NGS barcoding reveals high resistance of a hyperdiverse chironomid (Diptera) swamp fauna against invasion from adjacent freshwater reservoirs

Abstract

BackgroundMacroinvertebrates such as non-biting midges (Chironomidae: Diptera) are important components of freshwater ecosystems. However, they are often neglected in biodiversity and conservation research because invertebrate species richness is difficult and expensive to quantify with traditional methods. We here demonstrate that Next Generation Sequencing barcodes (“NGS barcodes”) can provide relief because they allow for fast and large-scale species-level sorting of large samples at low cost.ResultsWe used NGS barcoding to investigate the midge fauna of Singapore’s swamp forest remnant (Nee Soon Swamp Forest). Based on > 14.000 barcoded specimens, we find that the swamp forest maintains an exceptionally rich fauna composed of an observed number of 289 species (estimated 336 species) in a very small area (90 ha). We furthermore barcoded the chironomids from three surrounding reservoirs that are located in close proximity. Although the swamp forest remnant is much smaller than the combined size of the freshwater reservoirs in the study (90 ha vs. > 450 ha), the latter only contains 33 (estimated 61) species. We show that the resistance of the swamp forest species assemblage is high because only 8 of the 314 species are shared despite the close proximity. Moreover, shared species are not very abundant (3% of all specimens). A redundancy analysis revealed that ~ 21% of the compositional variance of midge communities within the swamp forest was explained by a range of variables with conductivity, stream order, stream width, temperature, latitude (flow direction), and year being significant factors influencing community structure. An LME analysis demonstrates that the total species richness decreased with increasing conductivity.ConclusionOur study demonstrates that midge diversity of a swamp forest can be so high that it questions global species diversity estimates for Chironomidae, which are an important component of many freshwater ecosystems. We furthermore demonstrate that small and natural habitat remnants can have high species turnover and can be very resistant to the invasion of species from neighboring reservoirs. Lastly, the study shows how NGS barcodes can be used to integrate specimen- and species-rich invertebrate taxa in biodiversity and conservation research.Electronic supplementary materialThe online version of this article (10.1186/s12983-018-0276-7) contains supplementary material, which is available to authorized users.

DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds

“…Morphological identification of Diptera larvae, especially Chironomidae, is often very difficult and complicated even for specialists, due to the lack of diagnostic characters (Baloğlu et al, 2018;Dobson, 2013;Silva & Wiedenbrug, 2014). Morphological identification of Diptera larvae, especially Chironomidae, is often very difficult and complicated even for specialists, due to the lack of diagnostic characters (Baloğlu et al, 2018;Dobson, 2013;Silva & Wiedenbrug, 2014).…”

“…However, identification/sorting of invertebrate using morphological properties to species level is difficult and expensive (Baloğlu, Clews, & Meier, 2018;Wang, Srivathsan, Foo, Yamane, & Meier, 2018). It has been shown that the cost of, for example, midge, identification using morphological properties is quite high due to the requirement of dissection and mounting of specimens onto microscopic slides (Baloğlu et al, 2018). As a result, the rarely used species-level data lead to the undesirable information of responses to stressors, because different species have different sensitivity to environmental parameters (Baloğlu et al, 2018;Beermann, Zizka, Elbrecht, Baranov, & Leese, 2018;Macher et al, 2015).…”

“…is typically based on identification of organisms by morphological properties (Briers, 2014;Le Viol, Mocq, Julliard, & Kerbiriou, 2009;Tixier, Rochfort, Grapentine, Marsalek, & Lafont, 2012). However, identification/sorting of invertebrate using morphological properties to species level is difficult and expensive (Baloğlu, Clews, & Meier, 2018;Wang, Srivathsan, Foo, Yamane, & Meier, 2018). It has been shown that the cost of, for example, midge, identification using morphological properties is quite high due to the requirement of dissection and mounting of specimens onto microscopic slides (Baloğlu et al, 2018).…”

Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches

“…Such transfer of methods may include, for instance, the use of the preservative ethanol to extract DNA without destroying the morphology of the organisms. Nevertheless, insect communities found in freshwater benthos and Malaise traps have different characteristics, with freshwater samples dominated by larval stages and often characterized by low diversity and abundances (see Baloğlu, Clews, and Meier () for exceptionally diverse kick net samples), while Malaise trap catches are dominated by adult insects and generally characterized by high diversity and abundances. As a consequence, the transfer of techniques between these types of samples demands specific testing and optimizing.…”

A new cost‐effective and fast direct PCR protocol for insects based on PBS buffer

“…direct PCR to amplify DNA in faecal samples (Kitpipit, Chotigeat, Linacre, & Thanakiatkrai, 2014). More recently, direct PCR has been used with next-generation sequencing (NGS) to metabarcode hundreds and thousands of samples at a very low cost per sample (less than 1 USD per barcode) (Baloğlu, Clews, & Meier, 2018;Meier, Wong, Srivathsan, & Foo, 2016;Wang, Srivathsan, Foo, Yamane, & Meier, 2018). However, the success rates of these NGS-based studies can still be improved (e.g.…”