Javier del Campo

Javier del Campo
Institute of Evolutionary Biology | IBE · Institute of Evolutionary Biology (CSIC-UPF)

PhD

About

160
Publications
27,924
Reads
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4,131
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Introduction
My research focuses on the study of the ecology and evolution of microbes and the microbiome. I am currently investigating microbial community ecology in marine animal-associated environments using cutting-edge sequencing technologies and computational biology. I hope that my research can help to have a better understanding of the role that microorganisms play in the response of animals to climate change.
Additional affiliations
February 2019 - January 2021
University of Miami
Position
  • Professor (Assistant)
May 2017 - January 2019
Institut de Ciències del Mar
Position
  • PostDoc Position
July 2013 - April 2017
University of British Columbia - Vancouver
Position
  • PostDoc Position
Education
September 1999 - September 2003

Publications

Publications (160)
Article
Full-text available
Understanding the origin and evolution of the eukaryotic cell and the full diversity of eukaryotes is relevant to many biological disciplines. However, our current understanding of eukaryotic genomes is extremely biased, leading to a skewed view of eukaryotic biology. We argue that a phylogeny-driven initiative to cover the full eukaryotic diversit...
Article
Full-text available
The diversity of heterotrophic flagellates is generally based on cultivated strains, on which ultrastructural, physiological, and molecular studies have been performed. However, the relevance of these cultured strains as models of the dominant heterotrophic flagellates in the marine planktonic environment is unclear. In fact, molecular surveys typi...
Article
Full-text available
The Opisthokonta clade includes Metazoa, Fungi and several unicellular lineages, such as choanoflagellates, filastereans, ichthyosporeans and nucleariids. To date, studies of the evolutionary diversity of opisthokonts have focused exclusively on metazoans, fungi and, very recently, choanoflagellates. Thus, very little is known about diversity among...
Article
Full-text available
Protists (unicellular eukaryotes) arguably account for most eukaryotic diversity and are central players of the biosphere. Known protist diversity and biology is largely based on cultured strains. Yet, environmental molecular surveys have unveiled entirely novel lineages that, as their prokaryotic counterparts, are essentially uncultured. Culture b...
Article
Full-text available
Eukaryote symbionts of animals are major drivers of ecosystems not only because of their diversity and host interactions from variable pathogenicity but also through different key roles such as commensalism and to different types of interdependence. However, molecular investigations of metazoan eukaryomes require minimising co-amplification of homo...
Chapter
Full-text available
Oceans are no longer inaccessible places for data acquisition. High-throughput technological advances applied to marine sciences ( from genes to global current patterns ) are generating Big Data sets at unprecedented rates. How to manage, store, analyse, use and transform this data deluge into knowledge is now a fundamental challenge for ocean scie...
Article
Full-text available
Cristamonadea is a large class of parabasalian protists that reside in the hindguts of wood-feeding insects, where they play an essential role in the digestion of lignocellulose. This group of symbionts boasts an impressive array of complex morphological characteristics, many of which have evolved multiple times independently. However, their divers...
Article
Full-text available
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 under...
Article
Full-text available
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 divid...
Article
The Stramenopiles are a large and diverse group of eukaryotes that possess various lifestyles required to thrive in a broad array of environments. The stramenopiles branch with the alveolates, rhizarians, and telonemids, forming the supergroup TSAR. Here, we present a new genus and species of aquatic nanoflagellated stramenopile: Mediocremonas medi...
Article
Studies of animal and plant microbiomes are burgeoning, but the majority of these focus on bacteria and rarely include micro-eukaryotes other than fungi. However, there is growing evidence that micro-eukaryotes living on and in larger organisms (e.g. plants, animals, macroalgae) are diverse and in many cases abundant. We present here a new combinat...
Preprint
Full-text available
The Stramenopiles are a large and diverse group of eukaryotes that possess various lifestyles required to thrive in a broad array of environments. The stramenopiles branch with the alveolates, rhizarians, and telonemids, forming the supergroup TSAR. Here, we present a new genus and species of aquatic nanoflagellated stramenopile: Mediocremonas medi...
Preprint
Full-text available
Microniche sampling can reveal highly specialized bacterial associations within the holobiont and also facilitate identification of core microbial symbionts that would otherwise be overlooked by bulk sampling methods. We characterized compartment-specific associations present within the model cnidarian Nematostella vectensis by dividing its morphol...
Article
Awareness of the roles host‐associated microbes play in host biology has escalated in recent years. However, microbiome studies have focused essentially on bacteria, and overall, we know little about the role of host‐associated eukaryotes outside of the field of parasitology. Despite that, eukaryotes and microeukaryotes in particular are known to b...
Article
The Fungi are a diverse kingdom, dominating terrestrial environments and driving important ecologies. Although fungi, and the related Opisthosporidia, interact with photosynthetic organisms on land and in freshwater as parasites, symbionts, and/or saprotrophic degraders [1, 2], such interactions in the marine environment are poorly understood [3-8]...
Article
Full-text available
Apicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including the causing agents of toxoplasmosis and malaria, and emergent diseases like cryptosporidiosis or babesiosis. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we...
Article
The application of metabarcoding to study animal‐associated microeukaryotes has been restricted because the universal barcode 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 host. As a result, when host‐associated microbial eukaryotes are analy...
Article
Full-text available
Apicomplexa is a group of obligate intracellular parasites that includes the causative agents of human diseases such as malaria and toxoplasmosis. Apicomplexans evolved from free-living phototrophic ancestors, but how this transition to parasitism occurred remains unknown. One potential clue lies in coral reefs, of which environmental DNA surveys h...
Article
This revision of the classification of eukaryotes follows that of Adl et al., 2012[J. Euk. Microbiol.59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted,environmental sampling in the intervening ye...
Preprint
Full-text available
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 b...
Preprint
Full-text available
Background: Unlike 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 barc...
Article
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 se...
Article
Full-text available
This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening...
Article
Full-text available
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 er...
Preprint
Full-text available
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 se...
Preprint
Full-text available
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 environmen...
Article
Recent surveys of marine microbial diversity have identified a previously unrecognised lineage of diplonemid protists as being amongst the most diverse heterotrophic eukaryotes in global oceans. Despite their monophyly (and assumed importance), they lack a formal taxonomic description, and are informally known as deep‐sea pelagic diplonemids (DSPDs...
Preprint
Full-text available
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 unde...
Article
Environmental sequences have become a major source of information. High‐throughput sequencing (HTS) surveys have been used to infer biogeographic patterns and distribution of broad taxa of protists. This approach is, however, more questionable for addressing low‐rank (less inclusive) taxa such as species and genera, because of the increased chance...
Article
Full-text available
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 env...
Preprint
Full-text available
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 er...
Article
Although previous studies, mostly based on microscopy analyses of a few groups of protists, have suggested that protists are abundant and diverse in litter and moss habitats, the overall diversity of moss and litter associated protists remains elusive. Here, high-throughput environmental sequencing was used to characterize the diversity and communi...
Article
Apicomplexans are a group of obligate intracellular parasites, but their retention of a relict non‐photosynthetic plastid reveals that they evolved from free‐living photosynthetic ancestors. The closest relatives of apicomplexans include photosynthetic chromerid algae (e.g., Chromera and Vitrella), non‐photosynthetic colpodellid predators (e.g., Co...
Article
High‐throughput sequencing (HTS) surveys, among the most common approaches currently used in environmental microbiology, require reliable reference databases to be correctly interpreted. The EukRef Initiative (eukref.org) is a community effort to manually screen available small subunit (SSU) rRNA gene sequences and produce a public, high‐quality, a...
Preprint
Full-text available
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 env...
Article
Full-text available
Photosynthetic picoeukaryotes contribute a significant fraction of primary production in the upper ocean. Micromonas pusilla is an ecologically relevant photosynthetic picoeukaryote, abundantly and widely distributed in marine waters. Grazing by protists may control the abundance of picoeukaryotes such as M. pusilla, but the diversity of the respon...
Article
Full-text available
Pseudotrichonympha is a large and structurally complex genus of parabasalian protists that play a key role in the digestion of lignocellulose in the termite hindgut. Like many termite symbionts, it has a conspicuous body plan that makes genus-level identification relatively easy, but species-level diversity of Pseudotrichonympha is understudied. Mo...
Article
Full-text available
Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell geno...
Article
Members of the genus Trichonympha are among the most well-known, recognizable and widely distributed parabasalian symbionts of lower termites and the wood-eating cockroach species of the genus Cryptocercus. Nevertheless, the species diversity of this genus is largely unknown. Molecular data have shown that the superficial morphological similarities...
Article
Our understanding of the origin of animals has been transformed by characterizing their most closely related, unicellular sisters: the choanoflagellates, filastereans, and ichthyosporeans. Together with animals, these lineages make up the Holozoa [ 1, 2 ]. Many traits previously considered “animal specific” were subsequently found in other holozoan...
Article
The study of marine microbial ecology has been completely transformed by molecular and genomic data: after centuries of relative neglect, genomics has revealed the surprising extent of microbial diversity and how microbial processes transform ocean and global ecosystems. But the revolution is not complete: major gaps in our understanding remain, an...
Article
The dinoflagellate Haidadinium ichthyophilum Buckland-Nicks, Reimchen and Garbary 1997 is an ectoparasite of the spine-deficient, three-spine stickleback Gasterosteus aculeatus L. Reimchen 1984, a fish endemic to Rouge Lake, Haida Gwaii. Haidadinium ichthyophilum proved difficult to assign taxonomically, because its morphology and complex life cycl...
Article
“X-cells” have long been associated with tumor-like formations (xenomas) in marine fish, including many of commercial interest. The name was first used to refer to the large polygonal cells that were found in epidermal xenomas from flatfish from the Pacific Northwest [ 1 ]. Similar looking cells from pseudobranchial xenomas had previously been repo...
Article
Full-text available
Temperate bacterial viruses (phages) may enter a symbiosis with their host cell, forming a unit called a lysogen. Infection and viral replication are disassociated in lysogens until an induction event such as DNA damage occurs, triggering viral-mediated lysis. The lysogen–lytic viral reproduction switch is central to viral ecology, with diverse eco...
Article
Full-text available
The bewildering organismal and functional complexity of microbial eukaryotes has long fascinated protistologists but exceeded the capacity of this research community to comprehensively study it. Lacking the critical mass for a strong scientific discipline, protistologists remain largely divided into various sub-communities (protozoology versus phyc...
Article
Labyrinthulomycetes are heterotrophic stramenopiles that are ubiquitous in a wide range of both marine and freshwater habitats and play important roles in decomposition of organic matter. The diversity and taxonomy of Labyrinthulomycetes has been studied for many years, but we nevertheless lack both a comprehensive reference database and up-to-date...
Article
Ostreobium is an endolithic algal genus thought to be an early-diverging lineage of the Bryopsidales (Ulvophyceae, Chlorophyta). Ostreobium can live in low-light conditions on calcium carbonate substrata in tropical conditions. It is best known as a symbiont of corals, where it lives deep within the animal skeleton and exchanges nitrogen and carbon...
Article
Recent global surveys of marine biodiversity have revealed that a group of organisms known as “marine diplonemids” constitutes one of the most abundant and diverse planktonic lineages. Though discovered over a decade ago, their potential importance was unrecognized, and our knowledge remains restricted to a single gene amplified from environmental...
Article
Full-text available
Environmental DNA and culture-based analyses have suggested that fungi are present in low diversity and in low abundance in many marine environments, especially in the upper water column. Here, we use a dual approach involving high-throughput diversity tag sequencing from both DNA and RNA templates and fluorescent cell counts to evaluate the divers...
Article
Full-text available
Graphical Abstract Highlights d Taxon-rich phylogenomics provides an evolutionary framework for the opisthokonts d Specialized osmotrophy evolved independently in fungi and animal relatives d Opisthokonts underwent independent secondary losses of the flagellum d The last opisthokont common ancestor had a complex repertoire of chitin synthases Corre...
Article
The opisthokonts are one of the major super-groups of eukaryotes. It comprises two major clades: 1) the Metazoa and their unicellular relatives and 2) the Fungi and their unicellular relatives. There is, however, little knowledge of the role of opisthokont microbes in many natural environments, especially among non-metazoan and non-fungal opisthoko...
Article
Full-text available
The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pat...
Data
Genes encoding cytoskeletal components in the 26 species.Most of components in the actomyosin complex were predicted in silico with some manual curation for P. falciparum and T. gondii. Definitions of the categories and details of how these genes are compiled are provided in the materials and method section.DOI: http://dx.doi.org/10.7554/eLife.0697...
Data
RNA-seq libraries of Chromera velia under various growth conditions.The list of growth conditions and the file names are given.DOI: http://dx.doi.org/10.7554/eLife.06974.023
Data
Summary of the genome assembly and the annotated genes of Chromera velia, Vitrella brassicaformis. Details of transposable elements on the genome are shown in Supplementary file 2. DOI: http://dx.doi.org/10.7554/eLife.06974.026
Data
Summary of transposable elements on the Chromera velia and Vitrella brassicaformis genomes. DOI: http://dx.doi.org/10.7554/eLife.06974.027
Data
Domains of extracellular proteins and example genes in chromerids. (a) Species abbreviations: Perkinsus marinus, P. mar; Chromera velia, C. vel; Vitrella brassicaformis, V. bra; and Cryptosporidium parvum, C. par. (b) Domain accession identifiers. Domain information can be retrieved at the NCBI Conserved Domain website: (http://www.ncbi.nlm.nih.gov...
Data
List of 24 species excluding Chomera and Vitrella used in this study and their data sources.DOI: http://dx.doi.org/10.7554/eLife.06974.004
Data
Genes encoding subunits of the endomembrane trafficking system.DOI: http://dx.doi.org/10.7554/eLife.06974.008
Data
List of genes implicated in invasion processes in apicomplexans.They were either annotated as implicated in invasion processes in P. falciparum or orthologs of those in other apicomplexans. Pubmed ID number or the database from which the annotation was obtained is listed in the last two columns.DOI: http://dx.doi.org/10.7554/eLife.06974.024