scholarly journals Linkages between reach-scale physical habitat and invertebrate assemblages in upland streams

2015 ◽  
Vol 66 (5) ◽  
pp. 438 ◽  
Author(s):  
Victoria S. Milner ◽  
Nigel J. Willby ◽  
David J. Gilvear ◽  
Charles Perfect
Keyword(s):  
Ecological Status ◽  
Biological Data ◽  
Species Level ◽  
Taxonomic Resolution ◽  
Initial Assessment ◽  
Physical Habitat ◽  
Biological Structure ◽  
Invertebrate Assemblages ◽  
Macroinvertebrate Species ◽  
Baetis Rhodani

Determining the influence of physical habitat on biological structure in minimally disturbed settings is important if the effects of alterations to physical habitat are to be understood. This study tested whether reach-scale differences in physical habitat influence macroinvertebrate community composition at 24 sites in the Cairngorm Mountains, Scotland. Stream reaches were classified into channel types based on a geomorphic typology (i.e. step-pool, bedrock, plane-bed and pool-riffle). PERMANOVA indicated an overall significant relationship between the geomorphic typology and macroinvertebrate species-level composition, and among all combinations of channel types (such as step-pool and pool-riffle, step-pool and bedrock). Most channel types were dominated by high abundances of Baetis rhodani, Rhithrogena semicolorata and Leuctra inermis, which are ubiquitous in unpolluted gravel-bedded Scottish streams. However, reflecting significant differences in abundance of commoner taxa between types, indicator value (IndVal) analysis revealed that pool-riffle reaches were characterised by elmids (Limnius sp. and Oulimnius sp.) and Caenis rivulorum, and step-pool reaches by Alainites muticus, B. rhodani, L. inermis and Brachyptera risi. Geomorphic typing of rivers provides a useful basis for the initial assessment of ecological status whereas abundance-based biological data processed at the appropriate taxonomic resolution should be sensitive to physical-habitat modifications.

scholarly journals Adding DNA barcoding to stream monitoring protocols – What’s the additional value and congruence between morphological and molecular identification approaches?

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0244598
Author(s):  
Simone Behrens-Chapuis ◽  
Fabian Herder ◽  
Matthias F. Geiger
Keyword(s):  
Dna Barcoding ◽  
Cost Benefit Analysis ◽  
Ecological Status ◽  
Species Level ◽  
Aquatic Macroinvertebrates ◽  
Taxonomic Resolution ◽  
Morphological Identification ◽  
Stream Monitoring ◽  
Monitoring Protocols ◽  
Additional Value

Although aquatic macroinvertebrates and freshwater fishes are important indicators for freshwater quality assessments, the morphological identification to species-level is often impossible and thus especially in many invertebrate taxa not mandatory during Water Framework Directive monitoring, a pragmatism that potentially leads to information loss. Here, we focus on the freshwater fauna of the River Sieg (Germany) to test congruence and additional value in taxa detection and taxonomic resolution of DNA barcoding vs. morphology-based identification in monitoring routines. Prior generated morphological identifications of juvenile fishes and aquatic macroinvertebrates were directly compared to species assignments using the identification engine of the Barcode of Life Data System. In 18% of the invertebrates morphology allowed only assignments to higher systematic entities, but DNA barcoding lead to species-level assignment. Dissimilarities between the two approaches occurred in 7% of the invertebrates and in 1% of the fishes. The 18 fish species were assigned to 20 molecular barcode index numbers, the 104 aquatic invertebrate taxa to 113 molecular entities. Although the cost-benefit analysis of both methods showed that DNA barcoding is still more expensive (5.30–8.60€ per sample) and time consuming (12.5h), the results emphasize the potential to increase taxonomic resolution and gain a more complete profile of biodiversity, especially in invertebrates. The provided reference DNA barcodes help building the foundation for metabarcoding approaches, which provide faster sample processing and more cost-efficient ecological status determination.

scholarly journals Phenology of myxomycetes in Turrialba, Costa Rica

Karstenia ◽  
2021 ◽  
pp. 1-12
Author(s):  
Carlos Rojas ◽  
Pedro A. Rojas ◽  
Steven L. Stephenson
Keyword(s):  
Costa Rica ◽  
Southern Oscillation ◽  
Biological Data ◽  
Species Level ◽  
Ecological Effect ◽  
Sampling Effort ◽  
Ecosystem Structure ◽  
Forest Patch ◽  
Local Climate ◽  
Substrate Quality

Long-term monitoring and phenological patterns of microbial communities are rare in the scientific literature. Myxomycetes have life cycle characteristics that allow both to be documented. The present study summarizes the integrated floristic and bioclimatic components of a 30-month assessment of myxomycete sporocarps in a premontane tropical forest in Turrialba, Costa Rica. Based on monthly visits and a standard sampling effort of 120 minutes per visit, myxomycetes were recorded on leaves, twigs, and logs on the ground by two to three people in 20-minute periods associated with six different collecting sites within a 34-hectare successional forest patch. Biological data were analyzed using three recorded climatic variables obtained <em>in situ</em> during the complete period of study. Also, the Oceanic Niño Index (ONI), provided by NOAA, an estimate of El Niño-Southern Oscillation (ENSO), was evaluated in the analyses. Overall, 54 species and 2245 records of myxomycetes were recorded, with an average of 14.5 species (range between 6-24) and 78.4 records (range between 20-110) detected each month. In general, neither the number of records nor the number of species were associated with individual climate variables, but multiple regression analyses showed that a combination of the accumulated precipitation of the four days before sampling and the average relative humidity can explain most of the fruiting dynamics (R2 = 0.56). When the ONI index was included in the analyses, the explained variability increased (R2 = 0.64), and when a categorization of months based on the same index was used, analyses showed that both the number of records and species evenness were affected by ENSO. At the species level, <em>Hemitrichia calyculata</em> was the only species observed during every month, closely followed by <em>Arcyria cinerea</em>, <em>A. denudata</em>, and <em>Physarum compressum</em>, recorded on most visits. Sporadic fruiting in some species such as <em>Tubifera microsperma</em>, <em>P. tenerum</em>, <em>P. bogoriense</em>, <em>P. melleum</em>, and <em>Metatrichia vesparia</em> could have been associated with local climate oscillations influenced by ENSO patterns. Phenological patterns were observed at the species level, indicating that in the Neotropics, under favorable conditions, myxomycete sporocarps are practically always present, but species assemblages vary temporally. These variations are primarily driven by local climate, but regional climate dynamics also affect fruiting patterns. Presumably, the remaining ecological effect on fruiting patterns in the Neotropics can be attributed to certain finer factors such as ecosystem structure, substrate quality/ availability, and biotic interactions. As such, phenomena such as climate change can have an important effect on the production of sporocarps by tropical myxomycetes, with subsequent effects of their ecological dynamics.

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.

Genetic diversity of three Aegla species (Decapoda, Anomura) revealed by AFLP and mtDNA markers

Crustaceana ◽  
2019 ◽  
Vol 92 (4) ◽  
pp. 445-462
Author(s):  
Bianca L. Zimmermann ◽  
Jober V. De Vargas Machado ◽  
Sandro Santos ◽  
Marlise L. Bartholomei-Santos
Keyword(s):  
Genetic Diversity ◽  
Distinct Species ◽  
Genetic Distances ◽  
Species Level ◽  
Taxonomic Resolution ◽  
Similar Species ◽  
Southern Brazil ◽  
Low Levels ◽  
Management And Conservation ◽  
Mtdna Markers

Abstract Representatives of the genus Aegla present a conserved morphology; thus, the increased use of molecular markers has raised many taxonomic issues. We used AFLP and mtDNA to investigate the genetic differentiation and phylogenetic relationships of morphologically similar species with overlapping distribution areas in southern Brazil: A. georginae, A. ludwigi, and A. platensis. While A. platensis is widely distributed, the critically endangered A. georginae and A. ludwigi have limited distributions. Although both markers showed populations with low levels of genetic variability, they differed markedly in revealing relationships between populations; according to AFLP, the genetic distances between A. platensis populations were as high as those between distinct species, a result not observed when considering mtDNA data. We emphasize that the use of multiple lines of evidence is necessary for defining correct levels of genetic diversity and a good species-level taxonomic resolution. Such features are essential for the management and conservation of Aegla species.

Taxonomic and numerical sufficiency in depth- and salinity-controlled marine paleocommunities

Paleobiology ◽  
2017 ◽  
Vol 43 (3) ◽  
pp. 463-478 ◽  
Author(s):  
Martin Zuschin ◽  
Rafał Nawrot ◽  
Mathias Harzhauser ◽  
Oleg Mandic ◽  
Adam Tomašových
Keyword(s):  
Compositional Data ◽  
Environmental Gradients ◽  
Community Response ◽  
Species Level ◽  
Taxonomic Resolution ◽  
Physical Parameters ◽  
Level Data ◽  
Numerical Transformation ◽  
Variation Explained ◽  
Intertidal Habitats

AbstractNumerical and taxonomic resolution of compositional data sets affects investigators’ abilities to detect and measure relationships between communities and environmental factors. We test whether varying numerical (untransformed, square-root- and fourth-root-transformed relative abundance and presence–absence data) and taxonomic (species, genera, families) resolutions reveals different insights into early to middle Miocene molluscan communities along bathymetric and salinity gradients. The marine subtidal has a more even species-abundance distribution, a higher number of rare species, and higher species:family and species:genus ratios than the three habitats—marine and estuarine intertidal, estuarine subtidal—with higher fluctuations in salinity and other physical parameters. Taxonomic aggregation and numerical transformation of data result in very different ordinations, although all habitats differ significantly from one another at all taxonomic and numerical levels. Rank correlations between species-level and higher-taxon, among-sample dissimilarities are very high for proportional abundance and decrease strongly with increasing numerical transformation, most notably in the two intertidal habitats. The proportion of variation explained by depth is highest for family-level data, decreases gradually with numerical transformation, and is higher in marine than in estuarine habitats. The proportion of variation explained by salinity is highest for species-level data, increases gradually with numerical transformation, and is higher in subtidal than in intertidal habitats. Therefore, there is no single best numerical and taxonomic resolution for the discrimination of communities along environmental gradients: the “best” resolution depends on the environmental factor considered and the nature of community response to it. Different numerical and taxonomic transformations capture unique aspects of metacommunity assembly along environmental gradients that are not detectable at a single level of resolution. We suggest that simultaneous analyses of community gradients at multiple taxonomic and numerical resolutions provide novel insights into processes responsible for spatial and temporal community stability.

scholarly journals Towards a Post-Graduate Level Curriculum for Biodiversity Informatics. Perspectives from the Global Biodiversity Information Facility (GBIF) Community

2021 ◽  
Vol 9 ◽  
Author(s):  
Fatima Parker-Allie ◽  
Francisco Pando ◽  
Anders Telenius ◽  
Jean Ganglo ◽  
Danny Vélez ◽  
...  
Keyword(s):  
Biological Data ◽  
Initial Assessment ◽  
Biodiversity Informatics ◽  
Global Biodiversity Information Facility ◽  
Policy Makers ◽  
Academic Teaching ◽  
E Learning ◽  
Learning Platforms ◽  
Global Biodiversity ◽  
Biodiversity Information

Biodiversity informatics is a new and evolving field, requiring efforts to develop capacity and a curriculum for this field of science. The main objective was to summarise the level of activity and the efforts towards developing biodiversity informatics curricula, for work-based training and/or academic teaching at universities, taking place within the Global Biodiversity Information Facility (GBIF) countries and its associated network. A survey approach was used to identify existing capacities and resources within the network. Most of GBIF Nodes survey respondents (80%) are engaged in onsite training activities, with a focus on work-based professionals, mostly researchers, policy-makers and students. Training topics include data mobilisation, digitisation, management, publishing, analysis and use, to enable the accessibility of analogue and digital biological data that currently reside as scattered datasets. An initial assessment of academic teaching activities highlighted that countries in most regions, to varying degrees, were already engaged in the conceptualisation, development and/or implementation of formal academic programmes in biodiversity informatics, including programmes in Benin, Colombia, Costa Rica, Finland, France, India, Norway, South Africa, Sweden, Taiwan and Togo. Digital e-learning platforms were an important tool to help build capacity in many countries. In terms of the potential in the Nodes network, 60% expressed willingness to be recruited or commissioned for capacity enhancement purposes. Contributions and activities of various country nodes across the network have been highlighted and a working curriculum framework has been defined.

scholarly journals Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer

2015 ◽  
Author(s):  
Alfonso Benítez-Páez ◽  
Kevin J. Portune ◽  
Yolanda Sanz
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Taxonomic Resolution ◽  
Universal Primers ◽  
Rrna Gene ◽  
Rdna Sequences ◽  
Dna Sequencer

AbstractBackgroundThe miniaturised and portable DNA sequencer MinIONTM has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide variety of genetic approaches. This technology has demonstrated great potential, especially in genome-wide analyses. In this study, we tested the ability of the MinIONTM system to perform amplicon sequencing in order to design new approaches to study microbial diversity using nearly full-length 16S rDNA sequences.ResultsUsing R7.3 chemistry, we generated more than 3.8 million events (nt) during a single sequencing run. These data were sufficient to reconstruct more than 90% of the 16S rRNA gene sequences for 20 different species present in a mock reference community. After read mapping and 16S rRNA gene assembly, consensus sequences and 2d reads were recovered to assign taxonomic classification down to the species level. Additionally, we were able to measure the relative abundance of all the species present in a mock community and detected a biased species distribution originating from the PCR reaction using ‘universal’ primers.ConclusionsAlthough nanopore-based sequencing produces reads with lower per-base accuracy compared with other platforms, the MinIONTM DNA sequencer is valuable for both high taxonomic resolution and microbial diversity analysis. Improvements in nanopore chemistry, such as minimising base-calling errors and the nucleotide bias reported here for 16S amplicon sequencing, will further deliver more reliable information that is useful for the specific detection of microbial species and strains in complex ecosystems.

scholarly journals Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1966 ◽  
Author(s):  
Vasco Elbrecht ◽  
Pierre Taberlet ◽  
Tony Dejean ◽  
Alice Valentini ◽  
Philippe Usseglio-Polatera ◽  
...  
Keyword(s):  
Species Level ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Reference Database ◽  
Bias Estimation ◽  
Knowing That ◽  
Dna Metabarcoding ◽  
Local Reference ◽  
Comprehensive Survey ◽  
Reference Databases

Cytochrome c oxidase I (COI) is a powerful marker for DNA barcoding of animals, with good taxonomic resolution and a large reference database. However, when used for DNA metabarcoding, estimation of taxa abundances and species detection are limited due to primer bias caused by highly variable primer binding sites across the COI gene. Therefore, we explored the ability of the 16S ribosomal DNA gene as an alternative metabarcoding marker for species level assessments. Ten bulk samples, each containing equal amounts of tissue from 52 freshwater invertebrate taxa, were sequenced with the Illumina NextSeq 500 system. The 16S primers amplified three more insect species than the Folmer COI primers and amplified more equally, probably due to decreased primer bias. Estimation of biomass might be less biased with 16S than with COI, although variation in read abundances of two orders of magnitudes is still observed. According to these results, the marker choice depends on the scientific question. If the goal is to obtain a taxonomic identification at the species level, then COI is more appropriate due to established reference databases and known taxonomic resolution of this marker, knowing that a greater proportion of insects will be missed using COI Folmer primers. If the goal is to obtain a more comprehensive survey the 16S marker, which requires building a local reference database, or optimised degenerated COI primers could be more appropriate.

An overview of the Syrphidae (Diptera) of Saudi Arabia

Zootaxa ◽  
2020 ◽  
Vol 4855 (1) ◽  
pp. 1-69
Author(s):  
HASSAN A. DAWAH ◽  
MOHAMMED A. ABDULLAH ◽  
SYED KAMRAN AHMAD ◽  
HATHAL AL-DHAFER ◽  
JAMES TURNER
Keyword(s):  
Saudi Arabia ◽  
World Wide ◽  
Wide Distribution ◽  
Biological Data ◽  
Species Level ◽  
Site Quality ◽  
Ecological Studies ◽  
Light Traps ◽  
Plant Pests ◽  
Malaise Traps

Despite the species richness of hoverflies (Diptera: Syrphidae) world-wide (about 6,200 species) and their role as agents for controlling plant pests, their significance as pollinators, and as bioindicators of site quality, hoverfly fauna of Saudi Arabia is poorly known. In exploring the biodiversity of Diptera in southwest Saudi Arabia a survey of the hoverfly fauna of Jazan, Asir, Najran and Al-Baha was performed mainly using Malaise traps, sweep nets and light traps from 2011 to 2014. Forty known species of Syrphidae were identified and recorded in this study, 19 of them new to Saudi Arabia. This makes the total number of Syrphidae species recorded in Saudi Arabia (including one species recorded by others) is 41. In addition, three taxa belonging to the genera Eumerus Meigen, Orthonevra Macquart, and Paragus Latreille that could not be identified safely to species level because there were no adequate identification keys or males were missing in the collected material. A key to the genera of Syrphidae occurring in Saudi Arabia is provided. The fauna of Syrphidae recorded in this study consists much more of Afrotropical zoogeographical elements than Palaearctic ones. A complete checklist of Syrphidae of Saudi Arabia is provided. Biological data, where known, and world-wide distribution of the studied taxa are provided. This paper is published with the purpose of assisting biogeographical, biological or ecological studies on syrphids in Saudi Arabia. 

scholarly journals Influence Of Urbanization On Ecological Status Of River In Amhara Region, Ethiopia 2019

2019 ◽  
Author(s):  
Melsew Setegn Alie
Keyword(s):  
Water Samples ◽  
Ecological Status ◽  
Working Party ◽  
Significant Degree ◽  
Biotic Index ◽  
Small Scale ◽  
P Value ◽  
Physical Habitat ◽  
Ecological Disturbance ◽  
Water Ecology

AbstractIntroductionUrbanization is one of the main causes for environmental problems due to the introduction of pollutants into water bodies. Lahi is crossing fintoselam. This river has long been used for a variety of purposes including source of public water supply, small scale irrigation, bathing, washing, animal watering, sand and stone dredging and recreation.ObjectiveTo assess the influence of Finoteselam town on ecological status of Lahi riverMethodsThe assessment were assessed using physicochemical parameters, physical habitat assessment, biotic indices /metrics, human activity by observation as well as macroinvertabretes samples from eleven sampling sites coded S1 to S11 along the river using the standard procedures. The assessments were involved in-situ measurements and collection of water samples in April 2019 then, analyzed the water samples in laboratory.ResultsThe biological analysis reveals a notable reduction of the diversity macroinvertabrates in the downstream direction where the minimum was at midstream sites. Upstream has significantly better macroinvertabrates assemblage than midstream (p-value<0.05). Physical habitat evaluation scores varied from 43 at S8 to 173 at S1 and relatively lower score were recorded at midstream sites. Low % of Ephemeroptera, Plecoptera and Trichoptera with high family biotic index and high % of Diptera with low biological monitoring working party also indicated water ecology deteriorated mainly at midstream sites. Multivariate analysis of classical analysis, canonical correspondence analysis and none metric multidimensional scaling also indicated ecological deterioration at midstream sites mainly at S5, S6, S7 and S8.ConclusionMidstream was relatively more polluted than upstream due to influence of pollutant from Finoteselam town. The ecological status of upstream segments of the river is very good with slight organic pollutions, and at midstream is poor and significant degree of organic pollutions; whereas the status of the downstream is fair with fairly substantial water pollution showing moderate ecological disturbance. In general, midstream the sampling stations show the deterioration in water ecology and thus necessitated a need for mitigation measure to save the Lahi.

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