Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing

Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2 cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18 S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2 g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes

Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity

The use of environmental DNA (eDNA) in biodiversity assessments offers a step-change in sensitivity, throughput and simultaneous measures of ecosystem diversity and function. There remains, however, a need to examine eDNA persistence in the wild through simultaneous temporal measures of eDNA and biota. Here, we use metabarcoding of two markers of different lengths, derived from an annual time series of aqueous lake eDNA to examine temporal shifts in ecosystem biodiversity and in an ecologically important group of macroinvertebrates (Diptera: Chironomidae). The analyses allow different levels of detection and validation of taxon richness and community composition (β-diversity) through time, with shorter eDNA fragments dominating the eDNA community. Comparisons between eDNA, community DNA, taxonomy and UK species abundance data further show significant relationships between diversity estimates derived across the disparate methodologies. Our results reveal the temporal dynamics of eDNA and validate the utility of eDNA metabarcoding for tracking seasonal diversity at the ecosystem scale

New insights about the introduction of the Portuguese oyster, Crassostrea angulata, into the North East Atlantic from Asia based on a highly polymorphic mitochondrial region

It is commonly presumed that the Portuguese oyster Crassostrea angulata was introduced into the North East (NE) Atlantic from Asia. The analysis of the nucleotide sequence of a highly polymorphic non-coding mitochondrial region (major noncoding region - MNR) of C. angulata samples collected in Europe (Portugal), Africa (Morocco) and Asia (Shantou and Taiwan) provided new insight into the introduction of this species into the NE Atlantic. Sixty haplotypes and a nucleotide diversity of 0.0077 were observed in 130 analyzed sequences. Higher nucleotide diversity levels were observed in NE Atlantic sites than in Asian sites and significant genetic differentiation was found between the two. Our results suggest that C. angulata might have been introduced to the NE Atlantic by multiple introductory events, though the exact origins remain unknown since none of the analyzed Asian sites seemed to have been a source of introduction. The nucleotide diversity of C. angulata was higher than that previously reported for Pacific oyster C. gigas in Europe and Asia for the same mitochondrial region. The results obtained in the present study suggest that NE Atlantic C. angulata stocks are a unique genetic resource, which highlights the importance of their conservation

Divergent national-scale trends of microbial and animal biodiversity revealed across diverse temperate soil ecosystems

Soil biota accounts for ~25% of global biodiversity and is vital to nutrient cycling and primary production. There is growing momentum to study total belowground biodiversity across large ecological scales to understand how habitat and soil properties shape belowground communities. Microbial and animal components of belowground communities follow divergent responses to soil properties and land use intensification; however, it is unclear whether this extends across heterogeneous ecosystems. Here, a national-scale metabarcoding analysis of 436 locations across 7 different temperate ecosystems shows that belowground animal and microbial (bacteria, archaea, fungi, and protists) richness follow divergent trends, whereas β-diversity does not. Animal richness is governed by intensive land use and unaffected by soil properties, while microbial richness was driven by environmental properties across land uses. Our findings demonstrate that established divergent patterns of belowground microbial and animal diversity are consistent across heterogeneous land uses and are detectable using a standardised metabarcoding approach

Glastir Monitoring & Evaluation Programme. First year annual report

The Welsh Government has commissioned a comprehensive new ecosystem monitoring and evaluation programme to monitor the effects of Glastir, its new land management scheme, and to monitor progress towards a range of international biodiversity and environmental targets. A random sample of 1 km squares stratified by landcover types will be used both to monitor change at a national level in the wider countryside and to provide a backdrop against which intervention measures are assessed using a second sample of 1 km squares located in areas eligible for enhanced payments for advanced interventions. Modelling in the first year has forecast change based on current understanding, whilst a rolling national monitoring programme based on an ecosystem approach will provide an evidence-base for on-going, adaptive development of the scheme by Welsh Government. To our knowledge, this will constitute the largest and most in-depth ecosystem monitoring and evaluation programme of any member state of the European Union

Genetic linkage mapping in the blue mussel Mytilus edulis and the European flat oyster Ostrea edulis, and the search for quantitative trait loci of resistance to a disease in O. edulis

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Analyse du succès reproducteurs chez des populations naturelles et d'écloserie d'huître plate Ostrea edulis L.

Cette étude vise à approfondir la connaissance de la biologie de la reproduction de l'huître plate Ostrea edulis afin de mieux comprendre comment les caractéristiques de la biologie de reproduction de l'espèce peuvent rendre compte des phénomènes de déficits en hétérozygote et de relation positive entre hétérozygotie et croissance. En particulier, elle vise à analyser le succès reproducteur en milieu naturel et dans les populations maintenues en écloserie. Cette étude repose sur l'utilisation de marqueurs microsatellites qui, du fait de leur fort polymorphisme, représentent des outils puissants d'assignation de parenté. Une première partie de l'étude a consisté à analyser les pontes issues de femelles incubantes prélevées dans le milieu naturel. Le nombre de pères ayant contribué à la descendance est très variable d'une femelle à l'autre et aucun patron particulier n'a pu être mis en évidence en fonction de la date d'échantillonnage. En revanche, une variance du succès reproducteur des mâle a pu être mise en évidence, puisque dans certains cas le mâle majoritaire a participé à plus de 90% des descendants. Une seconde partie de l'étude a consisté à analyser en milieu contrôlé des pontes en masse dont tous les géniteurs potentiels sont connus. Il nous a été difficile de trouver un logiciel adapté : aucun parent n'est connu de m^me que le sexe des géniteurs. Malgré tout, une faible taille efficace a pu être mise en évidence ainsi qu'une succession dans les géniteurs qui ont contribué à chacune des pontes. Les implications de la variance du succès reproducteur (qui implique un faible Ne) sur les déficits en hétérozygotes et l'hétérosis sont discutées. Cependant, ces résultats doivent être approfondis par l'utilisation d'autres outils d'analyse de parenté, notamment basés sur l'allocation fractionnée, qui permettrait d'obtenir une distribution plus fine du succès reproducteur. Parallèlement, le nombre de marqueurs génétiques utilisés doit être augmenté

Metabarcoding marine sediments: preparation of amplicon libraries: Chapter 12

PMID: 27460378The 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

Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing

Understanding how biodiversity changes in time and space is vital to assess the effects of environmental change on benthic ecosystems. Due to the limitations of morphological methods, there has been a rapid expansion in the application of high-throughput sequencing methods to study benthic eukaryotic communities. However, the effect of sample size and small-scale spatial variation on the assessment of benthic eukaryotic diversity is still not well understood. Here, we investigate the effect of different sample volumes in the genetic assessment of benthic metazoan and non-metazoan eukaryotic community composition. Accordingly, DNA was extracted from five different cumulative sediment volumes comprising 100% of the top 2 cm of five benthic sampling cores, and used as template for Ilumina MiSeq sequencing of 18 S rRNA amplicons. Sample volumes strongly impacted diversity metrics for both metazoans and non-metazoan eukaryotes. Beta-diversity of treatments using smaller sample volumes was significantly different from the beta-diversity of the 100% sampled area. Overall our findings indicate that sample volumes of 0.2 g (1% of the sampled area) are insufficient to account for spatial heterogeneity at small spatial scales, and that relatively large percentages of sediment core samples are needed for obtaining robust diversity measurement of both metazoan and non-metazoan eukaryotes