Biology subjects

del Campo, J.

Publications and source records attributed to del Campo, J..

26 records · Page 2Linked to original sources

bioRxiv2020

Microniche sampling of the microbiome in the Starlet Sea Anemone, Nematostella vectensis, reveals a compartment-specific dominance of Spirochetes

Sampling of different body regions can reveal highly specialized bacterial associations within the holobiont and facilitate identification of core microbial symbionts that would otherwise be overlooked by bulk sampling methods. Here we characterized compartment-specific associations present within the model cnidarian Nematostella vectensis by dividing its morphology into three distinct body regions. This sampling design allowed us to uncover a capitulum-specific dominance of spirochetes within N. vectensis. Bacteria from the family Spirochaetaceae made up 66% of the community in the capitulum, while only representing 1.2% and 0.1% of the communities in the mesenteries and physa, respectively. A phylogenetic analysis of the predominant spirochete sequence recovered from N. vectensis showed a close relation to spirochetes previously recovered from wild N. vectensis. These sequences clustered closer to the recently described genus Oceanispirochaeta, rather than Spirochaeta perfilievii, supporting them as members of this clade. This suggests a consistent and potentially important association between N. vectensis and spirochetes from the order Spirochaetales.

microbiology↗

bioRxiv2018

A new framework for the study of apicomplexan diversity across environments

Apicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including widespread intracellular pathogens of mammals such as Toxoplasma and Plasmodium (the agent of malaria), and emergent pathogens like Cryptosporidium and Babesia. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we know surprisingly little about their diversity and distribution in natural environments. In this study we analyze the distribution of apicomplexans across a range of both host-associated and free-living environments, covering animal hosts from cnidarians to mammals, and ecosystems from soils to fresh and marine waters. Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys such as Tara Oceans and VAMPS, as well as our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. This tree allowed us to identify and correct incongruences in the molecular identification of sequences, particularly within the hematozoans and the gregarines. Analyzing the diversity and distribution of apicomplexans in HTES studies with this curated reference database also showed a widespread, and quantitatively important, presence of apicomplexans across a variety of free-living environments. These data allow us to describe a remarkable molecular diversity of this group compared with our current knowledge, especially when compared with that identified from described apicomplexan species. This revision is most striking in marine environments, where potentially the most diverse apicomplexans apparently exist, but have not yet been formally recognized. The new database will be useful for both microbial ecology and epidemiological studies, and provide valuable reference for medical and veterinary diagnosis especially in cases of emerging, zoonotic, and cryptic infections.\n\nAuthor SummaryApicomplexans are important animal and human parasites, but little is known about their distribution and diversity in the natural environment. We have developed a phylogenetically informed and manually curated reference database for the SSU rRNA barcode gene, and analyzed all publicly available sequences from a broad range of environments, providing a needed framework to analyze high-throughput environmental sequencing (HTES) data. The reference database and the amplicon sequences identified a striking diversity of apicomplexans in the environment, including habitats not usually associated with this group (e.g. open ocean). The phylogenetic framework will underpin microbial ecology studies and provide valuable resources for medical and veterinary biology.

microbiology↗

bioRxiv2018

A universal set of primers to study animal associated microeukaryotic communities

BackgroundUnlike the study of bacterial microbiomes, the study of the microeukaryotes associated with animals has largely been restricted to visual identification or molecular targeting of particular groups. The application of high-throughput sequencing (HTS) approaches, such as those used to look at bacteria, has been restricted because the barcoding gene traditionally used to study microeukaryotic ecology and distribution in the environment, the Small Subunit of the Ribosomal RNA gene (18S rRNA), is also present in the animal host. As a result, when host-associated microbial eukaryotes are analyzed by HTS, the obtained reads tend to be dominated by host sequences.\n\nResultsWe have done an in-silico validation against the SILVA 18S rRNA reference database of contrametazoan primers that cover the V4 region of the 18S rRNA, and compared these with universal V4 18S rRNA primers that are widely used by the microbial ecology community. We observe that the contrametazoan primers recover only 2.6% of all the metazoan sequences present in SILVA, while the universal primers recover up to 20%. Among metazoans, the contrametazoan primers are predicted to amplify 74% of Porifera sequences and 4% and 15% of ctenophore and Cnidaria, respectively, while amplifying almost no sequences within Bilateria.\n\nWe tested these predictions in-vivo, and observed that contrametazoan primers amplify the 18SrRNA from two ctenophore species, but reduce significantly the metazoan signal from material derived from coral and from human samples. When compared in-vivo against universal primers, contrametazoan primers worked in 8 out of 9 samples, providing at worst a 2-fold decrease in the number of metazoan reads, and at best a 2800-fold decrease.\n\nConclusionsWe have validated an easy, inexpensive, and near-universal method for the study of microeukaryotes associated with animal hosts using 18S rRNA Illumina metabarcoding. This method will contribute to a better understanding of microbial communities, as they related to the wellbeing of animals and humans.

microbiology↗

bioRxiv2018

Phylogeny, evidence for a cryptic plastid, and distribution of Chytriodinium parasites (Dinophyceae) infecting copepods

Spores of the dinoflagellate Chytriodinium are known to infest copepod eggs causing their lethality. Despite the potential to control the population of such an ecologically important host, knowledge about Chytriodinium parasites is limited: we know little about phylogeny, parasitism, abundance, or geographical distribution. We carried out genome sequence surveys on four manually isolated sporocytes from the same sporangium to analyse the phylogenetic position of Chytriodinium based on SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize two genes related to the plastidial heme pathway, hemL and hemY. The results suggest the presence of a cryptic plastid in Chytriodinium and a photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the recovered SSU rRNA gene sequences from the sporocytes, we show that globally, Chytriodinium parasites are most abundant within the pico/nano- and mesoplankton of the surface ocean and almost absent within microplankton, a distribution indicating that they generally exist either as free-living spores or host-associated sporangia.

microbiology↗

bioRxiv2018

A widespread coral-infecting apicomplexan contains a plastid encoding chlorophyll biosynthesis

The Apicomplexa are an important group of obligate intracellular parasites that include the causative agents of human diseases like malaria and toxoplasmosis. They evolved from free-living, phototrophic ancestors, and how this transition to parasitism occurred remains an outstanding question. One potential clue lies in coral reefs, where environmental DNA surveys have uncovered several lineages of uncharacterized, basally-branching apicomplexans. Reef-building corals form a well-studied symbiotic relationship with the photosynthetic dinoflagellate Symbiodinium, but identification of other key microbial symbionts of corals has proven elusive. Here, we used community surveys, genomics, and microscopy to identify an apicomplexan lineage, which we name corallicola, that was found in high prevalence (>80%) across all major groups of corals. In-situ fluorescence and electron microscopy confirmed that corallicola lives intracellularly within the tissues of the coral gastric cavity, and possesses clear apicomplexan ultrastructural features. We sequenced the plastid genome, which lacked all genes for photosystem proteins, indicating that corallicola harbours a non-photosynthetic plastid (an apicoplast). However, the corallicola plastid differed from all other known apicoplasts because it retains all four genes involved in chlorophyll biosynthesis. Hence, corallicola shares characteristics with both its parasitic and free-living relatives, implicating it as an evolutionary intermediate, and suggesting that a unique ancestral biochemistry likely operated during the transition from phototrophy to parasitism.

microbiology↗

bioRxiv2018

Unbiased whole genomes from mammalian feces using fluorescence-activated cell sorting

Ecological flexibility, extended lifespans, and large brains, have long intrigued evolutionary biologists, and comparative genomics offers an efficient and effective tool for generating new insights into the evolution of such traits. Studies of capuchin monkeys are particularly well situated to shed light on the selective pressures and genetic underpinnings of local adaptation to diverse habitats, longevity, and brain development. Distributed widely across Central and South America, they are inventive and extractive foragers, known for their sensorimotor intelligence. Capuchins have the largest relative brain size of any monkey and a lifespan that exceeds 50 years, despite their small (3-5 kg) body size. We assemble a de novo reference genome for Cebus imitator and provide the first genome annotation of a capuchin monkey. Through high-depth sequencing of DNA derived from blood, various tissues and feces via fluorescence activated cell sorting (fecalFACS) to isolate monkey epithelial cells, we compared genomes of capuchin populations from tropical dry forests and lowland rainforests and identified population divergence in genes involved in water balance, kidney function, and metabolism. Through a comparative genomics approach spanning a wide diversity of mammals, we identified genes under positive selection associated with longevity and brain development. Additionally, we provide a technological advancement in the use of non-invasive genomics for studies of free-ranging mammals. Our intra- and interspecific comparative study of capuchin genomics provides new insights into processes underlying local adaptation to diverse and physiologically challenging environments, as well as the molecular basis of brain evolution and longevity. SIGNIFICANCESurviving challenging environments, living long lives, and engaging in complex cognitive processes are hallmark characteristics of human evolution. Similar traits have evolved in parallel in capuchin monkeys, but their genetic underpinnings remain unexplored. We developed and annotated a reference assembly for white-faced capuchin monkeys to explore the evolution of these phenotypes. By comparing populations of capuchins inhabiting rainforest versus dry forests with seasonal droughts, we detected selection in genes associated with kidney function, muscular wasting, and metabolism, suggesting adaptation to periodic resource scarcity. When comparing capuchins to other mammals, we identified evidence of selection in multiple genes implicated in longevity and brain development. Our research was facilitated by our new method to generate high- and low-coverage genomes from non-invasive biomaterials.

genomics↗

bioRxiv2018

EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

Environmental sequencing has greatly expanded our knowledge of micro-eukaryotic diversity and ecology by revealing previously unknown lineages and their distribution. However, the value of these data is critically dependent on the quality of the reference databases used to assign an identity to environmental sequences. Existing databases contain errors, and struggle to keep pace with rapidly changing eukaryotic taxonomy, the influx of novel diversity, and computational challenges related to assembling the high-quality alignments and trees needed for accurate characterization of lineage diversity. EukRef (eukref.org) is a community driven initiative that addresses these challenges by bringing together taxonomists with expertise spanning the complete eukaryotic tree of life and microbial ecologists that actively use environmental sequencing data for the purpose of developing reliable reference databases across the diversity of microbial eukaryotes. EukRef organizes and facilitates rigorous sequence data mining and annotation by providing protocols, guidelines and tools to do so.

microbiology↗

bioRxiv2018

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity

Although animals are among the best studied organisms, we still lack a full description of their diversity, especially for microscopic taxa. This is partly due to the time-consuming and costly nature of surveying animal diversity through morphological and molecular studies of individual taxa. A powerful alternative is the use of high-throughput environmental sequencing, providing molecular data from all organisms sampled. We here address the unknown diversity of animal phyla in marine environments using an extensive dataset designed to assess eukaryotic ribosomal diversity among European coastal locations. A multi-phylum assessment of marine animal diversity that includes water column and sediments, oxic and anoxic environments, and both DNA and RNA templates, revealed a high percentage of novel 18S rRNA sequences in most phyla, suggesting that marine environments have not yet been fully sampled at a molecular level. This novelty is especially high among Platyhelminthes, Acoelomorpha, and Nematoda, which are well studied from a morphological perspective and abundant in benthic environments. We also identified based on molecular data a potentially novel group of widespread tunicates. Moreover, we recovered a high number of reads for Ctenophora and Cnidaria in the smaller fractions suggesting their gametes might play a greater ecological role than previously suspected.

microbiology↗