Dynamic Soil Genes: Time and Neonicotinoid Seed Treatments Affect Agricultural Microbiomes

Posted on May 31, 2023   by Dr Mona Parizadeh

Dr Mona Parizadeh takes us behind the scenes of her latest publication 'Soil microbial gene expression in an agricultural ecosystem varies with time and neonicotinoid seed treatments' published in Microbiology.

My name is Mona Parizadeh. I am a postdoctoral fellow in the Arrieta lab at the University of Calgary, Canada. I specialize in microbial ecology, community ecology, computational biology, and bioinformatics. My research focuses on studying environmental effects on microbiomes, host-microbe and microbe-microbe interactions, and drivers of microbial community assembly in different environments. To address these objectives, I apply ecological theory and different high-throughput sequencing approaches, including meta-barcoding and meta-omics. During my Ph.D. under the supervision of Dr. Steven W. Kembel (Université du Québec à Montréal) and Dr. Benjamin Mimee (Agriculture and Agri-Food Canada), I studied the effects of host species, time and environmental stress and perturbations, like pesticide treatments, on microbial composition variation in agroecosystems.

Agriculture plays a critical role in feeding the growing global population. Sustainability in agriculture relies on maintaining soil quality and health, which is directly related to the diversity and dynamics of microbial communities. Soil microbial communities perform vital functions, such as nutrient cycling, and organic matter production and decomposition. Several factors influence the composition of microbial communities and gene expression patterns, including: time, soil management practices, environmental conditions, disturbances and perturbations (such as cultivation methods, drought, climate change, and pesticide treatments).

Neonicotinoids, also known as neonics, are a family of systemic and neuro-active insecticides widely used in recent years to control pests in both the soil and foliage. These chemicals are structurally similar to nicotine and have been predominantly employed as seed treatments in North America to control early-season insect pests in crops such as corn, soybean, and wheat. These treatments are often applied prophylactically without specific knowledge about the presence of the targeted pests. Neonicotinoid compounds are characterized by their small size and high solubility in water. Due to their systemic nature, plants absorb them from the seed coating and translocate them to various tissues and products, including guttation, nectar, and pollen. Neonicotinoids may remain active for extended periods, up to 200 days, in certain plant species. However, plants only absorb around 20% of the neonicotinoids present in the seed coating, while the remaining pesticide persists in the soil for up to three years. In recent years, neonicotinoid pesticides have gained widespread attention for their potential non-target effects on ecological communities and their functions. There has been extensive evidence that neonicotinoids affect beneficial organisms in agriculture, including insect pollinators, especially honeybees and butterflies, and soil invertebrates, such as earthworms. In response to these concerns, several regulatory measures have been implemented in various regions. In 2018, the European Union prohibited the outdoor use of several neonicotinoids. Similarly, in 2020, the United States Environmental Protection Agency banned the spray application of neonicotinoids and proposed limitations on their quantity and timing, particularly for crops in bloom. In Canada, the Quebec province implemented a requirement in 2018, mandating farmers to obtain prescriptions from agronomists before using neonicotinoids on crops. In 2021, Health Canada opted not to impose a complete ban on neonicotinoid application but instead imposed additional restrictions, such as implementing buffer zones around affected sectors and reducing the neonicotinoid seed treatment rate for certain crops like soybean and corn.

The above restrictions are mostly based on neonicotinoids' effects on beneficial invertebrates since they were initially considered more toxic to invertebrates. However, as reported in our previous research, they show non-target impacts on diversity and taxonomic composition of agricultural microbiomes. Gaining insights into the dynamics of soil microbial functions when faced with disturbances is also essential for evaluating their influence on ecosystem functioning and advancing the development of sustainable agricultural practices. Therefore, we decided to study the microbial functional activities and gene expression variations following neonicotinoid seed treatments in an experimental design of a 2-year soybean/corn crop rotation that was representing real farming conditions.

As we used metatranscriptomics to study soil microbial expressed genes and active functions, many challenges arose. Obtaining high-quality microbial RNA in sufficient quantities was one of these challenges. It took us several attempts before we found the appropriate kit and protocol. We then sent the extracted RNA to Genome Quebec for sequencing. The other challenge was determining a proper, efficient and accurate data-processing approach, for which we tried various pipelines and bioinformatics tools and software. It is also important to note that when it comes to gene annotations, a consistent and universally accepted method for labeling genes is lacking in the majority of reliable public genome databases. This poses a challenge in annotating gene expression at a community level in transcriptomic and metatranscriptomic studies like ours. However, we overcame these limitations by employing various strategies, such as utilizing multiple databases and implementing thorough data-cleaning processes.

Having surmounted these limitations and challenges, our findings revealed that soil microbial gene expression is influenced by both temporal variations and neonicotinoid seed treatments. Across various time intervals, genes associated with heat shock proteins, regulatory functions (such as soil respiration), and metabolic processes (like phosphonate breakdown and enzyme catalysis) were underexpressed in response to neonicotinoid seed treatment. Conversely, genes related to photosynthesis and DNA repair were overexpressed in the presence of neonicotinoid seed treatment. These results underscore the vital influence of time and temporal dynamics in shaping soil microbial gene expression. However, although gene expression in soil microbial communities fluctuates significantly over time, these communities are either highly resilient or resistant to alterations in gene expression triggered by neonicotinoid seed treatment. This resilience could potentially be attributed to functional redundancy in the genes that are expressed, despite the significant variation in the taxonomic composition of these microbial communities that we have previously documented. Understanding these dynamics is critical for assessing the impacts of agrochemicals on soil health and ecosystem functioning.