Ecology and taxonomy of free-living marine nematodes from Cienfuegos Bay, Caribbean Sea

Present thesis focuses on ecology of assemblages and taxonomy of free-living marine nematodes. Most of the data are from Cienfuegos, a semi-enclosed bay in the Caribbean Sea; but, we also provided data on biodiversity from other areas in Cuban marine waters. Four main topics are included: description of biodiversity patterns, a microcosm experiment about effects of organic enrichment on assemblages, a taxonomic revision of the genus Terschellingia de Man, 1888, and the description of four new genera for science. Spatial and temporal biodiversity patterns of free-living marine nematodes were studied in Cienfuegos Bay, a tropical semi-enclosed basin in the Caribbean Sea. Taxonomic (to species level) and functional (biological trait) approaches were applied for describing the assemblage structure and relating it to abiotic environment based on a sampling scheme in six subtidal stations and three months. Biological trait approach added relevant information to species pattern regarding relationships between diversity patterns and the abiotic environment. The most common trait combinations were deposit feeding nematodes, with intermediate colonising abilities of 2–3 (in a scale from 1 to 5), tail conical cylindrical or filiform and body slender; and their abundance were correlated with depth, organic matter and silt/clay fraction. The number of trait combinations and the number of species was highly correlated suggesting that the increase of biodiversity can lead to potential increase of functional diversity. Chemical pollution (organic enrichment and heavy metals) and hydrodynamic regime possibly drove the biodiversity patterns. The spatial distribution of assemblages is in agreement with the previously supposed existence of two well differentiated basins inside the bay, the northern basin more polluted than the southern one. The low hydrodynamic regime would determine a poor dispersion of nematodes resulting in high spatial variance in the assemblage structure; and also the associated hypoxic conditions and pollutants in sediments can explain the dominance of tolerant nematode species such as Daptonema oxycerca, Sabatieria pulchra, Terschellingia gourbaultae, and Terschellingia longicaudata. A comparison of spatial–temporal patterns of biodiversity between Cienfuegos Bay and other semi-enclosed bays in temperate regions suggests several similarities: nematode assemblages are strongly influenced by anthropogenic disturbance, temporal trends are weak or overridden by spatial ones, and few cosmopolitan genera/species tolerant to pollution and hypoxic conditions are dominant Marine nematodes from subtidal tropical sediments in Cienfuegos Bay were subjected to additions of phyto-detritus (microalgae Spirulina) in a microcosm experiment. The follow up of the experimental conditions was measured at days 0, 4, 15 and 30. Observed effects on the nematodes were a decrease in abundance and diversity, and changes in the taxonomic and trophic structure due to the organic enrichment. The results suggested that the nematodes were not food limited in the microcosms and probably neither in their natural environment. The main factor affecting the nematodes was probably the byproducts (hydrogen sulphide and ammonia) due to enhanced bacterial development in microcosms. Hypoxic conditions occurred in all experimental units, as well in the field suggesting a nematode assemblage adapted to naturally enriched sediments. However, tolerant (dominant) species showed a grade of sensitivity to reduced conditions, in increasing order: Spirinia parasitifera, Terschellingia longicaudata, Metalinhomoeus filiformis, and Sabatieria pulchra. We predict that further organic enrichment in sediments from Cienfuegos Bay may cause a phase shift into a strongly depleted benthic fauna and reduced conditions in water and sediments. The cosmopolitan and often ecologically dominant genus Terschellingia (Nematoda: Linhomoeidae), with 39 nominal species, is taxonomically a problematic taxon. Its species show high morphological plasticity, possess few diagnostic characters and identification keys are lacking. A revision of the genus was carried out based on morphological and morphometric data from the literature and from observations of specimens collected in Cienfuegos Bay, Caribbean Sea, Cuba. The diagnosis of the genus Terschellingia is amended. Of the current 39 nominal species, 16 are considered as valid species based on morphological characters related to size and position of amphidial fovea; presence and position of cephalic and cervical setae; presence, size, and shape of pharyngeal bulb; shape of spicular apparatus and shape of tail. Tabular and pictorial keys were provided based on these characters. Three sympatric species: T. communis, T. gourbaultae and T. longicaudata were redescribed based on recently collected Cuban specimens. Each of them showed relatively large differences in body size in comparison with the respective type specimens, suggesting possible variation due to local environmental differences. The highest intraspecific variation pertains for the most widely spread cosmopolitan species T. longicaudata, suggesting that morphological plasticity enhanced adaptation to different environmental conditions. The notable taxonomic inflation within the genus (14 species inquirenda, 9 junior synonyms), probably also present in other highly specious genera of marine nematodes, can lead to an overestimation of the alpha-diversity. Four new free-living marine nematode genera and species are described: Cienfuegia cachoi gen. nov., sp. nov. (Xyalidae, Chromadorida), Guitartia tridentata gen. nov., sp. nov. (Xyalidae, Chromadorida), Macrodontium gaspari gen. nov., sp. nov. (Microlaimidae, Chromadorida), and Pseudoterschellingia ibarrae gen. nov., sp. nov. (Linhomoeidae, Monhysterida). For each species, detailed morphological descriptions, drawings and photos are provided, tabular keys were built and relationships with other genera within each family are discussed. The following general discussion is focused on five topics: scientific novelties of the research, evaluation of techniques for environmental assessment, coupling between distribution patterns in the nature and microcosm experiments, ecological characterization of the four new species and biodiversity of free-living marine nematode in Cuban marine waters. Future research avenues are presented covering both experimental ecology and molecular taxonomy. Two appendixes are included regard to an ecological study of meio- and macrofaunal assemblages in Havana bay; and a taxonomic checklist of nematodes recorded by the author and colleagues from Cuban marine waters

Guitartia tridentata n. gen., n. sp (monhysterida: xyalidae) and macrodontium gaspari n. gen., n. sp (chromadorida: microlaimidae), free-living marine nematodes from the Caribbean sea

Two new genera of free-living marine nematodes are described from the muddy bottom of Cienfuegos Bay, Caribbean Sea. Guitartia n. gen. (Xyalidae, Monhysterida) is characterised by three long tooth-like structures in the stegostom, second and third circle of anterior sensilla separate and posterior genital branch of the female restricted to a long post-vulvar sac. The type species is Guitartia tridentata n. gen., n. sp. Within the Xyalidae, Guitartia n. gen. is morphologically close to Amphimonhystrella, Cobbia, Elzalia, Scaptrella and Valvaelaimus, all being characterised by sclerotised structures in the stoma and transverse striation of the body cuticle. Main features for discrimination are the type of stoma structure, the shape and relative size of amphidial fovea, the presence of a post-vulvar sac and gubernacular apophyses and the absence of terminal setae on the tail. Macrodontium n. gen. (Microlaimidae, Chromadorida) is characterised by a heavily sclerotised stoma with one large dorsal tooth and two smaller subventral teeth, sexual dimorphism in size and position of the amphidial fovea and males with a single anterior testis. The type species is Macrodontium gaspari n. gen., n. sp. Within the Microlaimidae, Macrodontium n. gen. is similar to the genera Acanthomicrolaimus and Bolbolaimus due to sclerotised stoma and presence of large dorsal tooth. The new genus is similar to Aponema in sexual dimorphism in the size of the amphidial fovea, monorchic males, presence of a gubernacular apophysis and conico-cylindrical tail shape. Morphological characters of diagnostic value within the family are the ornamentation of the body cuticle, relative length of cephalic sensilla, stoma sclerotisation and number of testes

A morphometric analysis of the genus Terschellingia (nematoda, Linhomoeidae) with redefinition of the genus and key to the species

The cosmopolitan and often ecologically dominant genus Terschellingia (Nematoda, Linhomoeidae), with 37 nominal species, is taxonomically a problematic taxon. Its species show high morphological plasticity, possess few diagnostic morphological characters and identification keys are lacking. A revision of the genus was carried out based on morphological and morphometric data from the literature and from light and electron microscopic observations of specimens collected in Cienfuegos Bay, Caribbean Sea, Cuba. The diagnosis of the genus Terschellingia is emended. Of the current 37 nominal species, 15 are considered as valid species based on morphological characters related to size and position of amphidial fovea, presence/position of cephalic and cervical setae, presence/ size/ shape of oesophageal bulb, shape of spicular apparatus and shape of tail. Tabular and pictorial keys were provided based on these characters. Three sympatric species: T. communis, T. gourbaultae, and T. longicaudata were redescribed based on recently collected Cuban specimens. Each of them showed relatively large differences in body size in comparison with the respective type specimens, suggesting possible variation due to local environmental differences. The highest intraspecific variation pertains for the most widely spread cosmopolitan species T. longicaudata, suggesting that morphological plasticity enhanced adaptation to different environmental conditions. The notable taxonomic inflation within the genus (13 species inquirendae, 9 junior synonyms), probably also present in other highly specious genera of marine nematodes, can lead to an overestimation of the alpha-diversity for some taxa

Biodiversity patterns of free-living marine nematodes in a tropical bay: Cienfuegos, Caribbean Sea

Spatial and temporal biodiversity patterns of free-living marine nematodes were studied in Cienfuegos Bay, a tropical semi-enclosed basin in the Caribbean Sea. Taxonomic (to species level) and functional (biological trait) approaches were applied for describing the assemblage structure and relating it to abiotic environment based on a sampling scheme in six subtidal stations and three months. Biological trait approach added relevant information to species pattern regarding relationships between diversity patterns and the abiotic environment. The most common morphotypes were deposit feeding nematodes, with colonising abilities of 2–3 (in a scale from 1 to 5), tail conical cylindrical or filiforme and body slender; and their abundance were correlated with depth, organic matter and silt/clay fraction. In spite of a high turnover of species, functional diversity of assemblages did not change notably in space and time. A result probably due to sampling of the habitat pool of species and to low heterogeneity of the studied muddy bottoms. Chemical pollution (organic enrichment and heavy metals) and hydrodynamic regime possibly drove the biodiversity patterns. Spatial distribution of assemblages support the existence of two well differentiated basins inside the bay, the northern basin more polluted than the southern one. The low hydrodynamic regime would determine a poor dispersion of nematodes resulting in high spatial variance in the assemblage structure; and also the associated hypoxic conditions and pollutants in sediments can explain the dominance of tolerant nematode species such as Daptonema oxycerca, Sabatieria pulchra, Terschellingia gourbaultae, and Terschellingia longicaudata. A comparison of spatial– temporal patterns of biodiversity between Cienfuegos Bay and other semi-enclosed bays in temperate regions suggests several similarities: nematode assemblages are strongly influenced by anthropogenic disturbance, temporal trends are weak or overridden by spatial ones, and few cosmopolitan genera/ species tolerant to pollution and hypoxic conditions are dominant

Extracellular reef metabolites across the protected Jardines de la Reina, Cuba Reef System

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Weber, L., Armenteros, M., Soule, M. K., Longnecker, K., Kujawinski, E. B., & Apprill, A. Extracellular reef metabolites across the protected Jardines de la Reina, Cuba Reef System. Frontiers in Marine Science, 7, (2020): 582161, https://doi.org/10.3389/fmars.2020.582161.Coral reef ecosystems are incredibly diverse marine biomes that rely on nutrient cycling by microorganisms to sustain high productivity in generally oligotrophic regions of the ocean. Understanding the composition of extracellular reef metabolites in seawater, the small organic molecules that serve as the currency for microorganisms, may provide insight into benthic-pelagic coupling as well as the complexity of nutrient cycling in coral reef ecosystems. Jardines de la Reina (JR), Cuba is an ideal environment to examine extracellular metabolites across protected and high-quality reefs. Here, we used liquid chromatography mass spectrometry (LC-MS) to quantify specific known metabolites of interest (targeted metabolomics approach) and to survey trends in metabolite feature composition (untargeted metabolomics approach) from surface and reef depth (6 – 14 m) seawater overlying nine forereef sites in JR. We found that untargeted metabolite feature composition was surprisingly similar between reef depth and surface seawater, corresponding with other biogeochemical and physicochemical measurements and suggesting that environmental conditions were largely homogenous across forereefs within JR. Additionally, we quantified 32 of 53 detected metabolites using the targeted approach, including amino acids, nucleosides, vitamins, and other metabolic intermediates. Two of the quantified metabolites, riboflavin and xanthosine, displayed interesting trends by depth. Riboflavin concentrations were higher in reef depth compared to surface seawater, suggesting that riboflavin may be produced by reef organisms at depth and degraded in the surface through photochemical oxidation. Xanthosine concentrations were significantly higher in surface reef seawater. 5′-methylthioadenosine (MTA) concentrations increased significantly within the central region of the archipelago, displaying biogeographic patterns that warrant further investigation. Here we lay the groundwork for future investigations of variations in metabolite composition across reefs, sources and sinks of reef metabolites, and changes in metabolites over environmental, temporal, and reef health gradients.This work was supported by the Dalio Foundation (now “OceanX”) and the National Science Foundation (OCE-1736288) (award to Amy Apprill). The mass spectrometry samples were analyzed at the WHOI FT-MS Users’ Facility with instrumentation funded by the National Science Foundation (grant OCE-1058448 to EK and MK) and the Simons Foundation (Award ID #509042, EK). Lastly, a portion of the publication fees was supported by the Massachusetts Institute of Technology (MIT) Open Access Article Publication Subvention fund from MIT Libraries

Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Babbin, A. R., Tamasi, T., Dumit, D., Weber, L., Rodríguez, M. V. I., Schwartz, S. L., Armenteros, M., Wankel, S. D., & Apprill, A. Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals. ISME Journal, (2020), doi:10.1038/s41396-020-00845-2.Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use 15N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N2O) production among five iconic species of reef-building corals (Acropora palmata, Diploria labyrinthiformis, Orbicella faveolata, Porites astreoides, and Porites porites) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N2O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis, at rates of ~1 nmol cm−2 d−1. In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N2O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.Research was conducted in the Gardens of the Queen, Cuba in accordance with the requirements of the Republic of Cuba, conducted under permit NV2370 and NV2568 issued by the Ministerio de Relaciones Exteriores. We gratefully acknowledge funding for this research by MIT Sea Grant award #2018-DOH-49-LEV, Simons Foundation award #622065, and MIT ESI seed funding to ARB, the MIT Montrym, Ferry, and mTerra Seed Grant Funds, and the generous contributions by Dr Bruce L. Heflinger

Metabarcoding free-living marine nematodes using curated 18S and CO1 reference sequence databases for species-level taxonomic assignments

High‐throughput sequencing has the potential to describe biological communities with high efficiency yet comprehensive assessment of diversity with species‐level resolution remains one of the most challenging aspects of metabarcoding studies. We investigated the utility of curated ribosomal and mitochondrial nematode reference sequence databases for determining phylum‐specific species‐level clustering thresholds. We compiled 438 ribosomal and 290 mitochondrial sequences which identified 99% and 94% as the species delineation clustering threshold, respectively. These thresholds were evaluated in HTS data from mock communities containing 39 nematode species as well as environmental samples from Vietnam. We compared the taxonomic description of the mocks generated by two read‐merging and two clustering algorithms and the cluster‐free Dada2 pipeline. Taxonomic assignment with the RDP classifier was assessed under different training sets. Our results showed that 36/39 mock nematode species were identified across the molecular markers (18S: 32, JB2: 19, JB3: 21) in UClust_ref OTUs at their respective clustering thresholds, outperforming UParse_denovo and the commonly used 97% similarity. Dada2 generated the most realistic number of ASVs (18S: 83, JB2: 75, JB3: 82), collectively identifying 30/39 mock species. The ribosomal marker outperformed the mitochondrial markers in terms of species and genus‐level detections for both OTUs and ASVs. The number of taxonomic assignments of OTUs/ASVs was highest when the smallest reference database containing only nematode sequences was used and when sequences were truncated to the respective amplicon length. Overall, OTUs generated more species‐level detections, which were, however, associated with higher error rates compared to ASVs. Genus‐level assignments using ASVs exhibited higher accuracy and lower error rates compared to species‐level assignments, suggesting that this is the most reliable pipeline for rapid assessment of alpha diversity from environmental samples

Mollusk and meiofauna communities data collected onboard the R/V Weatherbird II cruise WB0517 in the northwestern margin of Cuba from 2017-05-13 to 2017-05-23

Mollusk and meiofauna communities data were collected during an expedition of the R/V Weatherbird II cruise WB0517 to the northwestern margin of Cuba from 2017-05-13 to 2017-05-23. Sediment was collected using a multi-corer and three replicates were kept for these communities and preserved in a 10% buffered formalin. Mollusks (dead and alive shells) were sieved through a 0.5 mm sieve and species were identified from the top 10 cm of each core. The presence/absence of 129 mollusks species is presented in this dataset. Meiofauna was sieved through a 0.063 mm sieve and all the alive organisms were identified to their higher taxonomic level. The R/V Weatherbird II cruise WB0517 was led by chief scientist Dr. Steven A. Murawski with the objective of providing a baseline of fauna and sediments

Desmodora pontica Filipjev 1922

<i>Desmodora pontica</i> Filipjev, 1922 <p>Figs 6A–B, 7, Table 1</p> <p> <i>Desmodora pontica</i> Filipjev, 1922: 119.</p> <p> <i>Desmodora</i> (<i>Pseudochromadora</i>) <i>pontica</i> – Gerlach 1963: 84.</p> Material examined <p>10 ♂♂, 10 ♀♀ and 11 juveniles, deposited in the nematode collection at Centro de Investigaciones Marinas, Universidad de La Habana, CUBA.</p> Description <p>Cuticle coarsely striated (annuli ~ 2 μm width) in the anterior region but finer at mid-body region (annuli ~ 1 µm width). Strong head capsule with labial region clearly marked by a suture. Inner labial setae papilliform. Outer labial sensilla relatively long (2–3 µm long). Four cephalic setae (4–8 μm long); one circle of four subcephalic setae (4–8 μm long) posterior to the amphidial fovea. Amphidial fovea cryptospiral. Eight longitudinal rows of short somatic setae (2–4 μm long) running along the entire body length, continuing as four rows on the tail region. Buccal cavity narrow, elongate, with one dorsal tooth and two minute ventrosublateral teeth at the same level. Pharynx muscular with posterior bulb and plasmatic interruptions, internal lining well sclerotized. Cardia extended. Secretory-excretory system not observable. Posterior half of tail conspicuously punctuated and without striation.</p> <p>Male monorchic, anterior testis to the left of the intestine. Spicule strongly curved and cephalated. Gubernaculum a narrow rod. No supplements.</p> <p>Female didelphic, ovaries antidromously reflexed, both genital branches to the right of the intestine. Vulva a transversal slit.</p> <p>Juveniles are similar to adults, except for the development of the reproductive system.</p> Remarks <p> Suctorians (Ciliophora) are common commensals on <i>D. pontica</i>. The genus <i>Desmodora</i> de Man, 1889 is speciose, with a complicated taxonomy. It has included several subgenera later raised to genus level by Verschelde <i>et al.</i> (1998) (e.g., <i>Croconema</i>, <i>Pseudochromadora</i> and <i>Zalonema</i>) and a plethora of bad descriptions and doubtful species. The most comprehensive study about <i>Desmodora</i> has been made by Verschelde <i>et al.</i> (1998) and an outdated dichotomous key was provided by Wieser (1954). Our specimens resemble the descriptions of <i>D. pontica</i> by Schuurmans Stekhoven (1950) and Gerlach (1952). The female specimen depicted and described by Boucher (1975) as <i>D. pontica</i> differs in two important features: outer labial sensilla are considerable longer (i.e., as long as the cephalic setae) and the posterior border of the head capsule reaches the first cuticle annuli. Based on our material, males seem to have amphidial fovea well in the central part of the head capsule (i.e., no contact with the striation) and juveniles and females tend to have amphidial fovea posterior on the capsule (i.e., touching the first annuli).</p>Published as part of <i>Armenteros, Maickel, Ruiz-Abierno, Alexei & Decraemer, Wilfrida, 2014, Revision of Desmodorinae and Spiriniinae (Nematoda: Desmodoridae) with redescription of eight known species, pp. 1-32 in European Journal of Taxonomy 96</i> on page 13, DOI: 10.5852/ejt.2014.96, <a href="http://zenodo.org/record/3838898">http://zenodo.org/record/3838898</a&gt