Understanding the impacts of widespread forest die-offs across France, Germany, and China

Understanding the impacts of widespread forest die-offs across France, Germany, and China

Understanding the impacts of widespread forest die-offs across France, Germany, and China

Metabarcoding increases the taxonomic resolution and geographic scale at which researchers can assess the impacts of climate change on insect communities in forests

Entomologists studying tree dieback of Picea abies in Bavarian National Park.

PHOTO CREDIT: Heiner M. Elsner

Forests throughout the world are suffering from an increase in the frequency and severity of droughts as well as pathogen and insect infestations. These climate-exacerbated factors are leading to tree diebacks—the progressive death of tree branches—and subsequent large-scale forest die-offs, the effects of which are not well understood. Preliminary results from our study indicate that while the number of insect species along forest die-off gradients might not be affected, their composition is changing.

CLIMTREE is an international project funded by the Belmont Forum that assesses the impact of climate-induced forest die-off on invertebrate biodiversity in highland forests in France, Germany, and China. This project aims to better understand how tree mortality and associated changes in forest composition affect biodiversity and ecosystem functions.

Silver fir (Abies alba) dieback in the French eastern Pyrenees

PHOTO CREDIT: Carlos Lopez-Vaamonde

Our study measures changes in the insect communities along dieback and salvage-logging gradients of silver fir (Abies alba) forests in the French eastern and central Pyrenees, Norway, spruce (Picea abies) forests in the Bavarian Forest National Park, Germany, and Yunnan pine (Pinus yunnanensis) forests in Yunnan province, China. We examined patterns of variation in the species diversity of flying insects collected by Malaise traps. As these passive traps can collect a large number of specimens, we analyzed samples in bulk using DNA metabarcoding. This approach uses DNA barcode reference libraries to identify species from a mixed sample using high-throughput technologies that effectively provide large amounts of DNA sequence data.

Members of CLIMTREE assessing the level of decline of silver fir stands in Pays de Sault (French eastern Pyrenees)

PHOTO CREDIT: Carlos Lopez-Vaamonde

We also examined saproxylic beetles, a key functional group used as bioindicators in forest assessments of dead-wood availability. We collected these beetles using flight interception traps, and we also sampled specimens from natural history collections to build a DNA barcode reference library for the French saproxylic beetle fauna as a resource for future investigations.

The preliminary results from the 56 Malaise traps deployed in the French eastern and central Pyrenees have revealed more than 3,500 OTUs (Operational Taxonomic Units, a proxy for species) belonging to 18 insect orders, with considerable change in the compositions of the species detected along the dieback gradient as well as across a 4-month period. However, results to date do not suggest significant declines in species richness over the dieback gradient.

Rosalia alpina (Cerambycidae) is one of the 2,663 species of saproxylic beetles known to occur in France

PHOTO CREDIT: Carlos Lopez-Vaamonde

Polytrap flight interception trap

PHOTO CREDIT: Carl Moliard

Of the 55,571 saproxylic beetles collected by the flight interception traps, about 70% were morphologically identified to one of 284 species. Similar to the flying insects collected by Malaise traps, the diversity of beetles along dieback gradients did not decline. We are now trying to use a non-destructive metabarcoding approach that involves processing the collection media to determine whether we can uncover a comparable number of species with a morphology-based sorting approach. If results are similar, we will have a strong case for using this technique as a time-efficient alternative for biomonitoring moving forward.

Overall, there is an urgent need to obtain detailed baseline data on insect communities to quantify the impacts of climate change. By taking advantage of DNA metabarcoding approaches, our study is assessing biodiversity patterns at scales previously impossible and providing the data essential for evaluating future changes in insect communities. Our workflows are simple to use and provide an affordable, reliable, and repeatable method of assessing insect diversity in forests at a large geographical scale.

Written by

Lucas Sire

Lucas Sire

Institut de Recherche sur la Biologie de l’Insecte, Tours, France

Paul Schmidt Yañez

Paul Schmidt Yañez

Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany

Rodolphe Rougerie

Rodolphe Rougerie

Muséum National d’Histoire Naturelle, Paris, France

Christophe Bouget

Christophe Bouget

IRSTEA, Nogent-sur-Vernisson, France

Laurent Larrieu

Laurent Larrieu

Dynafor INRA & CRPF Occitanie, Toulouse, France

Douglas W. Yu

Douglas W. Yu

Kunming Institute of Zoology, Kunming, China

Michael T. Monaghan

Michael T. Monaghan

Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany

Institut Für Biologie, Freie Universität Berlin, Germany

Jörg Müller

Jörg Müller

Bavarian Forest National Park, Grafenau, Germany

Elisabeth A. Herniou

Elisabeth A. Herniou

Institut de Recherche sur la Biologie de l’Insecte, Tours, France

Carlos Lopez-Vaamonde

Carlos Lopez-Vaamonde

Institut de Recherche sur la Biologie de l’Insecte, Tours, France

INRA, Orléans, France

October 28, 2019
https://doi.org/10.21083/ibol.v9i1.5726

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Insects don’t talk, but new DNA-based technologies are helping to tell their stories

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Researchers unlock clues about vertebrate diversity by examining arthropod samples
Malaise trap deployed in Carajás National Forest in Brazil. PHOTO CREDIT: Christina Lynggaard

The study of arthropod diversity often uses primers solely targeting arthropod DNA, ignoring those originating from non-arthropod sources. Yet, some arthropods (e.g. sand flies, blowflies, mosquitoes) feed on vertebrates and vertebrate remains. By specifically targeting these vertebrate-feeding arthropods, invertebrate derived DNA (iDNA) can be used to understand vertebrate diversity as well. Our study has found that by using samples collected for arthropod diversity research, we can tap into a rich information source of vertebrate diversity.

Arthropods are highly abundant and provide vital ecosystem services such as pollination, decomposition of organic matter, and they serve as a food source for other animals. Because of this, hundreds to thousands of arthropod samples are collected globally every year for monitoring programs, conservation efforts, and ecosystem assessments.

However, identifying arthropod species based on physical characteristics is difficult, requiring specific expertise and a significant amount of time. Due to this, molecular analyses, such as DNA metabarcoding, are being used to identify the arthropods present in bulk samples, speeding-up the otherwise time-demanding identification process by screening the contents of hundreds of samples simultaneously.

Bulk arthropod sample

PHOTO CREDIT: Christina Lynggaard

In this study, bulk arthropod samples were collected using pitfall and Malaise traps deployed at the Carajás National Forest in Brazil and in the Udzungwa Mountains in Tanzania. Our aim was to study the arthropod diversity in these areas by using metabarcoding primers targeting arthropod DNA. Nevertheless, we conducted an additional analysis targeting vertebrate DNA remains in the bulk samples by using metabarcoding vertebrate primers.

We were able to detect vertebrate DNA in 19 per cent of our 265 analyzed samples, identifying more than 30 vertebrate taxa including mammals, amphibians and birds. For example, we found South American tapir (Tapirus terrestris), chirinda screeching frog (Arthroleptis xenodactyloides), velvety free-tailed bat (Molossus molossus), Zanzibar bushbaby (Paragalago zanzibaricus) and honeyguide greenbul (Baeopogon indicator). The presence of some species was further confirmed through visual observations during the sample collections.

Some cases represent the first time those vertebrate species have been detected in the area. This could indicate that we are detecting vertebrates that live in different areas to where the arthropods were collected or that with this method it is possible to detect local animals that are difficult to observe.

Tapir footprint found in one of the Brazilian study sites during bulk arthropod sample collection confirmed the presence of some of the detected vertebrate taxa PHOTO CREDIT: Christina Lynggaard

Bushbaby (Paragalago zanzibaricus) found in the Udzungwa Mountains in the Tanzanian study site during bulk arthropod sample collection confirmed the presence of some of the detected vertebrate taxa

PHOTO CREDIT: mnielsenphotography

The sensitivity of new DNA-based technologies is changing the way we explore and understand the relationships between species. Approaches like DNA metabarcoding can not only tell us about the different types of insects in our environment, but also what they eat and where they have been. Our study is the first to not target a specific invertebrate group to detect vertebrate DNA but instead to use bulk arthropod samples. We encourage others to consider bulk samples during environmental monitoring not only as a source for arthropod diversity information, but one for vertebrate diversity as well.

This study is published in the eDNA Journal.

Written by

Christina Lynggaard

Christina Lynggaard

The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark

Martin Nielsen

Martin Nielsen

The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark

Luisa Santos-Bay

Luisa Santos-Bay

The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark

NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
Markus Gastauer

Markus Gastauer

Instituto Tecnológico Vale, Belém, Pará, Brazil

Guilherme Oliveira

Guilherme Oliveira

Instituto Tecnológico Vale, Belém, Pará, Brazil

Kristine Bohmann

Kristine Bohmann

The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark

University of East Anglia, Norwich Research Park, Norwich, UK

October 17, 2019
https://doi.org/10.21083/ibol.v9i1.5727

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The deep connection between soil microbes and trees: DNA metabarcoding and reforestation

The deep connection between soil microbes and trees: DNA metabarcoding and reforestation

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Forest restoration can be better facilitated by considering the diversity and biomass of soil microbiomes

Aerial view of Laguna del Lagarto Lodge and primary forest, Costa Rica.

PHOTO CREDIT: Fritz Fucik

Tropical deforestation has contributed to the atmospheric rise in greenhouse gas levels, negative impacts on nutrient cycles, and declines in biodiversity. While forest restoration schemes are being implemented, the success of such efforts needs to be better evaluated. Our study demonstrates that soil microbial communities can guide the selection of key tree species important for local forest restoration processes and, ultimately, the global recovery of tropical forests.

 

2-year old logging road amongst Costa Rican primary forest with no vegetation re-growth due to severe soil degradation and compaction.

PHOTO CREDIT: Katie M. McGee

Tropical forests only comprise 7–10% of the Earth’s land surface but contain 20% of the planet’s carbon within the first three metres of soil. They also exchange more carbon dioxide (CO2) with the atmosphere than any other terrestrial ecosystem. Such characteristics make tropical areas critical for terrestrial primary productivity and global nutrient cycling. Yet, these important ecosystems are continually under threat from human-driven land-use practices.

Deforestation activities across the tropics contribute to the increase of atmospheric CO2 at levels comparable to fossil fuels1. If tropical deforestation were a country, it would be the third largest contributor of CO2 emissions (behind China and the United States), producing more than the European Union2. One of the main contributing factors, often ignored, is the large release of CO2 from the soil when forests are clear-cut; this occurs due to alterations in the respiration maintenance processes of soil microbes that result in a rapid release of the massive stock of soil carbon that has accumulated over time. Moreover, the soil in areas facing extraction-based land-use strategies have been so degraded that the capacity to recover and sustain biological productivity, and to capture and store carbon is significantly reduced.

Source Graph: Seymour and Busch (2016), Source Data: Busch and Engelmann (2015)

To remediate these consequences, restoration attempts have been implemented throughout the tropics. However, the success of these efforts is largely explored by studying charismatic organisms, such as birds, or by assessing plant biomass, with substantially less focus on soil dynamics. As soil microbes are key components in biogeochemical and nutrient cycling processes, it is thought that certain tree species and their affiliated soil microorganisms may help to serve as a principal pathway to ameliorate degraded soils. Many tropical trees can convert or ‘fix’ atmospheric nitrogen (N2) into ammonium through specialized root microbial symbionts. This conversion is critical to the growth and development of plants and soil microbes, yet the influence that N-fixing trees can have on the soil organisms in their immediate vicinity is still unclear.

The use of DNA-based identification techniques has significantly advanced research on soil microbial communities. Since the 1980s, popular methods have involved Terminal Restriction Fragment Length Polymorphism techniques and Sanger sequencing. However, all of these methods are time consuming, costly, and involve laborious processes. The more recent development of DNA metabarcoding has allowed us to rapidly and comprehensively characterize soil biotic communities.

DNA metabarcoding is a method that combines traditional marker gene surveys – targeting particular organisms using standardized PCR primers for specific gene regions – with next-generation sequencing. By comparing obtained DNA sequences to a standard reference library of known organisms, taxa present in an environmental sample such as soil can be identified with high confidence. This allows us to address ecological questions linked to environmental impact and biomonitoring in a more efficient manner.

Pentaclethra macroloba and its soil microbiome shown to effectively support forest restoration in northern Costa Rica.

PHOTO CREDIT: Katie M. McGee

Using DNA metabarcoding, our study investigated individual plant effects of the soil collected around two types of trees, Pentaclethra macroloba (Gavilán; nitrogen-fixing) and Dipteryx panamensis (Almendro; non-nitrogen-fixing), in Costa Rica’s northern region. We wanted to examine differences in the soil bacterial and fungal community composition. 

We found that each plant species contained a unique soil microbial community, and that the nitrogen-fixing tree, Pentaclethra, supported soil microbes and microbial biomass at levels similar to those measured in primary forests. This indicates their importance for the recovery of soils to a pre-disturbed state. In comparison to the non-N-fixer Dipteryx, Pentaclethra stimulates a soil microbial community that is more efficient in storing soil carbon into biomass, as opposed to carbon loss via aforementioned respiration maintenance processes. These effects appeared to be associated with the amount of soil ammonium that the Pentaclethra-soil is able to provide to the surrounding soil.

Our results indicate the importance of this N-fixing tree in building back up carbon storage as biomass in the soil as well as promoting plant and soil microbial growth. As such, we suggest the use of Pentaclethra and its associated soil microbiome as an important ecosystem restoration tool in facilitating early regeneration of secondary forests.

Our method of using soil microbes, characterized by DNA metabarcoding, is a novel approach that can be applied globally to guide regeneration efforts that most effectively improve the quality and fertility of degraded soils as well as inform restoration ecology and the policy surrounding it.

References:

1. Seymour F and Busch J (2016) Why forests? Why now? The science, economics, and politics of tropical forests and climate change. Center for Global Development. Washington, DC, USA. ISBN: 978-1-933286-85-3

2. Busch J and Engelmann J (2015) The Future of Forests: Emissions from Deforestation With and Without Carbon Pricing Policies, 2015– 2050. CGD Working Paper 411. Center for Global Development. Washington, DC, USA. 

Written by

Katie M. McGee

Katie M. McGee

Centre for Biodiversity Genomics, Guelph, ON, Canada

Mehrdad Hajibabaei

Mehrdad Hajibabaei

Centre for Biodiversity Genomics, Guelph, ON, Canada

May 23, 2019
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https://doi.org/10.21083/ibol.v9i1.5472

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