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

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dc.contributor.author Schmidt, Dietrich J. Epp
dc.contributor.author Kotze, David Johan
dc.contributor.author Hornung, Erzsebet
dc.contributor.author Setala, Heikki
dc.contributor.author Yesilonis, Ian
dc.contributor.author Szlavecz, Katalin
dc.contributor.author Dombos, Miklos
dc.contributor.author Pouyat, Richard
dc.contributor.author Cilliers, Sarel
dc.contributor.author Toth, Zsolt
dc.contributor.author Yarwood, Stephanie A.
dc.date.accessioned 2020-02-10T15:39:03Z
dc.date.available 2020-02-10T15:39:03Z
dc.date.issued 2019-10-10
dc.identifier.citation 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
dc.identifier.other PURE: 131801796
dc.identifier.other PURE UUID: 2468430b-707d-4ec4-bd47-21572871654e
dc.identifier.other WOS: 000491341300001
dc.identifier.other ORCID: /0000-0002-5230-4001/work/70953517
dc.identifier.uri http://hdl.handle.net/10138/311354
dc.description.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. en
dc.format.extent 17
dc.language.iso eng
dc.relation.ispartof Frontiers in Microbiology
dc.rights cc_by
dc.rights.uri info:eu-repo/semantics/openAccess
dc.subject urban
dc.subject soil metagenomics
dc.subject Ni-Fe hydrogenase
dc.subject nitrification
dc.subject microbiology
dc.subject methanogenesis
dc.subject DNRA
dc.subject ammonia oxidation
dc.subject AMMONIA MONOOXYGENASE
dc.subject BIOTIC HOMOGENIZATION
dc.subject SOIL CHARACTERISTICS
dc.subject FOREST SOILS
dc.subject NITROGEN
dc.subject DEPOSITION
dc.subject NITRIFICATION
dc.subject RESISTANCE
dc.subject PATTERNS
dc.subject METHANE
dc.subject 1181 Ecology, evolutionary biology
dc.title Metagenomics Reveals Bacterial and Archaeal Adaptation to Urban Land-Use : N Catabolism, Methanogenesis, and Nutrient Acquisition en
dc.type Article
dc.contributor.organization Ecosystems and Environment Research Programme
dc.contributor.organization Helsinki Institute of Sustainability Science (HELSUS)
dc.contributor.organization Helsinki Institute of Urban and Regional Studies (Urbaria)
dc.contributor.organization Urban Ecosystems
dc.contributor.organization Heikki Setälä / Principal Investigator
dc.description.reviewstatus Peer reviewed
dc.relation.doi https://doi.org/10.3389/fmicb.2019.02330
dc.relation.issn 1664-302X
dc.rights.accesslevel openAccess
dc.type.version publishedVersion

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