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MicroCity Report Summary

Project ID: 655159
Funded under: H2020-EU.1.3.2.

Periodic Reporting for period 1 - MicroCity (Microbes in the city: a metagenomic trait-based analysis of microbial metacommunity structure along urbanization gradients)

Reporting period: 2015-05-01 to 2017-04-30

Summary of the context and overall objectives of the project

Urbanization has become one of the most extreme forms of human-induced environmental changes with the dramatic expansion of urban land area over the past few decades. Urban areas fundamentally differ from natural areas in terms of geochemistry, climate and vegetation cover, and thus form unique ecosystems. Many studies have shown a broad and pronounced impact of urbanization on the ecology and functioning of ecosystems, communities and populations. Majority of these studies have focused on plants and animals, with only a limited number of studies so far focusing on microorganisms. Given the facts that microbes play a pivotal role of bacterial communities in driving biogeochemical cycles and overall ecosystem functioning, and are often the first responders to environmental perturbation; it is of utmost importance to gain insight into the ecological processes governing their community structure and function under anthropogenic stress. Understanding functional responses of microbes in natural systems with well-defined urbanization gradients can be crucial to predict and manage ecosystem functioning and ecosystem services to society.

In the MicroCity project, we capitalized on a sampling campaign, which included sampling of fresh-water ponds across well-defined gradients of urbanization in Flanders (Belgium). Belgium is a highly populated, strongly urbanized country where land is in high demand and therefore agricultural practices are intensive. This creates a mosaic of different types of often-strong anthropogenic impact, and it is key for conservation and biodiversity management and policies to take anthropogenic environments into consideration. Flanders therefore provides a strong model system for studying impacts of urbanization and intensive agriculture.

While taxon-focused approaches have dominated majority of research on microbial responses to urbanization, we here applied metagenomics in a molecular trait-based approach to identify the ecological processes that shape microbial metacommunities across environmental gradients associated with urbanization in Belgium. More specifically, we aimed to determine the impact of urbanization on biogeochemical cycles (genes associated with biogeochemical cycling, e.g. C, N, P and S cycles); on pesticide degradation pathways; and on mobile genetic elements in mediating evolutionary dynamics in microbial communities under anthropogenic stress.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We performed shotgun metagenomic sequencing (on Illumina HiSeq 2500 platform) of DNA extracted from water samples collected from freshwater ponds located across studied urbanization gradients. Quality trimmed and assembled scaffolds were used for gene prediction and were further summarized into a gene-catalog of ~10 million genes. This gene catalog was annotated against multiple databases including KEGG, Pfam, TIGRFAM and eggNOG to gain multi-view insights into functional responses of microbes to urbanization. Gene abundances were calculated by mapping metagenomic reads on the gene catalog. Molecular trait matrices of relative frequencies of KEGG pathways and modules associated with biogeochemical cycles, pesticide degradation and other relevant environmental pathways were created and their responses to urbanization (defined as percentage built-up area around studied ponds), abiotic and biotic variables and land-use variables were determined.

The resulting gene catalog of more than 10 million microbial genes, annotated against multiple databases is an extremely valuable resource, which will be useful for researchers studying microbial responses to anthropogenic stress in freshwater habitats. We found significant differences in nitrogen fixation pathways among urban and rural ponds with rural ponds showing a higher abundance of nif D genes. A marked difference in pathway of chemoautotrophic oxidation of sulfur compounds was noticed along the studied gradient of urbanization. In addition, we were also able to detect other metabolic processes relevant to environmental microbes, which varied between ponds situated in highly urbanized areas (built-up area more than 15%) and rural areas (built-up area less than 3%), namely ascorbate and aldarate metabolism, caprolactam degradation, selenocompound metabolism, folate biosynthesis, linoleic acid metabolism, biosynthesis of unsaturated fatty acids & pentose and glucouronate interconversion. We also found a significant difference in the abundance of a gene (K14541: urea carboxylase / allophanate hydrolase) involved in the atrazine degradation pathway between rural and urban ponds. Majority of these metabolic pathways were influenced by local factors rather than regional factors. Together, these results indicate strong differences in metabolic potential of microbial communities across various levels of urbanization and point towards the fact that microbial communities predominantly respond to land use changes on a local scale. This is important in policy decisions, as it informs us on the scale at which land use must be managed for optimum ecosystem functioning.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The central theme of this project – the effect of ever-increasing human influence on ecosystems and their services - is a relevant and timely topic and our findings are of broad public interest. Our results will be communicated primarily through two manuscripts in international peer-reviewed scientific journals and thereafter publicized in popular format.
This is a unique study combining high throughput metagenomics sequencing with metacommunity ecology to unravel functional responses of microbes to landscape-wide changes in land use. Although, this project mainly focused on impact of urbanization (defined here as percentage built-up area), we are also able to study microbial responses to other land use types (arable land, nature, grassland, cropland) through our study design. Our results will directly contribute to inform policy makers, the scientific community and the society at large on the impact of urbanization on ecosystem functions mediated by microbial communities. Also, information on the capacity to catabolize pollutants along land-use gradients is key information for policy-makers, industries, environmental consultancy agencies and land managers.

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