Description of Campanella hanchuanensis p. nov. (Ciliophora, Peritrichida): general morphology and isozyme pattern

Living and stained specimens of Campanella hanchuanensis sp. nov., collected near Hanchuan Power Plant, Hubei Province, China, were studied under light microscopy. Infraciliature was stained using a protargol staining technique. There is no bridge between concentric silver lines. The aboral ciliary wreath consists of 6 lines of basal bodies, with the middle 4 lines compacted and one lateral line each side separated. The other characters are similar to or the same as that described in Campanella umbellaria. The esterase isozyme was analyzed by micro-isoelectrofocussing. Campanella hanchuanensis sp. nov. has three bands of esterase near the cathode.Article信州大学理学部附属諏訪臨湖実験所報告 9: 87-94(1995)departmental bulletin pape

Comparative study on the gut microbiotas of four economically important Asian carp species

Gut microbiota of four economically important Asian carp species (silver carp, Hypophthalmichthys molitrix; bighead carp, Hypophthalmichthys nobilis; grass carp, Ctenopharyngodon idella; common carp, Cyprinus carpio) were compared using 16S rRNA gene pyrosequencing. Analysis of more than 590,000 quality-filtered sequences obtained from the foregut, midgut and hindgut of these four carp species revealed high microbial diversity among the samples. The foregut samples of grass carp exhibited more than 1,600 operational taxonomy units (OTUs) and the highest alpha-diversity index, followed by the silver carp foregut and midgut. Proteobacteria, Firmicutes, Bacteroidetes and Fusobacteria were the predominant phyla regardless of fish species or gut type. Pairwise (weighted) UniFrac distance-based permutational multivariate analysis of variance with fish species as a factor produced significant association (P &lt; 0.01). The gut microbiotas of all four carp species harbored saccharolytic or proteolytic microbes, likely in response to the differences in their feeding habits. In addition, extensive variations were also observed even within the same fish species. Our results indicate that the gut microbiotas of Asian carp depend on the exact species, even when the different species were cohabiting in the same environment. This study provides some new insights into developing commercial fish feeds and improving existing aquaculture strategies.</p

Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota

The 16S rRNA gene is one of the most commonly used molecular markers for estimating bacterial diversity during the past decades. However, there is no consistency about the sequencing depth (from thousand to millions of sequences per sample), and the clustering methods used to generate OTUs may also be different among studies. These inconsistent premises make effective comparisons among studies difficult or unreliable. This study aims to examine the necessary sequencing depth and clustering method that would be needed to ensure a stable diversity patterns for studying fish gut microbiota. A total number of 42 samples dataset of Siniperca chuatsi (carnivorous fish) gut microbiota were used to test how the sequencing depth and clustering may affect the alpha and beta diversity patterns of fish intestinal microbiota. Interestingly, we found that the sequencing depth (resampling 1000-11,000 per sample) and the clustering methods (UPARSE and UCLUST) did not bias the estimates of the diversity patterns during the fish development from larva to adult. Although we should acknowledge that a suitable sequencing depth may differ case by case, our finding indicates that a shallow sequencing such as 1000 sequences per sample may be also enough to reflect the general diversity patterns of fish gut microbiota. However, we have shown in the present study that strict pre-processing of the original sequences is required to ensure reliable results. This study provides evidences to help making a strong scientific choice of the sequencing depth and clustering method for future studies on fish gut microbiota patterns, but at the same time reducing as much as possible the costs related to the analysis.</p

Temporal-spatial Correlation Attention Network for Clinical Data Analysis in Intensive Care Unit

In recent years, medical information technology has made it possible for electronic health record (EHR) to store fairly complete clinical data. This has brought health care into the era of "big data". However, medical data are often sparse and strongly correlated, which means that medical problems cannot be solved effectively. With the rapid development of deep learning in recent years, it has provided opportunities for the use of big data in healthcare. In this paper, we propose a temporal-saptial correlation attention network (TSCAN) to handle some clinical characteristic prediction problems, such as predicting death, predicting length of stay, detecting physiologic decline, and classifying phenotypes. Based on the design of the attention mechanism model, our approach can effectively remove irrelevant items in clinical data and irrelevant nodes in time according to different tasks, so as to obtain more accurate prediction results. Our method can also find key clinical indicators of important outcomes that can be used to improve treatment options. Our experiments use information from the Medical Information Mart for Intensive Care (MIMIC-IV) database, which is open to the public. Finally, we have achieved significant performance benefits of 2.0\% (metric) compared to other SOTA prediction methods. We achieved a staggering 90.7\% on mortality rate, 45.1\% on length of stay. The source code can be find: \url{https://github.com/yuyuheintju/TSCAN}

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.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

Coordination and divergence in community assembly processes across co-occurring microbial groups separated by cell size

Setting the pace of life and constraining the role of members in food webs, body size can affect the structure and dynamics of communities across multiple scales of biological organization (e.g., from the individual to the ecosystem). However, its effects on shaping microbial communities, as well as underlying assembly processes, remain poorly known. Here, we analyzed microbial diversity in the largest urban lake in China and disentangled the ecological processes governing microbial eukaryotes and prokaryotes using 16S and 18S amplicon sequencing. We found that pico/nano-eukaryotes (0.22−20 μm) and micro-eukaryotes (20−200 μm) showed significant differences in terms of both community composition and assembly processes even though they were characterized by similar phylotype diversity. We also found scale dependencies whereby micro-eukaryotes were strongly governed by environmental selection at the local scale and dispersal limitation at the regional scale. Interestingly, it was the micro-eukaryotes, rather than the pico/nano-eukaryotes, that shared similar distribution and community assembly patterns with the prokaryotes. This indicated that assembly processes of eukaryotes may be coupled or decoupled from prokaryotes’ assembly processes based on eukaryote cell size. While the results support the important influence of cell size, there may be other factors leading to different levels of assembly process coupling across size classes. Additional studies are needed to quantitatively parse the influence of cell size versus other factors as drivers of coordinated and divergent community assembly processes across microbial groups. Regardless of the governing mechanisms, our results show that there are clear patterns in how assembly processes are coupled across sub-communities defined by cell size. These size-structured patterns could be used to help predict shifts in microbial food webs in response to future disturbance

Alpha-Tubulin and Small Subunit rRNA Phylogenies of Peritrichs Are Congruent and Do Not Support the Clustering of Mobilids and Sessilids (Ciliophora, Oligohymenophorea)

Peritrich ciliates have been traditionally subdivided into two orders, Sessilida and Mobilida within the subclass Peritrichia. However, all the existing small subunit (SSU) rRNA phylogenetic trees showed that the sessilids and mobilids did not branch together. To shed some light on this disagreement, we tested whether or not the classic Peritrichia is a monophyletic group by assessing the reliability of the SSU rRNA phylogeny in terms of congruency with alpha-tubulin phylogeny. For this purpose, we obtained 10 partial alpha-tubulin sequences from peritrichs and built phylogenetic trees based on alpha-tubulin nucleotide and amino acid data. A phylogenetic tree from the alpha-tubulin and SSU rRNA genes in combination was also constructed and compared with that from the SSU rRNA gene using a similar species sampling. Our results show that the mobilids and sessilids are consistently separated in all trees, which reinforces the idea that the peritrichs do not constitute a monophyletic group. However, in all alpha-tubulin gene trees, the urceolariids and trichodiniids do not group together, suggested mobilids may not be a monophyletic group

Impacts of algal blooms removal by chitosan-modified soils on zooplankton community in Taihu Lake, China

It is important to assess the effect on zooplankton when perform the environmental protection or restoration technology, especially removing algal blooms, because algae were the major primary producer in algal lakes. The influence on zooplankton community after half a year of algal blooms removed by chitosan-modified soils in Taihu Lake was assessed and the rationality of carrying out the process semiannually was evaluated in the present study. Morphological composition and genetic diversity of zooplankton community were investigated by microscope checkup and polymerase chain reaction-denatured gradient gel electrophoresis (PCR-DGGE). A total of 44 zooplankton taxa (23 protozoa, 17 rotifers, 3 copepoda and 1 cladocera) were detected by microscope checkup, and a total of 91 bands (28 bands amplified by primers F1427-GC and R1616, 63 bands amplified by primers Fung-GC and NS1) were detected by PCR-DGGE. The results of cluster analysis or detrended correspondence analysis indicated that there was no considerable difference in morphological composition of zooplankton and DGGE profiles between experimental and control sites, and DGGE profiles could represent the biologic diversity. The study showed that zooplankton community could recover original condition after half year of algal blooms removed by chitosan-modified soils and it was acceptable to apply this process semiannually. In addition, the results revealed that PCR-DGGE could be applied to investigate the impacts of the environmental protection or restoration engineering on zooplankton community diversity

Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China).

Uncovering which environmental factors govern community diversity patterns and how ecological processes drive community turnover are key questions related to understand the community assembly. However, the ecological mechanisms regulating long-term variations of bacterioplankton communities in lake ecosystems remain poorly understood. Here we present nearly a decade-long study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing with MiSeq platform. We found strong repeatable seasonal diversity patterns in terms of both common (detected in more than 50% samples) and dominant (relative abundance &gt;1%) bacterial taxa turnover. Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is a key environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern of bacterioplankton communities across the main lake areas within season was overwhelmed by their temporal variabilities. Phylogenetic analysis further indicated that 75%-82% of community turnover was governed by homogeneous selection due to consistent environmental conditions within seasons, suggesting that the microbial communities in Lake Donghu are mainly controlled by niche-based processes. Therefore, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout different lake areas