global diversity and distribution of aerobic anoxygenic phototrophs in the tropical and subtropical oceans

The aerobic anoxygenic phototrophic (AAP) bacteria are common in most marine environments but their global diversity and biogeography remain poorly characterized. Here, we analyzed AAP communities across 113 globally-distributed surface ocean stations sampled during the Malaspina Expedition in the tropical and subtropical ocean. By means of amplicon sequencing of the pufM gene, a genetic marker for this functional group, we show that AAP communities along the surface ocean were mainly composed of members of the Halieaceae (Gammaproteobacteria), which were adapted to a large range of environmental conditions, and of different clades of the Alphaproteobacteria, which seemed to dominate under particular circumstances, such as in the oligotrophic gyres. AAP taxa were spatially structured within each of the studied oceans, with communities from adjacent stations sharing more taxonomic similarities. AAP communities were composed of a large pool of rare members and several habitat specialists. When compared to the surface ocean prokaryotic and picoeukaryotic communities, it appears that AAP communities display an idiosyncratic global biogeographical pattern, dominated by selection processes and less influenced by dispersal limitation. Our study contributes to the understanding of how AAP communities are distributed in the horizontal dimension and the mechanisms underlying their distribution across the global surface ocean.

Global drivers of eukaryotic plankton biogeography in the sunlit ocean

[Figure: see text].

Diversity and ecology of protists revealed by metabarcoding

Protists are the dominant eukaryotes in the biosphere where they play key functional roles. While protists have been studied for over a century, it is the high-throughput sequencing of molecular markers from environmental samples - the approach of metabarcoding - that has revealed just how diverse, and abundant, these small organisms are. Metabarcoding is now routine to survey environmental diversity, so data have rapidly accumulated from a multitude of environments and at different sampling scales. This mass of data has provided unprecedented opportunities to study the taxonomic and functional diversity of protists, and how this diversity is organised in space and time. Here, we use metabarcoding as a common thread to discuss the state of knowledge in protist diversity research, from technical considerations of the approach to important insights gained on diversity patterns and the processes that might have structured this diversity. In addition to these insights, we conclude that metabarcoding is on the verge of an exciting added dimension thanks to the maturation of high-throughput long-read sequencing, so that a robust eco-evolutionary framework of protist diversity is within reach.

Tiara: deep learning-based classification system for eukaryotic sequences

MOTIVATION

With a large number of metagenomic datasets becoming available, eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step toward a better understanding of eukaryotic diversity.

RESULTS

We developed Tiara, a deep-learning-based approach for the identification of eukaryotic sequences in the metagenomic datasets. Its two-step classification process enables the classification of nuclear and organellar eukaryotic fractions and subsequently divides organellar sequences into plastidial and mitochondrial. Using the test dataset, we have shown that Tiara performed similarly to EukRep for prokaryotes classification and outperformed it for eukaryotes classification with lower calculation time. In the tests on the real data, Tiara performed better than EukRep in analyzing the small dataset representing eukaryotic cell microbiome and large dataset from the pelagic zone of oceans. Tiara is also the only available tool correctly classifying organellar sequences, which was confirmed by the recovery of nearly complete plastid and mitochondrial genomes from the test data and real metagenomic data.

AVAILABILITY AND IMPLEMENTATION

Tiara is implemented in python 3.8, available at https://github.com/ibe-uw/tiara and tested on Unix-based systems. It is released under an open-source MIT license and documentation is available at https://ibe-uw.github.io/tiara. Version 1.0.1 of Tiara has been used for all benchmarks.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Microbial eukaryotes assemblages and potential novel diversity in four tropical East-African Great Lakes

East-African Great Lakes are old and unique natural resources heavily utilized by their bordering countries. In those lakes, ecosystem functioning is dominated by pelagic processes, where microorganisms are key components, however protistan diversity is barely known. We investigated the community composition of small eukaryotes (< 10 µm) in surface waters of four African Lakes (Kivu, Edward, Albert and Victoria) by sequencing the 18S rRNA gene. Moreover, in the meromictic Lake Kivu, two stations were vertically studied. We found high protistan diversity distributed in 779 operational taxonomic units (OTUs), spanning in eleven high-rank lineages, being Alveolata (31%), Opisthokonta (20%) and Stramenopiles (17%) the most represented supergroups. Surface protistan assemblage were associated to conductivity and productivity gradients; whereas depth, had a strong effect on protistan community in Kivu, with higher contribution of heterotrophic organisms. Approximately 40% of OTUs had low similarity (< 90%) with reported sequences in public databases, these were mostly coming from deep anoxic waters of Kivu, suggesting a high extent of novel diversity. We also detected several taxa so far considered exclusive of marine ecosystems. Our results unveiled a complex and largely undescribed protistan community, in which several lineages have adapted to different niches after crossing the salinity boundary.

Olisthodiscus represents a new class of Ochrophyta

The phylogenetic diversity of Ochrophyta, a diverse and ecologically important radiation of algae, is still incompletely understood even at the level of the principal lineages. One taxon that has eluded simple classification is the marine flagellate genus Olisthodiscus. We investigated Olisthodiscus luteus K-0444 and documented its morphological and genetic differences from the NIES-15 strain, which we described as Olisthodiscus tomasii sp. nov. Phylogenetic analyses of combined 18S and 28S rRNA sequences confirmed that Olisthodiscus constitutes a separate, deep, ochrophyte lineage, but its position could not be resolved. To overcome this problem, we sequenced the plastid genome of O. luteus K-0444 and used the new data in multigene phylogenetic analyses, which suggested that Olisthodiscus is a sister lineage of the class Pinguiophyceae within a broader clade additionally including Chrysophyceae, Synchromophyceae, and Eustigmatophyceae. Surprisingly, the Olisthodiscus plastid genome contained three genes, ycf80, cysT, and cysW, inherited from the rhodophyte ancestor of the ochrophyte plastid yet lost from all other ochrophyte groups studied so far. Combined with nuclear genes for CysA and Sbp proteins, Olisthodiscus is the only known ochrophyte possessing a plastidial sulfate transporter SulT. In addition, the finding of a cemA gene in the Olisthodiscus plastid genome and an updated phylogenetic analysis ruled out the previously proposed hypothesis invoking horizontal cemA transfer from a green algal plastid into Synurales. Altogether, Olisthodiscus clearly represents a novel phylogenetically distinct ochrophyte lineage, which we have proposed as a new class, Olisthodiscophyceae.

Changes in protist communities in drainages across the Pearl River Delta under anthropogenic influence

Drainages in the Pearl River Delta urban agglomeration (PRDUA) host vital aquatic ecosystems and face enormous pressures from human activities in one of the largest urban agglomerations in the world. Despite being crucial components of aquatic ecosystems, the interactions and assembly processes of the protistan community are rarely explored in areas with serious anthropogenic disturbance. To elucidate the mechanisms of these processes, we used environmental DNA sequencing of 18S rDNA to investigate the influence of environmental factors and species interactions on the protistan community and its assembly in drainages of the PRDUA during summer. The protistan community showed a high level of diversity and a marked spatial pattern in this region. Community assembly was driven primarily by stochastic processes based on the Sloan neutral community model, explaining 74.28%, 75.82%, 73.67%, 74.40% and 51.24% of community variations in the BJ (Beijiang), XJ (Xijiang), PRD (Pearl River Delta), PRE (Pearl River Estuary) areas and in total, respectively. Meanwhile, environmental variables including temperature, pH, dissolved oxygen, transparency, nutrients and land use were strongly correlated with the composition and assembly of the protistan community, explaining 40.40% of variation in the protistan community. Furthermore, the bacterial community was simultaneously analysed by the 16S rDNA sequencing. Co-occurrence network analysis revealed that species interactions within bacteria (81.41% positive) or protists (82.80% positive), and those between bacteria and protists (50% positive and 50% negative) impacted the protistan community assembly. In summary, stochastic processes dominated, whereas species interactions and environmental factors also played important roles in shaping the protistan communities in drainages across the PRDUA. This study provides insights into the ecological patterns, assembly processes and species interactions underlying protistan dynamics in urban aquatic ecosystems experiencing serious anthropogenic disturbance.

Comparative genomics reveals new functional insights in uncultured MAST species

Heterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.

Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys

Small subunit rRNA (SSU rRNA) amplicon sequencing can quantitatively and comprehensively profile natural microbiomes, representing a critically important tool for studying diverse global ecosystems. However, results will only be accurate if PCR primers perfectly match the rRNA of all organisms present. To evaluate how well marine microorganisms across all 3 domains are detected by this method, we compared commonly used primers with >300 million rRNA gene sequences retrieved from globally distributed marine metagenomes. The best-performing primers compared to 16S rRNA of bacteria and archaea were 515Y/926R and 515Y/806RB, which perfectly matched over 96% of all sequences. Considering cyanobacterial and chloroplast 16S rRNA, 515Y/926R had the highest coverage (99%), making this set ideal for quantifying marine primary producers. For eukaryotic 18S rRNA sequences, 515Y/926R also performed best (88%), followed by V4R/V4RB (18S rRNA specific; 82%)-demonstrating that the 515Y/926R combination performs best overall for all 3 domains. Using Atlantic and Pacific Ocean samples, we demonstrate high correspondence between 515Y/926R amplicon abundances (generated for this study) and metagenomic 16S rRNA (median R² = 0.98, n = 272), indicating amplicons can produce equally accurate community composition data compared with shotgun metagenomics. Our analysis also revealed that expected performance of all primer sets could be improved with minor modifications, pointing toward a nearly completely universal primer set that could accurately quantify biogeochemically important taxa in ecosystems ranging from the deep sea to the surface. In addition, our reproducible bioinformatic workflow can guide microbiome researchers studying different ecosystems or human health to similarly improve existing primers and generate more accurate quantitative amplicon data. IMPORTANCE PCR amplification and sequencing of marker genes is a low-cost technique for monitoring prokaryotic and eukaryotic microbial communities across space and time but will work optimally only if environmental organisms match PCR primer sequences exactly. In this study, we evaluated how well primers match globally distributed short-read oceanic metagenomes. Our results demonstrate that primer sets vary widely in performance, and that at least for marine systems, rRNA amplicon data from some primers lack significant biases compared to metagenomes. We also show that it is theoretically possible to create a nearly universal primer set for diverse saline environments by defining a specific mixture of a few dozen oligonucleotides, and present a software pipeline that can guide rational design of primers for any environment with available meta'omic data.

Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S

Universal primers for SSU rRNA genes allow profiling of natural communities by simultaneously amplifying templates from Bacteria, Archaea, and Eukaryota in a single PCR reaction. Despite the potential to show relative abundance for all rRNA genes, universal primers are rarely used, due to various concerns including amplicon length variation and its effect on bioinformatic pipelines. We thus developed 16S and 18S rRNA mock communities and a bioinformatic pipeline to validate this approach. Using these mocks, we show that universal primers (515Y/926R) outperformed eukaryote-specific V4 primers in observed versus expected abundance correlations (slope = 0.88 vs. 0.67-0.79), and mock community members with single mismatches to the primer were strongly underestimated (threefold to eightfold). Using field samples, both primers yielded similar 18S beta-diversity patterns (Mantel test, p < 0.001) but differences in relative proportions of many rarer taxa. To test for length biases, we mixed mock communities (16S + 18S) before PCR and found a twofold underestimation of 18S sequences due to sequencing bias. Correcting for the twofold underestimation, we estimate that, in Southern California field samples (1.2-80 μm), there were averages of 35% 18S, 28% chloroplast 16S, and 37% prokaryote 16S rRNA genes. These data demonstrate the potential for universal primers to generate comprehensive microbiome profiles.

Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench

Microbial eukaryotes are widespread and play important roles in marine ecosystems. However, their ecological characteristics in the deep sea (>1,000 m), especially hadal trenches, were largely unknown. Here, we investigated the diversity and metabolic potentials of microbial eukaryotes along the whole water column of the Mariana Trench by metagenomics. Our results showed clear depth-related distribution of microbial eukaryotic community and associated metabolic potentials. Surface seawater was dominated by phototrophic/mixotrophic groups (e.g., Dinoflagellata) and genes involved in biosynthesis (photosynthesis and fatty acid biosynthesis), while deep (bathypelagic and/or hadal) seawaters were enriched with heterotrophic groups (e.g., Bicoecea) and genes related to digestion (lysosomal enzymes and V-type ATPase) and carbohydrate metabolism. Co-occurrence analysis revealed high intra-domain connectivity, indicating that microbial eukaryotic composition was more influenced by microbial eukaryotes themselves than bacteria. Increased abundance of genes associated with unsaturated fatty acid biosynthesis likely plays a role in resisting high hydrostatic pressure. Top1 and hupB genes, responsible for the formation and stabilization of DNA structure, were unique and abundant in the hadal zone and thus may be helpful to stabilize DNA structure in the deep sea. Overall, our results provide insights into the distribution and potential adaptability of microbial eukaryotes in the hadal zone.

Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate

Phagocytosis is a fundamental process in marine ecosystems by which prey organisms are consumed and their biomass incorporated in food webs or remineralized. However, studies searching for the genes underlying this key ecological process in free-living phagocytizing protists are still scarce, in part due to the lack of appropriate ecological models. Our reanalysis of recent molecular datasets revealed that the cultured heterotrophic flagellate Cafeteria burkhardae is widespread in the global oceans, which prompted us to design a transcriptomics study with this species, grown with the cultured flavobacterium Dokdonia sp. We compared the gene expression between exponential and stationary phases, which were complemented with three starvation by dilution phases that appeared as intermediate states. We found distinct expression profiles in each condition and identified 2056 differentially expressed genes between exponential and stationary samples. Upregulated genes at the exponential phase were related to DNA duplication, transcription and translational machinery, protein remodeling, respiration and phagocytosis, whereas upregulated genes in the stationary phase were involved in signal transduction, cell adhesion, and lipid metabolism. We identified a few highly expressed phagocytosis genes, like peptidases and proton pumps, which could be used to target this ecologically relevant process in marine ecosystems.

Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea

Marine snow is an important habitat for microbes, characterized by chemical and physical properties contrasting those of the ambient water. The higher nutrient concentrations in marine snow lead to compositional differences between the ambient water and the marine snow-associated prokaryotic community. Whether these compositional differences vary due to seasonal environmental changes, however, remains unclear. Thus, we investigated the seasonal patterns of the free-living and marine snow-associated microbial community composition and their functional potential in the northern Adriatic Sea. Our data revealed seasonal patterns in both, the free-living and marine snow-associated prokaryotes. The two assemblages were more similar to each other in spring and fall than in winter and summer. The taxonomic distinctness resulted in a contrasting functional potential. Motility and adaptations to low temperature in winter and partly anaerobic metabolism in summer characterized the marine snow-associated prokaryotes. Free-living prokaryotes were enriched in genes indicative for functions related to phosphorus limitation in winter and in genes tentatively supplementing heterotrophic growth with proteorhodopsins and CO-oxidation in summer. Taken together, the results suggest a strong influence of environmental parameters on both free-living and marine snow-associated prokaryotic communities in spring and fall leading to higher similarity between the communities, while the marine snow habitat in winter and summer leads to a specific prokaryotic community in marine snow in these two seasons.

Influence of Regional Oceanography and Hydrothermal Activity on Protist Diversity and Community Structure in the Okinawa Trough

Microbial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but the relative importance of factors shaping protist diversity, such as environmental selection and dispersal, remains difficult to parse. Water masses of a back-arc basin with hydrothermal activity provide a unique opportunity for studying the effects of dispersal and environmental selection on protist communities. In this study, we used metabarcoding to characterize protist communities in the Okinawa Trough, a back-arc spreading basin containing at least twenty-five active hydrothermal vent fields. Water was sampled from four depths at fourteen stations spanning the length of the Okinawa Trough, including three sites influenced by nearby hydrothermal vent sites. While significant differences in community structure reflecting water depth were present, protist communities were mostly homogeneous horizontally. Protist communities in the bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.

Ciliate diversity and distribution across horizontal and vertical scales in the open ocean

Ciliates are globally distributed eukaryotic organisms inhabiting virtually all environments on Earth. Although ciliates range from 10 µm to a few millimetres in cell size, they are repeatedly reported in the pico-sized fraction (<2-3 µm) of molecular surveys. Here, we used existing data sets (BioMarKs and Tara Oceans) with different size fractions to demonstrate that the ciliate pico-sized signal, probably derived from cell breakage during filtration, is informative and reliable to study marine ciliate biodiversity and biogeography. We then used sequences from the pico-eukaryotic fraction of two circumnavigation expeditions, Malaspina-2010 and Tara Oceans, to give insights into the taxonomic composition and horizontal and vertical distribution of ciliates in the global ocean. The results suggested a high homogeneity of ciliate communities along the ocean surface from temperate to tropical waters, with ciliate assemblages dominated by a few abundant and widely distributed taxa. Very few taxa were found in a single oceanic region, therefore suggesting a high level of ciliate cosmopolitanism in the global ocean. In vertical profiles, ciliates were detected up to 4,000 m depth, and a clear vertical community structuring was observed. Our results provided evidence supporting ciliates as deeply integrated organisms in the deep-sea trophic web, where they may play a relevant role as symbionts of metazoans and grazers of prokaryotes and small eukaryotes in the water column and in aggregates.