Impact of the Costa Concordia shipwreck on a Posidonia oceanica meadow: a multi-scale assessment from a population to a landscape level.

The Costa Concordia shipwreck permitted to assess how multiple disturbances affected marine biota at different spatial and temporal scales, evaluating the effects of mechanical and physical disturbances on Posidonia oceanica (L.) Delile, an endemic seagrass species of the Mediterranean Sea. To assess the impacts of the shipwreck and its salvaging from 2012 to 2017 at a population and a landscape level, a diversified approach was applied based on the application of a geographical information system coupled with seascape metrics and structural descriptors. Benthic habitat maps and seascape metrics highlighted cenotic transitions, as well as fragmentation and erosion phenomena, resulting in 9952 m2 of seagrass area impacted. Regression of the meadow was unveiled by both multivariate and interpolation analysis, revealing a clear spatio-temporal gradient of impacts based on distances from the wreck. Results highlighted the effectiveness of the descriptors involved that permitted to reveal temporal changes at both fine and large scales.

Dramatic loss of seagrass habitat under projected climate change in the Mediterranean Sea.

Although climate warming is affecting most marine ecosystems, the Mediterranean is showing earlier impacts. Foundation seagrasses are already experiencing a well-documented regression in the Mediterranean which could be aggravated by climate change. Here, we forecast distributions of two seagrasses and contrast predicted loss with discrete regions identified on the basis of extant genetic diversity. Under the worst-case scenario, Posidonia oceanica might lose 75% of suitable habitat by 2050 and is at risk of functional extinction by 2100, whereas Cymodocea nodosa would lose only 46.5% in that scenario as losses are compensated with gained and stable areas in the Atlantic. Besides, we predict that erosion of present genetic diversity and vicariant processes can happen, as all Mediterranean genetic regions could decrease considerably in extension in future warming scenarios. The functional extinction of Posidonia oceanica would have important ecological impacts and may also lead to the release of the massive carbon stocks these ecosystems stored over millennia.

Seagrass meadows.

Seagrass meadows are an important and threatened ecosystem.

Palaeoclimatic conditions in the Mediterranean explain genetic diversity of Posidonia oceanica seagrass meadows.

Past environmental conditions in the Mediterranean Sea have been proposed as main drivers of the current patterns of distribution of genetic structure of the seagrass Posidonia oceanica, the foundation species of one of the most important ecosystems in the Mediterranean Sea. Yet, the location of cold climate refugia (persistence regions) for this species during the Last Glacial Maximum (LGM) is not clear, precluding the understanding of its biogeographical history. We used Ecological Niche Modelling together with existing phylogeographic data to locate Pleistocene refugia in the Mediterranean Sea and to develop a hypothetical past biogeographical distribution able to explain the genetic diversity presently found in P. oceanica meadows. To do that, we used an ensemble approach of six predictive algorithms and two Ocean General Circulation Models. The minimum SST in winter and the maximum SST in summer allowed us to hindcast the species range during the LGM. We found separate glacial refugia in each Mediterranean basin and in the Central region. Altogether, the results suggest that the Central region of the Mediterranean Sea was the most relevant cold climate refugium, supporting the hypothesis that long-term persistence there allowed the region to develop and retain its presently high proportion of the global genetic diversity of P. oceanica.

Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes.

The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus.

Plastid Phylogenomic Analyses Resolve Tofieldiaceae as the Root of the Early Diverging Monocot Order Alismatales.

The predominantly aquatic order Alismatales, which includes approximately 4,500 species within Araceae, Tofieldiaceae, and the core alismatid families, is a key group in investigating the origin and early diversification of monocots. Despite their importance, phylogenetic ambiguity regarding the root of the Alismatales tree precludes answering questions about the early evolution of the order. Here, we sequenced the first complete plastid genomes from three key families in this order:Potamogeton perfoliatus(Potamogetonaceae),Sagittaria lichuanensis(Alismataceae), andTofieldia thibetica(Tofieldiaceae). Each family possesses the typical quadripartite structure, with plastid genome sizes of 156,226, 179,007, and 155,512 bp, respectively. Among them, the plastid genome ofS. lichuanensisis the largest in monocots and the second largest in angiosperms. Like other sequenced Alismatales plastid genomes, all three families generally encode the same 113 genes with similar structure and arrangement. However, we detected 2.4 and 6 kb inversions in the plastid genomes ofSagittariaandPotamogeton, respectively. Further, we assembled a 79 plastid protein-coding gene sequence data matrix of 22 taxa that included the three newly generated plastid genomes plus 19 previously reported ones, which together represent all primary lineages of monocots and outgroups. In plastid phylogenomic analyses using maximum likelihood and Bayesian inference, we show both strong support for Acorales as sister to the remaining monocots and monophyly of Alismatales. More importantly, Tofieldiaceae was resolved as the most basal lineage within Alismatales. These results provide new insights into the evolution of Alismatales as well as the early-diverging monocots as a whole.

Nitrate fertilisation does not enhance CO2 responses in two tropical seagrass species.

Seagrasses are often considered "winners" of ocean acidification (OA); however, seagrass productivity responses to OA could be limited by nitrogen availability, since nitrogen-derived metabolites are required for carbon assimilation. We tested nitrogen uptake and assimilation, photosynthesis, growth, and carbon allocation responses of the tropical seagrasses Halodule uninervis and Thalassia hemprichii to OA scenarios (428, 734 and 1213 µatm pCO2) under two nutrients levels (0.3 and 1.9 µM NO3(-)). Net primary production (measured as oxygen production) and growth in H. uninervis increased with pCO2 enrichment, but were not affected by nitrate enrichment. However, nitrate enrichment reduced whole plant respiration in H. uninervis. Net primary production and growth did not show significant changes with pCO2 or nitrate by the end of the experiment (24 d) in T. hemprichii. However, nitrate incorporation in T. hemprichii was higher with nitrate enrichment. There was no evidence that nitrogen demand increased with pCO2 enrichment in either species. Contrary to our initial hypothesis, nutrient increases to levels approximating present day flood plumes only had small effects on metabolism. This study highlights that the paradigm of increased productivity of seagrasses under ocean acidification may not be valid for all species under all environmental conditions.

A phylogeny and biogeographic analysis for the Cape-Pondweed family Aponogetonaceae (Alismatales).

The monocot family Aponogetonaceae (Alismatales) consists only of Aponogeton, with 57 species occurring in Africa, Madagascar, India and Sri Lanka, Southeast Asia and Australia. Earlier studies inferred a Madagascan or Australian origin for the genus. Aponogeton-like pollen is documented from the Late Cretaceous of Wyoming, the early mid-Eocene of Canada, and the late mid-Eocene of Greenland. We obtained nuclear and plastid DNA sequences for 42 species and generated a time-calibrated phylogeny, rooted on appropriate outgroups. Statistical biogeographic analyses were carried out with or without the fossils incorporated in the phylogeny. The recent-most common ancestor of living Aponogetonaceae appears to date to the mid-Eocene and to have lived in Madagascar or Africa (but not Australia). Three transoceanic dispersal events from Africa/Madagascar to Asia sometime during the Miocene could explain the observed species relationships. As inferred in earlier studies, an ancient Australian species is sister to all other Aponogetonaceae, while the remaining Australian species stem from an Asian ancestor that arrived about 5million years ago. The family's ancient Northern Hemisphere fossil record and deepest extant divergence between a single Australian species and an Africa/Madagascar clade are statistically well-supported and rank among the most unusual patters in the biogeography of flowering plants.

Morphological and physiological responses of seagrasses (Alismatales) to grazers (Testudines: Cheloniidae) and the role of these responses as grazing patch abandonment cues / Respuestas morfológicas y fisiológicas de los pastos marinos (Alismatales) a los herbívoros (Testudines: Cheloniidae) y el papel de estas respuestas como señales de abandono de parches de pastoreo

Green sea turtles, Chelonia mydas, are grazers influencing the distribution of seagrass within shallow coastal ecosystems, yet the drivers behind C. mydas patch use within seagrass beds are largely unknown. Current theories center on food quality (nutrient content) as the plant responds to grazing disturbances; however, no study has monitored these parameters in a natural setting without grazer manipulation. To determine the morphological and physiological responses potentially influencing seagrass recovery from grazing disturbances, seagrasses were monitored for one year under three different grazing scenarios (turtle grazed, fish grazed and ungrazed) in a tropical ecosystem in Akumal Bay, Quintana Roo, Mexico. Significantly less soluble carbohydrates and increased nitrogen and phosphorus content in Thalassia testudinum were indicative of the stresses placed on seagrasses during herbivory. To determine if these physiological responses were the drivers of the heterogeneous grazing behavior by C. mydas recorded in Akumal Bay, patches were mapped and monitored over a six-month interval. The abandoned patches had the lowest standing crop rather than leaf nutrient or rhizome soluble carbohydrate content. This suggests a modified Giving Up Density (GUD) behavior: the critical threshold where cost of continued grazing does not provide minimum nutrients, therefore, new patches must be utilized, explains resource abandonment and mechanism behind C. mydas grazing. This study is the first to apply GUD theory, often applied in terrestrial literature, to explain marine herbivore grazing behavior.

Las tortugas verdes, Chelonia mydas, son herbívoros que influencian la distribución de pastos marinos en sistemas costeros someros, sin embargo los factores que hay detrás del uso de un parche de pastos marinos por C. mydas son desconocidos. Teorías actuales se centran en calidad de alimento (contenido de nutrientes en tejido) conforme la planta responde a la alteración causada por el pastoreo; sin embargo no hay estudios que hayan monitoreado estos parámetros en un diseño natural sin manipulación del herbívoro. Para deter minar las respuestas morfológicas y fisiológicas (productividad, morfología y almacenamiento de nutrientes) que potencialmente influencian la recuperación de los pastos de la alteración por pastoreo, los pastos fueron monitoreados por un año en tres escenarios diferentes de pastoreo (pastoreo por tortuga, pastoreo por peces, sin pastoreo) en el sistema tropical Bahía de Akumal, Quintana Roo, México. Significativamente menos carbohidratos solubles y mayor contenido de nitrógeno y fósforo fueron indicativos del estrés causado por el pastoreo en los pastos. Para determinar si estas respuestas fisiológicas de los pastos son las causantes del heterogéneo comportamiento de pastoreo de C. midas, reportado en Akumal, se mapearon y monitorearon parches de pastos en intervalos de seis meses. Los parches abandonados tuvieron menor biomasa, en vez de bajo contenido de nutrientes en hoja, o de carbohidratos en raíces. Estos resultados sugieren un comportamiento modificado de renunciamiento por densidad: el umbral crítico donde el costo de pastoreo continuo no provee los nutrimentos mínimos, por lo tanto nuevos parches deberán ser utilizados, explicando así el abandono del recurso y mecanismo detrás del comportamiento de pastoreo por C. mydas. Este es el primer estudio en aplicar la teoría de renuncia por densidad, frecuentemente utilizada en la literatura terrestre, para explicar el comportamiento de pastoreo de herbívoros.

Changes in seagrass species composition in northwestern Gulf of Mexico estuaries: effects on associated seagrass fauna.

The objective of this study was to measure the communities associated with different seagrass species to predict how shifts in seagrass species composition may affect associated fauna. In the northwestern Gulf of Mexico, coverage of the historically dominant shoal grass (Halodule wrightii) is decreasing, while coverage of manatee grass (Syringodium filiforme) and turtle grass (Thalassia testudinum) is increasing. We conducted a survey of fishes, crabs, and shrimp in monospecific beds of shoal, manatee, and turtle grass habitats of South Texas, USA to assess how changes in sea grass species composition would affect associated fauna. We measured seagrass parameters including shoot density, above ground biomass, epiphyte type, and epiphyte abundance to investigate relationships between faunal abundance and these seagrass parameters. We observed significant differences in communities among three seagrass species, even though these organisms are highly motile and could easily travel among the different seagrasses. Results showed species specific relationships among several different characteristics of the seagrass community and individual species abundance. More work is needed to discern the drivers of the complex relationships between individual seagrass species and their associated fauna.

Spatial structure of seagrass suggests that size-dependent plant traits have a strong influence on the distribution and maintenance of tropical multispecies meadows.

BACKGROUND: Seagrass species in the tropics occur in multispecies meadows. How these meadows are maintained through species co-existence and what their ecological drivers may be has been an overarching question in seagrass biogeography. In this study, we quantify the spatial structure of four co-existing species and infer potential ecological processes from these structures. METHODS AND RESULTS: Species presence/absence data were collected using underwater towed and dropped video cameras in Pulau Tinggi, Malaysia. The geostatistical method, utilizing semivariograms, was used to describe the spatial structure of Halophila spp, Halodule uninervis, Syringodium isoetifolium and Cymodocea serrulata. Species had spatial patterns that were oriented in the along-shore and across-shore directions, nested with larger species in meadow interiors, and consisted of multiple structures that indicate the influence of 2-3 underlying processes. The Linear Model of Coregionalization (LMC) was used to estimate the amount of variance contributing to the presence of a species at specific spatial scales. These distances were <2.5 m (micro-scale), 2.5-50 m (fine-scale) and >50 m (broad-scale) in the along-shore; and <2.5 m (micro-scale), 2.5-140 m (fine-scale) and >140 m (broad-scale) in the across-shore. The LMC suggests that smaller species (Halophila spp and H. uninervis) were most influenced by broad-scale processes such as hydrodynamics and water depth whereas large, localised species (S. isoetifolium and C. serrulata) were more influenced by finer-scale processes such as sediment burial, seagrass colonization and growth, and physical disturbance. CONCLUSION: In this study, we provide evidence that spatial structure is distinct even when species occur in well-mixed multispecies meadows, and we suggest that size-dependent plant traits have a strong influence on the distribution and maintenance of tropical marine plant communities. This study offers a contrast from previous spatial models of seagrasses which have largely focused on monospecific temperate meadows.

New highly polymorphic microsatellite markers for the aquatic angiosperm Ruppia cirrhosa reveal population diversity and differentiation.

Ruppia cirrhosa is a clonal monoecious plant phylogenetically associated to seagrass families such as Posidoniaceae and Cymodoceaceae. It inhabits shallow waters that are important for productivity and as a biodiversity reservoir. In this study, we developed 10 polymorphic microsatellite loci for R. cirrhosa. Additionally, we obtained cross-amplification for two microsatellites previously described for Ruppia maritima. These 12 markers were tested in four R. cirrhosa populations from the southwest of Europe. The number of alleles per locus was high for most of the markers, ranging from 4 to 13. Two populations (Sicily and Cádiz) showed heterozygote deficit (p < 0.001). The four populations (Sicily, Murcia, Cádiz, and Tavira) were significantly differentiated (F(ST) ≠ 0; p < 0.001), corroborating the usefulness of these microsatellites on R. cirrhosa population genetics.

Comparative analysis of the venom proteome of four important Malaysian snake species

Naja kaouthia, Ophiophagus hannah, Bungarus fasciatus and Calloselasma rhodostoma are four venomous snakes indigenous to Malaysia. In the present study, their proteomic profile by two-dimensional gel electrophoresis (2-DE) have been separated and compared.

Hematology and plasma biochemistry of wild-caught Indian cobra Naja naja (Linnaeus, 1758)

Hematology and plasma biochemistry parameters are useful in the assessment and management of snake physiological status. Although reference ranges are readily available for many snake species, they are lacking for most venomous ophidians. We determined hematology and plasma biochemistry reference ranges for the wild-caught Indian cobra, Naja naja.

Hepatotoxicity and oxidative stress induced by Naja haje crude venom

Snake venoms are synthesized and stored in venom glands. Most venoms are complex mixtures of several proteins, peptides, enzymes, toxins and non-protein components. In the present study, we investigated the oxidative stress and apoptosis in rat liver cells provoked by Naja haje crude injection (LD50) after four hours. Wistar rats were randomly divided into two groups, the control group was intraperitoneally injected with saline solution while LD50-dose envenomed group was intraperitoneally injected with venom at a dose of 0.025 μg/kg of body weight. Animals were killed four hours after the injection. Lipid peroxidation, nitric oxide and glutathione levels were measured as oxidative markers in serum and liver homogenate. In addition, liver function parameters and activities of antioxidant enzymes were determined.

Comparative analysis of the venom proteome of four important Malaysian snake species

Naja kaouthia, Ophiophagus hannah, Bungarus fasciatus and Calloselasma rhodostoma are four venomous snakes indigenous to Malaysia. In the present study, their proteomic profile by two-dimensional gel electrophoresis (2-DE) have been separated and compared.

Hematology and plasma biochemistry of wild-caught Indian cobra Naja naja (Linnaeus, 1758)

Hematology and plasma biochemistry parameters are useful in the assessment and management of snake physiological status. Although reference ranges are readily available for many snake species, they are lacking for most venomous ophidians. We determined hematology and plasma biochemistry reference ranges for the wild-caught Indian cobra, Naja naja.

Morphological and physiological responses of seagrasses (Alismatales) to grazers (Testudines: Cheloniidae) and the role of these responses as grazing patch abandonment cues.

Green sea turtles, Chelonia mydas, are grazers influencing the distribution of seagrass within shallow coastal ecosystems, yet the drivers behind C. mydas patch use within seagrass beds are largely unknown. Current theories center on food quality (nutrient content) as the plant responds to grazing disturbances; however, no study has monitored these parameters in a natural setting without grazer manipulation. To determine the morphological and physiological responses potentially influencing seagrass recovery from grazing disturbances, seagrasses were monitored for one year under three different grazing scenarios (turtle grazed, fish grazed and ungrazed) in a tropical ecosystem in Akumal Bay, Quintana Roo, Mexico. Significantly less soluble carbohydrates and increased nitrogen and phosphorus content in Thalassia testudinum were indicative of the stresses placed on seagrasses during herbivory. To determine if these physiological responses were the drivers of the heterogeneous grazing behavior by C. mydas recorded in Akumal Bay, patches were mapped and monitored over a six-month interval. The abandoned patches had the lowest standing crop rather than leaf nutrient or rhi- zome soluble carbohydrate content. This suggests a modified Giving Up Density (GUD) behavior: the critical threshold where cost of continued grazing does not provide minimum nutrients, therefore, new patches must be utilized, explains resource abandonment and mechanism behind C. mydas grazing. This study is the first to apply GUD theory, often applied in terrestrial literature, to explain marine herbivore grazing behavior.

Comprehensive phylogenetic analyses of the Ruppia maritima complex focusing on taxa from the Mediterranean.

Recent molecular phylogenetic studies reported high diversity of Ruppia species in the Mediterranean. Multiple taxa, including apparent endemics, are known from that region, however, they have thus far not been exposed to phylogenetic analyses aimed at studying their relationships to taxa from other parts of the world. Here we present a comprehensive phylogenetic analyses of the R. maritima complex using data sets composed of DNA sequences of the plastid genome, the multi-copy nuclear ITS region, and the low-copy nuclear phyB gene with a primary focus on the Mediterranean representatives of the complex. As a result, a new lineage, "Drepanensis", was identified as the seventh entity of the complex. This lineage is endemic to the Mediterranean. The accessions included in the former "Tetraploid" entity were reclassified into two entities: an Asia-Australia-Europe disjunct "Tetraploid_α" with a paternal "Diploid" origin, and a European "Tetraploid_γ" originating from a maternal "Drepanensis" lineage. Another entity, "Tetraploid_ß", is likely to have been originated as a result of chloroplast capture through backcrossing hybridization between paternal "Tetraploid_α" and maternal "Tetraploid_γ". Additional discovery of multiple tetraploidizations as well as hybridization and chloroplast capture at the tetraploid level indicated that hybridization has been a significant factor in the diversification of Ruppia.

Eurasian origin of Alismatidae inferred from statistical dispersal-vicariance analysis.

Alismatidae is a wetland or aquatic herb lineage of monocots with a cosmopolitan distribution. Although considerable progress in systematics and biogeography has been made in the past several decades, geographical origin of this group remains unresolved. In this study, we used statistical dispersal-vicariance analysis implemented in program RASP to investigate the biogeography of Alismatidae. Six areas of endemism were used to describe the distribution: North America, South America, Eurasia, Africa, Southeast Asia and Australia. 18,000 trees retained from Bayesian inference of rbcL served as a framework to reconstruct the ancestral areas. The results suggested that the most recent common ancestor of Alismatidae most probably occurred in Eurasia, followed by a split into two major clades. The clade comprising Hydrocharitaceae, Butomaceae and Alismataceae mainly diversified in Eurasia and Africa. The other clade comprising the remaining families dispersed to southern hemisphere. Australia played an important role in diversification of this clade. Several families were suggested to have occurred in Australia, such as Ruppiaceae, Cymodoceaceae, Posidoniaceae and Zosteraceae.