scholarly journals It’s Complicated: Rapid Publication of Genomes in Microbiology Resource Announcements Can Be Both Part of the Problem and the Solution to Fungal Taxonomic Resolution

2021 ◽  
Vol 10 (48) ◽  
Author(s):  
Bradley Stevenson ◽  
Blake Stamps
Keyword(s):  
Taxonomic Resolution

scholarly journals Community structure of aquatic insects (Ephemeroptera, Plecoptera, and Trichoptera) in Cerrado streams of Paraguay, Paraná, and São Francisco river basins

2013 ◽  
Vol 13 (1) ◽  
pp. 97-107 ◽  
Author(s):  
Renato de Mei Romero ◽  
Mônica Ceneviva-Bastos ◽  
Gustavo Henrique Baviera ◽  
Lilian Casatti
Keyword(s):  
Community Structure ◽  
Aquatic Insects ◽  
Regional Differences ◽  
River Basins ◽  
Taxonomic Composition ◽  
Taxonomic Resolution ◽  
Sao Francisco River ◽  
Original Distribution ◽  
São Francisco River

We evaluated qualitatively and quantitatively the community structure of aquatic insects (Ephemeroptera, Plecoptera, and Trichoptera) in 19 streams in areas of Cerrado in the Paraguay, Paraná, and São Francisco river basins. The number of genera and taxonomic composition were compared at spatial (at the hydrographic basins level) and conservation levels (more preserved and less preserved areas). The influence of spatial and environmental factors in richness and abundance was also evaluated. The geographical distribution of Grumicha, Coryphorus, and Austrotinodes was expanded. The highest Trichoptera richness was found in the São Francisco river basin (F = 5,602, p = 0,004) and a higher number of Ephemeroptera genera occurred in the relatively less preserved sites (F = 6,835, p = 0,009). The pattern of genera distribution was different among basins (R = 0,0336, p = 0,001), but it was similar among relatively less and more preserved areas (R = -0,039, p = 0,737). These findings can be explained by the low impact level in these streams and also by the taxonomic resolution used in this study. Latitude and instream diversity were the most important factors to explain the variation in genera richness and abundance (p = 0.004 and p = 0.026, respectively). Hence, the regional differences can be attributed to spatial influences, quantity or quality of habitats and the original distribution of taxa within each basin.

scholarly journals Comparing the performance of different stream classification systems using aquatic macroinvertebrates

2013 ◽  
Vol 25 (4) ◽  
pp. 406-417 ◽  
Author(s):  
Márlon de Castro Vasconcelos ◽  
Adriano Sanches Melo ◽  
Albano Schwarzbold
Keyword(s):  
Randomization Test ◽  
Classification Systems ◽  
Data Type ◽  
Taxonomic Resolution ◽  
Stream Classification ◽  
Environment Variables ◽  
Family Level ◽  
Community Data ◽  
Performance Results ◽  
Classification Strength

AIM: We evaluated five stream classification systems observing: 1) differences in richness, abundance and macroinvertebrates communities among stream classes within classification systems; and 2) whether classification systems present better performance using macroinvertebrates. Additionally, we evaluated the effects of taxonomic resolution and data type (abundance and presence) on results. METHODS: Five stream classification systems were used, two based on hydroregions, one based on ecoregions by FEOW, a fourth one based on stream orders and the last one based on clusters of environment variables sampled in 37 streams at Rio Grande do Sul state, Brazil. We used a randomization test to evaluate differences of richness and abundance, a db-MANOVA to evaluate the differences of species assemblages and Classification Strength (CS) to evaluate the classifications performance. RESULTS: There were differences of richness and abundance among stream classes within each stream classification. The same result was found for community data, except for stream order classifications in family level. We observed that stream classes obtained for each stream classification differed in terms of environment variables (db-MANOVA). The classification based on environment variables showed higher CS values than other classification systems. The taxonomic resolution was important to the observed results. Data on genera level presented CS values 12% higher than family level for cluster classification, and the data type was dependent on the classification system and taxonomic resolution employed. CONCLUSION: Our results indicate that classifications based on cluster of environment variables was better than other stream classification systems, and similar results using genera level can be obtained for management programs using family resolution in a geographical context similar to this study.

scholarly journals Taxonomic Resolution of the Nematophagous Fungal Isolate ARF18 via Genome Sequencing

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Sandeep Sharma ◽  
Alex Z. Zaccaron ◽  
John B. Ridenour ◽  
Amy Bradshaw ◽  
Terry L. Kirkpatrick ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Novel Species ◽  
Biological Control Agent ◽  
Draft Genome ◽  
Control Agent ◽  
Nematophagous Fungus ◽  
Cyst Nematode ◽  
Fungal Isolate ◽  
Taxonomic Resolution

ABSTRACT The taxonomically uncharacterized nematophagous fungus ARF18, which parasitizes cysts, juveniles, and adults of the soybean cyst nematode (Heterodera glycines), was proposed as a nematode biological control agent in 1991. A 46.3-Mb draft genome sequence of this fungus is presented, and a tentative taxonomic identification as a novel species of Brachyphoris is proposed.

scholarly journals The use of DNA barcodes in food web construction—terrestrial and aquatic ecologists unite!

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 603-628 ◽  
Author(s):  
Tomas Roslin ◽  
Sanna Majaneva
Keyword(s):  
Food Web ◽  
Food Webs ◽  
Taxonomic Resolution ◽  
Dna Barcodes ◽  
Food Web Structure ◽  
Web Studies ◽  
Web Structure ◽  
Asking Questions ◽  
Web Construction ◽  
Interaction Webs

By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems—revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.

scholarly journals Pollinator importance networks illustrate the crucial value of bees in a highly speciose plant community

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Gavin Ballantyne ◽  
Katherine C. R. Baldock ◽  
Luke Rendell ◽  
P. G. Willmer
Keyword(s):  
Plant Species ◽  
Community Level ◽  
Taxonomic Resolution ◽  
Pollen Deposition ◽  
Pollinator Effectiveness ◽  
Flower Visitors ◽  
Pollinator Importance ◽  
Visitation Frequency ◽  
Pollinator Performance ◽  
Number Of Plant Species

AbstractAccurate predictions of pollination service delivery require a comprehensive understanding of the interactions between plants and flower visitors. To improve measurements of pollinator performance underlying such predictions, we surveyed visitation frequency, pollinator effectiveness (pollen deposition ability) and pollinator importance (the product of visitation frequency and effectiveness) of flower visitors in a diverse Mediterranean flower meadow. With these data we constructed the largest pollinator importance network to date and compared it with the corresponding visitation network to estimate the specialisation of the community with greater precision. Visitation frequencies at the community level were positively correlated with the amount of pollen deposited during individual visits, though rarely correlated at lower taxonomic resolution. Bees had the highest levels of pollinator effectiveness, with Apis, Andrena, Lasioglossum and Osmiini bees being the most effective visitors to a number of plant species. Bomblyiid flies were the most effective non-bee flower visitors. Predictions of community specialisation (H2′) were higher in the pollinator importance network than the visitation network, mirroring previous studies. Our results increase confidence in existing measures of pollinator redundancy at the community level using visitation data, while also providing detailed information on interaction quality at the plant species level.

scholarly journals A pilot study of the effect of deployment on the gut microbiome and traveler’s diarrhea susceptibility

2020 ◽  
Author(s):  
Blake W. Stamps ◽  
Wanda J. Lyon ◽  
Adam P. Irvin ◽  
Nancy Kelley-Loughnane ◽  
Michael S. Goodson
Keyword(s):  
Pilot Study ◽  
16S Rrna ◽  
Gut Microbiome ◽  
16S Rrna Gene Sequencing ◽  
Initial Study ◽  
Mitigation Strategies ◽  
Taxonomic Resolution ◽  
Rrna Gene ◽  
Traveler’S Diarrhea ◽  
Traveler's Diarrhea

AbstractTraveler’s diarrhea (TD) is a recurrent and significant issue for many travelers including the military. While many known enteric pathogens exist that are causative agents of diarrhea, our gut microbiome may also play a role in travelers’ diarrhea susceptibility. To this end we conducted a pilot study of the microbiome of warfighters prior to- and after deployment overseas to identify marker taxa relevant to traveler’s diarrhea. This initial study utilized full-length 16S rRNA gene sequencing to provide additional taxonomic resolution towards identifying predictive taxa.16S rRNA analyses of pre- and post-deployment fecal samples identified multiple marker taxa as significantly differentially abundant in subjects that reported diarrhea, including Weissella, Butyrivibrio, Corynebacterium, uncultivated Erysipelotrichaceae, Jeotgallibaca, unclassified Ktedonobacteriaceae, Leptolinea, and uncultivated Ruminiococcaceae. The ability to identify TD risk prior to travel will inform prevention and mitigation strategies to influence diarrhea susceptibility while traveling.

scholarly journals The use of eDNA and DNA metabarcoding in monitoring the ecological condition of Norwegian lakes

2021 ◽  
Vol 4 ◽  
Author(s):  
Sara Atienza Casas ◽  
Markus Majaneva ◽  
Thomas Jensen ◽  
Marie Davey ◽  
Frode Fossøy ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Ecological Status ◽  
Ecological Condition ◽  
Molecular Techniques ◽  
Taxonomic Resolution ◽  
Potential Cost ◽  
Running Water ◽  
National Monitoring ◽  
Monitoring Programs ◽  
Dna Metabarcoding

Biodiversity assessments using molecular identification of organisms through high-throughput sequencing techniques have been a game changer in ecosystem monitoring, providing increased taxonomic resolution, more objective identifications, potential cost reductions, and reduced processing times. The use of DNA metabarcoding of bulk samples and environmental DNA (eDNA) is now widespread but is not yet universally implemented in national monitoring programs. While bulk sample metabarcoding involves extraction of DNA from organisms in a sample, eDNA analysis involves obtaining DNA directly from environmental samples, which can include microorganisms, meiofauna-size taxa and macrofauna traces such as larval stages, skin and hair cells, gametes, faeces and free DNA bound to particles. In Norway, freshwater biomonitoring in compliance with the EU Water Framework Directive (WFD) is conducted on several administrative levels, including national monitoring programs for running water, small and large lakes. These programs typically focus on a fraction of the actual biodiversity present in the monitored habitats (Weigand 2019). DNA metabarcoding of both bulk samples and eDNA samples are relevant tools for future freshwater biomonitoring in Norway. The aim of this PhD project is to develop assessment protocols based on DNA-metabarcoding and eDNA of benthic invertebrates, microcrustaceans and fish that can be used as standard biomonitoring tools to assess the ecological condition of lakes. The main topics addressed will be: - Development of protocols throughout the eDNA-metabarcoding workflow (i.e. sampling, filtration, preservation, extraction, amplification and sequencing) suitable to execute biodiversity assessments and determine the ecological status of lakes. - Comparison of the results obtained using molecular tools and traditional morphology-based approaches in order to assess the feasibility of such techniques to be incorporated as standard biomonitoring tools, such as the ones implemented under the provisions of the WFD. - Evaluate the effect of improved taxonomic resolution from molecular techniques on determining the ecological status of lakes, both by broadening the number of taxa analyzed and by identifying more taxa to species level. - Assess the feasibility of using eDNA extracted from water samples, taken at different depths and fish densities, to measure fish abundance/biomass as a proxy to calculate the ecological quality indices regulated in the WFD. - Analyze the coverage and resolution provided by reference libraries for certain taxa, such as crustacea, in order to assess the reliability and precision of taxonomic assignments.

Can top-down and bottom-up forces explain phytoplankton structure in a subtropical and shallow groundwater-connected lake?

2015 ◽  
Vol 66 (12) ◽  
pp. 1106 ◽  
Author(s):  
Diego Frau ◽  
Melina Devercelli ◽  
Susana José de Paggi ◽  
Pablo Scarabotti ◽  
Gisela Mayora ◽  
...  
Keyword(s):  
Shallow Groundwater ◽  
Resource Limitation ◽  
River System ◽  
High Water ◽  
Taxonomic Resolution ◽  
Dominant Group ◽  
Top Down ◽  
Bottom Up ◽  
Physico Chemical ◽  
Phytoplankton Structure

Bottom-up and top-down control of phytoplankton is one of the most important hypothesis that explains and predicts the structure of aquatic community. Our aim was to elucidate whether predation and resource limitation can control phytoplankton composition and abundance in a subtropical shallow lake with groundwater connection to the river system. During 12 months, the lake was sampled at three points. Physico-chemical parameters, phytoplankton and zooplankton were sampled fortnightly, whereas fish were sampled every 3 months. The results showed that Euglenophyta dominated the total biovolume, followed by Dinophyta and Cryptophyta. As for the species composition, Chlorophyta was the dominant group (80 species recorded), followed by phylum Cyanobacteria (26 species recorded). Redundancy analysis (RDA) indicated that temperature and nitrate + nitrite concentration mainly explained biovolume changes, with zooplankton predation not having any measurable effect on phytoplankton during the high-water (HW) period. During low-water (LW) period top-down by fish was more important. At higher taxonomic resolution (species biovolume), phosphorus was another controlling factor. We concluded that phytoplankton in this lake is mainly regulated by hydrological changes as a macrofactor that affects nutrient availability and other environmental conditions. Even though bottom-up top-down forces do not have a central effect, we found evidence of positive nutrient influences at the HW period and fish effect at the LW period.

Sign in / Sign up

Export Citation Format

Share Document