Novel ecological niche of Cetobacterium somerae, an anaerobic bacterium in the intestinal tracts of freshwater fish

AIMS: This study was conducted to clarify the taxonomic status of Bacteroides type A strains with high vitamin B(12)-producing ability that is widely distributed in the intestinal tracts of freshwater fish. METHODS AND RESULTS: Seventeen strains of Bacteroides type A isolated from five fish species were all rod-shaped and gram-negative. The strains were positive for esculin hydrolysis, nitrate reduction, resistance to bile, acid phosphatase, and negative for the production of catalase and urease and the susceptibility to vancomycin. The G+C content of DNA from the 17 strains was 29 x 1-31 x 9 mol%, and 16S rDNA sequence analysis revealed a close phylogenetic relationship between Bacteroides type A strains and Cetobacterium somerae sharing 99 x 7-100% sequence similarity. In addition, strains were capable of producing vitamin B(12) at a rate of 1 x 82-13 x 98 ng ml(-1) in 48 h. CONCLUSION: Phenotypic and phylogenetic characteristics indicated that all isolates previously classified as Bacteroides type A strains belong to C. someare. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provided the important finding of novel niche of vancomycin-resistant bacteria such as C. somerae in the intestinal tract of freshwater fish.     

Composition and dispersal of riverine and lake phytoplankton communities in connected systems with different water retention times

1. Lake phytoplankton community structure may be influenced by both internal factors (predation, competition, resource constraints) and external ones, such as dispersal of materials and cells between connected habitats. However, little is known about the importance of cell dispersal for phytoplankton community structure in lakes. 2. We investigated the abundance and dispersal of phytoplankton cells between connected rivers and lakes, and analysed whether similarities in phytoplankton community composition between rivers and lakes were primarily related to cell import rates or to characteristics of the local habitat. We focused on lakes along a gradient of theoretical water retention times (TWRT). Two data sets from Swedish lakes were used; a seasonal study of two connected boreal forest lakes, differing in TWRT, and a multi‐lake study of 13 lakes with a continuous range of TWRTs. 3. Phytoplankton cells were transported and dispersed in all investigated rivers. In the seasonal study, cell import rates and similarities in phytoplankton community composition between the lake and its inlet(s) were much higher in the lake with a shorter TWRT. Phytoplankton community structure in different habitats was associated with total organic carbon (TOC). This indicates that local habitat characteristics may be important in determining lake phytoplankton community composition, even in the presence of substantial cell import. 4. The multi‐lake study also showed a negative relationship between TWRT and similarities in phytoplankton community composition between inlets and lakes. Moreover, similarity in community structure was related to both cell import rates from inlet to lake and differences in habitat characteristics between inlet and lake. However, the variable most strongly correlated with community structure was TOC, indicating that species sorting rather than a mass effect was the most important mechanism underlying the correlation between community structure and retention time. 5. Overall, our data suggest that local habitat characteristics may play a key role in determining community similarity in this set of lakes covering a large range of habitat connectedness. Due to the strong co‐variations between cell dispersal and TOC, it was hard to unequivocally disentangle the different mechanisms; hence, there is a need for further studies of the role of dispersal for phytoplankton community structures.     

Size-fractionated phytoplankton biomass and its implications for the dynamics of an oligotrophic tropical lake

1. Size-fractionated phytoplankton biomass was examined in relation to the hydrodynamics of tropical Lake Alchichica from 1999 to 2002.
2. Alchichica is a warm monomictic lake, in which mixing takes place from late December to early March. The lake is oligotrophic (mean total chlorophyll- a concentration 4.2 ± 4.2  μ g L⁻¹) and its phytoplankton biomass is dominated (72.3 ± 16.4%) by large individuals (>2  μ m). The degree of dominance of the large size class (nano- and microplankton) over the small size class (picoplankton) throughout the year is mainly determined by the availability of silicate and the Si/N ratio in the hypolimnion prior to the mixing period.
3. This is the first record of an oligotrophic tropical lake dominated by large size fractions of phytoplankton. Because of this dominance, the fate of most primary productivity is rapid sedimentation to the bottom followed by decomposition that promotes an anoxic hypolimnion.
4. Our findings in tropical Lake Alchichica challenge the idea that oligotrophic waters are dominated by small phytoplankton, as has been well established for the oligotrophic ocean and temperate lakes.     

Indirect effects of the algivorous fish Plecoglossus altivelis altivelis on the growth of two insectivorous benthic fish

1. Animals exploiting different resources may nevertheless interact if one species indirectly alters the abundance and distribution of the food of the other. To analyse this indirect effect, we conducted experiments in artificial pools and in the field to investigate the influence of the algivorous fish Plecoglossus altivelis altivelis (known as the ayu) on two species of insectivorous benthic fish, Pseudogobio esocinus esocinus and the goby Gymnogobius petschiliensis .
2. In the pool experiments, algal biomass was not correlated with the number of ayu, but the percentage of blue-green bacteria rose as the number increased. The number of aquatic macroinvertebrates on the upper surface of ceramic tiles placed in the pool bed decreased as the number of ayu increased.
3. Although ayu and the benthic species did not interact directly, the reduction in invertebrate abundance on the upper surface of tiles in the pool reduced the growth rate of the benthic insectivores.
4. In field experiments, the introduction of ayu into habitats with P. esocinus esocinus or G. petschiliensis reduced the growth rate of these benthic fish. In the field experiment that was carried out over 5 years in the G. petschiliensis habitat, the population density of the goby decreased when ayu were stocked.
5. The ayu is a strong interactor or bioengineer in streams, affecting not only benthic algae but also aquatic invertebrates and fishes. We conclude that to predict the outcome of interspecific interactions amongst fishes in streams with high algal production, possible indirect effects must be considered alongside better known direct effects.     

Construction of a taste-blind medaka fish and quantitative assay of its preference-aversion behavior

In vertebrates, the taste system provides information used in the regulation of food ingestion. In mammals, each cell group within the taste buds expresses either the T1R or the T2R taste receptor for preference-aversion discrimination. However, no such information is available regarding fish. We developed a novel system for quantitatively assaying taste preference-aversion in medaka fish. In this study, we prepared fluorescently labeled foods with fine cavities designed to retain tastants until they were bitten by the fish. The subjects were fed food containing a mixture of amino acids and inosine monophosphate (AN food), denatonium benzoate (DN food) or no tastant (NT food), and the amounts of ingested food were measured by fluorescence microscopy. Statistical analysis of the fluorescence intensities yielded quantitative measurements of AN food preference and DN food aversion. We then generated a transgenic fish expressing dominant-negative Galpha(i2) both in T1R-expressing and in T2R-expressing cells. The feeding assay revealed that the transgenic fish was unable to show a preference for AN food and an aversion to DN food. The assay system was useful for evaluating taste-blind behaviors, and the results indicate that the two taste signaling pathways conveying preferable and aversive taste information are conserved in fish as well as in mammals.     

Isolation and characterization of microsatellite markers for the ornamental discus fish Symphysodon discus and cross-species amplification in other Heroini cichlid species

The discus fishes (Symphysodon spp.) are economically important ornamental species. Thirteen microsatellite markers were developed from a CT(12) - and CA(12) -enriched whole genomic DNA library of Symphysodon discus. Allelic variability was tested on 44 individuals of two species (S. discus and S. aequifasciatus). Allelic richness ranged from two to 11 alleles per locus and observed heterozygosities from 0.083 to 0.998. All loci were at Hardy-Weinberg equilibrium, and no pair of loci showed linkage disequilibrium within a species. Cross-species amplification was also successfully performed in the Neotropical cichlids Uaru amphiacanthoides, Hoplarchus psittacus, Hypselecara coryphaenoides, Pterophyllum sp., Mesonauta sp. and Heros sp.     

PERMANENT GENETIC RESOURCES: Isolation and characterization of polymorphic trinucleotide and dinucleotide microsatellite loci for the ice goby, Leucopsarison petersii

Eleven microsatellite markers were isolated and characterized for the ice goby, Leucopsarion petersii, from genomic libraries enriched for (ATG)(9) and (CA)(16) . Twenty individuals from a single population were used to screen polymorphism in these loci. The number of alleles per locus and observed heterozygosity ranged from four to 22 and from 0.35 to 1.00, respectively. All loci did not significantly deviated from Hardy-Weinberg equilibrium, and there was no evidence of linkage disequilibrium between all loci-pairs. These loci showed Mendelian inheritance in a full-sib family. The high level of polymorphism of these loci will be useful for studies of population genetics.     

Sperm contamination in archived and contemporary herring samples

Studies using archived scales and otoliths to examine ancient fish populations have become increasingly common, despite many methodological challenges in ancient DNA research. Here, we describe a case of DNA contamination in both modern and historical samples of Pacific herring (Clupea pallasii), where the source of the contamination is likely from milt spillage during collection. We describe a series of experiments to remove contamination using pre-extraction wash treatments. Though contamination was easily removed from contemporary fin clippings, no method was successful at removing contamination from historical scales. We discuss the implications of our findings to the genetic analysis of archived samples.     

Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach

High throughput sequencing methods are widely used in analyses of microbial diversity, but are generally applied to small numbers of samples, which precludes characterization of patterns of microbial diversity across space and time. We have designed a primer-tagging approach that allows pooling and subsequent sorting of numerous samples, which is directed to amplification of a region spanning the nuclear ribosomal internal transcribed spacers and partial large subunit from fungi in environmental samples. To test the method for phylogenetic biases, we constructed a controlled mixture of four taxa representing the Chytridiomycota, Zygomycota, Ascomycota and Basidiomycota. Following cloning and colony restriction fragment length polymorphism analysis, we found no significant difference in representation in 19 of the 23 tested primers. We also generated a clone library from two soil DNA extracts using two primers for each extract and compared 456 clone sequences. Community diversity statistics and contingency table tests applied to counts of operational taxonomic units revealed that the two DNA extracts differed significantly, while the pairs of tagged primers from each extract were indistinguishable. Similar results were obtained using UniFrac phylogenetic comparisons. Together, these results suggest that the pig-tagged primers can be used to increase ecological inference in high throughput sequencing projects on fungi.