Local neighbourhood tree species composition effects in young forest stands : impact of stress, species identity and multitrophic interactions

In dit promotieonderzoek werd nagegaan hoe en waarom verschillen in boomsoortensamenstelling het functioneren van bosecosystemen kunnen beïnvloeden. Daarnaast werd gepoogd te testen hoe deze invloed kan veranderen indien er stresscondities voor de bomen optreden. Eerst werden biomassa en andere groeikarakteristieken gemeten in een Belgische Korte Omloophout site, waar verschillende hoogproductieve Zweedse wilgenklonen waren gemengd. De metingen werden uitgevoerd na twee en vier groeiseizoenen sinds de aanplant, voor de eerste oogst. Daarenboven werd gedurende drie groeiseizoenen de invloed op jonge zaailingen van eik nagegaan in twee Belgische jonge bosopstanden, die deel uitmaken van het FORBIO project. Hier werd zowel gekeken naar groei als bovengrondse en ondergrondse biomassa. Bovendien werden deze boomeigenschappen in verband gebracht met beschaduwing door naburige bomen en infecties door eikenmeeldauw, een belangrijke bladschimmel. Ook werd gekeken naar potentiële biologische controle van deze schimmel door het citroenlieveheersbeestje, zowel bij de situatie in het veld als onder beter gecontroleerde labo condities. De invloed van waterstress werd gesimuleerd door een experimentele behandeling waarbij een deel van de zomerse neerslag werd geïntercepteerd van de jonge boompjes

Improved standardization of transcribed digital specimen data

There are more than 1.2 billion biological specimens in the world's museums and herbaria. These objects are particularly important forms of biological sample and observation. They underpin biological taxonomy but the data they contain have many other uses in the biological and environmental sciences. Nevertheless, from their conception they are almost entirely documented on paper, either as labels attached to the specimens or in catalogues linked with catalogue numbers. In order to make the best use of these data and to improve the findability of these specimens, these data must be transcribed digitally and made to conform to standards, so that these data are also interoperable and reusable. Through various digitization projects, the authors have experimented with transcription by volunteers, expert technicians, scientists, commercial transcription services and automated systems. We have also been consumers of specimen data for taxonomical, biogeographical and ecological research. In this paper, we draw from our experiences to make specific recommendations to improve transcription data. The paper is split into two sections. We first address issues related to database implementation with relevance to data transcription, namely versioning, annotation, unknown and incomplete data and issues related to language. We then focus on particular data types that are relevant to biological collection specimens, namely nomenclature, dates, geography, collector numbers and uniquely identifying people. We make recommendations to standards organizations, software developers, data scientists and transcribers to improve these data with the specific aim of improving interoperability between collection datasets.Peer reviewe

A cost analysis of transcription systems

We compare different approaches to transcribing natural history data and summarise the advantages and disadvantages of each approach using six case studies from four different natural history collections. We summarise the main cost considerations when planning a transcription project and discuss the limitations we current have in understanding the costs behind transcription and data quality.Non peer reviewe

A botanical demonstration of the potential of linking data using unique identifiers for people

Natural history collection data available digitally on the web have so far only made limited use of the potential of semantic links among themselves and with cross-disciplinary resources. In a pilot study, botanical collections of the Consortium of European Taxonomic Facilities (CETAF) have therefore begun to semantically annotate their collection data, starting with data on people, and to link them via a central index system. As a result, it is now possible to query data on collectors across different collections and automatically link them to a variety of external resources. The system is being continuously developed and is already in production use in an international collection portal

Use of European open science cloud and national e-infrastructures for the long-term storage of digitised assets from natural history collections

Digitisation of Natural History Collections (NHC) has evolved from transcription of specimen catalogues in databases to web portals providing access to data, digital images, and 3D models of specimens. These portals increase global accessibility to specimens and help preserve the physical specimens by reducing their handling. The size of the NHC requires developing high-throughput digitisation workflows, as well as research into novel acquisition systems, image standardisation, curation, preservation, and publishing. Nowadays, herbarium sheet digitisation workflows (and fast digitisation stations) can digitise up to 6,000 specimens per day. Operating those digitisation stations in parallel, can increase the digitisation capacity. The high-resolution images obtained from these specimens, and their volume require substantial bandwidth, and disk space and tapes for storage of original digitised materials, as well as availability of computational processing resources for generating derivatives, information extraction, and publishing. While large institutions have dedicated digitisation teams that manage the whole workflow from acquisition to publishing, other institutions cannot dedicate resources to support all digitisation activities, in particular long-term storage. National and European e-infrastructures can provide an alternative solution by supporting different parts of the digitisation workflows. In the context of the Innovation and consolidation for large scale digitisation of natural heritage (ICEDIG Project 2018), three different e-infrastructures providing long-term storage have been analysed through three pilot studies: EUDAT-CINES, Zenodo, and National Infrastructures

Stronger diversity effects with increased environmental stress : a study of multitrophic interactions between oak, powdery mildew and ladybirds

Recent research has suggested that increasing neighbourhood tree species diversity may mitigate the impact of pests or pathogens by supporting the activities of their natural enemies and/or reducing the density of available hosts. In this study, we attempted to assess these mechanisms in a multitrophic study system of young oak (Quercus), oak powdery mildew (PM, caused by Erysiphe spp.) and a mycophagous ladybird (Psyllobora vigintiduo-punctata). We assessed ladybird mycophagy on oak PM in function of different neighbourhood tree species compositions. We also evaluated whether these species interactions were modulated by environmental conditions as suggested by the Stress Gradient Hypothesis. We adopted a complementary approach of a field experiment where we monitored oak saplings subjected to a reduced rainfall gradient in a young planted forest consisting of different tree species mixtures, as well as a lab experiment where we independently evaluated the effect of different watering treatments on PM infections and ladybird mycophagy. In the field experiment, we found effects of neighbourhood tree species richness on ladybird mycophagy becoming more positive as the target trees received less water. This effect was only found as weather conditions grew drier. In the lab experiment, we found a preference of ladybirds to graze on infected leaves from trees that received less water. We discuss potential mechanisms that might explain this preference, such as emissions of volatile leaf chemicals. Our results are in line with the expectations of the Natural Enemies Hypothesis and support the hypothesis that biodiversity effects become stronger with increased environmental stress

A benchmark dataset of herbarium specimen images with label data

More and more herbaria are digitising their collections. Images of specimens are made available online to facilitate access to them and allow extraction of information from them. Transcription of the data written on specimens is critical for general discoverability and enables incorporation into large aggregated research datasets. Different methods, such as crowdsourcing and artificial intelligence, are being developed to optimise transcription, but herbarium specimens pose difficulties in data extraction for many reasons. To provide developers of transcription methods with a means of optimisation, we have compiled a benchmark dataset of 1,800 herbarium specimen images with corresponding transcribed data. These images originate from nine different collections and include specimens that reflect the multiple potential obstacles that transcription methods may encounter, such as differences in language, text format (printed or handwritten), specimen age and nomenclatural type status. We are making these specimens available with a Creative Commons Zero licence waiver and with permanent online storage of the data. By doing this, we are minimising the obstacles to the use of these images for transcription training. This benchmark dataset of images may also be used where a defined and documented set of herbarium specimens is needed, such as for the extraction of morphological traits, handwriting recognition and colour analysis of specimens