Spring into action: Life in Earth’s rarest soils under threat

Spring into action: Life in Earth’s rarest soils under threat

Spring into action: Life in Earth’s rarest soils under threat

Springtails (Collembola) in the Antarctic indicate that unique soil biodiversity in the region faces biotic homogenization due to increased human activity

Invasive springtail (Collembola) in sub-Antarctic soil.

PHOTO CREDIT: Laura Phillips

Efforts to understand and protect Earth’s biodiversity have largely overlooked life present in the soil. However, soil biodiversity is critical to ecosystem health, playing an integral role in nutrient cycling, carbon storage, water filtration, and food production1.

The Antarctic, once a pristine wilderness, is undergoing rapid environmental change and increased human pressures. Yet the true diversity, uniqueness, and vulnerability of its soil communities are only beginning to be revealed. As tourism and science expeditions bring ever more passengers and cargo to Antarctica, human-induced transport of species (‘biological invasion’) – both into and throughout the region – presents a growing threat to soil biodiversity, as highlighted recently in our study.

The Antarctic terrestrial biome near McMurdo station. PHOTO CREDIT: Helena Baird

In the Antarctic region, which broadly covers approximately 30% of the planet’s surface, soil organisms represent the vast majority of terrestrial life. Antarctic soil organisms, which include nematodes, mites, springtails, fungi, and tardigrades, have eked out a largely isolated existence over millions of years in fragmented patches of ice-free land on the continent, or on the sub-Antarctic islands.

On the Antarctic continent, ice-free soil represents <1% of the total land area and can be found on mountain tops, scree slopes, valleys, and the coast. The sub-Antarctic islands encircle the continent, located in the frigid waters of the Southern Ocean and each is separated by up to thousands of kilometres of open ocean. Antarctic soil species are therefore highly isolated and possess unique adaptations to their harsh environment. They are at risk of being outcompeted, or ultimately even replaced, by invasive species as the climate warms2.

LEFT: Helena Baird and colleagues busy with sub-Antarctic fieldwork on Marion Island while king penguins watch in the background. RIGHT: Soil sampling with the use of a soil core – an undisturbed cylindrical sample.
PHOTO CREDIT: Charlene Janion-Scheepers

In our study, we used DNA barcoding to investigate the spread of an invasive springtail species, known to adversely affect native soil species, across the sub-Antarctic islands. Identification of numerous divergent barcode sequences revealed that the invasive has been introduced to Antarctica several times.

By comparing barcodes from Antarctic specimens in BOLD to those found elsewhere in the world, we could identify genetic lineages shared across countries which aligned with known shipping routes to the Southern Ocean, highlighting the utility of molecular tools in tracking invasion. For example, a shared barcode haplotype between Norway and the sub-Antarctic island of South Georgia accords directly with Norway’s long history of whaling on this island. That a well-known invasive species has been introduced on multiple occasions to such a remote region emphasises the importance of ongoing biosecurity monitoring, even for invasive species that have already established, since multiple invasions can introduce more genetic resilience and enable the invasive species to spread.

Research vessel as it approaches Possession island, Crozet archipelago, one of the sub-Antarctic islands in the region. PHOTO CREDIT: Helena Baird

Charlene Janion-Scheepers (left) and Helena Baird (right) sort soil species at sea using Berlese funnels.
PHOTO CREDIT: Steven Chown

Our study also explored the consequences of intra-regional human transport on native soil species. Antarctic soil organisms are typically highly endemic, even to local patches within the region. This raises the concern that increased human traffic throughout Antarctica could transport and ultimately homogenise soil populations, altering the region’s unique biogeography. Using genome-wide SNPs, we showed that a widespread native springtail species is indeed so distinct between sub-Antarctic islands that it is likely in the process of speciating. Clearly, future exchange of individuals among islands could possibly disrupt this biodiversity process, diluting the specific adaptations each population has evolved over millennia. Potential evolutionary consequences include a decrease in the fitness of island-specific populations, lineage extinction, or the loss of biodiversity by ‘reverse speciation’3.

Regardless of the outcome, the threat of disrupting biodiversity processes among these unique and fragile islands emphasises the importance of biosecurity for ships travelling throughout the Southern Ocean, particularly when passengers embark and disembark at multiple locations.

Taking a break to enjoy the view in the sub-Antarctic. PHOTO CREDIT: Helena Baird

One of the main hurdles to accurately predicting future changes to soil communities is a lack of basic biodiversity knowledge. In the Antarctic, molecular work such as metabarcoding continues to reveal far more soil diversity – most of which is locally endemic – than previously recognised4,5. This situation echoes worldwide, with biodiversity and biogeography patterns constantly revised as we probe the soil biome deeper. Fortunately, schemes such as the Global Soil Biodiversity Initiative are bringing fragile soil ecosystems under the spotlight, where we will be better served to protect them.

References:

1. Bardgett RD & van der Putten WH (2014) Belowground biodiversity and ecosystem functioning. Nature, 515. 2. Janion-Scheepers C, Phillips L, Sgrò CM, Duffy GA, Hallas R & Chown SL (2018) Basal resistance enhances warming tolerance of alien over indigenous species across latitude. Proceedings of the National Academy of Sciences, 115. 3. Seehausen O (2006) Conservation: losing biodiversity by reverse speciation. Current Biology, 16. 4. Czechowski P, Clarke LJ, Cooper A & Stevens MI (2016) A primer to metabarcoding surveys of Antarctic terrestrial biodiversity. Antarctic Science, 1-13. 5. Velasco-Castrillón A, McInnes SJ, Schultz MB, Arróniz-Crespo M, D’Haese CA, Gibson JAE, . . . Stevens MI (2015) Mitochondrial DNA analyses reveal widespread tardigrade diversity in Antarctica. Invertebrate Systematics, 29.

Read the complete manuscript in Evolutionary Applications.

Read more news about the Antarctic:

NEW AUSTRALIAN PROGRAM TO SECURE FUTURE FOR ANTARCTICA’S ENVIRONMENT AND BIODIVERSITY

The Australian Government has awarded $36 million to a new research program led by Monash University, Securing Antarctica’s Environmental Future (SAEF).

Written by

Helena Baird

Helena Baird

Monash University, School of Biological Sciences, Melbourne, Australia

June 4, 2020

doi: 10.21083/ibol.v10i1.6180

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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

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

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
doi: 10.21083/ibol.v9i1.5472

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