The rosette agent of chinook salmon (Oncorhynchus tshawytscha) is closely related to choanoflagellates,as determined by the phylogenetic analyses of its small ribosomal subunit RNA

The rosette agent of Chinook salmon (Oncorhynchus tshawytscha), initially described and characterized in the mid 1980s, is the cause of a serious infectious disease in the Pacific Northwest of North America. Previous work, utilizing rosette agent maintained by growth in embryo salmon cell-culture, has shown it to be a eukaryotic obligate intracellular parasite. However, its ultrastructural features do not suggest a relationship with any specific eukaryotic group. We have utilized a molecular approach to further investigate the phylogeny of rosette agent previously maintained in vitro during 1990 and 1991. We have amplified the genomic DNA encoding the small subunit ribosomal RNA (16S-like rRNA), and determined the complete DNA nucleotide sequence of this gene segment. Comparison with other eukaryotic 16S-like rRNA sequences suggests that the rosette agent shares a unique evolutionary history with choanoflagellates.     

Present-day genetic composition suggests contrasting demographic histories of two dominant chaetognaths of the North-East Atlantic, <Emphasis Type="Italic">Sagitta elegans</Emphasis> and <Emphasis Type="Italic">S. setosa</Emphasis>

Sagitta elegans and S. setosa are the two dominant chaetognaths in the North-East (NE) Atlantic. They are closely related and have a similar ecology and life history, but differ in distributional ranges. Sagitta setosa is a typical neritic species occurring exclusively above shelf regions, whereas S. elegans is a more oceanic species with a widespread distribution. We hypothesised that neritic species, because of smaller and more fragmented populations, would have been more vulnerable to population bottlenecks resulting from range contractions during Pleistocene glaciations than oceanic species. To test this hypothesis we compared mitochondrial Cytochrome Oxidase II DNA sequences of S. elegans and S. setosa from sampling locations across the NE Atlantic. Both species displayed very high levels of genetic diversity with unique haplotypes for every sequenced individual and an approximately three times higher level of nucleotide diversity in S. elegans (0.061) compared to S. setosa (0.021). Sagitta setosa mitochondrial DNA (mtDNA) haplotypes produced a star-like phylogeny and a uni-modal mismatch distribution indicative of a bottleneck followed by population expansion. In contrast, S. elegans had a deeper mtDNA phylogeny and a multi-modal mismatch distribution as would be expected from a more stable population. Neutrality tests indicated that assumptions of the standard neutral model were violated for both species and results from the McDonald-Kreitman test suggested that selection played a role in the evolution of their mitochondrial DNA. Congruent with these results, both species had much smaller effective population sizes estimated from genetic data when compared to census population sizes estimated from abundance data, with a factor of ~10⁸–10⁹ difference. Assuming that selective effects are comparable for the two species, we conclude that the difference in genetic signature can only be explained by contrasting demographic histories. Our data are consistent with the hypothesis that in the NE Atlantic, the neritic S. setosa has been more severely affected by population bottlenecks resulting from Pleistocene range shifts than the more oceanic S. elegans.     

基因间隔序列(ITS)在细菌分类鉴定和种群分析中的应用

Use of 16S -23S intergenic transcribed spacer (ITS) variability, as a relatively new method, is becoming an important supplement to the molecular methods based on 16S rRNA for which has a fairly constant size and is not divergent enough to give good separation in close relationships. This paper summarizes the structures and characteristics of ITS regions that are extremely variable in copy number, length and sequence per genome. The ITS region can be amplified easily taking advantage of conserved nucleotide stretches at the 5′of the 16S and 3′of the 23S gene, and the amplicon can contain different amounts of the 16S rDNA by choosing primers at different conserved areas within this gene. These primers are listed and discussed for perfecting the methodology of ITS. Furthermore, some recent progresses on the taxonomy, identification and community analysis of bacteria by means of ITS in epidemiology, ecology and artificial environment are reviewed, as well, the virtues and limitations of that method are discussed. Fig 2, Tab 1, Ref 51     

Two markers and one history: phylogeography of the edible common sea urchin Paracentrotus lividus in the Lusitanian region

Benthic marine invertebrates with long-lived larvae are believed to have dispersal capabilities that contribute to maintaining genetic uniformity among populations over large geographical scales. However, both hydrological and biological factors may limit the actual dispersal of such larvae. We studied the population genetic structure of the edible common sea urchin Paracentrotus lividus (Lamarck, 1816), to explore its dispersal patterns in the Atlanto-Mediterranean region and, more specifically, to ascertain the role of the Strait of Gibraltar in shaping the genetic structure of this species. For this purpose, we analysed 158 individuals for the mitochondrial 16S rRNA gene and 151 of these for the nuclear single-copy intron adenine nucleotide transporter (ANT) from 16 localities from the Atlantic and Mediterranean basins, spanning over 4,000 km. Mitochondrial 16S rRNA shows higher genetic diversity in the Mediterranean than in the Atlantic and reveals a sharp break between the populations of both basins, probably as a consequence of the barrier imposed by the Almería–Orán hydrological front, situated east of the Strait of Gibraltar. Both markers suggest that a recent population expansion has taken place in both basins, most probably following the Messinian salinity crisis. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The utility of the 16S gene in investigating cryptic speciation within the Brachionus plicatilis species complex

Recent reports indicate an extensive amount of molecular evolution separating cryptic taxa as well as significant population structure at a microgeographical scale. Appropriate molecular markers are particularly suitable for distinguishing cryptic biological species. In this study, we examine the phylogenetic utility of 16S rRNA in elucidating the evolutionary relationships within the recently described euryhaline Brachionus plicatilis species complex. In addition, we assess the applicability of this marker in the genetic identification and monitoring of rotifer populations. We have sequenced a 378-bp fragment of the mitochondrial 16S rRNA gene in laboratory reference strains, hatchery clones as well as collections from a wild population of the subsaline Lake Koroneia (Northern Greece). Also, restriction fragment length polymorphism (RFLP) analysis was performed with eight restriction endonucleases. Rotifer samples are distinguished into six genetically divergent lineages. Average sequence divergence between lineages is 0.1038. The evolutionary relationships and divergence time-scales revealed with the 16S sequence data are in agreement with previous analyses using different mitochondrial and nuclear markers. The 16S region appears to have several advantages over other regions of the genome regarding use of species-specific primers, ease of amplification from single specimens and undiluted informational content over both recent and more ancient separations. It has also exhibited maximum discriminatory power (100% success) between lineages during RFLP analysis. The 16S assayed region has proven especially informative and consistent in detecting, supporting and establishing the lineage status within the B. plicatilis species complex both from a phylogenetic perspective and as an identification tool.     

Seasonal population structure,vertical distribution and migration of the chaetognath Sagitta elegans in the Celtic Sea

The biology of the chaetognath Sagitta elegans Verrill has been much researched, but detailed studies of population structure have generally been conducted in coastal water where dynamic tidal conditions may cause difficulty in interpretation of data. The resolution of sampling examining vertical distribution and diurnal migration has also been rather coarse. During a series of eight cruises to a seasonally thermally stratified sampling site in the Celtic Sea in 1978 and 1979, detailed vertical zooplankton profiles were taken to study the seasonal population structure, vertical distribution and migration of this species. The overwintering stock of S. elegans (22 to 52 individuals m^-2, 0 to 90 m) had a wide range of lengths (5 to 20 mm) and matured in 1978 from early March, spawning several times before dying out by late July. Young produced by the overwintering stock started to mature in July and population numbers reached their highest in August (2483 m^-2, 132.8 mg C m^-2) when sea temperature peaked (17.1°C). By October, the population of S. elegans declined (284 m^-2), which was thought to be due to a combination of lower sea-water temperature, competition for and availability of food, and predation. Because of the length range of the overwintering population (5 to 20 mm), it is assumed that reproduction continued at a low level over the winter, although eggs were not found in January and February, the coldest months of the year. In summer, the smallest S. elegans (2 to 6 mm) were found in the near-surface waters and did not migrate, but as their lengths increased they occupied deeper depth ranges and a portion of the population started to migrate diurnally. Individuals which did not migrate and stayed in the warmer surface waters, or those which migrated into it, matured faster than those remaining in the colder water below the thermocline. Migration to surface waters by mature individuals seemed to be stopped by high surface temperatures (17°C) and a sharp thermocline (3 C°). As sea temperature increased during the year from the winter minimum of 7.7°C, S. elegans matured at a progressively shorter length (14 mm in March 1978 to 10 mm in August). There are probably only three generations of S. elegans a year in the Celtic Sea.     

Genetic differentiation in three Sepia species (Mollusca: Cephalopoda) from Galician waters (north-west Iberian Peninsula)

The systematics of the genus Sepia is not yet clear. Morphological evidence has led to S. officinalis Linnaeus, 1758 being considered as belonging to the subgenus Sepia sensu stricto, and S. orbignyana Férussac, 1826 and S. elegans Blainville, 1827 as belonging to the subgenus Rhombosepion. Samples of 30 individuals of S. officinalis and S. orbignyana from both sides of an oceanographic boundary off the north-west Iberian Peninsula, and a sample of S. elegans from the northern side, were collected in 1993–1994. Allozyme electrophoresis for 32 presumptive loci revealed low levels of genetic variability for the three Sepia species (mean expected heterozygosity estimates were <0.052). No significant differences in allozyme frequencies were detected among populations of either S. officinalis or S. orbignyana. The genetic identities (I) of S. officinalis and S. orbignyana (I=0.12) and of S. elegans (I=0.13) were significantly different from that of S. orbignyana and S. elegans (I=0.49). The former are typical of values for confamilial genera, and a new generic status is proposed for the latter two species, which become Rhombosepion orbignyana (Férussac, 1826) and R. elegans (Blainville, 1827).     

Mitochondrial and nuclear rRNA based copepod phylogeny with emphasis on the Euchaetidae (Calanoida)

Phylogenetic relationships within the copepod family Euchaetidae and between representatives of three copepod orders (Calanoida, Harpacticoida, and Poecilostomatoida) were investigated using partial nucleotide sequences of the mitochondrial 16S rRNA and the nuclear 28S rRNA genes. DNA isolation, polymerase chain reaction, cloning, and DNA sequencing techniques were customized for these crustaceans. Our results support the monophyly of each copepod order, but in contrast to traditional morphology-based phylogenies of copepod orders, the Poecilostomatoida are basal to the Calanoida and Harpacticoida on our DNA-based phylogenetic tree. Phylogenetic trees generated by maximum parsimony, neighbor-joining, and maximum-likelihood analyses support the classification of the genera Euchaeta and Paraeuchaeta in the family Euchaetidae; results, however, suggest that Euchaetaacuta Giesbrecht is more closely related to species of the genus Paraeuchaeta than to those of Euchaeta, although limited taxon sampling may be partially responsible for this result. Phylogenetic mapping using the most parsimonious 16S tree suggests that the morphological synapomorphies distinguishing the genus Euchaeta evolved independently twice during the history of the Euchaetidae. Further, phylogenetic mapping suggests that the most recent common ancestor of the Euchaetidae and the Aetideidae was a deep-living, vertically migrating copepod, and that a bathypelagic, vertically migrating lifestyle characteristic of Paraeuchaeta is an ancestral trait of the family Euchaetidae which was lost apomorphically by Euchaeta. The application of a molecular clock suggests that the sibling species Euchaeta rimana Bradford and Euchaeta marina (Prestandrea) diverged due to the emergence of the Panamanian land bridge. Received: 9 October 1997 / Accepted: 5 August 1998     

Interspecific and intraspecific identification of Dendrobium based on the psbAtrnH intergenic region sequences and the 5S rRNA gene spacer sequences北大核心CSCD

This research aimed to investigate the interspecific and intraspecific identification of Dendrobium by using the multi-locus method so as to provide a molecular basis for Dendrobium identification through the combination of chloroplast psbA-trnH intergenic region sequences and ribosome 5S rRNA gene spacer sequences. PCR direct sequencing was applied to detect the chloroplast psbA-trnH intergenic region sequences as well as the ribosome 5S rRNA gene spacer sequences of 12 Dendrobium species, while the psbA-trnH intergenic region sequences of Dendrobium denneanum dq-2 variety and dq- 5line were cloned and sequenced for single nucleotide polymorphism (SNP) analyzing. The sequences were analyzed by the software Sequencher4.14, Bioedit7.0, MEGA5.2 and Dansp5.0; the interspecific and intraspecific Kimara-2-Parameter(K2P) distances were also calculated. The phylogenetic tree (using Neighbor joining method) was constructed with Bulbophyllum odoratissimum and Bletilla striata as outgroup. The results showed an average length of chloroplast psbA-trnH gene sequences in Dendrobium as 742.3 bp, with 72 variable sites, including 33 information sites; the average length of the ribosome 5S rRNA gene spacer sequences in Dendrobium was 336.4 bp, with 213 variable sites including 139 information sites. Using psbAtrnH intergenic region sequences in combination with ribosome 5S rRNA gene spacer sequences can not only identify D. denneanum, D. hancockil, D. thysiflorum, D. devonianum, D. moniliforme, D. chrysotoxum, D. officinale, D. heterocarpum and D. nobile, but also differentiate D. officinale from different geographical populations, and distinguish the dq-2 variety and dq 5line with SNP in the multi locus of D. denneanum.     

Recovery of novel bacterial diversity from mangrove sediment

Bacteria in the surface sediments of a subtropical mangrove habitat were investigated using a cultivation-independent molecular approach. Phylogenetic analysis of nearly full-length 16S rRNA genes revealed a diversity of sequences that were mostly novel. Members from the five subdivisions of the Proteobacteria were detected, and they collectively represented the majority (67%) of the clone library. Sequence types affiliated with the Gammaproteobacteria constituted the largest portion (29%) of the library, and many of them were related to free-living and symbiotic sulfur-oxidizing bacteria. The Epsilonproteobacteria were the second most abundant group (16%), including only one sequence type clustering with PCR-generated bacterial clones previously recovered from deep-sea sediments. A substantial portion (8%) of the clones grouped within the Deltaproteobacteria, a subdivision with anaerobic sulfate or metal reduction as the predominant metabolic trait of its members. In addition, minor portions were affiliated with the Cytophaga–Flexibacter–Bacteroides group (9%), Actinobacteria (6%), Chloroflexi (5%), Firmicutes (4%), Fusobacteria (1%), and the Chlamydiae/Verrucomicrobia group, Fibrobacteres/Acidobacteria group and Planctomycetes (each < 1%). These results significantly expand our knowledge of the bacterial diversity of the unique mangrove environment.     

Using DNA barcoding to track seafood mislabeling in Los Angeles restaurants

Seafood mislabeling is common in both domestic and international markets. Studies on seafood fraud often report high rates of mislabeling (e.g., >70%), but these studies have been limited to a single sampling year, which means it is difficult to assess the impact of stricter governmental truth‐in‐labeling regulations. We used DNA barcoding to assess seafood labeling in 26 sushi restaurants in Los Angeles over 4 years. Seafood from 3 high‐end grocery stores were also sampled (n = 16) in 2014. We ordered 9 common sushi fish from menus, preserved tissue samples in 95% ethanol, extracted the genomic DNA, amplified and sequenced a portion of the mtDNA COI gene, and identified the resulting sequence to known fish sequences from the National Center for Biotechnology Information nucleotide database. We compared DNA results with the U.S. Food and Drug Administration (FDA) list of acceptable market names and retail names. We considered sushi‐sample labels that were inconsistent with FDA names mislabeled. Sushi restaurants had a consistently high percentage of mislabeling (47%; 151 of 323) from 2012 to 2015, yet mislabeling was not homogenous across species. Halibut, red snapper, yellowfin tuna, and yellowtail had consistently high (<77%) occurrences of mislabeling on menus, whereas mislabeling of salmon and mackerel were typically low (>15%). All sampled sushi restaurants had at least one case of mislabeling. Mislabeling of sushi‐grade fish from high‐end grocery stores was also identified in red snapper, yellowfin tuna, and yellowtail, but at a slightly lower frequency (42%) than sushi restaurants. Despite increased regulatory measures and media attention, we found seafood mislabeling continues to be prevalent.     

Colonization of the northwest Atlantic by the blue mussel, <Emphasis Type="Italic">Mytilus trossulus</Emphasis> postdates the last glacial maximum

Blue mussels in the genus Mytilus first arrived in the Atlantic Ocean from the Pacific during the Pliocene, following the opening of the Bering Strait. Repeated periods of glaciation throughout the Pleistocene led to re-isolation of the two ocean basins and the allopatric divergence of Mytilus edulis in the Atlantic and M. trossulus in the Pacific. Mytilus trossulus has subsequently colonized the northwest Atlantic (NW Atlantic) so that the two species are presently sympatric and hybridize throughout much of the Canadian Maritimes and the Gulf of Maine. To estimate when M. trossulus arrived in the NW Atlantic, we have examined sequence variation within a portion of the female mtDNA lineage large untranslated region (F-LUR) for 156 mussels sampled from three Pacific and eleven Atlantic populations of M. trossulus. Although we found no evidence of reciprocal monophyly for Pacific and NW Atlantic M. trossulus, limited gene flow between ocean basins has led to the divergence of unique sequence clades within each ocean basin. In contrast, relative genetic homogeneity indicates high levels of gene flow within each basin. Coalescence-based analysis of the F-LUR sequences suggests that M. trossulus recolonized the NW Atlantic from the northeast Pacific subsequent to a demographic expansion in the Pacific that occurred ~96,000 years before present (ybp). Estimates of timing of divergence for Pacific and NW Atlantic populations and the time since expansion among NW Atlantic sequence clades indicate that M. trossulus arrived in the NW Atlantic more recently, between 20,000 and 46,000 ybp. Given that these estimates overlap with the dates of peak ice in the NW Atlantic during the last glacial maximum (LGM, ~18,000–21,000 ybp), we suggest that colonization of the NW Atlantic by M. trossulus occurred during, but more likely just subsequent to, the LGM and was followed by rapid temporal and spatial expansion in the region.     

Chaetognaths and ctenophores in the holoplankton of the Bristol Channel

The geographical distributions, seasonal variations in numerical abundance and biomass (mg C m^-3) of the predators of the holoplankton of the Bristol Channel, between November 1973 and February 1975, are described. The predator numbers and biomass were dominated by the chaetognath Sagitta elegans Verrill. This species represented 96% of the holoplankton carnivore biomass in the outer, seaward region of the Channel and 60% in the inner region; the remainder being ctenophores. The maximum numerical abundance of S. elegans occurred in September at 129 individuals m^-3 (18 mg C m^-3). Juveniles (<5 mm) reached maximum numbers of 55 individuals m^-3 during June, August and September, demonstrating the reproductive activity of the population. The peak numbers were probably the result of the development of two major generations over the 90 d period from mid-June to mid-September. The tentaculate ctenophores were represented by Pleurobrachia pileus (O. F. Müller). The highest abundance was 81 individuals m^-3 (3.0 mg C m^-3) at a single site in July in the South Central Channel. However, June was the only month when the ctenophores dominated the carnivore biomass in all regions of the Channel; thereafter, S. elegans was more abundant. Reproduction of the ctenophore occurred from April to September, with juveniles reaching maximum abundance in June at 12 individuals m^-3. The estimated food demand of the population in May for the outer region of the Channel was approximately 31% of the daily production of copepods. When the population reached its peak abundance in June, the estimated food requirement outstripped the daily production of copepods and a decline in both the prey and predator standing stocks was observed. Similar estimations were derived for the inner region of the Channel. S. elegans increased from a standing stock of 0.038 mg C m^-3 in March to 6.35 mg C m^-3 in September. Estimates of the copepod production compared with the derived demand of the chaetognath population showed that the decline in the copepods in the late summer was the result of feeding by this predator. The holoplankton carnivore population was approximately 66% of the copepod standing stock for the 10 mo period November 1973 to September 1974 in the outer region of the Channel and 45% of that in the inner region. The carnivores formed the greater part of the total holoplankton biomass from September through the winter months to February, suggesting a predator-dominated community.     

Evidences showing 2,4-D ethyl ester and pencycuron-induced DNA damage in cyanobacteria and detection by PCR

The impact of 2,4-D ethyl ester and pencycuron in inducing DNA damage in three species of cyanobacteria-Anabaena fertilissima, Aulosira fertilissima, and Westiellopsis prolifica as evidenced by PCR-based assays: RAPD and 16S rRNA amplification was examined. Exposure of genomic DNA (in vitro) to pencycuron for 4 days did not produce severe damage in DNA fragments of all three cyanobacterial species whereas exposure to 2,4-D ethyl ester markedly inhibited the template activity of genomic DNA compared to untreated cultures of A. fertilissima. In A. fertilissima a single band of approximately 1000?bp was observed even after 16 days of exposure to 60?ppm pencycuron which suggests that certain segments of DNA are resistant to pencycuron DNA damaging effects. However, a significant effect was observed in the case of W. prolifica for 2,4-D ethyl ester and pencycuron where complete disappearance of fragments was not recorded even after 16 days of incubation and interestingly some new DNA bands were induced. Similar to the effects with RAPD profile, amplification of rRNA was significantly inhibited following exposure of genomic DNA to 2,4-D ethyl ester and pencycuron. Our findings clearly demonstrate that pesticide concentrations affected cyanobacterial DNA and lethality of these microbes might be due to irreversible DNA damage. Thus, it is postulated that PCR assays may be conveniently used for screening DNA damage produced by 2,4-D ethyl ester and pencycuron in all three cyanobacteria examined in this study.     

Genetic homogeneity and circum-Antarctic distribution of two benthic shrimp species of the Southern Ocean, Chorismus antarcticus and Nematocarcinus lanceopes

During the last years, molecular studies revealed significant population differentiation and cryptic species within various benthic and pelagic marine Antarctic taxa. This is unexpected due to the lack of obvious barriers to gene flow and strong current systems. Using mitochondrial (COI, 16S rDNA) and nuclear (28S rDNA: D2) gene fragments, we tested whether two circum-Antarctic benthic shrimps with planktotrophic larvae, Chorismus antarcticus and Nematocarcinus lanceopes, show patterns of regional differentiation. For both species, the 16S and the 28S fragment were invariant. However, for COI we found 24 different haplotypes for Chorismus antarcticus and 54 for Nematocarcinus lanceopes. No significant differentiation was observed among populations or regions. Furthermore, we found signatures of a population expansion in the late Pleistocene hinting at an impact of large-scale glaciations in particular on the shallow-water shrimp Chorismus antarcticus, supporting a (re)colonization and demographic expansion of this shrimp species in response to climate oscillation.     

Respiration and nitrogen excretion of zooplankton. IV. The influence of starvation on the metabolism and the biochemical composition of some species

Changes in the respiration, ammonia excretion and biochemical composition were studied for three species of starving zooplankton (Calanus finmarchicus, Sagitta elegans, and Acartia clausi). Over the period of starvation, the respiration rate of all three species followed the same pattern of an initial decrease followed by a more or less constant level. A similar pattern was observed for the ammonia excretion rate of S. elegans and A. clausi, whereas C. finmarchicus excretion appeared to oscillate between high and low levels of protein catabolism. Study of the biochemical changes showed that C. finmarchicus consumed primarily lipids, and at times proteins, to meet its energy requirement whereas S. elegans and A. clausi primarily used protein. Variations in the elemental composition as well as the O:N ratio confirmed that C. finmarchicus alternated between periods of protein-dominant catabolism and lipid-dominant catabolism during starvation. No similar change in catabolism was observed in the two other species. The results are discussed in terms of physiological mechanisms of resistance to starvation and were used to calculate the energy budget of S. elegans and C. finmarchicus during the period of total starvation. The significance of such budgets is discussed and some of the sources of error examined.Bedford Institute of Oceanography Contribution.     

Phylogenetic relationship among several genera of Dictyotaceae (Dictyotales, Phaeophyceae) based on 18S rRNA and partial rbcL gene sequences

The partial sequences of the 18S rRNA gene and the rbcL gene, RuBisCo spacer region of representatives of the Dictyotaceae were determined and compared to resolve their phylogenetic relationships. A total of 1,861 base pairs of 18S rDNA sequences were aligned and examined. There was a high similarity of nucleotide sequences within the tribe Dictyoteae (99.4-99.6%) and the tribe Zonarieae (92.8-99.8%). The largest intergeneric divergence within the Dictyotaceae was 7.31%, between Dilophus and Zonaria. The aligned 422 bases of partial rbcL gene sequences gave a similar phylogenetic relationship among taxa to those of the 18S rDNA sequences, although our alignment covered less than 30% of the whole gene. All genera of Dictyotales consisted of several clades forming a polychotomy in MP trees based on partial rbcL gene sequences and on 18S rDNA sequences. The genera within the tribe Dictyoteae formed a clade, a Dictyota-Phacydictyon-Dilophus clade, while genera of the tribe Zonarieae formed four clades: Padina; Distromium-Lobophora-Zonaria; Spatoglossum-Lobospira; and Dictyopteris-Spatoglossum. All genera of the Dictyotaceae included in these sequence analyses are classified into five groups, which have little phylogenetic resolution among them. The genera classified in the tribe Zonarieae according to Womersley's criteria do not appear to be monophyletic, based on our analyses. Although not all genera of Dictyotaceae were analysed, our data suggest that the status of the meristem cells should not be a criterion for separating tribes within the family Dictyotaceae and that other hierarchical systems should be adopted to properly reflect phylogenetic relationships.     

Characterisation and identification of carbofuran-utilising bacteria isolated from agricultural soil

A total of 96 bacterial cultures were isolated from soil. Seventeen bacterial isolates were selected following their cultivation on solid media containing 100 mg · L^?1 carbofuran as the sole source of carbon and nitrogen. Of the 17 isolates, 10F, 11M, 17N, 23B and 26M were specifically chosen because of their relatively higher growth efficiency and genetic diversity based on Box-polymerase chain reaction analysis. These bacterial cultures had 16S rRNA gene sequences that were most similar to Acinetobacter baumannii (10F), Agrobacterium tumefaciens (11M), Ochrobactrum anthropi (17N), Escherichia coli (23B) and Agrobacterium tumefaciens (26M) with 97, 95, 93, 95 and 94% similarity in their 16S rDNA gene sequence, respectively. Degradation rates of carbofuran in soil inoculated with these isolates were 1.9, 1.5, 1.6, 1.7 and 1.6 times, respectively, faster in comparison with uninoculated soil after 10 days of incubation. The maximum degradation rates of carbofuran (45 and 91%) were detected in soil inoculated with A. baumannii (10F) after 10 and 20 days’ incubation, respectively. These data indicate that these isolates may have the potential for use in bioremediation of pesticide contaminated soil.     

Cryptic speciation in the recently discovered American cycliophoran <Emphasis Type="Italic">Symbion americanus</Emphasis>; genetic structure and population expansion

Symbion americanus was recently described as the second species in the phylum Cycliophora, living commensally on the American commercial lobster Homarus americanus. A previous genetic analysis of American and European populations of cycliophorans suggested that haplotype divergence in S. americanus was much greater than in its European counterpart S. pandora. This study examined the population structure and demographics of 169 individuals thought to belong to S. americanus collected from lobsters over 13 North American localities (Nova Scotia, Canada to Maryland, USA) between October 2003 and January 2006. Cytochrome c oxidase subunit I sequence data clearly suggested the presence of three cryptic lineages in a species complex, often co-occurring in the same lobster specimens. One of these lineages, named the “G” lineage, was represented by very few individuals and therefore was excluded from subsequent statistical analyses. The other two sympatric lineages, named the “T” and “C” lineages, showed different population structure and demography. Although limited geographic structure was found in the T lineage, the C lineage showed higher nucleotide and haplotype diversity values, as well as more variation between localities. The data also indicated that the T lineage underwent a recent population expansion, suggesting that the C and T lineages may have speciated in allopatry but a subsequent population expansion may have been responsible for their current sympatric distribution. Studies on the anatomy and ecology of the sympatric lineages of this species complex should provide further information on the identity of the holotype of S. americanus, which currently cannot be ascribed to any of the three cryptic lineages.