Diversity and dynamics of a widespread bloom of the toxic dinoflagellate Alexandrium fundyense

Historically, cosmopolitan phytoplankton species were presumed to represent largely unstructured populations. However, the recent development of molecular tools to examine genetic diversity have revealed differences in phytoplankton taxa across geographic scales and provided insight into the physiology and ecology of blooms. Here we describe the genetic analysis of an extensive bloom of the toxic dinoflagellate Alexandrium fundyense that occurred in the Gulf of Maine in 2005. This bloom was notable for its intensity and duration, covering hundreds of kilometers and persisting for almost two months. Genotypic analyses based on microsatellite marker data indicate that the open waters of the northeastern U.S. harbor a single regional population of A. fundyense comprising two genetically distinct sub-populations. These subpopulations were characteristic of early- and late-bloom samples and were derived from the northern and southern areas of the bloom, respectively. The temporal changes observed during this study provide clear evidence of succession during a continuous bloom and show that selection can act on the timescale of weeks to significantly alter the representation of genotypes within a population. The effects of selection on population composition and turnover would be magnified if sexual reproduction were likewise influenced by environmental conditions. We hypothesize that the combined effects of differential growth and reproduction rates serves to reduce gene flow between the sub-populations, reinforcing population structure while maintaining the diversity of the overall regional population.     

Stimulation of Alexandrium fundyense growth by bacterial assemblages from the Bay of Fundy

AIMS: To evaluate the influence of marine bacterial assemblages from the Bay of Fundy on Alexandrium fundyense str. CB301 growth. METHODS AND RESULTS: Bacterial assemblages were collected from the Bay of Fundy during an Alexandrium spp. bloom, serially diluted to extinction and inoculated into axenic CB301 cultures. Bacterial assemblages dramatically enhanced CB301 growth. Retrieval and analysis of 16S rDNA fragments revealed an Alteromonas sp. strain to be the only detectable bacterium in all assemblages that promoted A. fundyense and the sole bacterium found in the most dilute inoculum that promoted A. fundyense. While this bacterium has not yet been isolated, other isolates obtained from the assemblages did not stimulate A. fundyense, indicating that the observed stimulation was not a general effect of marine bacteria. CONCLUSIONS: Bay of Fundy marine bacterial assemblages dominated by a member of the family Alteromonadaceae were found to dramatically stimulate growth of A. fundyense. SIGNIFICANCE AND IMPACT OF THE STUDY: These results show that native bacteria have the potential to dramatically promote the growth of A. fundyense and may play an important role in influencing A. fundyense dynamics in the Bay of Fundy.     

Microbial diversity and community structure in Fynbos soil

The Fynbos biome in South Africa is renowned for its high plant diversity and the conservation of this area is particularly important for the region. This is especially true in the case of endangered vegetation types on the lowlands such as Sand Fynbos, of which only small fragments remain. The question is thus whether the diversity of the above‐ground flora is mirrored in the below‐ground microbial communities. In order to determine the relationship of the above‐ and below‐ground communities, the soil community composition of both fungal and bacterial groups in Sand Fynbos was characterized over space and time. A molecular approach was used based on the isolation of total soil genomic DNA and automated ribosomal intergenic spacer analysis of bacterial and fungal communities. Soil from four different sites was compared to resolve the microbial diversity of eubacterial and fungal groups on a local (alpha diversity) scale as well as a landscape scale (beta diversity). The community structures from different sites were compared and found to exhibit strong spatial patterns which remained stable over time. The plant community data were compared with the fungal and the bacterial communities. We concluded that the microbial communities in the Sand Fynbos are highly diverse and closely linked to the above‐ground floral communities.     

Genetic diversity in natural populations of Piper cernuum

Piper cernuum is a native plant of the Brazilian Atlantic rain forest. This work studies the distribution of allozyme diversity in P. cernuum natural populations in order to establish a strategy for sustainable management and conservation. Leaf samples were collected in two Brazilian states. High divergences among populations (F(SR) = 0.380) and low divergences among regions (F(RT) = -0.069) and among gaps of the same population (F(GT) = 0.062) were found. No association between the geographical variation and the genetic distance was detected. An excess of heterozygotes was detected in the populations (F(IS) = -0.170), suggesting selection in favor of heterozygotes. The results, and the fact that the species depends on constant gap formation for maintenance of its dynamism, suggest that the founder effect is largely responsible for the structuring of populations. For sustainable management, the maintenance of plants/reproductive branches in the gaps is of major importance. The genotypes produced in these gaps are responsible for the establishment of new gaps and are the foundation for new populations, maintaining the dynamics of allele movement.     

Microbial community composition and functional diversity in the rhizosphere of maize

This study investigates the small-scale stratification of bacterial community composition and functional diversity in the rhizosphere of maize. Maize seedlings were grown in a microcosm with a horizontal mesh (53 M) creating a planar root mat and rhizosphere soil. An unplanted microcosm served as control. Thin slices of soil were cut at different distances from the mesh surface (0.2–5.0 mm) and analysed for bacterial community composition by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) of 16S rDNA and tested for activities of different enzymes involved in C, N, P and S cycling. Bacterial community composition and microbial functional diversity were affected by the presence of the maize roots. The bacterial composition showed a clear gradient up to 2.2 mm from the root surface, while no such gradient was observed in the unplanted pot. Invertase and phosphatase activities were higher in the close vicinity of maize roots (0.2–0.8 mm), whereas xylanase activity was unaffected. This study shows that the changes in bacterial community composition and functional diversity induced by roots may extend several millimetres into the soil.     

Polyamine profile in the paralytic shellfish poison-producing alga Alexandrium minutum

The polyamine profiles of the toxic dinoflagellate Alexandriumminutum during different growth stages were measured by high-performanceliquid chromatography. Both free and conjugated polyamines werefound, including putrescine, cadaverine, spermine, spermidineand norspermidine. During the growth cycle of A. minutum T1,the levels of norspermidine and putrescine in the free polyamineswere the highest after 3 days culture. Putrescine and cadaverinewere the major components in the conjugated polyamines. Theamount of conjugated amines was higher than that of free aminesduring the exponential phase of A. minutum T1.     

Genetic diversity of natural populations of Taxus mairei

Taxus mairei (Lemée & Lév.) S.Y. Hu ex T. S. Liu is a vulnerable tree species, and it is also a precious timber species in China. We used 13 microsatellites to assess the genetic diversity and differentiation of 665 T. mairei samples from 18 natural populations. A total of 291 alleles were detected. The average number of alleles (N_a?=?22.39), expected heterozygosity (H_e?=?0.74), polymorphic information content (PIC?=?0.86) and Shannon diversity index (I?=?1.66) of the loci indicated a high level of genetic diversity in natural T. mairei populations. Moreover, gene flow was more active among populations (N_m?=?1.62) than within populations. Among the 18 populations, the Xinfeng population in Jiangxi Province has the highest genetic diversity. Although each of the studied populations should be protected from further deforestation and agricultural expansion, the Xinfeng population deserves the highest conservation priority. The results based on analysis of molecular variance showed that genetic variation occurred mainly within populations (84.90%; P?<?0.001), which indicated that the degree of genetic differentiation of the natural populations of T. mairei was low. Based on UPGMA, the 18 populations were categorized into two groups. A Mantel test showed that there was no significant correlation between standard genetic distance and geographical distance or altitude differences among the populations. The genetic clustering results also indicated that there are varying degrees of gene penetration among natural populations of T. mairei. The information presented here forms the basis for the development of genetic guidelines for appropriate conservation programs.

     

Genetic diversity of the natural populations of Arabidopsis thaliana in China

Although extensive studies have been conducted on the genetic structure of Arabidopsis thaliana (A. thaliana) populations worldwide, the populations from China have never been studied. In this study, we collected 560 individuals from 19 natural populations of A. thaliana distributed in East China along the lower reaches of the Yangtze River, and two populations from northwest China (Xinjiang Province). We adopted two kinds of molecular marker, inter-simple sequence repeats (ISSRs) and random amplified polymorphic DNA (RAPDs) to investigate the genetic diversity within and among populations, and the correlation between the genetic and geographic distances. Thirteen ISSR primers produced 165 polymorphic bands (PPB) (96%) and 11 RAPD primers produced 162 polymorphic bands (98%) in about 560 individuals. The two marker systems generated similar patterns of genetic diversity in these natural populations. The AMOVA analysis indicated about 42-45% of the total genetic variation existed within populations, and found possible geographic structure. The Mantel test revealed a significant correlation between the geographic distance and the genetic distance of these populations in general. A close genetic relationship was found among four populations in the Jiangxi Province, and these always appeared clustered together as a monophyletic group in unweighted pair-group method with arithmetic averages dendrograms based on both ISSR and RAPD data sets. Based on the observation of recolonization and extinction of naturally distributed populations of A. thaliana, and the pattern of their genetic differentiation, the distribution of this species in China might be a result of natural dispersal under the strong influence of human activity.     

Microbial diversity in natural asphalts of the Rancho La Brea Tar Pits

Bacteria commonly inhabit subsurface oil reservoirs, but almost nothing is known yet about microorganisms that live in naturally occurring terrestrial oil seeps and natural asphalts that are comprised of highly recalcitrant petroleum hydrocarbons. Here we report the first survey of microbial diversity in ca. 28,000-year-old samples of natural asphalts from the Rancho La Brea Tar Pits in Los Angeles, CA. Microbiological studies included analyses of 16S rRNA gene sequences and DNA encoding aromatic ring-hydroxylating dioxygenases from two tar pits differing in chemical composition. Our results revealed a wide range of phylogenetic groups within the Archaea and Bacteria domains, in which individual taxonomic clusters were comprised of sets of closely related species within novel genera and families. Fluorescent staining of asphalt-soil particles using phylogenetic probes for Archaea, Bacteria, and Pseudomonas showed coexistence of mixed microbial communities at high cell densities. Genes encoding dioxygenases included three novel clusters of enzymes. The discovery of life in the tar pits provides an avenue for further studies of the evolution of enzymes and catabolic pathways for bacteria that have been exposed to complex hydrocarbons for millennia. These bacteria also should have application for industrial microbiology and bioremediation.     

Microbial diversity in natural environments: focusing on fundamental questions

Interactions with Gijs Kuenen and other Dutch scientists have led my lab to fundamental insights into the composition, structure and function of a hot spring cyanobacterial mat community that should influence our thinking about all microbial communities. By focusing on the distribution of molecular sequence variants of predominant mat phototrophs, we have discovered that small-scale sequence variation can be ecologically meaningful. By applying novel cultivation approaches, we have been able to obtain genetically relevant community members and thus to test the hypothesis that closely related sequence variants arose via adaptive evolutionary radiation. By applying the analytical tools of organic geochemistry we have gained insight into the metabolisms of major phototrophic members of the mat community as well as interactions between phototrophic guilds. These observations challenge traditional paradigms about prokaryotic species and cause us to consider evolutionary ecology theory as we develop genome-based methods for high-resolution analysis of the species-like fundamental units comprising microbial communities, and for investigating how such units coordinate the physiological activities within guilds of the community.     

Genetic diversity and molecular detection of three toxic dinoflagellate genera (Alexandrium,Dinophysis, and Karenia) from French coasts

The objectives of this study were 1) to study the genetic diversity of the Alexandrium, Dinophysis and Karenia genera along the French coasts in order to design probes targeting specific DNA regions, and 2) to apply PCR-based detection to detect these three toxic dinoflagellate genera in natural samples. Genetic diversity of these toxic taxa was first studied from either cultures or cells isolated from Lugol-fixed field samples. By this way, partial sequences of the large ribosomal subunit (LSU rDNA) including the variable domains D1 and D2 of A. minutum, Alexandrium species inside the tamarensis complex, the D. acuminata complex and K. mikimotoi were obtained. Next, specific primers were designed for a selection of toxic algae and used during semi-nested PCR detection. This method was tested over a 3-month period on water samples from the Bay of Concarneau (Brittany, France) and on sediment from the Antifer harbor (The English Channel, France). Specificity and sensitivity of this molecular detection were evaluated using the occurrence of target taxa reported by the IFREMER (Institut Fran?ais de Recherche pour l'Exploitation de la Mer) monitoring network based on conventional microscopic examination. This work presents the first results obtained on the biogeographical distribution of genotypes of these three toxic genera along the French coasts.     

Factors affecting levels of genetic diversity in natural populations.

Genetic variability is the clay of evolution, providing the base material on which adaptation and speciation depend. It is often assumed that most interspecific differences in variability are due primarily to population size effects, with bottlenecked populations carrying less variability than those of stable size. However, we show that population bottlenecks are unlikely to be the only factor, even in classic case studies such as the northern elephant seal and the cheetah, where genetic polymorphism is virtually absent. Instead, we suggest that the low levels of variability observed in endangered populations are more likely to result from a combination of publication biases, which tend to inflate the level of variability which is considered ''normal'', and inbreeding effects, which may hasten loss of variability due to drift. To account for species with large population sizes but low variability we advance three hypotheses. First, it is known that certain metapopulation structures can result in effective population sizes far below the census size. Second, there is increasing evidence that heterozygous sites mutate more frequently than equivalent homozygous sites, plausibly because mismatch repair between homologous chromosomes during meiosis provides extra opportunities to mutate. Such a mechanism would undermine the simple relationship between heterozygosity and effective population size. Third, the fact that related species that differ greatly in variability implies that large amounts of variability can be gained or lost rapidly. We argue that such cases are best explained by rapid loss through a genome-wide selective sweep, and suggest a mechanism by which this could come about, based on forced changes to a control gene inducing coevolution in the genes it controls. Our model, based on meiotic drive in mammals, but easily extended to other systems, would tend to facilitate population isolation by generating molecular incompatabilities. Circumstances can even be envisioned in which the process could provide intrinsic impetus to speciation.     

Modelling the population dynamics of the toxic dinoflagellate Alexandrium Tamarense in Hiroshima Bay, Japan

In the present study, a numerical model that simulates speciescompetition between the toxic dinoflagellate Alexandrium tamarenseand the non-toxic diatom Skeletonema costatum was constructedusing data from a number of experiments and field observations.In the model, not only vertical migration of swimming cellsbut also the encystment and excystment processes of A. tamarensewere taken into consideration. Sinking of S. costatum cellswas also considered. Both zooplankton and oysters, which areintensively cultured in this bay, feed on the phytoplanktonbut the contribution of grazing to the decrease in the celldensities of both species was small. The model predicts thatwhile sinking is one of the major processes that reduce thecell density of S. costatum, encystment of A. tamarense is acrucial process that determines the cessation of blooms of thisdinoflagellate. Advection and diffusion are also important physicalprocesses that affect, in positive and negative ways, the fluctuationof cell densities.