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 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 the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6684 ◽  
Author(s):  
Siyu Han ◽  
Yu Guan ◽  
Hailong Dou ◽  
Haitao Yang ◽  
Meng Yao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Gut Microbiota ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Panthera Pardus ◽  
Invasive Approach ◽  
Fecal Samples ◽  
Significant Difference

The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.

scholarly journals Single and Synergistic Effects of Solar Radiation, Water guard and Moringa oleifera Treatments on Bacterial Loads and Physicochemical Parameters of Surface Water in Umur and Bele Streams of Benue State

2018 ◽  
Vol 6 (3) ◽  
pp. 244-251
Author(s):  
G.M. Gberikon ◽  
I.I. Adeoti ◽  
I.O. Ogbonna
Keyword(s):  
Surface Water ◽  
Solar Radiation ◽  
Water Sample ◽  
Water Samples ◽  
Moringa Oleifera ◽  
Synergistic Effects ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Ph Values ◽  
Significant Difference

Bacteriological profiles of surface water samples treated with solar radiation, Moringa oleifera powder and water guard was carried out to ascertain their effectiveness in water treatment. Bacterial loads of the surface water collected from Umur and Bele streams in Gwer East Local Government area samples were determined before and after treatments and characterised using biochemical and molecular methods. Single and synergistic effects of these treatments on water quality were also examined. Bacteriological analysis showed that Umur stream had the highest bacterial loads of 4.47 x 103 cfu/mL while Bele had the lowest counts. There was significant reduction in the mean viable counts recorded for all the water samples (p ˂ 0.05). In the daily bacteria counts, the control water samples gave extremes values. There were no bacteria count recorded following combine treatment in water samples from Bele stream on the fifth day. Molecular analysis based on the 16S rRNA gene sequence showed bacterial strains to be phylogenetically close to bacterial strains which are capable of causing infectious diseases to man. Normal pH values were recorded in Umur stream while low pH values were recorded in Bele streams. Treatment impacted significantly on the pH of the water samples from Umur stream (p ˂ 0.05) while no significant difference was observed with water samples from Bele stream (p > 0.05). Treatment impacted significantly on turbidity in water sample from Umur stream (p ˂ 0.05). Sulphate was found to be within the permissible limit except for water sample from Bele stream which gave mean values within the range of 51.00 to 68.00 mg/L. Treatments impacted no significant difference on sulphate (p > 0.05). Surface water in these rural areas should be thoroughly treated before use. Int. J. Appl. Sci. Biotechnol. Vol 6(3): 244-251

scholarly journals Microbial Composition of Human Appendices from Patients following Appendectomy

mBio ◽  
2013 ◽  
Vol 4 (1) ◽  
Author(s):  
Caitriona M. Guinane ◽  
Amany Tadrous ◽  
Fiona Fouhy ◽  
C. Anthony Ryan ◽  
Eugene M. Dempsey ◽  
...  
Keyword(s):  
Human Health ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Evolutionary Development ◽  
Rrna Gene ◽  
Limited Data ◽  
Microbial Composition ◽  
Content Type ◽  
Study Results ◽  
Human Appendix

ABSTRACT The human appendix has historically been considered a vestige of evolutionary development with an unknown function. While limited data are available on the microbial composition of the appendix, it has been postulated that this organ could serve as a microbial reservoir for repopulating the gastrointestinal tract in times of necessity. We aimed to explore the microbial composition of the human appendix, using high-throughput sequencing of the 16S rRNA gene V4 region. Seven patients, 5 to 25 years of age, presenting with symptoms of acute appendicitis were included in this study. Results showed considerable diversity and interindividual variability among the microbial composition of the appendix samples. In general, however, Firmicutes was the dominant phylum, with the majority of additional sequences being assigned at various levels to Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria. Despite the large diversity in the microbiota found within the appendix, however, a few major families and genera were found to comprise the majority of the sequences present. Interestingly, also, certain taxa not generally associated with the human intestine, including the oral pathogens Gemella, Parvimonas, and Fusobacterium, were identified among the appendix samples. The prevalence of genera such as Fusobacterium could also be linked to the severity of inflammation of the organ. We conclude that the human appendix contains a robust and varied microbiota distinct from the microbiotas in other niches within the human microbiome. The microbial composition of the human appendix is subject to extreme variability and comprises a diversity of biota that may play an important, as-yet-unknown role in human health. IMPORTANCE There are currently limited data available on the microbial composition of the human appendix. It has been suggested, however, that it may serve as a “safe house” for commensal bacteria that can reinoculate the gut at need. The present study is the first comprehensive view of the microbial composition of the appendix as determined by high-throughput sequencing. We have determined that the human appendix contains a wealth of microbes, including members of 15 phyla. Important information regarding the associated bacterial diversity of the appendix which will help determine the role, if any, the appendix microbiota has in human health is presented.

scholarly journals Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

2015 ◽  
Vol 81 (20) ◽  
pp. 7067-7077 ◽  
Author(s):  
W. Ahmed ◽  
C. Staley ◽  
M. J. Sadowsky ◽  
P. Gyawali ◽  
J. P. S. Sidhu ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Water Samples ◽  
High Throughput Sequencing ◽  
Community Analysis ◽  
Fecal Pollution ◽  
Rrna Gene ◽  
Potential Sources

ABSTRACTIn this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways.

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