Multi-taxa environmental DNA inventories reveal distinct taxonomic and functional diversity in urban tropical forest fragments

Donald, Julian; Murienne, Jérôme; Chave, Jérôme; Iribar, Amaia; Louisanna, Eliane; Manzi, Sophie; Roy, Mélanie; Tao, Shengli; Orivel, Jérôme; Schimann, Heidy; Zinger, Lucie

doi:10.1016/j.gecco.2021.e01724

Cited by 15 publications

(11 citation statements)

References 96 publications

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“…Use of eDNA can greatly complement traditional species monitoring by enabling greater taxonomic resolution (Deiner et al 2017;Ruppert et al 2019), the detection of species which tend to avoid the presence of humans (Yonezawa et al 2020;Mas-Carrió et al 2021), or organisms such as bacteria and fungi which can be difficult to monitor using traditional observations (Frøslev et al 2019;Liddicoat et al 2022). Comparisons of eDNA with observational methods have also indicated their potential to help capture additional elements of ecologically relevant information, such as the functional diversity of various groups of species (Aglieri et al, 2021;Donald et al 2021;Sigsgaard et al 2021), particularly with regards to identifying ecological indicators (Yan et al 2018;Blattner et al 2021;Seymour et al 2021).…”

Section: Future Prospectsmentioning

confidence: 99%

Constructing ecological indices for urban environments using species distribution models

Simons

CALDWELL

et al. 2022

Urban Ecosyst

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In an increasingly urbanized world, there is a need to study urban areas as their own class of ecosystems as well as assess the impacts of anthropogenic impacts on biodiversity. However, collecting a sufficient number of species observations to estimate patterns of biodiversity in a city can be costly. Here we investigated the use of community science-based data on species occurrences, combined with species distribution models (SDMs), built using MaxEnt and remotely-sensed measures of the environment, to predict the distribution of a number of species across the urban environment of Los Angeles. By selecting species with the most accurate SDMs, and then summarizing these by class, we were able to produce two species richness models (SRMs) to predict biodiversity patterns for species in the class Aves and Magnoliopsida and how they respond to a variety of natural and anthropogenic environmental gradients.We found that species considered native to Los Angeles tend to have significantly more accurate SDMs than their non-native counterparts. For all species considered in this study we found environmental variables describing anthropogenic activities, such as housing density and alterations to land cover, tend to be more influential than natural factors, such as terrain and proximity to freshwater, in shaping SDMs. Using a random forest model we found our SRMs could account for approximately 54% and 62% of the predicted variation in species richness for species in the classes Aves and Magnoliopsida respectively. Using community science-based species occurrences, SRMs can be used to model patterns of urban biodiversity and assess the roles of environmental factors in shaping them.

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Section: Future Prospectsmentioning

confidence: 99%

Constructing ecological indices for urban environments using species distribution models

Simons

CALDWELL

et al. 2022

Urban Ecosyst

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“…Therefore, by only focusing on a single ecosystem function or attribute, the recovery of an ecosystem could be misrepresented. By combining different primers, soil eDNA can be used to detect species across taxonomic kingdoms from the same soil sample (Zinger et al 2016; Donald et al 2021) and could be used to monitor recovery across a range of organisms for a more holistic measure of restoration success. Indeed, eDNA studies are increasingly being used to capture species interactions and modifications to trophic web structures using machine learning techniques (Cordier et al 2019; Dubart et al 2022).…”

Section: Discussionmentioning

confidence: 99%

Soil environmental DNA metabarcoding can quantify local plant diversity for biomonitoring across varied environments

Duley

Iribar

Bisson

et al. 2022

Restoration Ecology

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Biomonitoring of plant communities is essential when evaluating outcomes of ecological restoration, but morphology‐based inventories can impede consistency across spatial and temporal scales. The Eden Project botanic garden (Cornwall, UK) offers an opportunity to test whether soil environmental DNA (eDNA) reflects plant species richness, community composition, and diversity. Furthermore, it enables the exploration of whether community complexity, environmental conditions, or sampling scale influence the similarity of soil eDNA‐derived results compared with those derived from classic botanical inventories. Survey plots were established encompassing a mixture of high‐ and low‐complexity plant assemblages, under either hot and humid or cool and dry conditions. Botanical inventories were conducted in quadrats up to 7 m around a soil eDNA sample plot. Soil samples were processed by metabarcoding of trnL p6 loop to determine plant eDNA identity and relative abundance. Differences in diversity and community composition were calculated before determining whether (1) inventory scale; (2) plant assembly complexity; (3) ambient conditions; (4) soil chemistry; (5) bulk root biomass and (6) soil respiration influenced the similarity of soil eDNA and botanical inventory methods. Inventory scale significantly determined the dissimilarity in both diversity and composition, with soil respiration, phosphorus, and C:N ratio also accounting for variation across sites. Our results demonstrate that soil eDNA metabarcoding is an effective approach for quantifying relative diversity in plant communities across broad habitat types and could be integrated into restoration monitoring strategies, but that its application requires an appropriate a priori knowledge of survey sites to best tailor soil eDNA survey implementation.

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“…All of these habitats are likely sources for mites that could be suspended by branch flows and stemflow as they drain to the surface. Mites also contribute to processes at the surface, including soil formation through burrowing, fragmentation of organic material, the production of faeces (Culliney, 2013; de Groot et al, 2016) and thereby support important ecosystem services of soils (de Groot et al, 2016; Donald et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

Stemflow metazoan transport from common urban tree species (São Paulo, Brazil)

et al. 2022

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For precipitation to reach the surface of vegetated ecosystems, it must first pass through the canopy. A portion of precipitation, stemflow, drains down branches to the stem. This stemflow may wash canopy-dwelling animals (metazoans) into the litter and soils below; however, stemflow metazoans transport has typically been ignored in past research. In fact, the visual presence of metazoans in stemflow collection bins was reported as "contamination" in past research. Thus, we know little about these organisms' transfer from plant canopies to the surface. To investigate this topic, we monitored metazoan concentrations and composition within stemflow that drained from eight urban tree species (n = 3 per species) over 12 months. Annual (±SE) stemflow recorded from all 24 sampled trees was 19.6 (±3.3) mm (2.3% rainfall). Analysis of 288 samples found 1,307 individuals distributed into seven classes (16 orders) and one organism at phylum level. Considering all trees (n = 24), the annual mean metazoan density in stemflow was 8.6 individuals L À1 . Among tree species, there were considerable variations, ranging from 1.0 to 17 individuals L À1 .Annual metazoan transport per tree ranged from 20 to 376 individuals m À2 y À1 . The most common taxa observed in stemflow from this site included Arachnida (10%), Collembola (33%) and Insecta (56%). Variability in metazoan density within and across species was high, but individual trees with the highest metazoan stemflow density and flux were those with large diameter and exfoliating bark structure. This study demonstrates that stemflow can transport a substantial and diverse meso-and macro-fauna to the surface of urban forests. Future work may be merited on the fate and/or role of these metazoans in litter and soil systems.

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Multi-taxa environmental DNA inventories reveal distinct taxonomic and functional diversity in urban tropical forest fragments

Cited by 15 publications

References 96 publications

Constructing ecological indices for urban environments using species distribution models

Constructing ecological indices for urban environments using species distribution models

Soil environmental DNA metabarcoding can quantify local plant diversity for biomonitoring across varied environments

Stemflow metazoan transport from common urban tree species (São Paulo, Brazil)

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