Short running title:High-throughput sequencing to unveil soil mesofauna Summary 1. Biological communities inhabiting the soil are among the most diversified, complex and yet most poorly studied of terrestrial ecosystems. The greatest knowledge gaps apply to the arthropod mesofauna (0.1-2 mm body size) because conventional morphological and molecular approaches are in many cases insufficient for the characterisation of these complex communities. The development of high-throughput sequencing (HTS) methodologies is required to solve current impediments and to further advance our understanding of belowground biodiversity. We propose a Flotation-Berlese-Flotation (FBF) protocol for sampling and specimenprocessing to obtain 'clean' DNA extractions of arthropod mesofauna from the soil. In addition, we developed and tested HTS protocols for the characterization of arthropod communities from these bulk DNA extractions using cox1 metabarcoding and shotgun metagenomic sequencing on the MiSeq Illumina platform. 3.The FBF protocol provided DNA of soil arthropods from sufficiently large volumes of soil and free from contaminating bacteria and inhibitors. Metabarcoding and metagenomic sequencing on two deep soil samples from Iberian grasslands revealed >100 species of Acari and Collembola from 28 families. Genome assembly straight from shotgun sequencing of bulk specimens produced partial and full mitogenomes for 54 species with average length of >6000 bp. Metabarcoding and metagenomic sequencing resulted in closely congruent OTUs but species numbers were highest with metabarcoding, while ~73% of species were confirmed by matching shotgun sequence reads and ~48% by contig assembly from those shotgun reads. Accepted ArticleThis article is protected by copyright. All rights reserved. 4.In combination, the FBF protocol together with the PCR-based and shotgun sequencing pipelines addressed most of the challenges of studying soil arthropod mesofauna on the MiSeq Illumina platform. They are powerful, cost-efficient tools for characterising soil diversity in a phylogenetic and community ecology context. These methodological developments of HTS approaches for the study of mesofauna will accelerate ecological and evolutionary studies, biomonitoring of soil arthropods, and progress in both theoretical and applied soil science.

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

The rate and depth of cattle dung incorporation into moorland soil may be an important factor influencing plant community dynamics through its effects on soil nutrient availability. This study traces the incorporation of 15N‐labelled dung into a moorland soil under two vegetation types in Dartmoor National Park, UK. Cores of treated and control soil 10 cm deep were collected at 2, 4, 8 and 16 week intervals and divided into 2 cm depth increments. Soil samples were freeze‐dried, ground and analysed for atom% 15N and %N content using continuous‐flow isotope‐ratio mass spectrometry. The contribution of dung N to the soil N pool was estimated by changes in atom% 15N of the soil.  The incorporation of dung dry matter into the soil was also calculated. The labile component of the dung N was incorporated deeper and more rapidly into soil under grass than under heather vegetation. The implications of these processes for the dynamics of upland plant communities are considered in relation to the ability of plants to compete for nutrients. Copyright © 2000 John Wiley & Sons, Ltd.

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Accurate estimates of methane (CH 4) fluxes from restored peatlands are needed to inform emission factor estimations and reporting. Flux measurements are usually taken during the daytime but such measurements may provide biased estimates of overall CH 4 emissions if night-time fluxes differ from daytime fluxes. Diurnal variations in CH 4 fluxes have been reported for a range of peatland types, but not for restored raised bogs which are important carbon stores in some countries. To help fill this knowledge gap, we investigated diurnal variations in CH 4 emissions from a restored raised bog. CH 4 fluxes from a restored raised bog were measured in two 24-hr field campaigns using flux chambers. Carbon dioxide (CO 2) fluxes were also monitored, as were a suite of complementary environmental variables. Night-time CH 4 fluxes were significantly greater than daytime fluxes during both campaigns, by 10.4% and 36.1%, respectively. In Campaign 1 air temperature was the best predictor of CH 4 fluxes, whereas in Campaign 2 net ecosystem exchange (NEE) values were the best predictor. This study shows that diurnal variations in CH 4 fluxes exist in a restored peatland and that current approaches biased to daytime measurements will underestimate CH 4 emissions from restored peatlands to the atmosphere. RÉSUMÉ Des estimations précises des flux de méthane (CH 4) à partir de tourbières perturbées sont requises pour informer les estimations de facteurs d'émission et la production de rapports. Les mesures de flux sont généralement prises pendant le jour, mais de telles mesures peuvent fournir des estimations biaisées des émissions totales de CH 4 si les flux nocturnes diffèrent des flux diurnes. Les variations journalières des flux de CH 4 de différent types de tourbières ont déjà été rapportés, mais pas pour les tourbières ombrotrophes restaurées, qui sont d'importants réservoirs de carbone dans certains pays. Pour combler ce manque de connaissances, nous avons évalué les variations journalières des émissions de CH 4 d'une tourbière ombrotrophe restaurée. Les flux de CH 4 ont été mesurés lors de deux campagnes de terrain de 24 heures à l'aide de chambres de débit. Les flux de dioxyde de carbone (CO 2) ont aussi été enregistrés, tout comme une série de variables environnementales complémentaires. Les flux de CH 4 nocturnes étaient significativement plus élevés que les flux diurnes lors des deux campagnes, respectivement par 10,4% et 36,1%. Lors de la Campagne 1, la température de l'air était le meilleur prédicteur des flux de CH 4 , tandis que lors de la Campagne 2, les valeurs d'échanges écosystémiques nets (EEN) étaient le meilleur prédicteur. Cette étude montre que des variations journalières des flux de CH 4 sont présentes dans une tourbière ombrotrophe restaurée et que les approches actuelles basées sur les mesures diurnes sous-estiment les émissions de CH 4 vers l'atmosphère.