Biology subjects

Marulanda-Gomez, A. M.

Publications and source records attributed to Marulanda-Gomez, A. M..

4 recordsLinked to original sources

bioRxiv2024

A paleogenomic approach to reconstruct historical responses of coral reefs to anthropogenic change

Coral reefs are declining worldwide due to anthropogenic environmental change. The foundation and health of these ecosystems rely on the harmonious functioning of all members of coral holobionts, i.e., cnidarian host, symbiotic microalgae, and associated microbiome. Coral stress responses often involve shifts in the taxonomic identity of their symbionts and microbiomes. Tracing back changes in coral holobiont composition over prolonged time periods can help us reconstruct health history of reefs and gain a better understanding of coral response to current stressors. Here, we focused on a major Caribbean reef-builder coral, Orbicella faveolata, from Varadero Reef, Colombia. This reef has undergone extensive freshwater sediment discharge and pollution for decades as result of urbanization. We show, for the first time, that paleogenomic and paleoclimatic approaches can be combined to reconstruct historical coral holobiont dynamics potentially associated with anthropogenic disturbances.

molecular biology↗

bioRxiv2024

The chromosome-level genome of the ctenophore Mnemiopsis leidyi A. Agassiz, 1865 reveals a unique immune gene repertoire

Ctenophora are basal marine metazoans, the sister group of all other animals. Mnemiopsis leidyi is one of the most successful invasive species worldwide with intense ecological and evolutionary research interest. Here, we generated a chromosome-level genome assembly of M. leidyi with a focus on its immune gene repertoire. The genome was 247.97 Mb, with N50 16.84 Mb, and 84.7% completeness. Its karyotype was 13 chromosomes. In this genome and that of two other ctenophores, Bolinopsis microptera and Hormiphora californensis, we detected a high number of protein domains related to potential immune receptors. Among those, proteins containing Toll/interleukin-1(TIR2) domain, NACHT domain, Scavenger Receptor Cystein-Rich (SRCR) domain, or C-type Lectin domain (CTLD) were abundant and presented unique domain architectures in M. leidyi. M. leidyi seems to lack bona fide Toll like Receptors, but it does possess a repertoire of 15 TIR2-domain containing genes. Besides, we detected a bona fide NOD-like receptor and 38 NACHT-domain containing genes. In order to verify the function of those domain containing genes, we exposed M. leidyi to the pathogen Vibrio coralliilyticus. Among the differentially expressed genes, we identified potential immune receptors, including four TIR2-domain containing genes, all of which were upregulated in response to pathogen exposure. To conclude, many common immune receptor domains, highly conserved across metazoans, are already present in Ctenophora. These domains have large expansions and unique architectures in M. leidyi, findings consistent with the basal evolutionary position of this group, but still might have conserved functions in immunity and host-microbe interaction.

genomics↗

bioRxiv2023

Transcriptomic responses of Mediterranean sponges upon encounter with seawater or symbiont microbial consortia

Sponges (phylum Porifera) constantly interact with microbes from the water column while filter-feeding and with the symbiotic partners they harbor within their mesohyl. Despite early observations on differential uptake between symbiont and seawater bacteria, it is still poorly understood how sponges discriminate between different microbial consortia. Initial evidence of the diverse repertoire of sponge immune receptors suggests their involvement in specific microbial recognition, yet experimental data is still scarce. We characterized the transcriptomic response of two sponge species, Aplysina aerophoba and Dysidea avara, upon incubation with two different microbial consortia, which were either enriched from ambient seawater or extracted from A. aerophoba. The sponges were sampled after 1 h, 3 h, and 5 h for RNA-Seq differential gene expression analysis. D. avara showed higher expression levels of genes related to immunity, ubiquitination, and signaling when incubated with A. aerophoba symbionts, than in incubations with seawater microbial consortia. Interestingly, the different bacteria consortia triggered changes in Nucleotide Oligomerization Domain (NOD)-Like Receptors (NLRs) gene expression in D. avara. We here provide the first experimental evidence for NLRs playing a role in distinguishing between different microbes in a sponge. In contrast, the response of A. aerophoba involved comparatively few genes and lacked genes encoding for immune receptors. This indicates that A. aerophoba is less responsive to microbial encounters than D. avara. Our study further reveals different transcriptomic responses between the two sponge species to microbes. The study of sponge responses to microbes aids in understanding the evolution of immune specificity and animal-microbe interactions. Significant statementAnimals rely on components of the immune system to recognize specific microbes, whether they are pathogens, food, or beneficial symbionts. However, in marine invertebrates, the mechanisms of microbial discrimination and specificity are not well understood. Our work suggests that:(i) the transcriptomic response by the sponge can be scaled according to the type of exposure, (ii) the response to microbial encounters is species-specific and (iii) NLRs seem to have a prominent role in the differential response to microorganisms, whether symbionts or food bacteria.

molecular biology↗

bioRxiv2023

A novel in-vivo phagocytosis assay to gain cellular insights on sponge-microbe interactions

Sponges harbor diverse, specific, and stable microbial communities, but at the same time, they efficiently feed on microbes from the surrounding water column. This filter-feeding lifestyle poses the need to distinguish between three categories of bacteria: food to digest, symbionts to incorporate, and pathogens to eliminate. How sponges discriminate between these categories is still largely unknown. Phagocytosis is conceivable as the cellular mechanism taking part in such discrimination, but experimental evidence is missing. We developed a quantitative in-vivo phagocytosis assay using an emerging experimental model, the sponge Halichondria panicea. We incubated whole sponge individuals with different particles, recovered the sponge (host) cells, and tracked the particles into the sponge cells to quantify the sponges phagocytic activity. Fluorescence-activated cell sorting (FACS) and fluorescent microscopy were used to quantify and verify phagocytic activity (i.e., the population of sponge cells with internalized particles). Sponges were incubated with a green microalgae to test the effect of particle concentration on the percentage of phagocytic activity, and to determine the timing where the maximum of phagocytic cells are captured in a pulse-chase experiment. Lastly, we investigated the application of our phagocytic assay with other particle types (i.e., bacteria and fluorescent beads). The percentage of phagocytic cells that had incorporated algae, bacteria, and beads ranged between 5 to 24 %. We observed that the population of phagocytic sponge cell exhibited different morphologies and sizes depending on the type of particle presented to the sponge. Phagocytosis was positively related to algal concentration suggesting that sponge cells adjust their phagocytic activity depending on the number of particles they encounter. Our results further revealed that sponge phagocytosis initiates within minutes after exposure to the particles. Fluorescent and TEM microscopy rectified algal internalization and potential digestion in sponge cells, and suggests translocation between choanocyte and archeocyte-like cells over time. To our knowledge, this is the first quantitative in-vivo phagocytosis assay established in sponges that could be used to further explore phagocytosis as a cellular mechanism for sponges to differentiate between different microorganisms.

cell biology↗