STARS Autumn Soil Science Conference 2021

The Canadian North: a new frontier for bioprospection in the face of anthropogenic change

Paul B. L. George^1,2,  Anne D. Jungbludt⁴, Alexander I. Culley^3,6, Jacques, Corbeil^1,2

1. Département de médicine moléculaire, Université Laval, Quebec City, Canada
2. Centre de recherche en données massives, Université Laval, Quebec City, Canada
3. Centre d’études nordiques, Université Laval, Quebec City, Canada
4. Life Sciences Department, Natural History Museum, London, UK
5. Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, Canada

Climate warming is causing significant changes to habitats in higher latitudes. Public attention has witnessed the dramatic loss of sea ice and its implications for indigenous populations and fauna. Moreover, rising temperatures destabilize soils in the Arctic and sub-Arctic, causing rapid and profound shifts in microbial biodiversity. As a result, there are concerns that undescribed microbes will go extinct as their unique habitats are lost, and others will be selected as new vegetation regimes take hold. Here, we characterise the soil communities from various habitats of Canada’s Arctic and sub-Arctic. More specifically, we apply modern sequencing techniques in addition to novel isolation methods to identify potential biomedical compounds and the organisms that produce them. Preliminary data is presented based on the 2021 field expedition to Whapmagoostui-Kuujjuuarapik, Québec. These villages are located in the Canadian sub-Arctic at the mouth of the Great Whale River on the eastern shore of Hudson Bay. Three soil cores of 30 cm depth x 10 cm diameter were collected from 5 habitats: forest, palsa, river shore, lakeshore, and Canadian Shield outcrops. Cores were frozen and transported to Université Laval for homogenisation. Samples will be incubated at different temperatures (+2 and +4 °C for 8 weeks), after which DNA will be extracted. Aliquots were set aside for immediate DNA extraction to establish baseline community composition under natural conditions. Experimental manipulations are ongoing; however, we will present our latest data and status of the EcoChip, a novel platform for the in situ isolation, monitoring, and culturing of bacteria in the field. Our hope is to better understand the consequences of global warming on these fragile ecosystems.

Use of untargeted metabolomics for assessing soil quality and microbial function

Emma Withers¹, Paul W. Hill¹, David R. Chadwick^1,2, Davey L. Jones^1,3

1. School of Natural Sciences, Environment Centre Wales, Bangor University, Gwynedd, LL57 2UW, UK.
2. Interdisciplinary Research Centre for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China.
3. SoilsWest, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.

Soils support a wide range of ecosystem services that underpin Earth system functioning. It is therefore essential that we have robust approaches to evaluate how anthropogenic perturbation affects soil quality and the delivery of these services. Metabolomics, the large-scale study of low molecular weight organic compounds in soil, offers one potential approach to characterise soils and evaluate the metabolic status of the soil biological community.

In this talk, I will introduce metabolomics and its uses in characterising the soil metabolome; its relationship with common chemical and physical soil quality indicators; and evaluate its discriminatory power and potential use as a soil quality indicator. Metabolomics has the potential to reveal important information regarding soil functional responses to environmental stimuli. In combination with complementary -omics techniques, it can be used to build a more holistic understanding of the complex molecular networks and metabolic pathways operating in the soil microbial community.

Big Questions About Big Data: Implications for Global Health and the Environment

Alex Williams

This talk represents a collection of thoughts and observations about the growing availability of very large datasets, the opportunities these present to researchers but also challenges and limitations associated with their use. The intention is to promote wider discussion about how the data landscape is changing and what it means for researchers now and in the future.

As the world is increasingly beset by concerns over climate change, global health and disease, ever greater interest is being paid to big data as a resource for the discovery and implementation of solutions to these issues. The opportunities presented by big data will be discussed, with particular reference to predicting emerging pathogens, Antimicrobial Resistance in the environment (AMR) as well as environmental monitoring more generally. The key challenges of analysing large quantities of data will also be discussed, including the role of machine learning, databases and their associated pitfalls. The importance of creating interfaces which allow the easy exploration of datasets (large or small) will also be discussed, with particular reference to app development.

To what extent is big data truly useful? Will it help to resolve threats to global health and the environment or conversely further exacerbate them?

Effect of random and oriented soil surface roughness on water infiltration, runoff and soil loss.

Sophia Bahddou¹, Wilfred Otten¹, Jane Rickson¹, Richard Whalley², Ho-Chul Shin², Mohamed El Gharous³

1. Cranfield University, Cranfield, UK
2. Rothamsted Research, Harpenden, UK
3. Mohammed VI Polytechnic University, Ben Guerir, Morocco

Soil erosion by water is a result of detachment of particles or small aggregates from the soil surface followed by transport of the detached material. One of the elements that affect surface runoff and soil erosion is the soil surface roughness (SSR). Most prior research reports that increasing roughness reduces generation of runoff and soil loss. In addition to that, it is widely found that across-slope oriented roughness created by tillage best controls soil and water losses. However, to date there have been no studies into the effect of both SSR and tillage orientations on runoff, infiltration and soil erosion (by raindrop splash and overland flow), occurring simultaneously under simulated rainfall. In this study, we compared the effects of up- and downslope oriented tillage (Treatment A), across-slope tillage (Treatment B) and random roughness (Treatment C), along with a smooth surface (Treatment D). We used a moderate slope of 10%, a rainfall intensity of 90 mm hr-1 and storm durations of 15 and 30 minutes. These conditions are comparable to erosion prone regions of Morocco. SSR was measured using the chain method before and after the rainfall event. Images of the soil surface were taken using a hand-held laser scanner to monitor the effect of rainfall and overland flow on the surface. The outcome of this study shows that rainfall and overland flow can decrease SSR, particularly in the random roughness treatment, decreasing SSR by 64% of the initial, pre-rainfall condition. This treatment generated significantly more runoff and soil loss and less infiltration than the other treatments (p < 0.001), but no significant difference was recorded between treatment C and the other treatments for raindrop splash erosion. Contrary to expectations, the across-slope oriented roughness did not always reduce runoff and soil erosion compared to the up- and downslope orientation.

Impact of a Simulated Methane Pulse Event on a Soil Microbial Community

Thomas Bott,^1,2 Dr. Simon Gregory, ¹ Prof. George Shaw,² Dr. Barbara Palumbo-Roe¹ Prof. Neil Crout²

1. British Geological Survey
2. Nottingham University

Methane is a major greenhouse gas. Soil microbial communities can act as a sink for methane from sub-surface sources. This worked assessed the resistance and resilience of soil microbial communities in response to a methane pulse event. Understanding how communities respond to methane is important to help mitigate future methane release, furthermore it provides insight into the use of microbial indicators of methane fluxes from soils.

To simulate a methane pulse, soil was packed into a column and repeatedly flushed with a 2.5% methane and air mix. A control mesocosm was also built and flushed with normal laboratory air. Mesocosms were deconstructed after two months of flushing, the soil potted and left to age in the laboratory over 18 months. Periodically, pots were destructively sampled. Methane oxidation rate was measured in microcosms and molecular ecology studies completed using qPCR and 16S rRNA sequencing. For qPCR, the relative abundance of methane mono-oxygenase genes, pmoA, mmoX and Methyolcella specific mmoX, was estimated using 16S rRNA as a proxy for total bacterial community size.

Overall, compared to the controls, a methane pulse event stimulated increases in particulate methane mono-oxygenase (pmoA) and changes in the methanotroph community structure. This was accompanied by increased rates of methane oxidation. Broader community changes were not seen using 16S rRNA sequencing. With increasing time from the initial pulse event, rate of methane oxidation declined but methanotrophic community structure remained in a disturbed state.

This work demonstrated that overall soil bacterial communities are resistant to this disturbance. Methane only impacted a small number of genera specialising in methane oxidation. Once disturbed, the methanotrophic community composition did not return to its pre-disturbed state despite a drop in methane oxidation rates, raising questions about the use of microbial indicators to detect methane fluxes in the field.

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