scholarly journals Distribution patterns of dinoflagellate communities along the Songhua River

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6733 ◽  
Author(s):  
Yangchun Gao ◽  
Yiyong Chen ◽  
Wei Xiong ◽  
Shiguo Li ◽  
Aibin Zhan
Keyword(s):  
Environmental Factors ◽  
Geographical Distribution ◽  
High Throughput ◽  
Environmental Variables ◽  
High Throughput Sequencing ◽  
Distribution Patterns ◽  
Freshwater Ecosystems ◽  
Songhua River ◽  
Significant Difference ◽  
The Songhua River

Background Dinoflagellates have the potential to pose severe ecological and economic damages to aquatic ecosystems. It is therefore largely needed to understand the causes and consequences of distribution patterns of dinoflagellate communities in order to manage potential environmental problems. However, a majority of studies have focused on marine ecosystems, while the geographical distribution patterns of dinoflagellate communities and associated determinants in freshwater ecosystems remain unexplored, particularly in running water ecosystems such as rivers and streams. Methods Here we utilized multiple linear regression analysis and combined information on species composition recovered by high-throughput sequencing and spatial and environmental variables to analyze the distribution patterns of dinoflagellate communities along the Songhua River. Results After high-throughput sequencing, a total of 490 operational taxonomic units (OTUs) were assigned to dinoflagellates, covering seven orders, 13 families and 22 genera. Although the sample sites were grouped into three distinctive clusters with significant difference (p < 0.05) in environmental variables, OTUs-based dinoflagellate communities among the three clusters showed no significant difference (p > 0.05). Among all 24 environmental factors, two environmental variables, including NO3-N and total dissolved solids (TDS), were selected as the significantly influential factors (p < 0.05) on the distribution patterns of dinoflagellate communities based on forward selection. The redundancy analysis (RDA) model showed that only a small proportion of community variation (6.1%) could be explained by both environmental (NO3-N and TDS) and dispersal predictors (watercourse distance) along the River. Variance partitioning revealed a larger contribution of local environmental factors (5.85%) than dispersal (0.50%) to the total variation of dinoflagellate communities. Discussion Our findings indicated that in addition to the two quantifiable processes in this study (species sorting and dispersal), more unquantifiable stochastic processes such as temporal extinction and colonization events due to rainfall may be responsible for the observed geographical distribution of the dinoflagellate community along the Songhua River. Results obtained in this study suggested that deeper investigations covering different seasons are needed to understand the causes and consequences of geographical distribution patterns of dinoflagellate biodiversity in river ecosystems.

scholarly journals Comparison of invertebrate diversity in lake waters and their resting eggs in sediments, as revealed by high-throughput sequencing (HTS)

2020 ◽  
pp. 19
Author(s):  
Xiaoyan Wang ◽  
Qing Wang ◽  
Yufeng Yang ◽  
Wenbo Yu
Keyword(s):  
High Throughput ◽  
Water Samples ◽  
High Throughput Sequencing ◽  
Essential Feature ◽  
Resting Eggs ◽  
Freshwater Ecosystems ◽  
Rrna Gene ◽  
Promising Alternative ◽  
Invertebrate Diversity ◽  
Significant Difference

Aquatic invertebrate diversity reflects water quality and the health of aquatic ecosystems and should be monitored as an essential feature of freshwater ecosystems. The resting eggs of aquatic invertebrates in sediments populate the overlying water. The diversity of invertebrates in waters and their resting eggs in sediments in Baiyangdian Lake, Xiongan, North China, were assessed using high-throughput sequencing (HTS) with a pair of 18S rRNA gene adaptor-linked primers. The total of 99 operational taxonomic units (OTUs) derived from 353,755 invertebrate sequences (mostly zooplankton) were revealed by this study. A total of 50 species in the water samples including 20 rotifers, 11 copepods, 1 cladoceran and 18 other species were sorted out. In the sediment 37 species, including 21 rotifers, 3 copepods, 1 cladoceran and 12 other species, were identified. There were 24 species in common between water and corresponding sediments. Invertebrate OTU richness in water samples was higher than that in sediments (p < 0.01), while there was no significant difference in the Shannon-Wiener index. These results suggest that HTS is a promising alternative for efficient biodiversity assessment and monitoring.

scholarly journals Distribution Patterns of Odonate Assemblages in Relation to Environmental Variables in Streams of South Korea

Insects ◽  
2018 ◽  
Vol 9 (4) ◽  
pp. 152 ◽  
Author(s):  
Da-Yeong Lee ◽  
Dae-Seong Lee ◽  
Mi-Jung Bae ◽  
Soon-Jin Hwang ◽  
Seong-Yu Noh ◽  
...  
Keyword(s):  
Land Use ◽  
Ecosystem Services ◽  
Environmental Factors ◽  
South Korea ◽  
Habitat Heterogeneity ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Distribution Patterns ◽  
Self Organizing Map ◽  
Factors Affecting

Odonata species are sensitive to environmental changes, particularly those caused by humans, and provide valuable ecosystem services as intermediate predators in food webs. We aimed: (i) to investigate the distribution patterns of Odonata in streams on a nationwide scale across South Korea; (ii) to evaluate the relationships between the distribution patterns of odonates and their environmental conditions; and (iii) to identify indicator species and the most significant environmental factors affecting their distributions. Samples were collected from 965 sampling sites in streams across South Korea. We also measured 34 environmental variables grouped into six categories: geography, meteorology, land use, substrate composition, hydrology, and physicochemistry. A total of 83 taxa belonging to 10 families of Odonata were recorded in the dataset. Among them, eight species displayed high abundances and incidences. Self-organizing map (SOM) classified sampling sites into seven clusters (A–G) which could be divided into two distinct groups (A–C and D–G) according to the similarities of their odonate assemblages. Clusters A–C were characterized by members of the suborder Anisoptera, whereas clusters D–G were characterized by the suborder Zygoptera. Non-metric multidimensional scaling (NMDS) identified forest (%), altitude, and cobble (%) in substrata as the most influential environmental factors determining odonate assemblage compositions. Our results emphasize the importance of habitat heterogeneity by demonstrating its effect on odonate assemblages.

Distribution and fate of synthetic musks in the Songhua River, Northeastern China: influence of environmental variables

2015 ◽  
Vol 22 (12) ◽  
pp. 9090-9099 ◽  
Author(s):  
Binyu Lu ◽  
Yujie Feng ◽  
Peng Gao ◽  
Zhaohan Zhang ◽  
Nan Lin
Keyword(s):  
Environmental Variables ◽  
Northeastern China ◽  
Songhua River ◽  
Synthetic Musks ◽  
The Songhua River

scholarly journals Comparison of the Intestinal Microbial Community in Ducks Reared Differently through High-Throughput Sequencing

2019 ◽  
Vol 2019 ◽  
pp. 1-14 ◽  
Author(s):  
Yan Zhao ◽  
Kun Li ◽  
Houqiang Luo ◽  
Longchuan Duan ◽  
Caixia Wei ◽  
...  
Keyword(s):  
Microbial Community ◽  
High Throughput ◽  
Water Contamination ◽  
High Throughput Sequencing ◽  
Free Access ◽  
Operational Taxonomic Units ◽  
Genus Level ◽  
Significant Difference ◽  
Access To Water ◽  
Poultry Droppings

Birds are an important source of fecal contamination in environment. Many of diseases are spread through water contamination caused by poultry droppings. A study was conducted to compare the intestinal microbial structure of Shaoxing ducks with and without water. Thirty 1-day-old Shaoxing ducks (Qingke No. 3) were randomly divided into two groups; one group had free access to water (CC), while the other one was restricted from water (CT). After 8 months of breeding, caecal samples of 10 birds from each group were obtained on ice for high-throughput sequencing. A total of 1507978 valid sequences were examined and clustered into 1815 operational taxonomic units (OTUs). At phylum level, Firmicutes (41.37%), Bacteroidetes (33.26%), Proteobacteria (13.67%), and Actinobacteria (8.26%) were found to dominate the microbial community in CC birds, while Firmicutes (53.62%), Bacteroidetes (33.06%), and Actinobacteria (11.13%) were uncovered to be the prime phyla in CT ducks. At genus level, Bacteroides (25.02%), Escherichia-Shigella (11.02%), Peptococcus (7.73%) and Parabacteroides (5.86%) were revealed to be the mainly genera in the CC group ducks, while Bacteroides (18.11%), Erysipelatoclostridium (10.94%), Ruminococcaceae_unclassified (10.43%), Lachnospiraceae_unclassified (5.26%), Coriobacteriales_unclassified (5.89%), and Faecalibacterium (4.2%) were detected to staple the microbial flora in the CT birds. One phylum and 13 genera were found to have the significant difference between the two bird groups (p<0.05). At phylum level, Proteobacteria in CT ducks were found to be obviously lower than ducks in CC birds (p<0.05). At genus level, Escherichia-Shigella (p<0.05) and Peptococcus (p<0.05) were found to be notably lower in CT birds, while Erysipelatoclostridium (p<0.05), Ruminococcaceae_unclassified (p<0.01), Coriobacteriales_unclassified (p<0.05), Faecalibacterium (p<0.01), Atopobiaceae_unclassified (p<0.01), Alistipes (p<0.05), Eggerthellaceae_unclassified (p<0.05), Prevotella_7 (<0.05), Rikenellaceae_RC9_gut_group (p<0.05), Prevotellaceae_uncultured (p<0.05), and Shuttleworthia (p<0.05) were observed to be prominently higher in CT ducks. In conclusion, the present study revealed the effects of keeping ducks away from swimming with obvious changes in the microbial community. Though higher microbial richness was found in the ducks without swimming, more pathogenic genera including Eggerthella, Erysipelatoclostridium, Alistipes, Prevotella_7, and Shuttleworthia; zoonotic genera including Eggerthella and Shuttleworthia; inflammatory genus Alistipes; anti-inflammatory Faecalibacterium genus; and tumor genus Rikenellaceae were examined in these ducks. The CT ducks also showed significant changes at genera level regarding the metabolism (Peptococcus, Ruminococcaceae, and Coriobacteriales).

scholarly journals Overwintering honeybees maintained dynamic and stable intestinal bacteria

2021 ◽  
Author(s):  
Peng Liu ◽  
Yujie Zhu ◽  
Liang Ye ◽  
Tengfei Shi ◽  
Lai Li ◽  
...  
Keyword(s):  
16S Rdna ◽  
High Throughput ◽  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Intestinal Bacteria ◽  
High Quality ◽  
Dynamic Changes ◽  
Ecological Balance ◽  
Significant Difference

Abstract Honeybee is an important pollinator for maintaining ecological balance. However, scientist found the bizarre mass death of bees in winter. Meanwhile, some reported that the differences composed of intestinal bacteria between healthy honeybees and CCD honeybees. It is essential that explored dynamic changes to the intestinal bacteria in overwintering honeybees. We collected bee samples before overwintering, during prophase of overwintering, metaphase of overwintering, anaphase of overwintering, telophase of overwintering, and after overwintering. By using high-throughput sequencing targeting the V3 − V4 regions of the 16S rDNA, the abundance of the intestinal bacteria were analyzed in overwintering honeybees. A total of 1,373,886 high-quality sequences were acquired and Proteobacteria (85.69%), Firmicutes (10.40%), Actinobacteria (3.66%), and Cyanobacteria (1.87%) were identified as major components of the intestinal bacteria. All core honeybee intestinal bacteria genera, such as Gilliamella, Bartonella, Snodgrassella, Lactobacillus, Frischella, Commensalibacter, and Bifidobacterium were detected. The abundance of Actinobacteria, Bartonella, and Bifidobacterium increased initially and then decreased in winter honeybees. There were no significant differences in the richness and evenness of the microbiota in overwintering honeybees; however, there was a statistically significant difference in the beta diversity of the intestinal bacteria after overwintering compared with that in other groups. Our results suggested that honeybees maintained their intestinal ecosystem balance, and increased the abundance of gut probiotics in response to environmental and nutrition pressures in winter.

scholarly journals The geographical distribution patterns of Chrysoteuchia Hübner in China and description of a new species (Lepidoptera, Crambidae)

ZooKeys ◽  
2019 ◽  
Vol 853 ◽  
pp. 109-118 ◽  
Author(s):  
Lu-Lan Jie ◽  
Jing-Bo Yang ◽  
Wei-Chun Li
Keyword(s):  
New Species ◽  
Geographical Distribution ◽  
Environmental Variables ◽  
Distribution Patterns ◽  
Annual Precipitation ◽  
Southeastern China ◽  
Present Distribution ◽  
Suitable Area ◽  
First Time ◽  
A New Species

The geographical distribution patterns ofChrysoteuchiaHübner in China are analysed with MaxEnt and ArcGIS based on known localities and nineteen environmental variables. The results suggest that southeastern China is a highly suitable area, and Bio11 (mean temperature of the coldest quarter), Bio12 (annual precipitation) and Bio18 (precipitation of the warmest quarter) are revealed to be the main variables affecting the present distribution patterns. Among them, Bio18 is the strongest predictor with a 24.3% contribution. Furthermore, a new species from Tibet is added to the genus,Chrysoteuchialandryisp. nov., and the male ofC.curvicavusis described for the first time. Images of adults and their genitalia are illustrated, and two maps showing the geographical distribution patterns ofChrysoteuchiain China are provided.

scholarly journals The Fungal Communities and Flavor Profiles in Different Types of High-Temperature Daqu as Revealed by High-Throughput Sequencing and Electronic Senses

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenchao Cai ◽  
Yu’ang Xue ◽  
Yurong Wang ◽  
Wenping Wang ◽  
Na Shu ◽  
...  
Keyword(s):  
High Temperature ◽  
Nitrogen Oxides ◽  
Organic Compounds ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Electronic Tongue ◽  
Illumina Miseq ◽  
Fungal Communities ◽  
Significant Difference ◽  
Distinct Character

Polymicrobial co-fermentation is among the distinct character of high-temperature Daqu. However, fungal communities in the three types of high-temperature Daqu, namely, white high-temperature Daqu, black high-temperature Daqu, and yellow high-temperature Daqu, are yet to be characterized. In this study, the fungal diversity, taste, and aroma profiles in the three types of high-temperature Daqu were investigated by Illumina MiSeq high-throughput sequencing, electronic tongue, and electronic nose, respectively. Ascomycota and Basidiomycota were detected as the absolute dominant fungal phylum in all types of high-temperature Daqu samples, whereas Thermomyces, Thermoascus, Aspergillus, Rasamsonia, Byssochlamys, and Trichomonascus were identified as the dominant fungal genera. The fungal communities of the three types of high-temperature Daqu differed significantly (p &lt; 0.05), and Thermomyces, Thermoascus, and Monascus could serve as the biomarkers in white high-temperature Daqu, black high-temperature Daqu, and yellow high-temperature Daqu, respectively. The three types of high-temperature Daqu had an extremely significant difference (p &lt; 0.01) in flavor: white high-temperature Daqu was characterized by sourness, bitterness, astringency, richness, methane, alcohols, ketones, nitrogen oxides, and sulfur organic compounds; black high-temperature Daqu was characterized by aftertaste-A, aftertaste-B, methane-aliph, hydrogen, and aromatic compounds; and yellow high-temperature Daqu was characterized by saltiness, umami, methane, alcohols, ketones, nitrogen oxides, and sulfur organic compounds. The fungal communities in the three types of high-temperature Daqu were significantly correlated with taste but not with aroma, and the aroma of high-temperature Daqu was mainly influenced by the dominant fungal genera including Trichomonascus, Aspergillus, Thermoascus, and Thermomyces. The result of the present study enriched and refined our knowledge of high-temperature Daqu, which had positive implications for the development of traditional brewing technique.

scholarly journals Distribution patterns of microsatellites and development of its marker in different genomic regions of forest musk deer genome based on high throughput sequencing

Aging ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 4445-4462
Author(s):  
Wen-Hua Qi ◽  
Ting Lu ◽  
Cheng-Li Zheng ◽  
Xue-Mei Jiang ◽  
Hang Jie ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Distribution Patterns ◽  
Musk Deer ◽  
Genomic Regions

scholarly journals Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

2018 ◽  
Author(s):  
Joeselle M. Serrana ◽  
Yo Miyake ◽  
Maribet Gamboa ◽  
Kozo Watanabe
Keyword(s):  
Community Composition ◽  
Environmental Variables ◽  
High Throughput Sequencing ◽  
Freshwater Ecosystems ◽  
Morphological Data ◽  
Morphological Identification ◽  
Biodiversity Assessment ◽  
Stream Macroinvertebrate ◽  
The Relationship ◽  
Diversity Metrics

AbstractConventional morphology-based identification is commonly used for routine assessment of freshwater ecosystems. However, cost and time efficient techniques such as high-throughput sequencing (HTS) based approaches may resolve the constraints encountered in conducting morphology-based surveys. Here, we characterized stream macroinvertebrate species diversity and community composition via metabarcoding and morphological analysis from environmental samples collected from the Shigenobu River Basin in Ehime Prefecture, Japan. We compared diversity metrics and assessed both approaches’ ability to evaluate the relationship between macroinvertebrate community and environmental variables. In total, we morphologically identified 45 taxa (3 families, six subfamilies, 31 genera, and five species) from 8,276 collected individuals from ten study sites. We detected 44 species by metabarcoding, with 35 species collapsed into 11 groups matching the morphologically identified taxa. A significant positive correlation between logged depth (number of HTS reads) and abundance of morphological taxa was observed, which implied that quantitative data can be used for subsequent analyses. Relatively higher estimates of alpha diversity were calculated from the metabarcoding data in comparison to morphology-based data. However, beta diversity estimates between metabarcoding and morphology data based on both incidence and abundance-based matrices were correlated proving that community differences between sampling sites were preserved in the molecular data. Also, both models were significant, but metabarcoding data (93%) explained a relatively higher percentage of variation in the relationship between community composition and the environmental variables than morphological data (91%). Overall, we present both the feasibility and limitations of HTS-driven estimations of taxonomic richness, community composition, and diversity metrics, and that metabarcoding was proven comparable and more sensitive against morphology-based analysis for stream macroinvertebrate biodiversity assessment and environmental monitoring.

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