scholarly journals Multi-marker metabarcoding resolves subtle variations in freshwater condition: Bioindicators, ecological traits, and trophic interactions

2021 ◽  
Author(s):  
Chloe Victoria Robinson ◽  
Teresita M Porter ◽  
Victoria Carley Maitland ◽  
Michael TG Wright ◽  
Mehrdad Hajibabaei
Keyword(s):  
Habitat Degradation ◽  
Good Condition ◽  
Scale Up ◽  
Ecological Condition ◽  
Trophic Levels ◽  
Ecological Traits ◽  
Dna Metabarcoding ◽  
Trophic Network ◽  
Condition Indicator ◽  
Stability And Resilience

Freshwater systems are experiencing rapid biodiversity losses resulting from high rates of habitat degradation. Ecological condition is typically determined through identifying either macroinvertebrate or diatom bioindicator assemblages and comparing them to their known tolerance to stressors. These comparisons are typically conducted at family or genus levels depending on the availability of taxonomic keys and expertise for focal groups. The objective of this study was to test whether a more taxonomically comprehensive assessment of communities in benthic samples can provide a different perspective of ecological conditions. DNA metabarcoding was used to identify macroinvertebrates and diatoms from kick-net samples collected from sites with different habitat status. Sites with good condition were associated with higher beta diversity as well as slightly higher directed connectance and modularity indicating higher resilience compared with fair condition sites. Indicator value and correlation analyses used DNA metabarcoding data to detect 29 site condition indicator species consistent with known bioindicators and expected relative tolerances. DNA metabarcoding and trophic network analysis also recovered 11 keystone taxa. This study demonstrates the importance of taxonomic breadth across trophic levels for generating biotic data to study ecosystem status, with the potential to scale-up ecological assessments of freshwater condition, trophic stability, and resilience.

scholarly journals High and specific diversity of protists in the deep-sea basins dominated by diplonemids, kinetoplastids, ciliates and foraminiferans

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Alexandra Schoenle ◽  
Manon Hohlfeld ◽  
Karoline Hermanns ◽  
Frédéric Mahé ◽  
Colomban de Vargas ◽  
...  
Keyword(s):  
Carbon Cycling ◽  
Deep Sea ◽  
Trophic Levels ◽  
Earth System ◽  
Parasitic Species ◽  
Unicellular Eukaryotes ◽  
The Earth ◽  
Dna Metabarcoding ◽  
Global Carbon ◽  
Pelagic Communities

AbstractHeterotrophic protists (unicellular eukaryotes) form a major link from bacteria and algae to higher trophic levels in the sunlit ocean. Their role on the deep seafloor, however, is only fragmentarily understood, despite their potential key function for global carbon cycling. Using the approach of combined DNA metabarcoding and cultivation-based surveys of 11 deep-sea regions, we show that protist communities, mostly overlooked in current deep-sea foodweb models, are highly specific, locally diverse and have little overlap to pelagic communities. Besides traditionally considered foraminiferans, tiny protists including diplonemids, kinetoplastids and ciliates were genetically highly diverse considerably exceeding the diversity of metazoans. Deep-sea protists, including many parasitic species, represent thus one of the most diverse biodiversity compartments of the Earth system, forming an essential link to metazoans.

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.

scholarly journals Environmental DNA metabarcoding reveals comparable responses to agricultural stressors on different trophic levels of a freshwater community

2020 ◽  
Author(s):  
Kevin Beentjes ◽  
Henrik Barmentlo ◽  
Ellen Cieraad ◽  
Menno Schilthuizen ◽  
Berry van der Hoorn ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Trophic Levels ◽  
Dna Metabarcoding ◽  
Freshwater Community

Food niche overlap between sympatric potential competitors increases with habitat alteration at different trophic levels in rain-forest reptiles (omnivorous tortoises and carnivorous vipers)

2006 ◽  
Vol 22 (6) ◽  
pp. 695-704 ◽  
Author(s):  
Luca Luiselli
Keyword(s):  
Rain Forest ◽  
Habitat Degradation ◽  
Niche Overlap ◽  
Independent Study ◽  
Trophic Levels ◽  
Habitat Alteration ◽  
Forest Region ◽  
Reptile Species ◽  
Kinixys Erosa ◽  
Food Niche

Comparisons of sympatric reptile species were used to assess the variation in niche overlap for food between potential competitors at different trophic levels. Omnivorous tortoises and carnivorous vipers inhabiting the rain-forest region of West Africa were used as study models. Food niche overlap between species increased with habitat alteration in both the independent study systems: tortoises (Kinixys homeana and Kinixys erosa) and vipers (Bitis gabonica and Bitis nasicornis) showed lower values of Pianka's niche overlap index in the pristine habitat than in the altered habitat, and these differences in overlap values did not depend on chance after Monte Carlo simulations. There were higher inter-habitat food niche overlaps within-species than between-species. Permutation tests (assessed after 5000 iterations) revealed that, for both study systems, the P-values became significantly smaller with fewer resource states, thus showing the niche overlap between species really increases after habitat alteration. The observed increases in food niche overlap between species accomplished with rain-forest habitat degradation in turn may be predicted to have cumulative effects on reducing the level of forest biodiversity.

scholarly journals Bacterial microbiota similarity between predators and prey in a blue tit trophic network

2021 ◽  
Author(s):  
Hélène Dion-Phénix ◽  
Anne Charmantier ◽  
Christophe de Franceschi ◽  
Geneviève Bourret ◽  
Steven W. Kembel ◽  
...  
Keyword(s):  
Spatial Scales ◽  
Trophic Levels ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
16S Rrna Gene Sequences ◽  
Blue Tit ◽  
Trophic Networks ◽  
Bacterial Microbiota ◽  
Trophic Network ◽  
Blue Tits

AbstractTrophic networks are composed of many organisms hosting microbiota that interact with their hosts and with each other. Yet, our knowledge of the factors driving variation in microbiota and their interactions in wild communities is limited. To investigate the relation among host microbiota across a trophic network, we studied the bacterial microbiota of two species of primary producers (downy and holm oaks), a primary consumer (caterpillars), and a secondary consumer (blue tits) at nine sites in Corsica. To quantify bacterial microbiota, we amplified 16S rRNA gene sequences in blue tit feces, caterpillars, and leaf samples. Our results showed that hosts from adjacent trophic levels had a more similar bacterial microbiota than hosts separated by two trophic levels. Our results also revealed a difference between bacterial microbiota present on the two oak species, and among leaves from different sites. The main drivers of bacterial microbiota variation within each trophic level differed across spatial scales, and sharing the same tree or nest box increased similarity in bacterial microbiota for caterpillars and blue tits. This study quantifies host microbiota interactions across a three-level trophic network and illustrates how the factors shaping bacterial microbiota composition vary among different hosts.

Ecological condition of central Australian arid-zone rivers

2002 ◽  
Vol 45 (11) ◽  
pp. 225-232 ◽  
Author(s):  
S.C. Choy ◽  
C.B. Thomson ◽  
J.C. Marshall
Keyword(s):  
Water Chemistry ◽  
Life Histories ◽  
Arid Zone ◽  
Good Condition ◽  
Ecological Integrity ◽  
Ecological Condition ◽  
Spatial And Temporal Variability ◽  
Human Influence ◽  
Management Interventions ◽  
Wide Range

Australian arid-zone rivers are known to be ecologically variable and go through “boom and bust” cycles based on highly variable and unpredictable flow regimes. They are facing increasing pressure from land and water resources development and, whilst they are considered to be still in relatively good condition, no studies have yet been carried out to verify this. Such baseline studies are crucial if we are to assess any ecological changes in response to development and management interventions. The ecological condition of four of these endorheic rivers (Georgina, Diamantina, Cooper-Thomson and Bulloo) flowing into the Lake Eyre and Bulloo Basins in central Australia was assessed using several criteria (level of human influence, habitat condition, water chemistry and aquatic macroinvertebrate composition). Using criteria based on the level of human influence, most of the sites were assessed to be relatively unimpacted (reference) condition. The most discernible and widespread impact was riparian and bank damage by stock access. However, the level of this impact was considered to be only moderate. Most aquatic macroinvertebrates found in the area are considered to be opportunistic and tolerant of a wide range of environmental conditions, but with their life histories known to be linked to flow conditions. Their trophic guild was dominated by collectors and predators. The AusRivAS modelled observed to expected values of macroinvertebrate composition indicated that there were differences in ecological condition between sites (e.g. different waterholes) and between times (e.g. seasons and years). Overall, 75% of sites were assessed to be good condition with the remainder being mildly impaired. Water chemistry of the sites was characterised by high spatial and temporal variability with low conductivity and alkaline pH, relatively high turbidity, total nitrogen and total phosphorus, and wide-ranging dissolved oxygen. Given the high variability in water quality and ecological condition within a catchment, there was little evidence of any overall difference in these factors between the catchments. However, given that the hydrology of each river system is distinctly different, one might expect some differences in ecological structure and function at finer scale. Periods of hydrological isolation (eg. to allow natural dryouts) as well as the maintenance of natural connectivity (eg. instream, overbank and floodplain wetting) are both necessary for the maintenance of ecological integrity of these systems.

scholarly journals Long-term persistence of structured habitats: seagrass meadows as enduring hotspots of biodiversity and faunal stability

2019 ◽  
Vol 286 (1912) ◽  
pp. 20191861 ◽  
Author(s):  
A. Challen Hyman ◽  
Thomas K. Frazer ◽  
Charles A. Jacoby ◽  
Jessica R. Frost ◽  
Michał Kowalewski
Keyword(s):  
Habitat Degradation ◽  
Gulf Coast ◽  
Habitat Types ◽  
Marine Systems ◽  
Spatial Stability ◽  
Seagrass Meadows ◽  
Key Driver ◽  
Mollusc Assemblages ◽  
Stability And Resilience

Ecological studies indicate that structurally complex habitats support elevated biodiversity, stability and resilience. The long-term persistence of structured habitats and their importance in maintaining biodiverse hotspots remain underexplored. We combined geohistorical data (dead mollusc assemblages, ‘DA’) and contemporary surveys (live mollusc assemblages, ‘LA’) to assess the persistence of local seagrass habitats over multi-centennial timescales and to evaluate whether they acted as long-term drivers of biodiversity, stability and resilience of associated fauna. We sampled structured seagrass meadows and open sandy bottoms along Florida's Gulf Coast. Results indicated that: (i) LA composition differed significantly between the two habitat types, (ii) LA from seagrass sites were characterized by significantly elevated local biodiversity and significantly higher spatial stability, (iii) DA composition differed significantly between the two habitat types, and (iv) fidelity between LA and DA was significantly greater for seagrass habitats. Contemporary results support the hypotheses that local biodiversity and spatial stability of marine benthos are both elevated in structured seagrass habitats. Geohistorical results suggest that structured habitats persist as local hotspots of elevated biodiversity and faunal stability over centennial-to-millennial timescales; indicating that habitat degradation and concomitant loss within structurally complex marine systems is a key driver of declining biodiversity and resilience.

scholarly journals DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions

2021 ◽  
Vol 9 (2) ◽  
pp. 361
Author(s):  
Davide Francioli ◽  
Guillaume Lentendu ◽  
Simon Lewin ◽  
Steffen Kolb
Keyword(s):  
High Throughput Sequencing ◽  
Methodological Approach ◽  
Soil Microbial Communities ◽  
Cost Effective ◽  
Trophic Levels ◽  
Gene Markers ◽  
Dna Metabarcoding ◽  
Terrestrial Environments ◽  
Sequencing Platforms

Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.

scholarly journals Selective logging shows no impact on the dietary breadth of the fawn leaf-nosed bat (Hipposideros cervinus)

2021 ◽  
Author(s):  
David Richard Hemprich-Bennett ◽  
Victoria A Kemp ◽  
Joshua Blackman ◽  
Owen T Lewis ◽  
Matthew J Struebig ◽  
...  
Keyword(s):  
Habitat Degradation ◽  
Forest Disturbance ◽  
Taxonomic Composition ◽  
Selective Logging ◽  
Dietary Breadth ◽  
Disturbance Gradient ◽  
Dna Metabarcoding ◽  
Invaluable Tool ◽  
Logging Disturbance ◽  
The Tropics

Logging activities degrade forest habitats across large areas of the tropics, but the impacts on trophic interactions that underpin forest ecosystems are poorly understood. DNA metabarcoding provides an invaluable tool to investigate such interactions, allowing analysis at a far greater scale and resolution than has previously been possible. We analysed the diet of the insectivorous fawn leaf-nosed bat Hipposideros cervinus across a forest disturbance gradient in Borneo, using a dataset of ecological interactions from an unprecedented number of bat-derived faecal samples. Bats predominantly consumed insects from the orders Lepidoptera, Blattodea, Diptera and Coleoptera, and the taxonomic composition of their diet remained relatively consistent across sites regardless of logging disturbance. There was little difference in the richness of prey consumed in each logging treatment, indicating potential resilience of this species to habitat degradation. In fact, bats consumed a high richness of prey items, and intensive sampling is needed to reliably compare feeding ecology over multiple sites regardless of the bioinformatic procedures used.

scholarly journals Putting the “Beaver” Back in Beverley Brook: Rapid Shifts in Community Composition Following the Restoration of a Degraded Urban River

Water ◽  
2021 ◽  
Vol 13 (24) ◽  
pp. 3530
Author(s):  
Daniel M. Perkins ◽  
Toby Hull ◽  
Niamh Bubb ◽  
Alex Cunningham ◽  
Rory Glackin ◽  
...  
Keyword(s):  
Water Quality ◽  
Large Scale ◽  
Habitat Degradation ◽  
Urban River ◽  
Trophic Levels ◽  
Apex Predators ◽  
Natural Processes ◽  
Basal Resources ◽  
Average Body Mass ◽  
Source Populations

Widespread habitat degradation has caused dramatic declines in aquatic biodiversity. Reconfiguring channels and adding physical structures to rivers has become common practice in order to reinstate natural processes and restore biodiversity. However, the effectiveness of such measures is often questioned, especially in urban settings where overriding factors (e.g., water quality) might constrain biotic responses to increased habitat heterogeneity. We monitored invertebrate and fish communities before and up to five years after extensive restoration of Beverley Brook, a small, urban river flowing through a Royal Park in London, UK. Total invertebrate density was 5–148% higher with restoration across the monitoring period, and there was an increase in evenness but not invertebrate richness. Riverflies (Ephmemeroptera and Trichoptera) and crustaceans (Amphipoda, Asellidae) showed marked increases in density with restoration, suggesting improved flow, enhanced water quality, and greater quantity of basal resources. Fish biomass increased by 282% with restoration as did fish richness and the average body mass of three common fish species. Our results provide evidence for the effectiveness of common restoration methods in increasing standing stocks across trophic levels, from basal resources to apex predators. However, we primarily observed changes in the density of existing taxa rather than the development of novel assemblages, suggesting that large-scale factors, such as water quality and the lack of adequate source populations, might be important for understanding changes in biodiversity following river restoration.

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