scholarly journals Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

2021 ◽  
Vol 5 ◽  
Author(s):  
Till-Hendrik Macher ◽  
Robin Schütz ◽  
Jens Arle ◽  
Arne J. Beermann ◽  
Jan Koschorreck ◽  
...  
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Bird Species ◽  
Sampling Strategy ◽  
Environmental Dna ◽  
Federal State ◽  
Vertebrate Species ◽  
Biodiversity Monitoring ◽  
Species Detection ◽  
Terrestrial Species

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., when drinking). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 22.2%, and 7.4% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 24.8% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 68.9% and 77.3%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.

scholarly journals Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species

2021 ◽  
Author(s):  
Till-Hendrik Macher ◽  
Robin Schuetz ◽  
Jens Arle ◽  
Arne J. Beermann ◽  
Jan Koschorreck ◽  
...  
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Bird Species ◽  
Sampling Strategy ◽  
Environmental Dna ◽  
Federal State ◽  
Vertebrate Species ◽  
Biodiversity Monitoring ◽  
Species Detection ◽  
Terrestrial Species

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because water in a catchment flows to the lowest point in the landscape, often a stream, it can often collect traces of terrestrial species via surface or subsurface runoff along its way or when specimens come into direct contact with water (e.g., for drinking purposes). Thus, fish eDNA metabarcoding data can provide information on fish but also on other vertebrate species that live in riparian habitats. This additional data may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2 km stretch of the river Mulde (Germany), we collected 18 1-L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 24%, and 7% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 25% more detected fish and lamprey species, mammal, and bird species richness increased disproportionately by 69% and 84%, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true, when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called 'bycatch'. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy is chosen carefully. With the increased use of eDNA metabarcoding as part of national fish bioassessment and monitoring programs, the complimentary information provided on bycatch can be used for biodiversity monitoring and conservation on a much broader scale.

scholarly journals Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream-associated vertebrate species

2021 ◽  
Vol 4 ◽  
Author(s):  
Till-Hendrik Macher ◽  
Robin Schütz ◽  
Jens Arle ◽  
Arne Beermann ◽  
Jan Koschorreck ◽  
...  
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Bird Species ◽  
Sampling Strategy ◽  
Freshwater Ecosystems ◽  
Federal State ◽  
Vertebrate Species ◽  
Species Detection ◽  
Terrestrial Species ◽  
Biological Replication

Fast, reliable, and comprehensive biodiversity monitoring data are needed for environmental decision making and management. Recent work on fish environmental DNA (eDNA) metabarcoding shows that aquatic diversity can be captured fast, reliably, and non-invasively at moderate costs. Because freshwater ecosystems act as sinks in the landscape, they also collect traces of terrestrial species via surface runoff or when specimens come into direct contact with water (e.g., for drinking purposes). Thus, fish eDNA metabarcoding data can provide information on fish but also on other, even terrestrial vertebrate species that live in riparian habitats. This data become available and may offer a much more comprehensive approach for assessing vertebrate diversity at no additional costs. Studies on how the sampling strategy affects species detection especially of stream-associated communities, however, are scarce. We therefore performed an analysis on the effects of biological replication on both fish as well as (semi-)terrestrial species detection. Along a 2-km stretch of the river Mulde (Germany), we collected 18 1L water samples and analyzed the relation of detected species richness and quantity of biological replicates taken. We detected 58 vertebrate species, of which 25 were fish and lamprey, 18 mammals, and 15 birds, which account for 50%, 24% and 7% of all native species to the German federal state of Saxony-Anhalt. However, while increasing the number of biological replicates resulted in only 25 % more detected fish and lamprey species, mammal and bird species richness increased disproportionately by 69 % and 84 %, respectively. Contrary, PCR replicates showed little stochasticity. We thus emphasize to increase the number of biological replicates when the aim is to improve general species detections. This holds especially true, when the focus is on rare aquatic taxa or on (semi-)terrestrial species, the so-called ‘bycatch’. As a clear advantage, this information can be obtained without any additional sampling or laboratory effort when the sampling strategy regarding biological replication is chosen carefully. With the consideration of frequent eDNA metabarcoding as part of national biomonitoring programs, the additional information provided by the bycatch can be used to further investigate the state of the environment and its biodiversity on a much broader scale.

Impacts of Buffelgrass (Pennisetum ciliare) on a Forb Community in South Texas

2009 ◽  
Vol 2 (2) ◽  
pp. 130-140 ◽  
Author(s):  
Joseph P. Sands ◽  
Leonard A. Brennan ◽  
Fidel Hernández ◽  
William P. Kuvlesky ◽  
James F. Gallagher ◽  
...  
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Grassland Birds ◽  
Bird Species ◽  
South Texas ◽  
Breeding Period ◽  
Stem Density ◽  
Grass Cover ◽  
Canopy Coverage ◽  
Useable Space

AbstractSince the 1950s, many south Texas rangelands have been seeded with buffelgrass, a perennial C4 bunchgrass native to Africa that is believed to contribute to reductions in biodiversity. Forb species represent a critical habitat component throughout the breeding period for many wildlife species as seed (summer to fall), as green vegetative material (spring to summer), and as habitat for arthropods (spring to summer). Reductions in richness and diversity of crucial ecosystem components such as forbs and arthropods have large implications for grassland birds and other wildlife. We sampled annual and perennial forbs within 1-m2 quadrats on 15 study plots (1 ha; n = 20 quadrats/plot) at Chaparral Wildlife Management Area, in LaSalle and Dimmit counties, Texas, during 2005 and 2006. Study plots were divided into five light-buffelgrass plots (0 to 5% buffelgrass canopy coverage), five moderate-buffelgrass plots (5 to 25% buffelgrass canopy coverage), and five heavy-buffelgrass plots (> 25% buffelgrass canopy coverage). Buffelgrass in study plots was composed of naturalized plants, and was not deliberately planted. During 2005 we observed that plots with > 25% buffelgrass had a 73% reduction in forb canopy of native species, a 64% reduction in native forb species richness, and a 77% reduction in native forb stem density compared to plots with 0 to 5% buffelgrass. These trends in native forb reduction (−79% native forb canopy, −65% forb species richness, −80% forb stem density) were nearly identical in 2006, even with greatly reduced rainfall. Simple linear regression revealed negative relationships between buffelgrass cover, total exotic grass cover (buffelgrass and Lehmann lovegrass), and total grass cover and the richness, coverage, and density of forbs/m2. Reductions in diversity may have larger implications regarding ecosystem function and available useable space and densities of desired bird species such as northern bobwhite.

scholarly journals Reinforcement of Environmental DNA Based Methods (Sensu stricto) in Biodiversity Monitoring and Conservation: A Review

Biology ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1223
Author(s):  
Pritam Banerjee ◽  
Gobinda Dey ◽  
Caterina M. Antognazza ◽  
Raju Kumar Sharma ◽  
Jyoti Prakash Maity ◽  
...  
Keyword(s):  
Conservation Biology ◽  
Natural Populations ◽  
Monitoring Program ◽  
Environmental Dna ◽  
Sensu Stricto ◽  
High Accuracy ◽  
Rapid Expansion ◽  
Research Progress ◽  
Biodiversity Monitoring ◽  
Species Detection

Recently developed non-invasive environmental DNA-based (eDNA) techniques have enlightened modern conservation biology, propelling the monitoring/management of natural populations to a more effective and efficient approach, compared to traditional surveys. However, due to rapid-expansion of eDNA, confusion in terminology and collection/analytical pipelines can potentially jeopardize research progression, methodological standardization, and practitioner adoption in several ways. Present investigation reflects the developmental progress of eDNA (sensu stricto) including highlighting the successful case studies in conservation management. The eDNA technique is successfully relevant in several areas of conservation research (invasive/conserve species detection) with a high accuracy and authentication, which gradually upgrading modern conservation approaches. The eDNA technique related bioinformatics (e.g., taxon-specific-primers MiFish, MiBird, etc.), sample-dependent methodology, and advancement of sequencing technology (e.g., oxford-nanopore-sequencing) are helping in research progress. The investigation shows that the eDNA technique is applicable largely in (i) early detection of invasive species, (ii) species detection for conservation, (iii) community level biodiversity monitoring, (iv) ecosystem health monitoring, (v) study on trophic interactions, etc. Thus, the eDNA technique with a high accuracy and authentication can be applicable alone or coupled with traditional surveys in conservation biology. However, a comprehensive eDNA-based monitoring program (ecosystem modeling and function) is essential on a global scale for future management decisions.

Bushland modification and styles of urban development: their effects on birds in south-east Queensland

1998 ◽  
Vol 25 (1) ◽  
pp. 41 ◽  
Author(s):  
Sven R. Sewell ◽  
Carla P. Catterall
Keyword(s):  
Species Richness ◽  
Native Species ◽  
Bird Species ◽  
Individual Species ◽  
Bird Abundance ◽  
Bird Species Richness ◽  
Forest Clearing ◽  
Major Response ◽  
Forest Remnants ◽  
High Species Richness

Variation in bird assemblages associated with forest clearing and urbanisation in the greater Brisbane area was assessed by counting birds in sites within six habitat categories: large remnants, small remnants, no- understorey remnants, canopy suburbs (original trees present), planted suburbs, and bare suburbs. Total bird abundance and species richness were generally highest in canopy suburbs. Individual species showed many significant abundance differences among the habitat types, and were classified into three major response categories: bushland species (3 in summer, 13 in winter), tolerant species (13 in summer, 13 in winter), and suburban species (12 in summer, 11 in winter). The commonly proposed notion that urbanisation results in lowered bird species richness and increases in introduced species is broadly consistent with the observed differences between bare suburbs and large remnants. However, it does not adequately describe the situation in the planted and canopy suburbs, where there was high species richness and extremely high abundance of some native species (including noisy miners, lorikeets, friarbirds, and butcherbirds) but low abundance of a majority of the species common in the original habitats (including fantails, wrens, whistlers, and other small insectivores). Retained forest remnants are essential for the latter group. Urban plantings of prolifically flowering native species do not reverse the effects of deforestation, but promote a distinctive group of common native suburban bird species. Origins of the urban bird assemblage are discussed.

scholarly journals Environmental DNA metabarcoding for biodiversity monitoring of a highly-diverse tropical fish community in a coral-reef lagoon: Estimation of species richness and detection of habitat segregation

2020 ◽  
Author(s):  
Shin-ichiro Oka ◽  
Hideyuki Doi ◽  
Kei Miyamoto ◽  
Nozomi Hanahara ◽  
Tetsuya Sado ◽  
...  
Keyword(s):  
Species Richness ◽  
Coral Reef ◽  
Fish Species ◽  
Environmental Dna ◽  
Seagrass Beds ◽  
Biodiversity Monitoring ◽  
Reef Lagoon ◽  
Coral Reef Lagoon ◽  
Offshore Reef ◽  
Reef Edge

AbstractAn environmental DNA (eDNA) metabarcoding approach has been widely used for biodiversity monitoring of fishes, although it has rarely been applied to tropical and subtropical aquatic ecosystems, where species diversity is remarkably high. This study examined the extent to which species richness can be estimated in a small coral reef lagoon (1500 × 900 m) near Okinawa Island, southern Japan, where the surrounding waters are likely to harbor more than 1500 species of fish. During 2015–2017, a total of 16 capture-based surveys were conducted to create a faunal list of fish species, followed by eDNA metabarcoding based on seawater samples taken from 11 sites in the lagoon on a day in May 2019. We also tested whether eDNA metabarcoding could detect differences between adjacent fish communities inhabiting the offshore reef edge and shore-side seagrass beds within the lagoon. A total of 217 fish species were confirmed by the capture-based samplings, while 291 fish species were detected by eDNA metabarcoding, identifying a total of 410 species distributed across 119 families and 193 genera. Of these 410 species, only 96 (24% of the total) were commonly identified by both methods, indicating that capture-based surveys failed to collect a number of species detected by eDNA metabarcoding. Interestingly, two different approaches to estimate species richness based on eDNA data yielded values close to the 410 species, including one that suggested an additional three or more eDNA surveys from 11 sites (36 samples) would detect 90% of the 410 species. In addition, non-metric multi-dimensional scaling for fish assemblages clearly distinguished between the fish communities of the offshore reef edge and those of the shore-side seagrass beds.

scholarly journals Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: a case study on a threatened amphibian

2018 ◽  
Author(s):  
Lynsey R. Harper ◽  
Lori Lawson Handley ◽  
Christoph Hahn ◽  
Neil Boonham ◽  
Helen C. Rees ◽  
...  
Keyword(s):  
Species Richness ◽  
Large Scale ◽  
Gasterosteus Aculeatus ◽  
Abiotic Factors ◽  
Environmental Dna ◽  
Hypothesis Generation ◽  
Vertebrate Species ◽  
Mammal Species ◽  
Negatively Associated ◽  
Fulica Atra

AbstractEnvironmental DNA (eDNA) metabarcoding is revolutionising biodiversity monitoring, but has unrealised potential for ecological hypothesis generation and testing. Here, we validate this potential in a large-scale analysis of vertebrate community data generated by eDNA metabarcoding of 532 UK ponds. We test biotic associations between the threatened great crested newt (Triturus cristatus) and other vertebrates as well as abiotic factors influencing T. cristatus detection at the pondscape. Furthermore, we test the status of T. cristatus as an umbrella species for pond conservation by assessing whether vertebrate species richness is greater in ponds with T. cristatus and higher T. cristatus Habitat Suitability Index (HSI) scores. T. cristatus detection was positively correlated with amphibian and waterfowl species richness. Specifically, T. cristatus was positively associated with smooth newt (Lissotriton vulgaris), common coot (Fulica atra), and common moorhen (Gallinula chloropus), but negatively associated with common toad (Bufo bufo). T. cristatus detection did not significantly decrease as fish species richness increased, but negative associations with common carp (Cyprinus carpio), three-spined stickleback (Gasterosteus aculeatus) and ninespine stickleback (Pungitius pungitius) were identified. T. cristatus detection was negatively correlated with mammal species richness, and T. cristatus was negatively associated with grey squirrel (Sciurus carolinensis). T. cristatus detection was negatively correlated with larger pond area, presence of inflow, and higher percentage of shading, but positively correlated with HSI score, supporting its application to T. cristatus survey. Vertebrate species richness was significantly higher in T. cristatus ponds and broadly increased as T. cristatus HSI scores increased. We reaffirm reported associations (e.g. T. cristatus preference for smaller ponds) but also provide novel insights, including a negative effect of pond inflow on T. cristatus. Our findings demonstrate the prospects of eDNA metabarcoding for ecological hypothesis generation and testing at landscape scale, and dramatic enhancement of freshwater conservation, management, monitoring and research.

Functional evenness of bird communities varies along the elevational gradient in Europe: Conservation implications

2019 ◽  
Author(s):  
Federico Morelli ◽  
Yanina
Keyword(s):  
Species Richness ◽  
Elevation Gradient ◽  
Bird Species ◽  
Elevational Gradient ◽  
Negative Association ◽  
Bird Communities ◽  
Breeding Bird ◽  
Bird Species Richness ◽  
Large Spatial Scale ◽  
Functional Evenness

ContextThe negative association between elevation and species richness is a well-recognized pattern in macro-ecology. ObjectivesThe aim of this study was to investigate changes in functional evenness of breeding bird communities along an elevation gradient in Europe. MethodsUsing the bird data from the EBCC Atlas of European Breeding Birds we estimated an index of functional evenness which can be assumed as a measure of the potential resilience of communities.ResultsOur findings confirm the existence of a negative association between elevation and bird species richness in all European eco regions. However, we also explored a novel aspect of this relationship, important for conservation: Our findings provide evidence at large spatial scale of a negative association between the functional evenness (potential community resilience) and elevation, independent of the eco region. We also found that the Natura2000 protected areas covers the territory most in need of protection, those characterized by bird communities with low potential resilience, in hilly and mountainous areas.ConclusionsThese results draw attention to European areas occupied by bird communities characterized by a potential lower capacity to respond to strong ecological changes, and, therefore, potentially more exposed to risks for conservation.

Sign in / Sign up

Export Citation Format

Share Document