Metagenomics Reveals Bacterial and Archaeal Adaptation to Urban Land-Use : N Catabolism, Methanogenesis, and Nutrient Acquisition

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Schmidt , D J E , Kotze , D J , Hornung , E , Setala , H , Yesilonis , I , Szlavecz , K , Dombos , M , Pouyat , R , Cilliers , S , Toth , Z & Yarwood , S A 2019 , ' Metagenomics Reveals Bacterial and Archaeal Adaptation to Urban Land-Use : N Catabolism, Methanogenesis, and Nutrient Acquisition ' , Frontiers in Microbiology , vol. 10 , 2330 . https://doi.org/10.3389/fmicb.2019.02330

Title: Metagenomics Reveals Bacterial and Archaeal Adaptation to Urban Land-Use : N Catabolism, Methanogenesis, and Nutrient Acquisition
Author: Schmidt, Dietrich J. Epp; Kotze, David Johan; Hornung, Erzsebet; Setala, Heikki; Yesilonis, Ian; Szlavecz, Katalin; Dombos, Miklos; Pouyat, Richard; Cilliers, Sarel; Toth, Zsolt; Yarwood, Stephanie A.
Contributor: University of Helsinki, Ecosystems and Environment Research Programme
University of Helsinki, Ecosystems and Environment Research Programme
Date: 2019-10-10
Language: eng
Number of pages: 17
Belongs to series: Frontiers in Microbiology
ISSN: 1664-302X
URI: http://hdl.handle.net/10138/311354
Abstract: Urbanization results in the systemic conversion of land-use, driving habitat and biodiversity loss. The "urban convergence hypothesis" posits that urbanization represents a merging of habitat characteristics, in turn driving physiological and functional responses within the biotic community. To test this hypothesis, we sampled five cities (Baltimore, MD, United States; Helsinki and Lahti, Finland; Budapest, Hungary; Potchefstroom, South Africa) across four different biomes. Within each city, we sampled four land-use categories that represented a gradient of increasing disturbance and management (from least intervention to highest disturbance: reference, remnant, turf/lawn, and ruderal). Previously, we used amplicon sequencing that targeted bacteria/archaea (16S rRNA) and fungi (ITS) and reported convergence in the archaeal community. Here, we applied shotgun metagenomic sequencing and QPCR of functional genes to the same soil DNA extracts to test convergence in microbial function. Our results suggest that urban land-use drives changes in gene abundance related to both the soil N and C metabolism. Our updated analysis found taxonomic convergence in both the archaeal and bacterial community (16S amplicon data). Convergence of the archaea was driven by increased abundance of ammonia oxidizing archaea and genes for ammonia oxidation (QPCR and shotgun metagenomics). The proliferation of ammonia-oxidizers under turf and ruderal land-use likely also contributes to the previously documented convergence of soil mineral N pools. We also found a higher relative abundance of methanogens (amplicon sequencing), a higher relative abundance of gene sequences putatively identified as Ni-Fe hydrogenase and nickel uptake (shotgun metagenomics) under urban land-use; and a convergence of gene sequences putatively identified as contributing to the nickel transport function under urban turf sites. High levels of disturbance lead to a higher relative abundance of gene sequences putatively identified as multiple antibiotic resistance protein marA and multidrug efflux pump mexD, but did not lead to an overall convergence in antibiotic resistance gene sequences.
Subject: urban
soil metagenomics
Ni-Fe hydrogenase
nitrification
microbiology
methanogenesis
DNRA
ammonia oxidation
AMMONIA MONOOXYGENASE
BIOTIC HOMOGENIZATION
SOIL CHARACTERISTICS
FOREST SOILS
NITROGEN
DEPOSITION
NITRIFICATION
RESISTANCE
PATTERNS
METHANE
1181 Ecology, evolutionary biology
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