Josephine Bay Paul Center in Comparative Molecular Biology and Evolution

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The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution explores the evolution and interaction of genomes of diverse organisms that play significant roles in environmental biology and human health. This dynamic research program integrates the powerful tools of genome science, molecular phylogenetics, and molecular ecology to advance our understanding of how living organisms are related to each other, to provide the tools to quantify and assess biodiversity, and to identify genes and underlying mechanisms of biomedical importance. Projects span all evolutionary time scales, ranging from deep phylogenetic divergence of ancient eukaryotic and prokaryotic lineages, to ecological analyses of how members of diverse communities contribute and respond to environmental change.

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Now showing 1 - 20 of 285
  • Article
    Sargasso Sea Vibrio bacteria: underexplored potential pathovars in a perturbed habitat
    (Elsevier, 2023-08-10) Mincer, Tracy J. ; Bos, Ryan P. ; Zettler, Erik R. ; Zhao, Shiye ; Asbun, Alejandro A. ; Orsi, William D. ; Guzzetta, Vincent S. ; Amaral-Zettler, Linda A.
    We fully sequenced the genomes of 16 Vibrio cultivars isolated from eel larvae, plastic marine debris (PMD), the pelagic brown macroalga Sargassum, and seawater samples collected from the Caribbean and Sargasso Seas of the North Atlantic Ocean. Annotation and mapping of these 16 bacterial genome sequences to a PMD-derived Vibrio metagenome-assembled genome created for this study showcased vertebrate pathogen genes closely-related to cholera and non-cholera pathovars. Phenotype testing of cultivars confirmed rapid biofilm formation, hemolytic, and lipophospholytic activities, consistent with pathogenic potential. Our study illustrates that open ocean vibrios represent a heretofore undescribed group of microbes, some representing potential new species, possessing an amalgam of pathogenic and low nutrient acquisition genes, reflecting their pelagic habitat and the substrates and hosts they colonize.
  • Article
    Human milk-associated bacterial communities associate with the infant gut microbiome over the first year of life
    (Frontiers Media, 2023-04-17) Lundgren, Sara N. ; Madan, Juliette C. ; Karagas, Margaret R. ; Morrison, Hilary G. ; Christensen, Brock C. ; Hoen, Anne G.
    Mosquitoes represent the most important pathogen vectors and are responsible for the spread of a wide variety of poorly treatable diseases. Wolbachia are obligate intracellular bacteria that are widely distributed among arthropods and collectively represents one of the most promising solutions for vector control. In particular, Wolbachia has been shown to limit the transmission of pathogens, and to dramatically affect the reproductive behavior of their host through its phage WO. While much research has focused on deciphering and exploring the biocontrol applications of these WO-related phenotypes, the extent and potential impact of the Wolbachia mobilome remain poorly appreciated. Notably, several Wolbachia plasmids, carrying WO-like genes and Insertion Sequences (IS), thus possibly interrelated to other genetic units of the endosymbiont, have been recently discovered. Here we investigated the diversity and biogeography of the first described plasmid of Wolbachia in Culex pipiens (pWCP) in several islands and continental countries around the world—including Cambodia, Guadeloupe, Martinique, Thailand, and Mexico—together with mosquito strains from colonies that evolved for 2 to 30 years in the laboratory. We used PCR and qPCR to determine the presence and copy number of pWCP in individual mosquitoes, and highly accurate Sanger sequencing to evaluate potential variations. Together with earlier observation, our results show that pWCP is omnipresent and strikingly conserved among Wolbachia populations within mosquitoes from distant geographies and environmental conditions. These data suggest a critical role for the plasmid in Wolbachia ecology and evolution, and the potential of a great tool for further genetic dissection and possible manipulation of this endosymbiont.
  • Article
    pWCP is a widely distributed and highly conserved Wolbachia plasmid in Culex pipiens and Culex quinquefasciatus mosquitoes worldwide
    (Springer, 2023-04-28) Ghousein, Amani ; Tutagata, Jordan ; Schrieke, Hans ; Etienne, Manuel ; Chaumeau, Victor ; Boyer, Sebastien ; Pages, Nonito ; Roiz, David ; Eren, A Murat ; Cambray, Guillaume ; Reveillaud, Julie
    Mosquitoes represent the most important pathogen vectors and are responsible for the spread of a wide variety of poorly treatable diseases. Wolbachia are obligate intracellular bacteria that are widely distributed among arthropods and collectively represents one of the most promising solutions for vector control. In particular, Wolbachia has been shown to limit the transmission of pathogens, and to dramatically affect the reproductive behavior of their host through its phage WO. While much research has focused on deciphering and exploring the biocontrol applications of these WO-related phenotypes, the extent and potential impact of the Wolbachia mobilome remain poorly appreciated. Notably, several Wolbachia plasmids, carrying WO-like genes and Insertion Sequences (IS), thus possibly interrelated to other genetic units of the endosymbiont, have been recently discovered. Here we investigated the diversity and biogeography of the first described plasmid of Wolbachia in Culex pipiens (pWCP) in several islands and continental countries around the world-including Cambodia, Guadeloupe, Martinique, Thailand, and Mexico-together with mosquito strains from colonies that evolved for 2 to 30 years in the laboratory. We used PCR and qPCR to determine the presence and copy number of pWCP in individual mosquitoes, and highly accurate Sanger sequencing to evaluate potential variations. Together with earlier observation, our results show that pWCP is omnipresent and strikingly conserved among Wolbachia populations within mosquitoes from distant geographies and environmental conditions. These data suggest a critical role for the plasmid in Wolbachia ecology and evolution, and the potential of a great tool for further genetic dissection and possible manipulation of this endosymbiont.
  • Article
    Plastics select for distinct early colonizing microbial populations with reproducible traits across environmental gradients
    (Applied Microbiology International, 2023-05-03) Bos, Ryan P. ; Kaul, Drishti ; Zettler, Erik R. ; Hoffman, Jeffrey M. ; Dupont, Christopher L. ; Amaral-Zettler, Linda A. ; Mincer, Tracy J
    Little is known about early plastic biofilm assemblage dynamics and successional changes over time. By incubating virgin microplastics along oceanic transects and comparing adhered microbial communities with those of naturally occurring plastic litter at the same locations, we constructed gene catalogues to contrast the metabolic differences between early and mature biofilm communities. Early colonization incubations were reproducibly dominated by Alteromonadaceae and harboured significantly higher proportions of genes associated with adhesion, biofilm formation, chemotaxis, hydrocarbon degradation and motility. Comparative genomic analyses among the Alteromonadaceae metagenome assembled genomes (MAGs) highlighted the importance of the mannose-sensitive hemagglutinin (MSHA) operon, recognized as a key factor for intestinal colonization, for early colonization of hydrophobic plastic surfaces. Synteny alignments of MSHA also demonstrated positive selection for mshA alleles across all MAGs, suggesting that mshA provides a competitive advantage for surface colonization and nutrient acquisition. Large-scale genomic characteristics of early colonizers varied little, despite environmental variability. Mature plastic biofilms were composed of predominantly Rhodobacteraceae and displayed significantly higher proportions of carbohydrate hydrolysis enzymes and genes for photosynthesis and secondary metabolism. Our metagenomic analyses provide insight into early biofilm formation on plastics in the ocean and how early colonizers self-assemble, compared to mature, phylogenetically and metabolically diverse biofilms.
  • Article
    SAG-RAD: a method for single-cell population genomics of unicellular eukaryotes
    (Oxford University Press, 2023-04-20) Gollnisch, Raphael ; Wallenius, Joel ; Gribble, Kristin E. ; Ahrén, Dag ; Rengefors, Karin
    Sequencing of reduced representation libraries enables genotyping of many individuals for population genomic studies. However, high amounts of DNA are required, and the method cannot be applied directly on single cells, preventing its use on most microbes. We developed and implemented the analysis of single amplified genomes followed by restriction-site-associated DNA sequencing to bypass labor-intensive culturing and to avoid culturing bias in population genomic studies of unicellular eukaryotes. This method thus opens the way for addressing important questions about the genetic diversity, gene flow, adaptation, dispersal, and biogeography of hitherto unexplored species.
  • Article
    Metabolic independence drives gut microbial colonization and resilience in health and disease
    (BioMed Central, 2023-04-17) Watson, Andrea R. ; Füssel, Jessika ; Veseli, Iva ; DeLongchamp, Johanna Zaal ; Silva, Marisela ; Trigodet, Florian ; Lolans, Karen ; Shaiber, Alon ; Fogarty, Emily ; Runde, Joseph M. ; Quince, Christopher ; Yu, Michael K. ; Söylev, Arda ; Morrison, Hilary G. ; Lee, Sonny T. M. ; Kao, Dina ; Rubin, David T. ; Jabri, Bana ; Louie, Thomas ; Eren, A. Murat
    Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge.Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients.These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
  • Article
    A phylogenomic approach to resolving interrelationships of polyclad flatworms, with implications for life-history evolution
    (The Royal Society, 2023-03-29) Goodheart, Jessica A. ; Collins, Allen G. ; Cummings, Michael P. ; Egger, Bernhard ; Rawlinson, Kate A.
    Platyhelminthes (flatworms) are a diverse invertebrate phylum useful for exploring life-history evolution. Within Platyhelminthes, only two clades develop through a larval stage: free-living polyclads and parasitic neodermatans. Neodermatan larvae are considered evolutionarily derived, whereas polyclad larvae are hypothesized to be ancestral due to ciliary band similarities among polyclad and other spiralian larvae. However, larval evolution has been challenging to investigate within polyclads due to low support for deeper phylogenetic relationships. To investigate polyclad life-history evolution, we generated transcriptomic data for 21 species of polyclads to build a well-supported phylogeny for the group. The resulting tree provides strong support for deeper nodes, and we recover a new monophyletic clade of early branching cotyleans. We then used ancestral state reconstructions to investigate ancestral modes of development within Polycladida and more broadly within flatworms. In polyclads, we were unable to reconstruct the ancestral state of deeper nodes with significant support because early branching clades show diverse modes of development. This suggests a complex history of larval evolution in polyclads that likely includes multiple losses and/or multiple gains. However, our ancestral state reconstruction across a previously published platyhelminth phylogeny supports a direct developing prorhynchid/polyclad ancestor, which suggests that a larval stage in the life cycle evolved along the polyclad stem lineage or within polyclads.
  • Article
    Ectodermal Wnt signaling, cell fate determination, and polarity of the skate gill arch skeleton
    (eLife Sciences Publications, 2023-03-20) Rees, Jenaid M. ; Sleight, Victoria A. ; Clark, Stephen J. ; Nakamura, Tetsuya ; Gillis, J Andrew
    The gill skeleton of cartilaginous fishes (sharks, skates, rays, and holocephalans) exhibits a striking anterior-posterior polarity, with a series of fine appendages called branchial rays projecting from the posterior margin of the gill arch cartilages. We previously demonstrated in the skate (Leucoraja erinacea) that branchial rays derive from a posterior domain of pharyngeal arch mesenchyme that is responsive to Sonic hedgehog (Shh) signaling from a distal gill arch epithelial ridge (GAER) signaling centre. However, how branchial ray progenitors are specified exclusively within posterior gill arch mesenchyme is not known. Here, we show that genes encoding several Wnt ligands are expressed in the ectoderm immediately adjacent to the skate GAER, and that these Wnt signals are transduced largely in the anterior arch environment. Using pharmacological manipulation, we show that inhibition of Wnt signalling results in an anterior expansion of Shh signal transduction in developing skate gill arches, and in the formation of ectopic anterior branchial ray cartilages. Our findings demonstrate that ectodermal Wnt signalling contributes to gill arch skeletal polarity in skate by restricting Shh signal transduction and chondrogenesis to the posterior arch environment and highlights the importance of signalling interactions at embryonic tissue boundaries for cell fate determination in vertebrate pharyngeal arches.
  • Article
    Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution
    (American Association for the Advancement of Science, 2023-02-22) Kiefl, Evan ; Esen, Ozcan C. ; Miller, Samuel E. ; Kroll, Kourtney L. ; Willis, Amy D. ; Rappé, Michael S. ; Pan, Tao ; Eren, A. Murat
    Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynonymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.
  • Article
    Dual functions of labial resolve the hox logic of chelicerate head segments
    (Oxford University Press, 2023-02-17) Gainett, Guilherme ; Klementz, Benjamin C. ; Blaszczyk, Pola O. ; Bruce, Heather S. ; Patel, Nipam H. ; Sharma, Prashant P.
    Despite an abundance of gene expression surveys, comparatively little is known about Hox gene function in Chelicerata. Previous investigations of paralogs of labial (lab) and Deformed (Dfd) in a spider have shown that these play a role in tissue maintenance of the pedipalp segment (lab-1) and in patterning the first walking leg identity (Dfd-1), respectively. However, extrapolations of these data across chelicerates are hindered by the existence of duplicated Hox genes in arachnopulmonates (e.g., spiders and scorpions), which have resulted from an ancient whole genome duplication (WGD) event. Here, we investigated the function of the single-copy ortholog of lab in the harvestman Phalangium opilio, an exemplar of a lineage that was not subject to this WGD. Embryonic RNA interference against lab resulted in two classes of phenotypes: homeotic transformations of pedipalps to chelicerae, as well as reduction and fusion of the pedipalp and leg 1 segments. To test for combinatorial function, we performed a double knockdown of lab and Dfd, which resulted in a homeotic transformation of both pedipalps and the first walking legs into cheliceral identity, whereas the second walking leg is transformed into a pedipalpal identity. Taken together, these results elucidate a model for the Hox logic of head segments in Chelicerata. To substantiate the validity of this model, we performed expression surveys for lab and Dfd paralogs in scorpions and horseshoe crabs. We show that repetition of morphologically similar appendages is correlated with uniform expression levels of the Hox genes lab and Dfd, irrespective of the number of gene copies.
  • Article
    The common morphospecies Cypridopsis vidua (O.F. MÜLLER, 1776) (Crustacea, Ostracoda) is not an obligate parthenogen
    (Royal Belgian Zoology Society, 2023-01-19) Martens, Koen ; Shribak, Michael ; Arkhipova, Irina ; Schön, Isa
    The common non-marine ostracod Cypridopsis vidua (O.F. Müller, 1776) is used as a proxy in various biological disciplines, such as (palaeo-)ecology, evolutionary biology, ecotoxicology and parasitology. This morphospecies was considered to be an obligate parthenogen. We report on the discovery of the first population of C. vidua with males from Woods Hole (MA, USA) and determine that it is a population with mixed reproduction. We describe the morphology of the males and of the sexual and asexual females. We illustrate a copula of a male and a sexual female as well insemination in a sexual female, showing that males are functional. Therefore, Cypridopsis vidua is a morphospecies with mixed reproduction, not a full apomictic parthenogen. We use, for the first time, polychromatic polarization microscope technology to illustrate soft parts of ostracods. In addition, we compare the sexual species C. bisexualis, C. okeechobei, C. howei and C. schwartzi and conclude that these species, especially the latter three, are morphologically very close to C. vidua.
  • Article
    Site specialization of human oral veillonella species
    (American Society for Microbiology, 2023-01-25) Giacomini, Jonathan J. ; Torres-Morales, Julian ; Dewhirst, Floyd E. ; Borisy, Gary G. ; Mark Welch, Jessica L.
    Veillonella species are abundant members of the human oral microbiome with multiple interspecies commensal relationships. Examining the distribution patterns ofspecies across the oral cavity is fundamental to understanding their oral ecology. In this study, we used a combination of pangenomic analysis and oral metagenomic information to clarifytaxonomy and to test the site specialist hypothesis for thegenus, which contends that most oral bacterial species are adapted to live at specific oral sites. Using isolate genome sequences combined with shotgun metagenomic sequence data, we showed thatspecies have clear, differential site specificity: Veillonella parvula showed strong preference for supra- and subgingival plaque, while closely related V. dispar, as well as more distantly related V. atypica, preferred the tongue dorsum, tonsils, throat, and hard palate. In addition, the provisionally namedsp. Human Microbial Taxon 780 showed strong site specificity for keratinized gingiva. Using comparative genomic analysis, we identified genes associated with thiamine biosynthesis and the reductive pentose phosphate cycle that may enablespecies to occupy their respective habitats.Understanding the microbial ecology of the mouth is fundamental for understanding human physiology. In this study, metapangenomics demonstrated that differentspecies have clear ecological preferences in the oral cavity of healthy humans, validating the site specialist hypothesis. Furthermore, the gene pool of differentspecies was found to be reflective of their ecology, illuminating the potential role of vitamins and carbohydrates in determiningdistribution patterns and interspecies interactions.
  • Article
    Spatio-temporal patterns of Synechococcus oligotypes in Moroccan lagoonal environments
    (Nature Research, 2023-01-03) Chaouni, Bouchra ; Idrissi Azami, Abdellah ; Raoui, Sanae ; Amzazi, Saaïd ; Nejjari, Chakib ; Bakkali, Fadil ; Zaid, El Houssine ; Hamamouch, Noureddine ; Amaral-Zettler, Linda ; Ghazal, Hassan
    Synechococcus are unicellular cyanobacteria susceptible to environmental fluctuations and can be used as bioindicators of eutrophication in marine ecosystems. We examined their distribution in two Moroccan lagoons, Marchica on the Mediterranean coast and Oualidia on the Atlantic, in the summers of 2014 and 2015 using 16S rRNA amplicon oligotyping. Synechococcus representatives recruited a higher number of reads from the 16S rRNA in Marchica in comparison to Oualidia. We identified 31 Synechococcus oligotypes that clustered into 10 clades with different distribution patterns. The Synechococcus community was mainly represented by oligotype 1 (clade III) in Marchica. Cooccurring clades IV and I had an important relative abundance in Marchica in the summer of 2014, which is unusual, as these clades are widespread in cold waters. Moreover, Clades VII and subcluster “5.3” formed a sizeable percentage of the Synechococcus community in Marchica. Notably, we found low Synechococcus sequence counts in the Atlantic Lagoon. These results showed that the relative abundance of Synechococcus reads is not constant over space and time and that rare members of the Synechococcus community did not follow a consistent pattern. Further studies are required to decipher Synechococcus dynamics and the impact of environmental parameters on their spatial and temporal distributions.
  • Article
    A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome
    (Nature Research, 2022-11-18) Chitale, Poonam ; Lemenze, Alexander D. ; Fogarty, Emily C. ; Shah, Avi ; Grady, Courtney ; Odom-Mabey, Aubrey R. ; Johnson, W. Evan ; Yang, Jason H. ; Eren, A. Murat ; Brosch, Roland ; Kumar, Pradeep ; Alland, David
    H37Rv is the most widely used Mycobacterium tuberculosis strain, and its genome is globally used as the M. tuberculosis reference sequence. Here, we present Bact-Builder, a pipeline that uses consensus building to generate complete and accurate bacterial genome sequences and apply it to three independently cultured and sequenced H37Rv aliquots of a single laboratory stock. Two of the 4,417,942 base-pair long H37Rv assemblies are 100% identical, with the third differing by a single nucleotide. Compared to the existing H37Rv reference, the new sequence contains ~6.4 kb additional base pairs, encoding ten new regions that include insertions in PE/PPE genes and new paralogs of esxN and esxJ, which are differentially expressed compared to the reference genes. New sequencing and de novo assemblies with Bact-Builder confirm that all 10 regions, plus small additional polymorphisms, are also present in the commonly used H37Rv strains NR123, TMC102, and H37Rv1998. Thus, Bact-Builder shows promise as an improved method to perform accurate and reproducible de novo assemblies of bacterial genomes, and our work provides important updates to the primary M. tuberculosis reference genome.
  • Article
    The diversity and functional capacity of microbes associated with coastal macrophytes
    (American Society for Microbiology, 2022-08-22) Miranda, Khashiff ; Weigel, Brooke L. ; Fogarty, Emily C. ; Veseli, Iva A. ; Giblin, Anne E. ; Eren, A. Murat ; Pfister, Catherine A.
    Coastal marine macrophytes exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their hosts through metabolisms that are unique to microbial taxa. Here, we characterized the metabolic functions of macrophyte-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus, and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.), the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 63 metagenome-assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic activity. Host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis in addition to a range of nitrogen and sulfur metabolisms that recycle dissolved inorganic nutrients into forms more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms and contributes to the functional capabilities of microbes and their influences on carbon and nitrogen cycling in nearshore ecosystems.
  • Article
    The contributions of maternal age heterogeneity to variance in lifetime reproductive output
    (The University of Chicago Press, 2022-03-28) van Daalen, Silke F. ; Hernández, Christina M. ; Caswell, Hal ; Neubert, Michael G. ; Gribble, Kristin E.
    Variance among individuals in fitness components reflects both genuine heterogeneity between individuals and stochasticity in events experienced along the life cycle. Maternal age represents a form of heterogeneity that affects both the mean and the variance of lifetime reproductive output (LRO). Here, we quantify the relative contribution of maternal age heterogeneity to the variance in LRO using individual-level laboratory data on the rotifer Brachionus manjavacas to parameterize a multistate age × maternal age matrix model. In B. manjavacas, advanced maternal age has large negative effects on offspring survival and fertility. We used multistate Markov chains with rewards to quantify the contributions to variance in LRO of heterogeneity and of the stochasticity inherent in the outcomes of probabilistic transitions and reproductive events. Under laboratory conditions, maternal age heterogeneity contributes 26% of the variance in LRO. The contribution changes when mortality and fertility are reduced to mimic more ecologically relevant environments. Over the parameter space where populations are near stationarity, maternal age heterogeneity contributes an average of 3% of the variance. Thus, the contributions of maternal age heterogeneity and individual stochasticity can be expected to depend strongly on environmental conditions; over most of the parameter space, the variance in LRO is dominated by stochasticity.
  • Article
    Editorial: microbial communities and metabolisms involved in the degradation of cellular and extracellular organic biopolymers
    (Frontiers Media, 2022-01-04) Ruff, S. Emil
    Most organic matter on Earth occurs in the form of macromolecules and complex biopolymers, which include the building blocks of every organism. Plant, animal, fungal, and microbial cells largely consist of macromolecules belonging to four compound classes: proteins, polysaccharides, nucleic acids, and lipids (Figure 1). The percentage of these compounds per dry weight can vary greatly between lineages, but also between individuals of the same species or developmental stages of the same organism. Living and lysing cells release a substantial quantity and variety of macromolecules to the environment. These compounds often contain nitrogen, phosphorus, and sulfur, in addition to carbon, and are thus ideal food sources for heterotrophic organisms. Although the degradation of biopolymers and macromolecules has received considerable attention, many knowledge gaps remain, particularly in very complex ecosystems such as soils and sediments.
  • Article
    Common environmental pollutants negatively affect development and regeneration in the sea anemone Nematostella vectensis holobiont
    (Frontiers Media, 2021-12-23) Klein, Sylvia ; Frazier, Victoria ; Readdean, Timothy ; Lucas, Emily ; Diaz-Jimenez, Erica P. ; Sogin, Mitchell L. ; Ruff, S. Emil ; Echeverri, Karen
    The anthozoan sea anemone Nematostella vectensis belongs to the phylum of cnidarians which also includes jellyfish and corals. Nematostella are native to United States East Coast marsh lands, where they constantly adapt to changes in salinity, temperature, oxygen concentration and pH. Its natural ability to continually acclimate to changing environments coupled with its genetic tractability render Nematostella a powerful model organism in which to study the effects of common pollutants on the natural development of these animals. Potassium nitrate, commonly used in fertilizers, and Phthalates, a component of plastics are frequent environmental stressors found in coastal and marsh waters. Here we present data showing how early exposure to these pollutants lead to dramatic defects in development of the embryos and eventual mortality possibly due to defects in feeding ability. Additionally, we examined the microbiome of the animals and identified shifts in the microbial community that correlated with the type of water that was used to grow the animals, and with their exposure to pollutants.
  • Article
    Developmental exposure to non-dioxin-like polychlorinated biphenyls promotes sensory deficits and disrupts dopaminergic and GABAergic signaling in zebrafish
    (Nature Research, 2021-09-24) Brun, Nadja R. ; Panlilio, Jennifer M. ; Zhang, Kun ; Zhao, Yanbin ; Ivashkin, Evgeny ; Stegeman, John J. ; Goldstone, Jared V.
    The most abundant polychlorinated biphenyl (PCB) congeners found in the environment and in humans are neurotoxic. This is of particular concern for early life stages because the exposure of the more vulnerable developing nervous system to neurotoxic chemicals can result in neurobehavioral disorders. In this study, we uncover currently unknown links between PCB target mechanisms and neurobehavioral deficits using zebrafish as a vertebrate model. We investigated the effects of the abundant non-dioxin-like (NDL) congener PCB153 on neuronal morphology and synaptic transmission linked to the proper execution of a sensorimotor response. Zebrafish that were exposed during development to concentrations similar to those found in human cord blood and PCB contaminated sites showed a delay in startle response. Morphological and biochemical data demonstrate that even though PCB153-induced swelling of afferent sensory neurons, the disruption of dopaminergic and GABAergic signaling appears to contribute to PCB-induced motor deficits. A similar delay was observed for other NDL congeners but not for the potent dioxin-like congener PCB126. The effects on important and broadly conserved signaling mechanisms in vertebrates suggest that NDL PCBs may contribute to neurodevelopmental abnormalities in humans and increased selection pressures in vertebrate wildlife.
  • Article
    Microbial communities under distinct thermal and geochemical regimes in axial and off-axis sediments of Guaymas Basin
    (Frontiers Media, 2021-02-12) Teske, Andreas P. ; Wegener, Gunter ; Chanton, Jeffrey P. ; White, Dylan ; MacGregor, Barbara J. ; Hoer, Daniel ; de Beer, Dirk ; Zhuang, Guangchao ; Saxton, Matthew A. ; Joye, Samantha B. ; Lizarralde, Daniel ; Soule, S. Adam ; Ruff, S. Emil
    Cold seeps and hydrothermal vents are seafloor habitats fueled by subsurface energy sources. Both habitat types coexist in Guaymas Basin in the Gulf of California, providing an opportunity to compare microbial communities with distinct physiologies adapted to different thermal regimes. Hydrothermally active sites in the southern Guaymas Basin axial valley, and cold seep sites at Octopus Mound, a carbonate mound with abundant methanotrophic cold seep fauna at the Central Seep location on the northern off-axis flanking regions, show consistent geochemical and microbial differences between hot, temperate, cold seep, and background sites. The changing microbial actors include autotrophic and heterotrophic bacterial and archaeal lineages that catalyze sulfur, nitrogen, and methane cycling, organic matter degradation, and hydrocarbon oxidation. Thermal, biogeochemical, and microbiological characteristics of the sampling locations indicate that sediment thermal regime and seep-derived or hydrothermal energy sources structure the microbial communities at the sediment surface.