Applying pollen DNA metabarcoding to the study of plant–pollinator interactions1

@article{Bell2017ApplyingPD,
  title={Applying pollen DNA metabarcoding to the study of plant–pollinator interactions1},
  author={Karen L. Bell and Julie Fowler and Kevin S. Burgess and Emily K. Dobbs and David L. Gruenewald and Brice Lawley and Connor Morozumi and Berry J. Brosi},
  journal={Applications in Plant Sciences},
  year={2017},
  volume={5}
}
Premise of the study: To study pollination networks in a changing environment, we need accurate, high-throughput methods. Previous studies have shown that more highly resolved networks can be constructed by studying pollen loads taken from bees, relative to field observations. DNA metabarcoding potentially allows for faster and finer-scale taxonomic resolution of pollen compared to traditional approaches (e.g., light microscopy), but has not been applied to pollination networks. Methods: We… 

Using Metabarcoding to Investigate the Strength of Plant-Pollinator Interactions From Surveys of Visits to DNA Sequences

The ongoing decline in pollinators and increasing concerns about pollination services require a better understanding of complex pollination networks, particularly their response to global climate

Genome-skimming provides accurate quantification for pollen mixtures Authors

TLDR
It is concluded that genome-skimming is a feasible approach to identifying and quantifying pollen compositions for mixed pollen samples and is expected to improve the understanding of pollen diversity transported by pollinators and their ecological roles in the plant-pollinator networks.

Harnessing the power of metabarcoding in the ecological interpretation of plant-pollinator DNA data: strategies and consequences of reads filtering

TLDR
Results clearly indicated that pruning type shapes species composition and that to apply or not a threshold dramatically impacts ecological indices, potentially increasing the risk of misinterpreting DNA metabarcoding data under an ecological point of view.

Plant–pollinator interactions over time: Pollen metabarcoding from bees in a historic collection

TLDR
The results showed that small, insect‐carried pollen samples from historic bee specimens collected from as early as 1914 can be used to obtain pollen metabarcodes, providing a faster, more accurate method of determining pollen provenance, without the need for expert palynologists.

Capabilities and limitations of using DNA metabarcoding to study plant–pollinator interactions

TLDR
Some strengths and limitations of using DNA metabarcoding to identify plant species present in bee pollen loads, make ecological inferences about foraging behaviour and provide guidance for future research are examined.

Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches

Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or

Quantitative Amplicon Sequencing for Meta-DNA Analysis Reveals Patterns in Pollen Use by Bees

TLDR
It is determined that bee visitation behaviors are generally predictive of the pollens that bees carry while foraging, and that some bees carry multiple species of Clarkia at the same time, indicating that Clarkia likely compete via interspecific pollen transfer.

Generalisation and specialisation in hoverfly (Syrphidae) grassland pollen transport networks revealed by DNA metabarcoding

TLDR
It is found that Eristalis hoverflies transport pollen from 65 plant taxa, more than previously appreciated, and networks were generalised at the site and species level, suggesting some degree of functional redundancy, and were more generalised in late summer compared to early summer.

Experimental quantification of pollen with DNA metabarcoding using ITS1 and trnL

TLDR
This study investigated the relationships between the amount of pollen grains in mock solutions and the abundance of high-throughput sequence reads and how the relationship was affected by the pollen counting methodology, the number of PCR cycles, the type of markers and plant species whose pollen grains have different characteristics.

Genome‐skimming provides accurate quantification for pollen mixtures

TLDR
It is concluded that genome‐skimming is a feasible approach to identifying and quantifying mixed pollen samples and is expected to improve the understanding in studies that involve plant–pollinator interactions, such as pollen preference in corbiculate bees, pollen diet analyses and identification of landscape pollen resource use from beehives.
...

References

SHOWING 1-10 OF 54 REFERENCES

Using metabarcoding to reveal and quantify plant-pollinator interactions

TLDR
If metabarcoding may circumvent the limits of conventional methodologies in detecting and quantifying plant-pollinator interactions, it holds great promise for investigating diverse facets of interactions and will provide a new perception of pollination networks as a whole.

Rank-based characterization of pollen assemblages collected by honey bees using a multi-locus metabarcoding approach1

TLDR
The findings suggest metabarcoding data from plastid loci, as opposed to the ribosomal locus, are more reliable for quantitative characterization of pollen assemblages, underscoring the need for discovering novel barcodes and barcode combinations optimized for molecular palynology.

Evaluating multiplexed next-generation sequencing as a method in palynology for mixed pollen samples.

TLDR
Next-generation sequencing of amplicons from the highly variable, species-specific internal transcribed spacer 2 region of nuclear ribosomal DNA presents a useful and efficient workflow to identify pollen at the genus and species level without requiring specialised palynological expert knowledge.

Pollen DNA barcoding: current applications and future prospects.

TLDR
The nascent field of pollen DNA barcoding is reviewed and potential new applications of this technology are discussed, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.

Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach

TLDR
A new primer-adapter design for high throughput sequencing with the Illumina technology that uses a dual-indexing strategy, where sample-specific combinations of forward and reverse identifiers attached to the barcode marker allow high sample throughput with a single sequencing run.

Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences

TLDR
Although honey bees are considered to be supergeneralists in their foraging choices, there are certain key species or plant groups that are particularly important in the honey bees environment that require further investigation.

Plant-Pollinator Interactions over 120 Years: Loss of Species, Co-Occurrence, and Function

TLDR
Using historic data sets, the degree to which global change over 120 years disrupted plant-pollinator interactions in a temperate forest understory community in Illinois, USA is quantified and it is suggested that networks will be less resilient to future changes.

Plant-pollinator networks: adding the pollinator's perspective.

TLDR
This study of a Mediterranean scrubland community in NE Spain supplement data from an intensive field survey with the analysis of pollen loads carried by pollinators, revealing the existence of four clearly defined modules that were not apparent when only field survey data were used.

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci

TLDR
The results show that a pre-compiled, curated reference database is not essential for genus- level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation.

Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well

TLDR
Resolution to the contentious debate on plant barcoding should involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barc coding systems.
...