Limits...
Elucidating the diet of the island flying fox ( Pteropus hypomelanus ) in Peninsular Malaysia through Illumina Next-Generation Sequencing

View Article: PubMed Central - HTML - PubMed

ABSTRACT

There is an urgent need to identify and understand the ecosystem services of pollination and seed dispersal provided by threatened mammals such as flying foxes. The first step towards this is to obtain comprehensive data on their diet. However, the volant and nocturnal nature of bats presents a particularly challenging situation, and conventional microhistological approaches to studying their diet can be laborious and time-consuming, and provide incomplete information. We used Illumina Next-Generation Sequencing (NGS) as a novel, non-invasive method for analysing the diet of the island flying fox (Pteropus hypomelanus) on Tioman Island, Peninsular Malaysia. Through DNA metabarcoding of plants in flying fox droppings, using primers targeting the rbcL gene, we identified at least 29 Operationally Taxonomic Units (OTUs) comprising the diet of this giant pteropodid. OTU sequences matched at least four genera and 14 plant families from online reference databases based on a conservative Least Common Ancestor approach, and eight species from our site-specific plant reference collection. NGS was just as successful as conventional microhistological analysis in detecting plant taxa from droppings, but also uncovered six additional plant taxa. The island flying fox’s diet appeared to be dominated by figs (Ficus sp.), which was the most abundant plant taxon detected in the droppings every single month. Our study has shown that NGS can add value to the conventional microhistological approach in identifying food plant species from flying fox droppings. At this point in time, more accurate genus- and species-level identification of OTUs not only requires support from databases with more representative sequences of relevant plant DNA, but probably necessitates in situ collection of plant specimens to create a reference collection. Although this method cannot be used to quantify true abundance or proportion of plant species, nor plant parts consumed, it ultimately provides a very important first step towards identifying plant taxa and spatio-temporal patterns in flying fox diets.

No MeSH data available.


Relative abundance of 8 OTUs detected in flying fox droppings.Relative abundance of 8 OTUs detected in flying fox droppings across 8 months (Mar–Oct 2015) at two different roosting sites on Tioman Island, Tekek (two roosts) and Juara (three roosts). OTU 1, Ficus; OTU 3, Anacardiaceae; OTU 4, Rubiaceae; OTU 5, Rubiaceae; OTU 6, Diospyros; OTU 7, Moraceae; OTU 8, Lamiales; OTU 13, Terminalia; Others, pooled OTUs with <5% relative abundance at each roost.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5391789&req=5

fig-2: Relative abundance of 8 OTUs detected in flying fox droppings.Relative abundance of 8 OTUs detected in flying fox droppings across 8 months (Mar–Oct 2015) at two different roosting sites on Tioman Island, Tekek (two roosts) and Juara (three roosts). OTU 1, Ficus; OTU 3, Anacardiaceae; OTU 4, Rubiaceae; OTU 5, Rubiaceae; OTU 6, Diospyros; OTU 7, Moraceae; OTU 8, Lamiales; OTU 13, Terminalia; Others, pooled OTUs with <5% relative abundance at each roost.

Mentions: The results from our NGS analysis of island flying fox droppings over eight months suggest that the diet at both Juara and Tekek during this time was dominated by four different plant taxa (Table 1; Fig. 2): OTU 1 (Ficus sp.), OTU 3 (likely to be Mangifera indica based on sequence match with site-specific plant reference collection) and OTUs 4 & 5 (Rubiaceae). Spatio-temporal patterns in the relative abundance of these four taxa in the diet were observed during the sampling period (Fig. 2). For example, OTU 5 appeared to be consumed in similar proportions at both Juara and Tekek across all months whereas OTU 4 was consistently consumed in low proportions in Tekek yet consumed irregularly in Juara over the same period (Fig. 3). Even between different roosts in the same site, spatio-temporal differences were observed, such as for OTU 7 (Fig. S5).


Elucidating the diet of the island flying fox ( Pteropus hypomelanus ) in Peninsular Malaysia through Illumina Next-Generation Sequencing
Relative abundance of 8 OTUs detected in flying fox droppings.Relative abundance of 8 OTUs detected in flying fox droppings across 8 months (Mar–Oct 2015) at two different roosting sites on Tioman Island, Tekek (two roosts) and Juara (three roosts). OTU 1, Ficus; OTU 3, Anacardiaceae; OTU 4, Rubiaceae; OTU 5, Rubiaceae; OTU 6, Diospyros; OTU 7, Moraceae; OTU 8, Lamiales; OTU 13, Terminalia; Others, pooled OTUs with <5% relative abundance at each roost.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5391789&req=5

fig-2: Relative abundance of 8 OTUs detected in flying fox droppings.Relative abundance of 8 OTUs detected in flying fox droppings across 8 months (Mar–Oct 2015) at two different roosting sites on Tioman Island, Tekek (two roosts) and Juara (three roosts). OTU 1, Ficus; OTU 3, Anacardiaceae; OTU 4, Rubiaceae; OTU 5, Rubiaceae; OTU 6, Diospyros; OTU 7, Moraceae; OTU 8, Lamiales; OTU 13, Terminalia; Others, pooled OTUs with <5% relative abundance at each roost.
Mentions: The results from our NGS analysis of island flying fox droppings over eight months suggest that the diet at both Juara and Tekek during this time was dominated by four different plant taxa (Table 1; Fig. 2): OTU 1 (Ficus sp.), OTU 3 (likely to be Mangifera indica based on sequence match with site-specific plant reference collection) and OTUs 4 & 5 (Rubiaceae). Spatio-temporal patterns in the relative abundance of these four taxa in the diet were observed during the sampling period (Fig. 2). For example, OTU 5 appeared to be consumed in similar proportions at both Juara and Tekek across all months whereas OTU 4 was consistently consumed in low proportions in Tekek yet consumed irregularly in Juara over the same period (Fig. 3). Even between different roosts in the same site, spatio-temporal differences were observed, such as for OTU 7 (Fig. S5).

View Article: PubMed Central - HTML - PubMed

ABSTRACT

There is an urgent need to identify and understand the ecosystem services of pollination and seed dispersal provided by threatened mammals such as flying foxes. The first step towards this is to obtain comprehensive data on their diet. However, the volant and nocturnal nature of bats presents a particularly challenging situation, and conventional microhistological approaches to studying their diet can be laborious and time-consuming, and provide incomplete information. We used Illumina Next-Generation Sequencing (NGS) as a novel, non-invasive method for analysing the diet of the island flying fox (Pteropus hypomelanus) on Tioman Island, Peninsular Malaysia. Through DNA metabarcoding of plants in flying fox droppings, using primers targeting the rbcL gene, we identified at least 29 Operationally Taxonomic Units (OTUs) comprising the diet of this giant pteropodid. OTU sequences matched at least four genera and 14 plant families from online reference databases based on a conservative Least Common Ancestor approach, and eight species from our site-specific plant reference collection. NGS was just as successful as conventional microhistological analysis in detecting plant taxa from droppings, but also uncovered six additional plant taxa. The island flying fox&rsquo;s diet appeared to be dominated by figs (Ficus sp.), which was the most abundant plant taxon detected in the droppings every single month. Our study has shown that NGS can add value to the conventional microhistological approach in identifying food plant species from flying fox droppings. At this point in time, more accurate genus- and species-level identification of OTUs not only requires support from databases with more representative sequences of relevant plant DNA, but probably necessitates in situ collection of plant specimens to create a reference collection. Although this method cannot be used to quantify true abundance or proportion of plant species, nor plant parts consumed, it ultimately provides a very important first step towards identifying plant taxa and spatio-temporal patterns in flying fox diets.

No MeSH data available.