scholarly journals Monitoring riverine fish communities through eDNA metabarcoding: determining optimal sampling strategies along an altitudinal and biodiversity gradient

2018 ◽  
Vol 2 ◽  
Author(s):  
Jonas Bylemans ◽  
Dianne M. Gleeson ◽  
Mark Lintermans ◽  
Christopher M. Hardy ◽  
Matthew Beitzel ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Species Abundance ◽  
Spatial Sampling ◽  
Optimal Sampling ◽  
Sampling Strategies ◽  
Sampling Intensity ◽  
Fish Biodiversity ◽  
Adequate Sampling ◽  
Riverine Fish ◽  
The Impact

Monitoring aquatic biodiversity through DNA extracted from environmental samples (eDNA) combined with high-throughput sequencing, commonly referred to as eDNA metabarcoding, is increasing in popularity within the scientific community. However, sampling strategies, laboratory protocols and analytical pipelines can influence the results of eDNA metabarcoding surveys. While the impact of laboratory protocols and analytical pipelines have been extensively studied, the importance of sampling strategies on eDNA metabarcoding surveys has not received the same attention. To avoid underestimating local biodiversity, adequate sampling strategies (i.e. sampling intensity and spatial sampling replication) need to be implemented. This study evaluated the impact of sampling strategies along an altitudinal and biodiversity gradient in the upper section of the Murrumbidgee River (Murray-Darling Basin, Australia). An eDNA metabarcoding survey was used to determine the local fish biodiversity and evaluate the influence of sampling intensity and spatial sampling replication on the biodiversity estimates. The results show that optimal eDNA sampling strategies varied between sites and indicate that river morphology, species richness and species abundance affect the optimal sampling intensity and spatial sampling replication needed to accurately assess the fish biodiversity. While the generality of the patterns will need to be confirmed through future studies, these findings provide a basis to guide future eDNA metabarcoding surveys in river systems.

scholarly journals Impact of satellite viewing-swath width on global and regional aerosol optical thickness statistics and trends

2014 ◽  
Vol 7 (7) ◽  
pp. 2313-2335 ◽  
Author(s):  
P. R. Colarco ◽  
R. A. Kahn ◽  
L. A. Remer ◽  
R. C. Levy
Keyword(s):  
Optical Thickness ◽  
Radiative Forcing ◽  
Aerosol Optical Thickness ◽  
Spatial Sampling ◽  
Sampling Strategies ◽  
Data Set ◽  
Modis Data ◽  
Aerosol Loading ◽  
The Impact ◽  
Single Pixel

Abstract. We use the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite aerosol optical thickness (AOT) product to assess the impact of reduced swath width on global and regional AOT statistics and trends. Along-track and across-track sampling strategies are employed, in which the full MODIS data set is sub-sampled with various narrow-swath (~ 400–800 km) and single pixel width (~ 10 km) configurations. Although view-angle artifacts in the MODIS AOT retrieval confound direct comparisons between averages derived from different sub-samples, careful analysis shows that with many portions of the Earth essentially unobserved, spatial sampling introduces uncertainty in the derived seasonal–regional mean AOT. These AOT spatial sampling artifacts comprise up to 60% of the full-swath AOT value under moderate aerosol loading, and can be as large as 0.1 in some regions under high aerosol loading. Compared to full-swath observations, narrower swath and single pixel width sampling exhibits a reduced ability to detect AOT trends with statistical significance. On the other hand, estimates of the global, annual mean AOT do not vary significantly from the full-swath values as spatial sampling is reduced. Aggregation of the MODIS data at coarse grid scales (10°) shows consistency in the aerosol trends across sampling strategies, with increased statistical confidence, but quantitative errors in the derived trends are found even for the full-swath data when compared to high spatial resolution (0.5°) aggregations. Using results of a model-derived aerosol reanalysis, we find consistency in our conclusions about a seasonal–regional spatial sampling artifact in AOT. Furthermore, the model shows that reduced spatial sampling can amount to uncertainty in computed shortwave top-of-atmosphere aerosol radiative forcing of 2–3 W m−2. These artifacts are lower bounds, as possibly other unconsidered sampling strategies would perform less well. These results suggest that future aerosol satellite missions having significantly less than full-swath viewing are unlikely to sample the true AOT distribution well enough to obtain the statistics needed to reduce uncertainty in aerosol direct forcing of climate.

Designing For Diversity: Implications for Research and Practice

2020 ◽  
Vol 64 (1) ◽  
pp. 563-567
Author(s):  
Abigail R. Wooldridge ◽  
Rod D. Roscoe ◽  
Rod D. Roscoe ◽  
Shannon C. Roberts ◽  
Rupa Valdez ◽  
...  
Keyword(s):  
Interdisciplinary Teams ◽  
Team Science ◽  
Participatory Methods ◽  
Sampling Strategies ◽  
Design Problems ◽  
Sociotechnical System ◽  
The Past ◽  
Diversity Committee ◽  
The Impact ◽  
Equity And Inclusion

The Diversity Committee of HFES has led sessions at the Annual Meeting for the past three years focused on improving diversity, equity and inclusion in the society as well as providing support to human factors and ergonomics (HF/E) researchers and practitioners who aim to apply HF/E knowledge and principles to improve diversity, equity and inclusion through their work. In this panel, we bring together researchers actively engaged in designing technology and systems by considering issues of diversity, equity and inclusion to share insights and methods. Topics include the thoughtful design of sampling strategies and research approaches, alternative and participatory methods to understand the impact of automation and technology on equity, scoping design problems to be inclusive and equitable through interdisciplinary partnerships, and the application of sociotechnical system design and team science to develop interdisciplinary teams. By sharing our experiences, we hope to prepare others to successfully approach these topics.

Effects of pH shock on microaerobic activated sludge system with a graphene oxide/nano-magnetic powder composite

2020 ◽  
Vol 35 (3) ◽  
pp. 457-463
Author(s):  
Huixia Lan ◽  
Xiangzhi Wang ◽  
Shixin Qi ◽  
Da Yang ◽  
Hao Zhang
Keyword(s):  
Graphene Oxide ◽  
Activated Sludge ◽  
High Throughput Sequencing ◽  
Impact Resistance ◽  
Magnetic Powder ◽  
Blank Group ◽  
Activated Sludge System ◽  
Ph Shock ◽  
Dominant Bacteria ◽  
The Impact

AbstractUsing the acclimated activated sludge from the pulping middle-stage effluent, the effect of pH shock on the micro-oxygen activated sludge system with a nano-magnetic powder/graphene oxide composite was studied. The results showed that the removal rates of chemical oxygen demand (CODCr) and ultraviolet adsorption at 254 nm (UV254) decreased. Also, the sludge settling performance was poor due to the impact of pH, but the impact resistance of nano-magnetic powder/graphene oxide group (MGO group) was higher and the recovery was faster. Results of high throughput sequencing indicated that the diversity of microbial community was reduced by the impact of pH, but it was significantly higher in MGO group than in the blank group. The dominant bacteria after pH shock or recovery in both of the system had a large difference. The percentage of the dominant bacteria in the MGO group was higher than that in the blank group. The MGO group had higher electron transfer system (ETS) activity which made the system having a strong pH impact resistance.

scholarly journals Assessing Habitat Vulnerability and Loss of Naturalness: Applying the GLOBIO3 Model in the Czech Republic

2021 ◽  
Vol 13 (10) ◽  
pp. 5355
Author(s):  
Vilém Pechanec ◽  
Ondřej Cudlín ◽  
Miloš Zapletal ◽  
Jan Purkyt ◽  
Lenka Štěrbová ◽  
...  
Keyword(s):  
Land Use ◽  
Czech Republic ◽  
Habitat Quality ◽  
Species Abundance ◽  
Biodiversity Loss ◽  
Infrastructure Development ◽  
Natural Habitats ◽  
The Czech Republic ◽  
New Equation ◽  
The Impact

Global and regional biodiversity loss is caused by several drivers including urban development, land use intensification, overexploitation of natural resources, environmental pollution, and climate change. The main aim of our study was to adapt the GLOBIO3 model to the conditions of the Czech Republic (CR) to assess loss of naturalness and biodiversity vulnerability at the habitat level on a detailed scale across the entire CR. An additional aim was to assess the main drivers affecting the biodiversity of habitat types. The GLOBIO3 model was adapted to CZ-GLOBIO by adapting global to local scales and using habitat quality and naturalness data instead of species occurrence data. The total mean species abundance (MSA) index of habitat quality, calculated from the spatial overlay of the four MSA indicators by our new equation, reached the value 0.62. The total value of MSA for natural and near-natural habitats was found to be affected mainly by infrastructure development and fragmentation. Simultaneously, intensity of land use change and atmospheric nitrogen deposition contributed primarily to the low total value of MSA for distant natural habitats. The CZ-GLOBIO model can be an important tool in political decision making to reduce the impact of the main drivers on habitat biodiversity in the CR.

scholarly journals 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

scholarly journals Assessing Genotypic and Environmental Effects on Endophyte Communities of Fraxinus (Ash) Using Culture Dependent and Independent DNA Sequencing

2021 ◽  
Vol 7 (7) ◽  
pp. 565
Author(s):  
Anindita Lahiri ◽  
Brian R. Murphy ◽  
Trevor R. Hodkinson
Keyword(s):  
Community Composition ◽  
Environmental Effects ◽  
High Throughput Sequencing ◽  
Fungal Community Composition ◽  
Species Identity ◽  
Ash Dieback ◽  
Hymenoscyphus Fraxineus ◽  
Culture Independent ◽  
The Impact ◽  
Culture Dependent

Fraxinus excelsior populations are in decline due to the ash dieback disease Hymenoscyphus fraxineus. It is important to understand genotypic and environmental effects on its fungal microbiome to develop disease management strategies. To do this, we used culture dependent and culture independent approaches to characterize endophyte material from contrasting ash provenances, environments, and tissues (leaves, roots, seeds). Endophytes were isolated and identified using nrITS, LSU, or tef DNA loci in the culture dependent assessments, which were mostly Ascomycota and assigned to 37 families. Few taxa were shared between roots and leaves. The culture independent approach used high throughput sequencing (HTS) of nrITS amplicons directly from plant DNA and detected 35 families. Large differences were found in OTU diversity and community composition estimated by the contrasting approaches and these data need to be combined for estimations of the core endophyte communities. Species richness and Shannon index values were highest for the leaf material and the French population. Few species were shared between seed and leaf tissue. PCoA and NMDS of the HTS data showed that seed and leaf microbiome communities were highly distinct and that there was a strong influence of Fraxinus species identity on their fungal community composition. The results will facilitate a better understanding of ash fungal ecology and are a step toward identifying microbial biocontrol systems to minimize the impact of the disease.

scholarly journals Optimal Sampling Strategies for Detecting Zoonotic Disease Epidemics

2014 ◽  
Vol 10 (6) ◽  
pp. e1003668 ◽  
Author(s):  
Jake M. Ferguson ◽  
Jessica B. Langebrake ◽  
Vincent L. Cannataro ◽  
Andres J. Garcia ◽  
Elizabeth A. Hamman ◽  
...  
Keyword(s):  
Zoonotic Disease ◽  
Optimal Sampling ◽  
Sampling Strategies ◽  
Disease Epidemics

scholarly journals A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5382 ◽  
Author(s):  
Fernanda Cornejo-Granados ◽  
Luigui Gallardo-Becerra ◽  
Miriam Leonardo-Reza ◽  
Juan Pablo Ochoa-Romo ◽  
Adrian Ochoa-Leyva
Keyword(s):  
Developmental Stage ◽  
High Throughput Sequencing ◽  
Meta Analysis ◽  
Biological Factor ◽  
Rrna Gene ◽  
Wild Type ◽  
Biological Factors ◽  
Sequencing Data ◽  
Freshwater Environment ◽  
The Impact

The shrimp or prawn is the most valuable traded marine product in the world market today and its microbiota plays an essential role in its development, physiology, and health. The technological advances and dropping costs of high-throughput sequencing have increased the number of studies characterizing the shrimp microbiota. However, the application of different experimental and bioinformatics protocols makes it difficult to compare different studies to reach general conclusions about shrimp microbiota. To meet this necessity, we report the first meta-analysis of the microbiota from freshwater and marine shrimps using all publically available sequences of the 16S ribosomal gene (16S rRNA gene). We obtained data for 199 samples, in which 63.3% were from marine (Alvinocaris longirostris, Litopenaeus vannamei and Penaeus monodon), and 36.7% were from freshwater (Macrobrachium asperulum, Macrobrachium nipponense, Macrobranchium rosenbergii, Neocaridina denticulata) shrimps. Technical variations among studies, such as selected primers, hypervariable region, and sequencing platform showed a significant impact on the microbiota structure. Additionally, the ANOSIM and PERMANOVA analyses revealed that the most important biological factor in structuring the shrimp microbiota was the marine and freshwater environment (ANOSIM R = 0.54, P = 0.001; PERMANOVA pseudo-F = 21.8, P = 0.001), where freshwater showed higher bacterial diversity than marine shrimps. Then, for marine shrimps, the most relevant biological factors impacting the microbiota composition were lifestyle (ANOSIM R = 0.341, P = 0.001; PERMANOVA pseudo-F = 8.50, P = 0.0001), organ (ANOSIM R = 0.279, P = 0.001; PERMANOVA pseudo-F = 6.68, P = 0.001) and developmental stage (ANOSIM R = 0.240, P = 0.001; PERMANOVA pseudo-F = 5.05, P = 0.001). According to the lifestyle, organ, developmental stage, diet, and health status, the highest diversity were for wild-type, intestine, adult, wild-type diet, and healthy samples, respectively. Additionally, we used PICRUSt to predict the potential functions of the microbiota, and we found that the organ had more differentially enriched functions (93), followed by developmental stage (12) and lifestyle (9). Our analysis demonstrated that despite the impact of technical and bioinformatics factors, the biological factors were also statistically significant in shaping the microbiota. These results show that cross-study comparisons are a valuable resource for the improvement of the shrimp microbiota and microbiome fields. Thus, it is important that future studies make public their sequencing data, allowing other researchers to reach more powerful conclusions about the microbiota in this non-model organism. To our knowledge, this is the first meta-analysis that aims to define the shrimp microbiota.

scholarly journals Heat Stress Alters the Intestinal Microbiota and Metabolomic Profiles in Mice

2021 ◽  
Vol 12 ◽  
Author(s):  
Chaoyue Wen ◽  
Siyu Li ◽  
Jiaojiao Wang ◽  
Yimin Zhu ◽  
Xin Zong ◽  
...  
Keyword(s):  
Heat Stress ◽  
Fatty Acid ◽  
High Temperature ◽  
Intestinal Microbiota ◽  
High Throughput Sequencing ◽  
Acid Metabolism ◽  
Core Body Temperature ◽  
Control Group ◽  
Serum Biochemical ◽  
The Impact

BackgroundHeat stress has negative effects on the intestinal health of humans and animals. However, the impact of heat stress on intestinal microbial and metabolic changes remains elusive. Here, we investigated the cecal microbial and metabolic profiles in mice in response to heat stress.MethodsThe mouse heat stress model was constructed by simulating a high-temperature environment. Twenty mice were randomly assigned to two groups, the control group (CON, 25°C) and the heat treatment group (HS, 40°C from 13:00 to 15:00 every day for 7 days). Serum and cecal contents were collected from the mice for serum biochemical analysis, 16S rRNA high-throughput sequencing, and non-targeted metabolomics.ResultsBoth core body temperature and water intake were significantly increased in the HS group. Serum biochemical indicators were also affected, including significantly increased triglyceride and decreased low-density lipoprotein in the heat stress group. The composition and structure of intestinal microbiota were remarkably altered in the HS group. At the species level, the relative abundance of Candidatus Arthromitus sp. SFB-mouse-Japan and Lactobacillus murinus significantly reduced, while that of Lachnospiraceae bacterium 3-1 obviously increased after HS. Metabolomic analysis of the cecal contents clearly distinguished metabolite changes between the groups. The significantly different metabolites identified were mainly involved in the fatty acid synthesis, purine metabolism, fatty acid metabolism, cyanoamino acid metabolism, glyceride metabolism, and plasmalogen synthesis.ConclusionIn summary, high temperature disrupted the homeostatic balance of the intestinal microbiota in mice and also induced significant alterations in intestinal metabolites. This study provides a basis for treating intestinal disorders caused by elevated temperature in humans and animals and can further formulate nutritional countermeasures to reduce heat stress-induced damage.

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