The distribution of coastal fish eDNA sequences in the Anthropocene

Aim

Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors.

Location

Tropical, temperate and polar coastal areas.

Time period

Present day.

Major taxa studied

Marine fishes.

Methods

We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on α- and β-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α- and β-diversity measured from our barcodes, and phylogenetic but also functional diversity.

Results

We show that fish eDNA MOTU and sequence α- and β-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity.

Main conclusions

Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.     

Early cytokine and chemokine gene expression in lymph nodes of macaques infected with simian immunodeficiency virus is predictive of disease outcome and vaccine efficacy.

Competitive PCR was used to evaluate the expression of cytokine, granzyme B, and chemokine genes in lymph nodes of macaques recently infected with the simian immunodeficiency virus (SIV) pathogenic molecular clone SIVmac239 (n = 16), the nonpathogenic vaccine strain SIVmac239 delta nef (n = 8), and the nonpathogenic molecular clone SIVmac1A11 (n = 8). For both SIVmac239 and its nef-deleted derivative, strong expression was observed as early as 7 days postinfection for interleukin 1beta (IL-1beta), IL-6, tumor necrosis factor alpha, gamma interferon, and IL-13. The levels of gene induction were equally intense for both viruses despite a lower viral load for SIVmac239 deltanef compared with that for SIVmac239. However, the nature of the cytokine network activation varied with the viral inocula. Primary infection with SIVmac239 was characterized by a higher level of IL-4, IL-10, MIP-1alpha, MIP-1beta, MCP-1, and RANTES gene expression and a lower level of IL-12 and granzyme B gene expression compared with infection with SIVmac239 delta nef. Thus, infection with nef-deleted SIV was associated with a preferential Th1 versus Th2 pattern of cytokine production. Infection with SIVmac1A11 was characterized by a delayed immune response for all markers tested. The unique patterns of cytokine and chemokine gene expression in lymph nodes correlated nicely with the pathogenic potential of the SIV strains used as well as with differences in their ability to serve as protective vaccines.     

A newZornia species in the Flora of Cuba

A newZornia species from Cuba, the endemicZornia arenicola sp. nova, is described. It was found on moving sand dunes between the town of Guane and the village of Cortes (Pinar del Rio province).     

In vivo expression of IL-1 beta and IL-6 genes during viral infections in human.

Macrophage infiltration is a constant feature of human virus-infected tissues. However, the in situ functional status of these cells remains undetermined. In order to document an activation of macrophages in virus-infected tissues, the expression of IL-1 beta and IL-6 genes was analyzed using in situ hybridization. Several tissues were studied, as well as infections induced by different viruses: lymph nodes infected by HIV-1 (9 cases) or EBV (one case), lungs infected by CMV (5 cases) or adenovirus (1 case), livers infected by HBV, either chronically (2 cases) or acutely (7 cases presenting a fulminant hepatitis). With the exception of fulminant HBV hepatitis, IL-1 beta and IL-6 genes were expressed in all cases. IL-1 beta and IL-6 genes were usually coordinately regulated, as cells containing IL-1 beta or IL-6 mRNA were present in identical amounts and displayed a similar distribution. Analysis of the location and the morphology of monokine gene-expressing cells indicated that both small macrophages and endothelial cells expressed IL-1 beta and IL-6 genes. However, neither tingible body macrophages present in lymph node follicles nor Kupffer cells expressed these genes at a detectable level. Infected cells themselves were also negative for monokine gene expression. These findings indicate that expression of IL-1 beta and IL-6 genes by reactive cells may play a role in viral spreading limitation as well as virus-induced tissue damage.     

C32 human melanoma cell endogenous lectins: characterization and implication in vesicle-mediated melanin transfer to keratinocytes.

To optimize skin pigmentation in order to help body prevention against UV radiation, the mechanism of melanin pigment transfer from melanocytes to keratinocytes must be elucidated. Melanin transfer to keratinocytes requires specific recognition between keratinocytes and melanocytes or melanosomes. Cell surface sugar-specific receptor (membrane lectin) expression was studied in human C32 melanoma cells, an amelanotic melanoma, by flow cytometry analysis of neoglycoprotein binding as an approach to the molecular specificity. Sugar receptors on melanocytes are mainly specific for alpha-L-fucose. Their expression is enhanced upon treatment by the diacylglycerol analogue 1-oleoyl-2-acetylglycerol, which can induce melanin synthesis in amelanotic human melanoma cells in a dose-dependent manner. Flow cytometry analyses showed a small-sized population of vesicles distinguishable from large cells by their fluorescence properties upon neoglycoprotein binding. Sorting indicated that the small-sized subpopulation is composed of vesicles produced by melanocytic cells. Upon vesicle formation, a selective concentration of sugar receptors specific for 6-phospho-beta-D-galactosides appears in the resulting melanocytic vesicles. Vesicles are recognized and taken up by cultured keratinocytes and a partial inhibitory effect was obtained upon cell incubation in the presence of neoglycoproteins, indicating a possible participation of sugar receptors in this recognition. The validity for such a model to help in understanding the natural melanin transfer by melanosomes is confirmed by electron microscopy, which demonstrates the presence of melanin inside keratinocytic cells upon incubation with melanocytic vesicles.     

Contribution to the knowledge of the savanna and forb-rich communities of Pinar del Rio Province (Cuba)

Phytosociological analysis of savanna and forb-rich communities in the Pinar del Rio Province was done in the area of Remates de Guane; one locality lies on the seashore in the western part of the province. Altogether six associations were distinguished. Five of them, viz.Sclerio curtissii-Centelletum erectae, Schultezio guianensis-Rhynchosporetum fascicularis, Cassio diphyllae-Hypericetum stypheloidis, Polygalo squamifoliae-Dichromenetum seslerioidis andPhyllantho juncei-Aristidetum, all newly described in this paper, are classified into the order ofAcoelorapho-Colpothrinacetalia Bal.-Tul. inBal.-Tul. etCapote 1985 with two alliances. One association, thePaspalo debilis-Asteretum grisebachii Bal.-Tul. etCapote 1992, was put into the order ofAsteretalia grisebachii Bal.-Tul. inBal.-Tul. etCapote 1992 with one alliance bound to inland moving dunes. The plant composition reflects soil quality, above all the water regime. Very interesting is the presence of theByrsonimo crassifoliae-Andropogonetalia teneris-species in the association ofPolygalo-Dichromeneteum seslerioidis indicating the rich presence of stones in the upper part of the soil profile.     

A new savanna-like community of the sierra del rosario mountains,Cuba

This communication describes a new savanna-like community, theBletio purpureae-Andropogonetum gracilis Balátová-Tulá?ková etR. Capote ass. nov., found in the woodless eastern part of the Sierra del Rosario Mountains (western part of Cuba). From the phytosociological point of view, it belongs to the allianceAchlaenion piptostachyae Balátová-Tulá?ková all. nov., the orderAchlaenetalia piptostachyae Balátová-Tulá?ková ord. nov., and the classSclerio baldwinii-Andropogonetea gracilis Balátová-Tulá?ková cl. nov. In the area under study four subassociations were distinguished: theBletio-Andropogonetum typicum Balátová-Tulá?ková et.R. Capote subass. nov., theB.-A. rhynchosporetosum fascicularis Balátová-Tulá?ková etR. Capote subass. nov., theB.-A. cassietosum aeschynomenes Balátová-Tulá?ková etR. Capote subass. nov., and theB.-A. stenandrietosum droseroidis Balátová-Tulá?ková etR. Capote subass. nov.     

Beitrag zur Kenntnis der chemischen Zusammensetzung derPhragmiti-Magnocaricetea und derAgropyro-Rumicion-Arten

Zwanzig Pflanzen der KlassePhragmiti-Magnocaricetea (Kennarten der einzelnen pflanzen-soziologischen Einheiten) und des VerbandesAgropyro-Rumicion crispi wurden den chemischen Analysen unterzogen. Die Pflanzenproben wurden auf den Wiesen der Trockengebiete S-Mährens und der SW-Slowakei gesammelt, u. zw. aus den pflanzensoziologisch, definierbaren Einheiten (Assoziationen der VerbändePhragmition, Caricion gracilis, Caricion rostratae undAgropyro-Rumicion). Die Resultate wurden mit der chemischen Zusammensetzung der in anderen Gebieten vorkommenden Pflanzen verglichen. Es zeigten sich Zusammenhänge zwischen der genetisch bedingten chemischen Zusammensetzung bestimmter Artengruppen und den Eigenschaften des Substrats. In diesem Sinne gibt es allgemeine Unterschiede zwischen den VerbändenCaricion gracilis undCaricion rostratae. Die Arten desAgropyro-Rumicion zeigen im Durchschnitt engere Bindung an die Gesellschaften desCnidion-Verbandes als an dasCaricion gracilis.