Seasonal variation of dominant free-floating and attached Ulva species in Rudong coastal area,China

In this paper, species compositions and seasonal variations of attached Ulva species on Porphyra aquaculture rafts and free floating Ulva species at Rudong coastal area, Jiangsu Province of China were investigated during 2010–2011. Based on the sequences analysis of nuclear-encoded ITS (including 5.8S rDNA regions) and 5S rDNA spacer regions, dominant species of both attached and free-floating Ulva samples were identified as Ulva compressa, Ulva linza, Ulva prolifera and Ulva flexuosa. Phylogenetic tree based on sequences of ITS and 5S rDNA spacer regions for attached and free-floating Ulva species was constructed, respectively. Species compositions of the Ulva population attached on aquaculture rafts varied with seasons, and U. prolifera was only found on aquaculture rafts in March 2011 during the 2010–2011 Porphyra yezoensis cultivation season, which had the same sequences of ITS and 5S rDNA spacer regions as that of the dominant species bloomed in the Yellow Sea of China in 2008. Dominant species of the free-floating Ulva population at the early stage of the green tide were U. compressa, U. flexuosa, and U. linza. Free-floating U. prolifera appeared in the middle of May, 2011. ITS sequence similarity rates of U. compressa and U. flexuosa between the attached and free-floating species were 100%. And ITS and 5S rDNA spacer sequences of the attached and the free-floating U. prolifera population also showed no differences. Further study showed that there were two types of free-floating U. prolifera population (Type 5S-A and Type 5S-B) based on 5S rDNA spacer sequences. The present study would provide some useful information for clarifying the outbreak mechanism of green tides occurred in the Yellow Sea, China.     

Genetic variation of <Emphasis Type="Italic">Ulva (Enteromorpha) prolifera</Emphasis> (Ulvales,Chlorophyta)—the causative species of the green tides in the Yellow Sea,China

Ulva (Enteromorpha) prolifera, widely distributed from the intertidal to the upper subtidal zones around the world, was the dominant species of the massive green tides in the Yellow Sea in the summers of 2007, 2008, and 2009. However, little is known about its intra-species genetic diversity. In this study, six attached and seven floating U. prolifera samples collected from different sites distributed from the north of the Yellow Sea to the south of the East China Sea were taken in inter-simple sequence repeat (ISSR) analysis. Based on the results of the 90 polymorphic bands from four ISSR primers, the genetic diversity level of the floating samples (H = 0.1663, I = 0.2608) was found to be lower than that of the attached samples (H = 0.2105, I = 0.3346). Unweighted pair-group mean analysis (UPGMA) and principal coordinate analysis (PCoA) suggested that floating U. prolifera samples in the Yellow Sea from 2007 to 2009 had a close genetic relationship, and the floating samples were separated from the attached samples. Genetic differentiation and limited gene flow among attached U. prolifera populations were indicated by analysis of molecular variance.     

Morphological and molecular characterization of free-floating and attached green macroalgae Ulva spp. in the Yellow Sea of China

During the summer of 2008 and 2009, massive algal blooms repeatedly broke out in the Yellow Sea of China. These were undoubtedly caused by the accumulations of one or more species in the macroalgal genus Ulva. In previous reports, morphological observation indicated that the species involved in this phenomenon is Ulva prolifera but molecular analyses indicated that the species belongs to an Ulva linza–procera–prolifera (LPP) clade. Correct identification of the bloom species is required to understand and manage the blooms, but the taxonomic status of the bloom species remains unclear. In the current study, the taxonomic status of 22 selected specimens from the Yellow Sea was assessed by using both morphological and molecular (ITS and rbcL sequences) data. In addition, 5S rDNA analyses were performed for those samples clustering in the LPP clade, and phylogenetic tree and ribotype analyses were constructed for determining the possible origin of the bloom. Three free-floating and two attached Ulva species were distinguished and described: Ulva compressa Linnaeus and Ulva pertusa Kjellman were found in free-floating samples; U. linza Linnaeus was found on rocks; and U. prolifera O.F. Müller was found in both habitats. Diversity in free-floating Ulva of the Yellow Sea appears to be greater than previously thought. The dominant free-floating Ulva species, U. prolifera, was not closely related to local populations attached to rocks but was closely related to populations from Japan.     

Discrimination of the common macroalgae (Ulva and Blidingia) in coastal waters of Yellow Sea,northern China,based on restriction fragment-length polymorphism (RFLP) analysis

Since 2007, reoccurring large-scale green algae blooms have caused deleterious effects to the estuarine ecosystem of Yellow Sea, northern China and subsequent economical losses. Previous surveys indicated the green tides were initiated in the coastal water of southern Jiangsu province where Porphyra farming was intensively conducted; however, the main ‘seed source’ of floating green algae is still under debate. Ulva prolifera was confirmed to be the major causative species of green tides. The multiple sympatric ulvoid species in the natural environment has complicated species identification in both field surveys and laboratory studies due to their morphological plasticity. Thus, we developed a genetic identification key based on restriction fragment length polymorphism (RFLP) analysis of the ITS nuclear marker to discriminate the common Ulva and Blidingia species in the Yellow Sea. Ten genetic lineages (1 in Blidingia, 9 in Ulva) were detected along the coast of China through phylogenetic analysis of ITS sequences. They can be separated by virtual restriction digestion using the four selected restriction enzymes (BspT107 I, EcoO109 I, Hin1 I and VpaK11B I). With additional PCR amplification of the 5S spacer region, we were able to discriminate U. prolifera from Ulva linza. Using this genetic key, we screened macroalgal samples collected from the coast of the Yellow Sea, and the results indicated 6 common lineages (U. prolifera, U. linza, Ulva compressa, Ulva pertusa, Clade 6 and Blidingia sp.) in this region, which could be explicitly distinguished by a single enzyme (BspT107 I) coupled with 5S spacer polymorphism. U. prolifera was confirmed to be present on the Porphyra aquaculture rafts with seasonal variation in the species composition. This genetic key will facilitate our long-term field surveys to investigate the origin of the floating U. prolifera and furthermore to explore its bloom dynamics along the coast of the Yellow Sea. It also provided a framework for the future inclusion of more Ulva species, which will expand the usage of this key.     

Ulva diversity in the Yellow Sea during the large‐scale green algal blooms in 2008–2009

In the Yellow Sea of China, large‐scale green tides have broken out for three consecutive years from 2007 to 2009. As part of the efforts to localize the algal source, two cruises were conducted in the early stage and the outbreak stage of the bloom in 2009. We analyzed the morphological and genetic diversity of drifting Ulva specimens and culture‐derived isolates from seawater sampled in different localities. For phylogenetic analyses, the nuclear encoded ribosomal DNA internal transcribed spacer region (ITS nrDNA) and the plastid encoded large subunit of ribulose‐1, 5‐bisphosphate carboxylase/oxgenase gene (rbcL) were used. Our molecular and morphological data indicate that the dominant free‐floating Ulva species in 2008 and 2009 possibly belonged to a single strain of the U. linza‐procera‐prolifera (LPP) clade. The ITS sequences from bloom‐forming algal samples with dense branches were identical to those from U. linza‐like specimens without branches derived from the Yellow Sea. Microscopic individuals of the dominant Ulva strain were detected in eight stations, revealing that spore dispersal in the water helped to enlarge biomass in the water during the outbreak stage of green tide in the Yellow Sea.     

Somatic cells serve as a potential propagule bank of <Emphasis Type="Italic">Enteromorpha prolifera</Emphasis> forming a green tide in the Yellow Sea,China

For the last 2 years, vast accumulations of the unattached filamentous green alga, Enteromorpha prolifera, have occurred during summer along the coastal region of the Yellow Sea, China. However, algae do not seem to occur after the end of the fertile season. It has been suggested that banks of microscopic forms of the algae, primarily spores, function as a survival mechanism for this opportunistic alga. Therefore, in this study, field surveys and laboratory cultures were conducted to determine if somatic cells were serving as a propagule bank to enable the algae to survive through periods of unfavorable conditions. Laboratory experiments demonstrated that somatic regeneration was one of the most important approaches by which E. prolifera colonized and flourished in the study area. Indeed, at least 19.32% of somatic cells from the filamentous segments could survive for 2 months under various temperatures (0, 5, 10, 15, 20, and 30°C at an irradiance of 60 μmol photons m⁻² s⁻¹) and irradiances (darkness, 5 10, 15, 20 and 30 μmol photons m⁻² s⁻¹ at a temperature of 20°C). Additionally, greater than 35.85% of the somatic cells could survive at 0°C or in darkness for 2 months, and no less than 15.99% of these cells resumed growth when the temperature and irradiance were adjusted to the normal levels (20°C and 60 μmol photons m⁻² s⁻¹). Furthermore, the results of field surveys revealed that viable E. prolifera was widespread in high quantities in the sediment of the Yellow Sea when the macroalga was absent. Taken together, the results of this study suggest that somatic cells may act as an overwintering stage for the annual spring bloom of E. prolifera. These findings should be useful in future studies conducted to behavior of somatic cells in green tide as well as in the management of future spring blooms of E. prolifera.     

Effects of crude oil on major functional characteristics of macroalgae of the Barents Sea

On the basis of experimental research on the influence of crude oil on basic functional characteristics (growing speed, photosynthesis, and breadth) of macroalgae of the Barents Sea (Laminaria saccharina, Fucus vesiculosus, Ascophyllum nodosum, Porphyra umbilicalis, Palmaria palmata, and Enteromorpha prolifera) it was shown that kelp are more resistant to the influence of oil carbohydrates while red and green algae are less resistant. Under the short-term influence of oil toxins photosynthesis is depressed and respiration increases, under long-term influence the rate of growth is reduced.     

Trace metal interactions in the macroalga Enteromorpha prolifera (O. F. Müller) J.Ag., grown in water of the Scheldt estuary (Belgium & SW Netherlands), in response to cadmium exposure

The littoral macroalga Enteromorpha prolifera was sampled along the Scheldt estuary at Lillo (Belgium), Bath and Ellewoutsdijk (SW Netherlands). The algae were incubated in water from the same locations with salinities of 7, 14 and 23%, at about 50 molquanta m^–2 s^–1 irradiance and 15 °C. One series of cultures was exposed to 400 nm Cd, a second series served as a control. Temporal changes in cadmium, copper, iron, lead and zinc contents of E. prolifera were monitored with atomic absorption spectroscopy in a 21 day experiment. Both synergistic and antagonistic metal interactions became evident in response to cadmium uptake. During the first 8 days of incubation iron contents increased in both cadmium-exposed and control algae. However, iron contents were relatively higher in cadmium-exposed algae. Similar, but weaker synergisms were also found between lead/cadmium and coper/cadmium. Zinc contents decreased in controls and cadmium-exposed algae, but were significantly lower in cadmium-exposed algae. A distinct antagonism between cadmium and zinc was observed in cadmium-exposed algae.     

Nuclear and chloroplast DNA sequences data support the origin of Potamogeton intortusifolius J.B. He in China as a hybrid between P. perfoliatus Linn. and P. wrightii Morong

Internal transcribed spacers (ITS) of nuclear ribosomal DNA and chloroplast rbcL gene sequence data were used to test the hypothesis that natural populations of Potamogeton intortusifolius J.B. He in China originated from hybridization between P. perfoliatus Linn. and P. wrightii Morong. Based on ITS sequences data, P. intortusifolius possessed heterozygous rDNA genotypes which confirmed the hybrid origin of P. intortusifolius. Chloroplast rbcL gene sequences of P. intortusifolius from Yichang population revealed the same chloroplast haplotype as P. perfoliatus and the samples of P. intortusifolius from Weinan population had the same chloroplast haplotype as P. wrightii, which indicated that both putative parental species had been the maternal parent and that the two populations of P. intortusifolius had independent origins. This study confirms P. intortusifolius as a reciprocal hybrid. Because P. × intortusifolius in China has the same hybrid origin as P. × anguillanus Koidz. in Japan, it is suggested that P. × intortusifolius should be a synonym of P. × anguillanus.     

Invasion of protein coding genes by green algal ribosomal group I introns

The spread of group I introns depends on their association with intron-encoded homing endonucleases. Introns that encode functional homing endonuclease genes (HEGs) are highly invasive, whereas introns that only encode the group I ribozyme responsible for self-splicing are generally stably inherited (i.e., vertical inheritance). A number of recent case studies have provided new knowledge on the evolution of group I introns, however, there are still large gaps in understanding of their distribution on the tree of life, and how they have spread into new hosts and genic sites. During a larger phylogenetic survey of chlorophyceaen green algae, we found that 23 isolates contain at least one group I intron in the rbcL chloroplast gene. Structural analyses show that the introns belong to one of two intron lineages, group IA2 intron-HEG (GIY-YIG family) elements inserted after position 462 in the rbcL gene, and group IA1 introns inserted after position 699. The latter intron type sometimes encodes HNH homing endonucleases. The distribution of introns was analyzed on an exon phylogeny and patterns were recovered that are consistent with vertical inheritance and possible horizontal transfer. The rbcL 462 introns are thus far reported only within the Volvocales, Hydrodictyaceae and Bracteacoccus, and closely related isolates of algae differ in the presence of rbcL introns. Phylogenetic analysis of the intron conserved regions indicates that the rbcL699 and rbcL462 introns have distinct evolutionary origins. The rbcL699 introns were likely derived from ribosomal RNA L2449 introns, whereas the rbcL462 introns form a close relationship with psbA introns.     

Tempo-spatial distribution and species diversity of green algae micro-propagules in the Yellow Sea during the large-scale green tide development

From 2008 to 2013, vast green tides mainly composed of Ulva prolifera consecutively invaded the coast of Qingdao (36°06′N, 120°25′E, PR China) in June and July. Previous studies have shown that the early green tides initially formed in the Porphyra yezoensis aquaculture area of the Subei Shoal, southern Yellow Sea. To date, multiple studies have demonstrated that green algae micro-propagules play an important role in the formation of green tides. In this study, we aimed to assess the temporal and spatial distribution of green algae micro-propagules in an extensive area of the Yellow Sea and to determine the species diversity of propagules during the development of the large-scale green tide. We found that the quantity of micro-propagules increased with the free-floating biomass from the initial generation to the development phase of the green tide in mid May. From late May to mid June, the micro-propagule density decreased sharply despite a continuous increase of the floating macroalgae biomass. In addition, our data indicate that the coastal area of the Subei Shoal has always been the distribution center of the micro-propagules, even prior to the large-scale green tide formation. Furthermore, diverse green algae species, including Ulva prolifera, Ulva linza, Ulva flexuosa, Ulva compressa, Ulva pertusa and Blidingia sp., were identified among the micro-propagules in the survey sea area. Finally, we determined that the distribution of U. prolifera micro-propagules is closely related to the floating algal mats and attached macroalgae on Porphyra aquaculture rafts.     

Host-parasite relationship of the geoduck Panopea abbreviata and the green alga Coccomyxa parasitica in the Argentinean Patagonian coast

The association of the geoduck Panopea abbreviata and the green alga Coccomyxa parasitica is described. The identity of the green alga was confirmed by molecular studies; the alga was found within the hemocytes that infiltrate the connective tissue of the geoduck siphons. Cytological characteristics of hemocytes were not altered by algal infection; very often the algae were seen enveloped by a digestive vacuole within the hemocyte cytoplasm, evidencing diverse degrees of resorption. Connective cells of siphons were rarely infected by C. parasitica. The mean prevalence of C. parasitica was higher (82%) in San Matías Gulf (42°00′S, 65°05′W) than in San José Gulf (45%) (40°32′S, 64°02′W); except for spring, when the two locations showed no differences in prevalences (80%). Independently of location, season and host size, infected geoducks showed lower condition index values than uninfected ones. Regarding other bivalve species, only one specimen of the razor clam Ensis macha was found infected, and none of the oysters Ostrea puelchana and Pododesmus rudis and scallop Aequipecten tehuelchus was parasitized by the green alga.     

Interactions of Algae within the Community of <Emphasis Type="Italic">Gracilaria gracilis</Emphasis> (Rhodophyta)

Interactions among the unattached red alga Gracilaria gracilis, the dominant species of an algal community, and associated algal species Chaetomorpha linum, Enteromorpha prolifera f. prolifera, and Polysiphonia sp. were studied during and after an algal bloom. It was shown that during their bloom the associated algae Enteromorpha and Polysiphonia sp. significantly decreased the photosynthetic rate of G. gracilis but did not affect its growth rate. It is suggested that the inhibition of Gracilaria gracilis photosynthesis is connected to the impact of extracellular metabolites excreted by Chaetomorpha linum, Enteromorpha prolifera f. prolifera, and Polysiphonia sp. In laboratory experiments, the photosynthetic rate of the associated species was enhanced in the presence of Gracilaria. However, no significant alterations were observed in the content of chlorophyll a, growth, and the dark respiration rates of associated algae when they were kept together with Gracilaria. It was suggested that allelopathic interactions observed among algal species during the formation of the monospecific Gracilaria community, as well as during algal blooms, are not determinative.     

Acid phosphatase in Enteromorpha

Extracts of the alga Enteromorpha linza hydrolysed glucose-6-phosphate, p-nitrophenylphosphate 2′-, 3′-, and 5′-adenosine monophosphates with an optimum at pH 5. Cytidine and uridine-5′-nucleoside diphosphates, and 2′-, and 3′-adenosine monophosphates were relatively poorly hydrolysed. Zn²⁺ (10 mM) inhibited the hydrolysis of all substrates, whereas Mg²⁺ (10 mM) may be stimulatory. It is suggested that the hydrolysis of these phosphomonoesters was due to the activity of a non-specific acid phosphatase (orthophosphoric monoester phosphohydrolase, E.C. 3.1.3.2).     

Application of DNA Barcodes in Asian Tropical Trees – A Case Study from Xishuangbanna Nature Reserve,Southwest China

Background

Within a regional floristic context, DNA barcoding is more useful to manage plant diversity inventories on a large scale and develop valuable conservation strategies. However, there are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world.

Methodology and Principal Findings

A DNA barcoding database of an Asian tropical trees with high diversity was established at Xishuangbanna Nature Reserve, Yunnan, southwest China using rbcL and matK as standard barcodes, as well as trnH–psbA and ITS as supplementary barcodes. The performance of tree species identification success was assessed using 2,052 accessions from four plots belonging to two vegetation types in the region by three methods: Neighbor-Joining, Maximum-Likelihood and BLAST. We corrected morphological field identification errors (9.6%) for the three plots using rbcL and matK based on Neighbor-Joining tree. The best barcode region for PCR and sequencing was rbcL (97.6%, 90.8%), followed by trnH–psbA (93.6%, 85.6%), while matK and ITS obtained relative low PCR and sequencing success rates. However, ITS performed best for both species (44.6–58.1%) and genus (72.8–76.2%) identification. With trnH–psbA slightly less effective for species identification. The two standard barcode rbcL and matK gave poor results for species identification (24.7–28.5% and 31.6–35.3%). Compared with other studies from comparable tropical forests (e.g. Cameroon, the Amazon and India), the overall performance of the four barcodes for species identification was lower for the Xishuangbanna Nature Reserve, possibly because of species/genus ratios and species composition between these tropical areas.

Conclusions/Significance

Although the core barcodes rbcL and matK were not suitable for species identification of tropical trees from Xishuangbanna Nature Reserve, they could still help with identification at the family and genus level. Considering the relative sequence recovery and the species identification performance, we recommend the use of trnH–psbA and ITS in combination as the preferred barcodes for tropical tree species identification in China.     

Molecular Analysis of Anisakis Type I Larvae in Marine Fish from Three Different Sea Areas in Korea

Anisakiasis, a human infection of Anisakis L3 larvae, is one of the common foodborne parasitic diseases in Korea. Studies on the identification of anisakid larvae have been performed in the country, but most of them have been focused on morphological identification of the larvae. In this study, we analyzed the molecular characteristics of 174 Anisakis type I larvae collected from 10 species of fish caught in 3 different sea areas in Korea. PCR-RFLP and sequence analyses of rDNA ITS and mtDNA cox1 revealed that the larvae showed interesting distribution patterns depending on fish species and geographical locations. Anisakis pegreffii was predominant in fish from the Yellow Sea and the South Sea. Meanwhile, both A. pegreffii and A. simplex sensu stricto (A. simplex s.str.) larvae were identified in fish from the East Sea, depending on fish species infected. These results suggested that A. pegreffii was primarily distributed in a diverse species of fish in 3 sea areas around Korea, but A. simplex s.str. was dominantly identified in Oncorhynchus spp. in the East Sea.     

Potential use of DNA barcoding for the identification of Salvia based on cpDNA and nrDNA sequences

An effective DNA marker for authenticating the genus Salvia was screened using seven DNA regions (rbcL, matK, trnL–F, and psbA–trnH from the chloroplast genome, and ITS, ITS1, and ITS2 from the nuclear genome) and three combinations (rbcL + matK, psbA–trnH + ITS1, and trnL–F + ITS1). The present study collected 232 sequences from 27 Salvia species through DNA sequencing and 77 sequences within the same taxa from the GenBank. The discriminatory capabilities of these regions were evaluated in terms of PCR amplification success, intraspecific and interspecific divergence, DNA barcoding gaps, and identification efficiency via a tree-based method. ITS1 was superior to the other marker for discriminating between species, with an accuracy of 81.48%. The three combinations did not increase species discrimination. Finally, we found that ITS1 is a powerful barcode for identifying Salvia species, especially Salvia miltiorrhiza.     

Space competition between seagrass and Caulerpa prolifera (Forsskaal) Lamouroux following simulated disturbances in Lassing Park, FL

An experimental study was conducted in Tampa Bay, FL to examine the response to disturbance of two co-occurring subtidal plants: the alga Caulerpa prolifera and the seagrass Halodule wrightii (Ascherson). Some recent studies have called into question the assumption that fast-growing rhizoidal Caulerpa species have the potential to outcompete and rapidly replace local seagrasses. In the Fall of 2002 an abrupt appearance of Caulerpa prolifera was noted in a shallow embayment in Tampa Bay previously dominated by seagrasses. Natural disturbance events were simulated by excavating 0.5 × 0.5 m plots in an area with monospecific C. prolifera and mixed C. prolifera and H. wrightii. Above and below-ground biomass were removed, and recovery of above-ground cover into the newly created gaps was monitored over 15 months. In addition to measuring the recovery of both species, the spatial pattern of Caulerpa recovery from the simulated disturbances was also analyzed. Simulated gaps were rapidly (5-8 months, depending on sampling resolution) and exclusively reoccupied by C. prolifera, with the recovery occurring predominantly via lateral expansion from gap edges rather than colonization by fragments. Therefore, while rhizoidal algae may or may not be able to supplant existing seagrasses by overgrowth or other forms of direct competition, disturbance events that remove seagrass and create bare areas may allow C. prolifera to replace seagrasses over time via preemption of space should an algal bloom such as this be persistent.     

Phylogenetics,biogeography, and evolutionary trends of the Phalaenopsis sumatrana complex inferred from nuclear and chloroplast DNA

Phylogenetic trees inferred from the internal transcribed spacers 1 and 2 (ITS1 + ITS2) region from nuclear ribosomal DNA (nrDNA) and the intergenic spacer of atpB-rbcL from chloroplast DNA (cpDNA) were used to clarify the phylogenetics and evolutionary trends of the Phalaenopsis sumatrana complex. The P. sumatrana complex includes the two species P. sumatrana and Phalaenopsis corningiana as well as a problem species, Phalaenopsis zebrina, according to the concepts of Sweet (1980) and Christenson (2001). Based on the phylogenetic tree inferred from the ITS sequence, the accessions of P. sumatrana cannot be separated from those of P. corningiana. In contrast, the accessions of P. zebrina can be separated from those of both P. sumatrana and P. corningiana. However, analyses of the sequences of the atpB-rbcL spacer apparently cannot discriminate among these three species of the P. sumatrana complex. An inspection of the morphological characters of the plants of the P. sumatrana complex and the floral fragrances of P. zebrina can be used to separate it from both P. sumatrana and P. corningiana. Based on the molecular data and floral fragrances, P. zebrina perhaps should not be treated as a synonym of P. sumatrana. On the evolutionary trend of the P. sumatrana complex, P. zebrina was suggested to be the relative origin group of the P. sumatrana complex based on the phylogenetic tree and biogeography.