- Bonn, Nordrhein-Westfalen, Germany
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Marine sediment communities are major contributors to biogeochemical cycling and benthic ecosystem functioning, but they are poorly described, particularly in remote regions such as Antarctica. We analysed patterns and drivers of... more
Marine sediment communities are major contributors to biogeochemical cycling and benthic ecosystem functioning, but they are poorly described, particularly in remote regions such as Antarctica. We analysed patterns and drivers of diversity in metazoan and prokaryotic benthic communities of the Antarctic Peninsula with metabarcoding approaches. Our results show that the combined use of mitochondrial Cox1, and 16S and 18S rRNA gene regions recovered more phyla, from metazoan to non-metazoan groups, and allowed correlation of possible interactions between kingdoms. This higher level of detection revealed dominance by the arthropods and not nematodes in the Antarctic benthos and further eukaryotic diversity was dominated by benthic protists: the world’s largest reservoir of marine diversity. The bacterial family Woeseiaceae was described for the first time in Antarctic sediments. Almost 50% of bacteria and 70% metazoan taxa were unique to each sampled site (high alpha diversity) and har...
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Forest habitats host enormous diversity, but little is known about the seasonal turnover of arthropod species between the above- and below ground forest layers. In this study, we used metabarcoding approaches to uncover arthropod... more
Forest habitats host enormous diversity, but little is known about the seasonal turnover of arthropod species between the above- and below ground forest layers. In this study, we used metabarcoding approaches to uncover arthropod diversity in different forest types and seasons. Our study shows that metabarcoding soil eDNA and Malaise trap bulk samples can provide valuable insights into the phenology and life cycles of arthropods. We found major differences in arthropod species diversity between soil samples and Malaise traps, with only 11.8% species overlap. Higher diversity levels were found in Malaise traps in summer whereas soil samples showed a diversity peak in winter, highlighting the seasonal habitat preferences and life strategies of arthropods. We conclude that collecting time series of bulk arthropod samples and eDNA in the same locations provides a more complete picture of local arthropod diversity and turnover rates and may provide valuable information on climate induced...
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The accurate assessment of community composition and ultimately species identification is of utmost importance in any ecological and evolutionary study. Advances in sequencing technologies have allowed the unraveling of levels of... more
The accurate assessment of community composition and ultimately species identification is of utmost importance in any ecological and evolutionary study. Advances in sequencing technologies have allowed the unraveling of levels of biodiversity never imagined before when applied to large-scale environmental DNA studies (also termed metabarcoding/metagenetics/metasystematics/environmental barcoding). Here, we describe a detailed protocol to assess eukaryotic biodiversity in marine sediments, identifying key steps that should not be neglected when preparing Next-Generation Sequencing (NGS) amplicon libraries: DNA extraction, multiple PCR amplification of DNA barcode markers with index/ tag-primers, and final Illumina MiSeq sequencing library preparation.
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Eukaryotic diversity in environmental samples is often assessed via PCR-based amplification of nSSU genes. However, estimates of diversity derived from pyrosequencing environmental data sets are often inflated, mainly because of the... more
Eukaryotic diversity in environmental samples is often assessed via PCR-based amplification of nSSU genes. However, estimates of diversity derived from pyrosequencing environmental data sets are often inflated, mainly because of the formation of chimeric sequences during PCR amplification. We have analyzed the effect of sample richness, evenness and phylogenetic diversity on the formation of chimeras using an nSSU data set derived from 454 Roche pyrosequencing of replicated, large control pools of closely and distantly related nematode mock communities, of known intragenomic identity and richness. Chimera formation in eukaryotes was higher in both richer and more genetically diverse samples, and compared with prokaryote datasets gives a different perspective of chimera formation in pyrosequenced environmental data sets. Further to this, methods to prepare and analyse massive pyrosequencing datasets in this case from European coast samples were tested using different pipelines and in...
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ABSTRACT Salinas (saltworks) are particularly important for the estuarine waterbirds that breed in Mediterranean countries, where nesting habitats are often scarce. Here we analyze the use of habitats by waterbirds breeding in a salinas... more
ABSTRACT Salinas (saltworks) are particularly important for the estuarine waterbirds that breed in Mediterranean countries, where nesting habitats are often scarce. Here we analyze the use of habitats by waterbirds breeding in a salinas complex on the Ria Formosa in southern Portugal. The results should assist in determining the value of salinas for breeding waterbirds and in drawing up appropriate conservation prescriptions. The species recorded were Black-winged Stilt Himantopus himantopus, Pied Avocet Recurvirostra avosetta, Kentish Plover Charadrius alexandrinus, Little Tern Sterna albifrons, Mallard Anas platyrhynchos and Little Grebe Tachybaptus ruficollis. Our study suggests that each species chooses to use different ponds depending on water level and salinity. Knowledge of such patterns is useful in determining good conservation management.
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Research Interests: Genetics, Computational Biology, Gene expression, Phylogeny, Cell line, and 16 moreCartilage, Animals, Clinical Sciences, Chondrocytes, Amino Acid Profile, Osteogenesis, Bone Formation, SIGNAL PEPTIDE, S100 protein family, Amino Acid Sequence, Base Sequence, Calcium Binding Protein, Sea Bream, Full Length Movies, cDNA library, and Molecular Sequence Data
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Fish has been recently recognized as a suitable vertebrate model and represents a promising alternative to mammals for studying mechanisms of tissue mineralization and unravelling specific questions related to vertebrate bone formation.... more
Fish has been recently recognized as a suitable vertebrate model and represents a promising alternative to mammals for studying mechanisms of tissue mineralization and unravelling specific questions related to vertebrate bone formation. The recently developed Sparus aurata (gilthead seabream) osteoblast-like cell line VSa16 was used to construct a cDNA subtractive library aimed at the identification of genes associated with fish tissue mineralization. Suppression subtractive hybridization, combined with mirror orientation selection, identified 194 cDNA clones representing 20 different genes up-regulated during the mineralization of the VSa16 extracellular matrix. One of these genes accounted for 69% of the total number of clones obtained and was later identified as theS. aurata osteopontin-like gene. The 2138-bp full-length S. aurata osteopontin-like cDNA was shown to encode a 374 amino-acid protein containing domains and motifs characteristic of osteopontins, such as an integrin receptor-binding RGD motif, a negatively charged domain and numerous post-translational modifications (e.g. phosphorylations and glycosylations). The common origin of mammalian osteopontin and fish osteopontin-like proteins was indicated through an in silico analysis of available sequences showing similar gene and protein structures and was further demonstrated by their specific expression in mineralized tissues and cell cultures. Accordingly, and given its proven association with mineral formation and its characteristic protein domains, we propose that the fish osteopontin-like protein may play a role in hard tissue mineralization, in a manner similar to osteopontin in higher vertebrates.
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Biodiversity assessment is the key to understanding the relationship between biodiversity and ecosystem functioning, but there is a well-acknowledged biodiversity identification gap related to eukaryotic meiofaunal organisms. Meiofaunal... more
Biodiversity assessment is the key to understanding the relationship between biodiversity and ecosystem functioning, but there is a well-acknowledged biodiversity identification gap related to eukaryotic meiofaunal organisms. Meiofaunal identification is confounded by the small size of taxa, morphological convergence and intraspecific variation. However, the most important restricting factor in meiofaunal ecological research is the mismatch between diversity and the number of taxonomists that are able to simultaneously identify and catalogue meiofaunal diversity. Accordingly, a molecular operational taxonomic unit (MOTU)-based approach has been advocated for en mass meiofaunal biodiversity assessment, but it has been restricted by the lack of throughput afforded by chain termination sequencing. Contemporary pyrosequencing offers a solution to this problem in the form of environmental metagenetic analyses, but this represents a novel field of biodiversity assessment. Here, we provide an overview of meiofaunal metagenetic analyses, ranging from sample preservation and DNA extraction to PCR, sequencing and the bioinformatic interrogation of multiple, independent samples using 454 Roche sequencing platforms. We report two examples of environmental metagenetic nuclear small subunit 18S (nSSU) analyses of marine and tropical rainforest habitats and provide critical appraisals of the level of putative recombinant DNA molecules (chimeras) in metagenetic data sets. Following stringent quality control measures, environmental metagenetic analyses achieve MOTU formation across the eukaryote domain of life at a fraction of the time and cost of traditional approaches. The effectiveness of Roche 454 sequencing brings substantial advantages to studies aiming to elucidate the molecular genetic richness of not only meiofaunal, but also all complex eukaryotic communities.