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Metabarcoding and Metagenomics
Number of Followers: 0  

  This is an Open Access Journal Open Access journal
ISSN (Online) 2534-9708
Published by Pensoft Homepage  [26 journals]
  • Dropping Hints: Estimating the diets of livestock in rangelands using DNA
           metabarcoding of faeces

    • Abstract: Metabarcoding and Metagenomics 2: e22467
      DOI : 10.3897/mbmg.2.22467
      Authors : Timothy Lee, Yohannes Alemseged, Andrew Mitchell : The introduction of domesticated animals into new environments can lead to considerable ecological disruption, and it can be difficult to predict their impact on the new ecosystem. In this study, we use faecal metabarcoding to characterize the diets of three ruminant taxa in the rangelands of south-western New South Wales, Australia. Our study organisms included goats (Capra aegagrus hircus) and two breeds of sheep (Ovis aries): Merinos, which have been present in Australia for over two hundred years, and Dorpers, which were introduced in the 1990s. We used High-Throughput Sequencing methods to sequence the rbcL and ITS2 genes of plants in the faecal samples, and identified the samples using the GenBank and BOLD online databases, as well as a reference collection of sequences from plants collected in the study area. We found that the diets of all three taxa were dominated by the family Malvaceae, and that the Dorper diet was more diverse than the Merino diet at both the family and the species level. We conclude that Dorpers, like Merinos, are potentially a threat to some vulnerable species in the rangelands of New South Wales. HTML XML PDF
      PubDate: Wed, 14 Mar 2018 15:18:51 +020
       
  • Quantitative monitoring of multispecies fish environmental DNA using
           high-throughput sequencing

    • Abstract: Metabarcoding and Metagenomics 2: e23297
      DOI : 10.3897/mbmg.2.23297
      Authors : Masayuki Ushio, Hiroaki Murakami, Reiji Masuda, Tetsuya Sado, Masaki Miya, Sho Sakurai, Hiroki Yamanaka, Toshifumi Minamoto, Michio Kondoh : Effective ecosystem conservation and resource management require quantitative monitoring of biodiversity, including accurate descriptions of species composition and temporal variations of species abundance. Accordingly, quantitative monitoring of biodiversity has been performed for many ecosystems, but it is often time- and effort-consuming and costly. Recent studies have shown that environmental DNA (eDNA), which is released to the environment from macro-organisms living in a habitat, contains information about species identity and abundance. Thus, analysing eDNA would be a promising approach for more efficient biodiversity monitoring. In the present study, internal standard DNAs (i.e. known amounts of short DNA fragments from fish species that have never been observed in a sampling area) were added to eDNA samples, which were collected weekly from a coastal marine ecosystem in Maizuru Bay, Japan (from April 2015 to March 2016) and metabarcoding analysis was performed using Illumina MiSeq to simultaneously identify fish species and quantify fish eDNA copy numbers. A correction equation was obtained for each sample using the relationship between the number of sequence reads and the added amount of the standard DNAs and this equation was used to estimate the copy numbers from the sequence reads of non-standard fish eDNA. The calculated copy numbers showed significant positive correlations with those determined by quantitative PCR, suggesting that eDNA metabarcoding with standard DNA enabled useful quantification of eDNA. Furthermore, for samples that show a high level of PCR inhibition, this method might allow more accurate quantification than qPCR because the correction equations generated using internal standard DNAs would include the effect of PCR inhibition. A single run of Illumina MiSeq produced >70 quantitative fish eDNA time series in this study, showing that this method could contribute to more efficient and quantitative monitoring of biodiversity. HTML XML PDF
      PubDate: Wed, 14 Mar 2018 9:23:23 +0200
       
  • Using DNA metabarcoding for assessing chironomid diversity and community
           change in mosquito controlled temporary wetlands

    • Abstract: Metabarcoding and Metagenomics 2: e21060
      DOI : 10.3897/mbmg.2.21060
      Authors : Kathrin Theissinger, Anna Kästel, Vasco Elbrecht, Jenny Makkonen, Susanne Michiels, Susanne Schmidt, Stefanie Allgeier, Florian Leese, Carsten Brühl : The biocide Bacillus thuringiensis var. israelensis (Bti) is widely applied for mosquito control in temporary wetlands of the German Upper Rhine Valley. Even though Bti is considered environmentally friendly, several studies have shown non-target effects on chironomids, a key food resource in wetland ecosystems. Chironomids have been proposed as important indicators for monitoring freshwater ecosystems, however, morphological determination is very challenging. In this study, we investigated the effectiveness of metabarcoding for chironomid diversity assessment and tested the retrieved chironomid operational taxonomic units (OTUs) for possible changes in relative abundance and species diversity in relation to mosquito control actions in four temporary wetlands. Three of these wetlands were, for the first year after 20 years of Bti treatment, partly left Bti-untreated in a split field design, and one wetland has never been treated with Bti. Our metabarcoding approach detected 54 chironomid OTUs across all study sites, of which almost 70% could be identified to species level comparisons against the BOLD database. We showed that metabarcoding increased chironomid species determination by 70%. However, we found only minor significant effects of Bti on the chironomid community composition, even though Bti reduced chironomid emergence by 65%. This could be due to a time lag of chironomid recolonization, since the study year was the first year of Bti intermittence after about 20 years of Bti application in the study area. Subsequent studies will have to address if and how the chironomid community composition will recover further in the now Bti-untreated temporary wetlands to assess effects of Bti. HTML XML PDF
      PubDate: Mon, 15 Jan 2018 14:52:37 +020
       
  • Geographic distance and mountain ranges structure freshwater protist
           communities on a European scalŠµ

    • Abstract: Metabarcoding and Metagenomics 2: e21519
      DOI : 10.3897/mbmg.2.21519
      Authors : Jens Boenigk, Sabina Wodniok, Christina Bock, Daniela Beisser, Christopher Hempel, Lars Grossmann, Anja Lange, Manfred Jensen : Protists influence ecosystems by modulating microbial population size, diversity, metabolic outputs and gene flow. In this study we used eukaryotic ribosomal amplicon diversity from 218 European freshwater lakes sampled in August 2012 to assess the effect of mountain ranges as biogeographic barriers on spatial patterns and microbial community structure in European freshwaters. The diversity of microbial communities as reflected by amplicon clusters suggested that the eukaryotic microbial inventory of lakes was well-sampled at the European and at the local scale. Our pan-European diversity analysis indicated that biodiversity and richness of high mountain lakes differed from that of lowland lakes. Further, the taxon inventory of high-mountain lakes strongly contributed to beta-diversity despite a low taxon inventory. Even though ecological factors, in general, strongly affect protist community pattern, we show that geographic distance and geographic barriers significantly contribute to community composition particularly for high mountain regions which presumably act as biogeographic islands. However, community composition in lowland lakes was also affected by geographic distance but less pronounced as in high mountain regions. In consequence protist populations are locally structured into distinct biogeographic provinces and community analyses revealed biogeographic patterns also for lowland lakes whereby European mountain ranges act as dispersal barriers in particular for short to intermediate distances whereas the effect of mountain ranges levels off on larger scale. HTML XML PDF
      PubDate: Tue, 2 Jan 2018 10:26:33 +0200
       
  • Combining NCBI and BOLD databases for OTU assignment in metabarcoding and
           metagenomic datasets: The BOLD_NCBI _Merger

    • Abstract: Metabarcoding and Metagenomics 1: e22262
      DOI : 10.3897/mbmg.1.22262
      Authors : Jan-Niklas Macher, Till-Hendrik Macher, Florian Leese : HTML XML PDF
      PubDate: Fri, 15 Dec 2017 15:03:10 +020
       
  • Disentangling higher trophic level interactions in the cabbage aphid food
           web using high-throughput DNA sequencing

    • Abstract: Metabarcoding and Metagenomics 1: e13709
      DOI : 10.3897/mbmg.1.13709
      Authors : Marie-Caroline Lefort, Stephen Wratten, Antonino Cusumano, Yann-David Varennes, Stephane Boyer : The lack of understanding of complex food-web interactions has been a major gap in the history of biological control. In particular, a better understanding of the functioning of pest food-webs and how they vary between native and invaded geographical ranges is of prime interest for biological control research and associated integrated pest management. Technical limitations associated with the deciphering of complex food-webs can now be largely overcome by the use of high throughput DNA sequencing techniques such as Illumina MiSeq. We tested the efficiency of this next generation sequencing technology in a metabarcoding approach, to study aphid food-webs using the cabbage aphid as model. We compared the variations in structure and composition of aphid food-webs in the species’ native range (United Kingdom, UK) and in an invaded range (New Zealand, NZ). We showed that Illumina MiSeq is a well suited technology to study complex aphid food-webs from aphid mummies. We found an unexpectedly high top down pressure in the NZ cabbage aphid food-web, which coupled to a large ratio of consumer species / prey species and a lack of potential inter-specific competition between primary parasitoids, could cause the NZ food-web to be more vulnerable than the UK one. This study also reports for the first time the occurrence of a new hyperparasitoid species in NZ, as well as new associations between hyperparasitoids parasitoids and the cabbage aphid in this country. We conclude that the complexity of aphid food-webs in agricultural systems could often be underestimated, particularly at higher trophic levels; and that the use of high throughput DNA sequencing tools, could largely help to overcome this impediment. HTML XML PDF
      PubDate: Wed, 18 Oct 2017 14:38:41 +030
       
  • Ready for the deluge! Introducing the new Metabarcoding and Metagenomics
           (MBMG) journal

    • Abstract: Metabarcoding and Metagenomics 1: e14791
      DOI : 10.3897/mbmg.1.14791
      Authors : Florian Leese, Dirk Steinke, Alexander Weigand, Lyubomir Penev : HTML XML PDF
      PubDate: Wed, 20 Sep 2017 15:15:10 +030
       
  • Short COI markers for freshwater macroinvertebrate metabarcoding

    • Abstract: Metabarcoding and Metagenomics 1: e14625
      DOI : 10.3897/mbmg.1.14625
      Authors : Ecaterina Vamos, Vasco Elbrecht, Florian Leese : Species diversity of metazoan bulk samples can be rapidly assessed using cytochrome c oxidase I (COI) metabarcoding. However, in some applications often only degraded DNA is available, e.g. from poorly conserved museum specimens, environmental DNA (eDNA) filtered from water or gut content analyses. Here universal primer sets targeting only a short COI fragment are advantageous, as they often can still amplify short DNA fragments. Using PrimerMiner, we optimised two universal primer sets targeting freshwater macroinvertebrates based on NCBI and BOLD reference sequences. The fwh1 and fwh2 primer sets targeting a 178 and 205 bp region were tested in vitro by sequencing previously used freshwater macroinvertebrate mock communities as well as three monitoring samples from Romanian streams of unknown composition. They were further evaluated in silico for their suitability to amplify other insect groups. The fwh1 primer sets showed the most consistent amplification in silico and in vitro, detecting 92% of the taxa present in the mock communities, and allowing clear differentiation between the three macroinvertebrate communities from the Romanian streams. In silico analysis indicates that the short primers are likely to perform well even for non-freshwater insects. Comparing the performance of the new fwh1 primer sets to a highly degenerate primer set targeting a longer fragment (BF2+BR2) revealed that detection efficiency is slightly lower for the new primer set. Nevertheless, the shorter new primer pairs might be useful for studies that have to rely on degraded or poorly conserved DNA and thus be of importance for biomonitoring, conservation biological or molecular ecological studies. Furthermore, our study highlights the need for in silico evaluation of primer sets in order to detect design errors in primers (fwhR2) and find optimal universal primer sets for the target taxa of interest. HTML XML PDF
      PubDate: Wed, 20 Sep 2017 10:33:01 +030
       
  • Functional and phylogenetic analysis of the core transcriptome of
           Ochromonadales

    • Abstract: Metabarcoding and Metagenomics 1: e19862
      DOI : 10.3897/mbmg.1.19862
      Authors : Nadine Graupner, Jens Boenigk, Christina Bock, Manfred Jensen, Sabina Marks, Sven Rahmann, Daniela Beisser : Background Most protist lineages consist of members with diverging features e.g. different modes of nutrition and adaptations for life in different habitat types and climatic zones. The nutritional mode is particularly variable in chrysophytes and they are therefore an excellent model group to study the core genes and metabolic pathways of a functionally diverse lineage. The objective of our study is the identification of the joint genetic repertoire expressed in closely related chrysophytes as well as the extent of variation on species and strain level. Therefore, we investigated the transcriptomes of six strains belonging to four species of Ochromonadales. We performed analyses on metabolic pathway level as well as on sequence level. Results We could identify 1,574 core genes shared between all six investigated strains of Ochromonadales. Most of these core genes were affiliated with the primary metabolism. Phylogenetic analysis of 166 protein-coding core genes supported a close relation of Poteriospumella lacustris and Poterioochromonas malhamensis and resolved for more than 50% of investigated genes the relationship of strains affiliated with the species P. lacustris. Further, we found diverging phylogenetic patterns for genes interacting with the environment. Conclusions In Ochromonadales, a functionally diverse lineage, the core transcriptome represents only a minor part of the individual transcriptomes. But this small fraction of genes comprises the basal metabolism essential for life in several protist lineages. Phylogenetic analyses of these genes indicate a similar degree of conservation as observed for genes coding for ribosomal proteins. HTML XML PDF
      PubDate: Wed, 20 Sep 2017 9:13:36 +0300
       
 
 
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