Spatiotemporal heterogeneity of plankton communities in Lake Donghu, China, as revealed by PCR-denaturing gradient gel electrophoresis and its relation to biotic and abiotic factors

The 16S and 18S rRNA genes of planktonic organisms derived from five stations with nutrient gradients in Lake Donghu, China, were studied by PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting, and the relationships between the genetic diversity of the plankton community and biotic/abiotic factors are discussed. The concentrations of total nitrogen (TN), total phosphorus (TP), NH4-N and As were found to be significantly related (P < 0.05) to morphological composition of the plankton community. Both chemical and morphological analyses suggested that temporal heterogeneity was comparatively higher than spatial heterogeneity in Lake Donghu. Although the morphological composition was not identical to the DGGE fingerprints in characterizing habitat similarity, the two strongest eutrophic stations (I and II) were always initially grouped into one cluster. Canonical correspondence analysis suggested that the factors strongly correlated with the first two ordination axes were seasonally different. The concentrations of TN and TP and the densities of rotifers and crustaceans were generally the main factors related to the DGGE patterns of the plankton communities. The study suggested that genetic diversity as depicted by metagenomic techniques (such as PCR-DGGE fingerprinting) is a promising tool for ecological study of plankton communities and that such techniques are likely to play an increasingly important role in assessing the environmental conditions of aquatic habitats.

Genetic diversity of plankton community as depicted by PCR-DGGE fingerprinting and its relation to morphological composition and environmental factors in lake donghu

To collect information about the genetic diversity of the plankton community and to study how plankton respond to environmental conditions, plankton samples were collected from five stations representing different trophic levels in a shallow, eutrophic lake (Lake Donghu), and investigated by PCR-DGGE fingerprinting. A total of 100 bands (61 of 16S rDNA bands and 39 of 18S rDNA bands) were detected. The DGGE bands unique to any single station accounted for 38% of the total bands, whereas common bands detected at all five stations accounted for only 11%. Using UPGMA clustering and MDS ordination of DGGE fingerprints, stations I and II were found to initially group together into one cluster, which was later joined by station V. Stations III and IV were isolated into two separate groups of one station each. Some differences in grouping relationships were found when analysis was completed on the basis of chemical characteristics and morphological composition, with zooplankton composition showing the greatest variability. However, the most similar stations (I and II) were always initially grouped into one cluster. Moreover, stations that exhibited the same or similar trophic level (stations III and IV), but different concentrations of heavy metals, were further differentiated by the DGGE method. Results of the present study indicated that PCR-DGGE fingerprinting was more sensitive than the traditional methods, as other studies suggested. Additionally, PCR-DGGE appears to be more appropriate for diversity characterization of the plankton community, as it is more canonical, systematic, and effective. Most importantly, fingerprinting results are more convenient for the comparative analyses between different studies. Therefore, the use of the described fingerprinting analysis may provide an operable and sensitive biomonitoring approach to identify critical, and potentially negative, stress within an aquatic ecosystem.

Crustacean zooplankton distribution patterns and their biomass as related to trophic indicators of 29 shallow subtropical lakes

A comparative limnological study was carried out to present a snapshot of crustacean zooplankton communities and their relations to environmental factors to test whether there is a consistent relationship between crustacean biomass and trophic indicators among lake groups with similar trophic conditions. The study lakes showed a wide range of trophic status, with total phosphorus (TP) ranging from 0.008 to 1.448mgL(-1), and chlorophyll a from 0.7 to 146.1 mu g L-1, respectively. About 38 species of Crustacea were found, of which Cladocera were represented by 25 taxa (20 genera), and Copepoda by 13 taxa (I I genera). The most common and dominant species were Bosmina coregoni, Moina micrura, Diaphanosoma brachyurum, Cyclops vicinus, Thermocyclops taihokuensis, Mesocyclops notius and Sinocalanus dorrii. Daphnia was rare in abundance. Canonical correspondence analysis showed that except for four species (D. hyalina, S. dorrii, C. vicinus and M. micrura), almost all the dominant species had the same preference for environmental factors. Temperature, predatory cyclopoids and planktivorous fishes seem to be the key factors determining species distribution. TP was a relatively better trophic indicator than chlorophyll a to predict crustacean biomass. Within the three groups of lakes, however, there was no consistent relationship between crustacean biomass and trophic indicators. The possible reason might be that top-down and bottom-up control on crustaceans vary with lake trophic state. The lack of significant negative correlation between crustacean biomass and chlorophyll a suggests that there was little control of phytoplankton biomass by macrozooplankton in these shallow subtropical lakes. (c) 2007 Elsevier GmbH. All rights reserved.

Driving forces shaping phytoplankton assemblages in two subtropical plateau lakes with contrasting trophic status

1. We studied driving forces shaping phytoplankton assemblages in two subtropical plateau lakes with contrasting trophic status, the oligotrophic deep Lake Fuxian and the eutrophic shallow Lake Xingyun. 2. Phytoplankton samples were taken monthly for a year and phytoplankton species were sorted into the main taxonomic groups and associations proposed by Reynolds. A canonical correspondence analysis (CCA) was used to test the occurrence of these classification schemes and to determine their discriminatory power. 3. The results suggest that the major driving forces in Lake Fuxian were physical variables, and particularly the underwater light climate, whereas, nutrients were the important driving force in Lake Xingyun. 4. Top-down control through zooplankton grazing in Lake Fuxian was hardly ever a significant determinant itself, because of the scarcity of zooplankton and their low grazing efficiency of predation while a dominance of inedible cyanobacteria throughout the year rendered top-down controls ineffective failing in Lake Xingyun. Hence phytoplankton communities in both lakes appear to be regulated primarily by bottom-up controls.

Identification and characterization of two homologues of interferon-stimulated gene ISG15 in crucian carp

ISG15 is one of the most strongly induced genes upon viral infection, interferon (IFN) stimulation, and lipopolysaccharide, (LPS) stimulation, and only one copy has been found in mammals so far. Here two fish ISG15 genes, termed CaISG15-1 and CaISG15-2, have been cloned and sequenced from UV-inactivated GCHV (grass carp haemorrhagic virus)-infected and IFN-produced CAB cells (crucian carp Carassius auratus blastulae embryonic cells) by suppression subtractive hybridization. The full-length cDNA sequences of two crucian carp ISG15 encode a 155-amino-acid protein and a 161-amino-acid protein, both of which show 78.9% identity overall and possess the characteristic structures of mammalian ISG15 proteins including two tandem ubiquitin-like domains and the C-terminal canonical LRLRGG motif. In CAB cells treated with different stimuli including active virus, UV-inactivated GCHV and IFN containing supernatant (ICS), the expression of both CaISG15-1 and CaISG15-2 was up-regulated but displayed different kinetics. Poly I:C and LPS were also able to induce an increase in mRNA for both genes. In CAB cells responsive to active GCHV, UV-inactivated GCHV, CAB ICS, Poly 1:12 and LPS, CaISG15-1 was upregulated more significantly than CaISG15-2. These results suggest that there are two ISG15 homologues in crucian carp, both of which might play distinct roles in innate immunity against viral and bacterial infection. (c) 2006 Elsevier Ltd. All rights reserved.

Environmental mechanism of change in cyanobacterial species composition in the northeastern part of Lake Dianchi (China)

Environmental mechanism of change in cyanobacterial species composition in the northeastern part of Lake Dianchi (also called Macun Bay and Haidong Bay) was studied using canonical correlation analysis (CCA), but also bottom-up control and top-down control were fully discussed. Results from CCA suggest: (1) the abundance and dominance of Microcystis aeruginosa in Macun Bay and Haidong Bay are influenced by total phosphorus (TP), nitrate (NO3--N), nitrite (NO2--N), dissolved oxygen (DO) and water temperature (WT); (2) water temperature has a positive correlation with the abundance of M. aeruginosa and it also has negative correlations with the abundances of Anabaena flos-aquae and Aphanizomenonon flos-aquae; and (3) abundances of both Anabaena flos-aquae and Aphanizomenon flos-aquae have positive correlations with ammonia-N (NH4+-N). Furthermore, cyanobacterial species composition has no significant correlations with light and size-fractioned iron in this study. Grazers, cyanophages and viruses were able to control cyanobacterial blooms and change the composition of cyanobacterial species. Though we studied physical and chemical factors intensely enough, we still are not able to predict the change in the composition of cyanobacterial blooms, because of plankton system in a chaotic behavior.

Community structure of small fishes in a shallow macrophytic lake (Niushan Lake) along the middle reach of the Yangtze River, China

This study describes the current status of the small fish community in Niushan Lake in China, and examines the spatial and seasonal variations of the community in relation to key environmental factors. Based on macrophyte cover conditions, the lake was divided into three major habitat types: (1) Potamogeton maackianus habitat, (2) Potamogeton maackianus and Myriophyllum spicatum habitat, and (3) uncovered or less-covered habitat. Fish were sampled quantitatively in the three habitat types by block nets seasonally from September 2002 to August 2003. A total of 10 469 individuals from 27 fish species were caught, among which 20 species were considered as small fishes. Rhodeus ocellatus, Paracheilognathus imberbis, Pseudorasbora parva, Micropercops swinhonis and Cultrichthys erythropterus were recognized as dominant small fishes according to their abundance and occurrence. It was noted that (1) small fishes predominated the total number of fish species in the lake, which reflected to some degree the size diminution phenomenon of fish resources; (2) many small fishes had plant detritus as their food item, which was consistent with the abundance of macrophyte detritus in the lake and implied the importance of detritus in supporting small fish secondary production. Canonical correspondence analysis suggested that the spatial distributions of most small fishes were associated with complex macrophyte cover conditions. Macrophyte biomass was positively correlated with species richness, diversity index and the catch per unit of effort (CPUE) of the fish community. Water depth had no significant effects on species diversity and distribution of the small fishes. Correspondence analysis revealed a higher occurrence of the small fishes and higher abundance of individuals in summer and autumn. Seasonal length-frequency distributions of several species indicated that more larval and juvenile individuals appeared in spring and summer. This study provides some baseline information which will be essential to long-term monitoring of small fish communities in the Yangtze lakes.

Effects of seasonal succession and water pollution on the protozoan community structure in an eutrophic lake

The purpose of the research is to study the seasonal succession of protozoa community and the effect of water quality on the protozoa community to characterize biochemical processes occurring at a eutrophic Lake Donghu, a large shallow lake in Wuhan City, China. Samples of protozoa communities were obtained monthly at three stations by PFU (polyurethane foam unit) method over a year. Synchronously, water samples also were taken from the stations for the water chemical quality analysis. Six major variables were examined in a principal component analysis (PCA), which indicate the fast changes of water quality in this station I and less within-year variation and a comparatively stable water quality in stations II and III. The community data were analyzed using multivariate techniques, and we show that clusters are rather mixed and poorly separated, suggesting that the community structure is changing gradually, giving a slight merging of clusters form the summer to the autumn and the autumn to the winter. Canonical correspondence analysis (CCA) was used to infer the relationship between water quality variables and phytoplankton community structure, which changed substantially over the survey period. From the analysis of cluster and CCA, coupled by community pollution value (CPV), it is concluded that the key factors driving the change in protozoa community composition in Lake Donghu was water qualities rather than seasons. (c) 2006 Elsevier Ltd. All rights reserved.

Distribution of the macroinvertebrate communities in the Xiangxi River system and relationships with environmental factors

Surveys of macroinvertebrates were carried out in the Xiangxi River system during July of 2001. Among the 121 taxa collected, Ephemeroptera, Trichoptera, and Diptera dominated (41.7, 26.0, and 24.5% of the total relative abundance, respectively). Two-way indictor species analysis and detrended correspondence analysis divided the 49 sites into four groups based on species composition and relative abundance. Canonical correspondence analysis indicated that elevation, SiO2, pH, conductivity, hardness, and NO2-N were significant environmental factors affecting the distribution of macroinvertebrates.

Benthic algae of the Xiangxi River, China

From June 2000 to June 2002, four sites on the mainstem of the Xiangxi River and one site on each of its major tributaries were sampled 16 times each for benthic algae. All total, 223 taxa (most to species and variety levels) were found (193 Bacillariophyta, 20 Chlorophyta, nine Cyanophyta and one Xanthophyta). The diatoms Cocconeis placentula, Achnanthes linearis, and Diatoma vulgare dominated the system, with relative abundance of 33.3%, 18.8%, and 6.4%, respectively. The abundances of all the other taxa were under 5%, and 210 taxa collectively contributed less than 1% of the total abundance. Taxa diversity peaked in winter and reached a minimum in summer. Species richness varied considerably but was not significantly different over time. Maximum algal density occurred in later winter/spring (1.4 x 10(9) ind./m(2)) but was not significantly different from the minimum density, which occurred in August. Chlorophyll a showed similar seasonal fluctuation but also was not significantly different over time. Canonical correspondence analysis demonstrated that water hardness, depth, conductivity, and alkalinity had important influences on variation of epilithic algae in the Xiangxi River system.

Linear dimensionality reduction: Survey, insights, and generalizations

© 2015 John P. Cunningham and Zoubin Ghahramani. Linear dimensionality reduction methods are a cornerstone of analyzing high dimensional data, due to their simple geometric interpretations and typically attractive computational properties. These methods capture many data features of interest, such as covariance, dynamical structure, correlation between data sets, input-output relationships, and margin between data classes. Methods have been developed with a variety of names and motivations in many fields, and perhaps as a result the connections between all these methods have not been highlighted. Here we survey methods from this disparate literature as optimization programs over matrix manifolds. We discuss principal component analysis, factor analysis, linear multidimensional scaling, Fisher's linear discriminant analysis, canonical correlations analysis, maximum autocorrelation factors, slow feature analysis, sufficient dimensionality reduction, undercomplete independent component analysis, linear regression, distance metric learning, and more. This optimization framework gives insight to some rarely discussed shortcomings of well-known methods, such as the suboptimality of certain eigenvector solutions. Modern techniques for optimization over matrix manifolds enable a generic linear dimensionality reduction solver, which accepts as input data and an objective to be optimized, and returns, as output, an optimal low-dimensional projection of the data. This simple optimization framework further allows straightforward generalizations and novel variants of classical methods, which we demonstrate here by creating an orthogonal-projection canonical correlations analysis. More broadly, this survey and generic solver suggest that linear dimensionality reduction can move toward becoming a blackbox, objective-agnostic numerical technology.

Structure of macrozoobenthos of the East Dongting nature reserve, with emphasis on relationships with environmental variables

Ecological survey of macrozoobenthos assemblages was carried out at 32 sites in the East Dongting Nature Reserve, located in the northern region of the East Dongting Lake in the middle basin of the Yangtze River, China. All total 51 taxa including 18 oligochaetes, 15 mollusks, 14 insects and four other animals were recorded. Mollusks composed the dominant group and accounted for more than 70% of the total abundance. Assemblages were composed mainly of scrapers (66.7%) and collector-gatherers (nearly 20%), and to a lesser extent collector-filterers (roughly 12%), predators (ca. 7%), and shredders (ca. 6%). Two-way indicator species analysis, detrended correspondence, and canonical correspondence analysis (CCA) were employed to identify the relationships between macrozoobenthos assemblages and environmental variables. Thirty-two sites were separated into four site groups based on composition and relative abundance of benthic macroinvertebrates. CCA detected that water depth, pH, conductivity, SiO2, total nitrogen, total phosphorus, alkalinity, hardness, and Ca2+, were significant environmental factors influencing the pattern of macozoobenthos. In this minimal subset, water depth, pH, alkalinity and hardness were the most influential variables.

Distribution of epilithic algae in the Xiangxi River system and their relationships with environmental factors

The spatial pattern of epilithic algae in the Xiangxi River system was studied in relation to several environmental factors by two-way indictor species analysis (TWINSPAN), detrended correspondence analysis (DCA), and canonical correspondence analysis (CCA). Eighty-nine taxa including diatoms, green algae, and blue-green algae were observed. Diatoms were dominant, and Cocconeis placentula, Cymbella minuta, Diatoma vulgare, and Gomphonema angustatum appeared in most of sampling sites. By TWINSPAN and DCA, thirty-one sites were divided into three groups based on composition and relative richness of benthic algae. CCA indicated that SiO2, pH, total phosphorus, Ca2+, velocity, elevation, and Cl- were significant environmental factors affecting the distribution of algae communities. In this minimal subset, SiO2 and pH were the most influential variables.

Dietary-morphological relationships of fishes in Liangzi Lake, China

Species in Liangzi Lake were clustered into four trophic groups: Hemiramphus kurumeus and Hemiculter bleekeri bleekeri fed predominantly on terrestrial insects; Carassius auratus auratus and Abbottina rivularis on non-animal food; Hypseleotris swinhonis, Ctenogobius giurinus, Pseudorasbora parva and Toxabramis swinhonis on cladocerans or copepods; Culterichthys erythropterus on decapod shrimps. Gut length, mouth width, mouth height, gill raker length and gill raker spacing, varied widely among species. With the exception of three species pairs (H. swinhonis, C. glurinus; C. erythropterus, H. kurumeus; T. swinhonis, H. bleekeri bleekeri), principal components analysis of morphological variables revealed over-dispersion of species. Canonical correspondence analysis of dietary and morphological data revealed five significant dietary-morphological correlations. The first three roots explained > 85% of the total variance. The first root reflected mainly the relationship of gut length to non-animal feud, with an increase in gut length associated with an increase in non-animal food. The second root was influenced strongly by the relationship of the gill raker spacing to consumption of copepods, with an increase in gill raker spacing associated positively with copepods in the diet. The third root was influenced by the relationship of mouth gape to consumption of fish and decapod shrimps, with an increase in mouth gape associated with more fish and decapod shrimps in the diet. These significant dietary-morphological relationships supported the eco-morphological hypotheses that fish morphology influence food use, and morphological variation is important in determining ecological segregation of co-existing fish species. (C) 2001 The Fisheries Society of the British Isles.

Raman scattering of folded acoustic phonons in self-assembled Si/Ge dot superlattices

Self-assembled Si/Ge dot multilayers with small, uncorrelated dots fabricated by molecular beam epitaxy in the Stranski-Krastanov growth mode are studied by Raman scattering of folded longitudinal acoustic (FLA) modes. The FLA Raman spectra are analyzed and modeled with respect to mode frequencies and the spectral envelope of mode intensities. The deduced average superlattice properties are consistent with results from atomic force microscopy. The simple Rytov model used for Si/Ge layer structures reproduces very well the frequencies of the FLA modes up to 150 cm(-1). The nonlinearity of phonon dispersion curves in bulk Si for large momenta, however, becomes important for modeling the higher frequencies of observed FLA modes up to 22nd order. The effective dot layer width and an activation energy for thermal intermixing of 2.1+/-0.2 eV are determined from the spectral envelopes of FLA mode intensities of as-grown and annealed Si/Ge dot multilayers. (C) 2004 American Institute of Physics.