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.

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.

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.

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_β", 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.

An integrative method for the evaluation, monitoring, and comparison of seagrass habitat structure

Assessing environmental condition is essential for the management of coasts and their resources, but better management decisions occur when large databases are simplified into more manageable units of information. Here we present the habitat structure index (HSI), which enables rapid assessment and direct comparison of seagrass habitat structure using scores of 0 (poor) to 100 (excellent) based on integrating five habitat variables: area, continuity, proximity, percentage cover, and species identity. Acquiring data to calculate the HSI can be done in situ or from video recordings, and requires relatively simple methodology of belt transects, estimating percentage cover, and basic taxonomy. Spatiotemporal comparisons can usefully identify locations and periods of seagrass habitat change, potentially providing an early warning indicator of habitat damage and decline in environmental quality. Overall, the integrative approach of the HSI represents a step toward simplifying the exchange of environmental information among researchers, coastal managers, and governing bodies.

The mitochondrial genome of an aquatic plant, Spirodela polyrhiza

BACKGROUND

Spirodela polyrhiza is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral features than the Poales. Its complete sequence of the mitochondrial (mt) genome could provide clues for the understanding of the evolution of mt genomes in plant.

METHODS

Spirodela polyrhiza mt genome was sequenced from total genomic DNA without physical separation of chloroplast and nuclear DNA using the SOLiD platform. Using a genome copy number sensitive assembly algorithm, the mt genome was successfully assembled. Gap closure and accuracy was determined with PCR products sequenced with the dideoxy method.

CONCLUSIONS

This is the most compact monocot mitochondrial genome with 228,493 bp. A total of 57 genes encode 35 known proteins, 3 ribosomal RNAs, and 19 tRNAs that recognize 15 amino acids. There are about 600 RNA editing sites predicted and three lineage specific protein-coding-gene losses. The mitochondrial genes, pseudogenes, and other hypothetical genes (ORFs) cover 71,783 bp (31.0%) of the genome. Imported plastid DNA accounts for an additional 9,295 bp (4.1%) of the mitochondrial DNA. Absence of transposable element sequences suggests that very few nuclear sequences have migrated into Spirodela mtDNA. Phylogenetic analysis of conserved protein-coding genes suggests that Spirodela shares the common ancestor with other monocots, but there is no obvious synteny between Spirodela and rice mtDNAs. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly four-fifths of the Spirodela mitochondrial genome is of unknown origin and function. Although it contains a similar chloroplast DNA content and range of RNA editing as other monocots, it is void of nuclear insertions, active gene loss, and comprises large regions of sequences of unknown origin in non-coding regions. Moreover, the lack of synteny with known mitochondrial genomic sequences shed new light on the early evolution of monocot mitochondrial genomes.

Ecological status of seagrass ecosystems: An uncertainty analysis of the meadow classification based on the Posidonia oceanica multivariate index (POMI)

Quantifying the uncertainty associated with monitoring protocols is essential to prevent the misclassification of ecological status and to improve sampling design. We assessed the Posidonia oceanica multivariate index (POMI) bio-monitoring program for its robustness in classifying the ecological status of coastal waters within the Water Framework Directive. We used a 7-year data set covering 30 sites along 500 km of the Catalonian coastline to examine which version of POMI (14 or 9 metrics) maximises precision in classifying the ecological status of meadows. Five factors (zones within a site, sites within a water body, depth, years and surveyors) that potentially generate classification uncertainty were examined in detail. Of these, depth was a major source of uncertainty, while all the remaining spatial and temporal factors displayed low variability. POMI 9 matched POMI 14 in all factors, and could effectively replace it in future monitoring programs.

Molecular phylogenetic analyses of Tofieldiaceae (Alismatales): family circumscription and intergeneric relationships

Tofieldiaceae are a small monocot family comprising about 20 species, mostly distributed in the Northern Hemisphere, with some in northern South America. To clarify the family circumscription, the number of distinguishable genera in the family, and relationships among the genera, we conducted molecular analyses of cpDNA (matK and non-coding trnL-trnL-trnF region) sequences of 17 associated species of Tofieldiaceae, along with 14 species of Acorales, Alismatales, Dioscoreales, Pandanales, and Liliales. Results showed that Tofieldiaceae are monophyletic, comprising all the species assignable to Harperocallis, Isidrogalvia, Pleea, Tofieldia, and Triantha, thus supporting the original family circumscription. Within the family, Pleea is sister to the rest of the family, in which Isidrogalvia is sister to Harperocallis, and Tofieldia to Triantha. Morphological characters supporting the relationships among the genera were briefly discussed.

[Antioxidant effect and polyphenol content of Syringodium filiforme (Cymodoceaceae)]

The marine phanerogam Syringodium filiforme, known as "manatee grass", is a common species that grows in coastal areas associated to Thalassia testudinum. With the aim to describe some of its possible chemical characteristics, this study was performed with a sample of 1.2 kg, collected in March 2009, in Guanabo beach, Havana, Cuba. The sample was dried (less than 12% humidity) and a total extract prepared; other three extracts were prepared with the use of solvents of increasing polarity. The phytochemical screening and analytical determinations of each fraction were undertaken Total polyphenol content was determined using pyrogallol as reference's standard; chlorophyll a and b and anthocyanin content were also quantified. Total extract and fractions antioxidant activity were evaluated by using the free radical scavenging activity assay with 1,1-Diphenyl-2-Picrylhydrazyl reactive (knowing as DPPH's method). The phytochemical screening of the different extracts detected the presence of high concentrations of flavonoids, phenols, terpenes, antocyanins, reducing sugars and alkaloids. The total extract and methanol fraction showed significant free radical scavenging properties, while the petroleum ether fraction showed moderate activity, and the chloroform fraction and the aqueous soluble precipitate (residual salt) obtained didn't show antioxidant properties against free radicals. The results of this work confirmed the potentialities of this species for biological purposes.

[Does sea-grass biomass control the density of peracarids (Crustacea: Peracarida) in tropical lagoons?]

We analyzed the time-space variation of the peracarid crustaceans that inhabit seagrasses of the Alvarado Lagoon System, Veracruz, Gulf of Mexico. The organisms were collected from 108 samples in six sites with Ruppia maritima beds (December 1992 to November 1994). The assemblage was composed of 11 species. Eight species of Amphipoda (Hourstonius laguna, Cerapus benthophilus, Apocorophium louisianum, Grandidierella bonnieroides, Leptocheirus rhizophorae, Gammarus mucronatus, Melita longisetosa and Haustorius sp.), one of Isopoda (Cassidinidea ovalis) and two of Tanaidacea (Discapseudes holthuisi and Leptochelia savignyi) were identified. Taxocoenosis, density and biomass of peracarids showed seasonal pulses related to R. maritima biomass, salinity variation, epicontinental affluent and inlets. The species C. ovalis, G. mucronatus, A. louisianum and D. holthuisi were dominant.

[Seagrass monitoring at Perezoso, Cahuita, Costa Rica (CARICOMP site)]

The seagrass of Perezoso (Cahuita National Park, Caribbean coast of Costa Rica) was monitored using the CARICOMP protocol. Productivity (2.7 +/- 1.15 g/m2/d; n=74) was intermediate, compared to other Caribbean sites. Total biomass was intermediate to high (750-1500 g/m2) at most CARICOMP sites (Colombia, Cuba, Mexico, Puerto Rico and Venezuela) including Costa Rica (822.8 +/- 391.84 g/m2; n=32). Turnover rates were high (5.5 +/- 1.36%; n=74) compared to what was found in March and August at other sites. Shoot densities average 725 shoots/m2, in the Caribbean region, while in Costa Rica the value was higher (1184 +/- 335.5 shoots/m2). Average leaf length and width in the entire region were 14.4 cm and 10.6 mm, respectively, similar to what we found, but leaf area index average 3.4 m2 m(-2), higher than what was found in Costa Rica (0.92 m2 m(-2)). At Cahuita, seagrass productivity was significantly lower in March 2005 compared with the previous six years, and biomass has decreased with time. Seagrass productivity and biomass are being affected by the maximum temperatures, which increased by almost 10 degrees C from 1999 to 2005, and show a high negative correlation. Turnover rate and temperature were not correlated. Recreational boating, swimming and nutrient loading from deforested lands in the coast, the upstream rivers and local pollution are potential sources of impact to the seagrass beds at Cahuita.

Flower-like terminal structures in racemose inflorescences: a tool in morphogenetic and evolutionary research

Terminal flower-like structures (TFLS) occur in many angiosperms that possess indeterminate inflorescences such as spikes, racemes, or spadices. We describe and review TFLS in early-divergent angiosperms, especially the magnoliid order Piperales and the monocot order Alismatales, in which floral interpretation is controversial. Essentially similar TFLS occur in a wide range of taxa. Among magnoliids, they occur in some Piperales (Saururaceae and a few Piperaceae), but are absent from Chloranthaceae. Among monocots, they occur in some early-divergent families such as Acoraceae, Aponogetonaceae, Juncaginaceae, Potamogetonaceae, and Ruppiaceae. Similar TFLS with obscure organ identity are recorded in mutants of Arabidopsis. TFLS can often be interpreted as pseudanthia (close aggregations of reduced flowers), but in some cases the entire terminal pseudanthium is very similar to a true flower. In some cases, elaborated TFLS could therefore have given rise to what are normally termed 'true' (i.e. euanthial) flowers. Data presented here on terminal pseudanthia in Potamogeton and Ruppia support a pseudanthial evolutionary origin of reproductive units in the alismatid families Zannichelliaceae and Cymodoceaceae. Furthermore, in some alismatid species, either the entire inflorescence apex or an individual primordium at or near the inflorescence tip can be transformed into a filamentous or tubular (or intermediate) structure. A tubular structure enclosing stamens and carpels is described in Piper. This indicates that pseudanthium formation can provoke morphological novelties, perhaps due to new patterns of overlap between expression zones of regulatory genes and/or new spatial constraints.

Biosystematic studies on the family Tofieldiaceae I. Phylogeny and circumscription of the family inferred from DNA sequences of matK and rbcL

In order to specify phylogenetic positions of the genera of Tofieldiaceae (Tofieldia, Triantha, Pleea, Harperocallis, Isidrogalvia), and to suggest reasonable circumscription of the family and genera of Tofieldiaceae, we determined DNA sequences of matK and rbcL for each genus of the family, and analyzed them phylogenetically with the 45 families and 113 genera of the monocots other than Tofieldiaceae, whose matK and rbcL sequences have already been reported. We found that Tofieldia, Triantha, Pleea, and Harperocallis form the same clade, which receives 100% bootstrap support. This clade can be regarded as corresponding to Tofieldiaceae, and is embedded in the clade of Alismatales (98%). On the other hand, Isidrogalvia is not included in this Tofieldiaceae clade, and positioned as sister to Narthecium (100%), embedded in the clade of Nartheciaceae (Dioscoreales) (100%). In the Tofieldiaceae, Pleea first diverges from the remaining three genera (100%), and then, Harperocallis diverges from the Tofieldia- Triantha complex (100%). In the Tofieldia- Triantha complex, five Tofieldia species form the same clade (100%), and two Triantha species form another clade (100%). Thus, Isidrogalvia should be transferred from Tofieldiaceae to Nartheciaceae. As Isidrogalvia, as well as the Nartheciaceae, have the carpels that are fully connate into a single style, Isidrogalvia fits the Nartheciaceae well with respect to carpel connation. After this transfer, the Tofieldiaceae correspond mainly to plants with almost free carpels and three styles. Pleea is better treated as an independent genus than included in Tofieldia. Triantha can be treated either as an independent genus or as congeneric with Tofieldia.

Requiem for an eastern Pacific seagrass bed

Few papers concerning seagrasses of the eastern Pacific have been published. This paper presents the first ecological data on the seagrass, Ruppia maritima, from a non-lagoonal setting in the eastern Pacific. A 5000 m2 patch formed by R. maritima, at Playa Iguanita, Bahía Culebra, Pacific coast of Costa Rica was studied. Plant density and leaf length of R. maritima were determined along two transects on different dates. Above and below ground biomass were calculated along one transect. Plant density ranged from 1590 to 8630 individuals m(-2) along the two transects, with means of 5990 +/- 1636 and 6100 +/- 1876 plants m(-2) for transect 1 and 2, respectively. Longest leaf length per plant varied between 0.5 and 23.0 cm. Leaf biomass (LB) ranged from 10 to 97 gm(-2), and root-rhizome biomass (RB) from 31 to 411 gm(-2), resulting in RB:LB ratios of 3.07 to 15.27. Total biomass at Bahía Culebra was lower than at tropical lagoons on the Pacific coast of Mexico, but higher than in the Gulf of Mexico. The below ground: above ground biomass ratio was much higher at Bahía Culebra than at other sites on the Pacific coast of Mexico and the Gulf of Mexico. Another seagrass present at Bahía Culebra was Halophila baillonii, with low densities on the deepest section of the patch. At least 44 invertebrate species associated with the seagrass bed have also been identified. The patch at Playa Iguanita and other sites within Bahía Culebra, as well as their associated organisms, disappeared after a severe storm in June 1996. No seagrasses have been found in the area or in any other location on the Pacific coast of Costa Rica since then.