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Epp Schmidt DJ, Kotze DJ, Hornung E, Setälä H, Yesilonis I, Szlavecz K, Dombos M, Pouyat R, Cilliers S, Tóth Z, Yarwood S. Metagenomics Reveals Bacterial and Archaeal Adaptation to Urban Land-Use: N Catabolism, Methanogenesis, and Nutrient Acquisition. Front Microbiol 2019; 10:2330. [PMID: 31649656 PMCID: PMC6795690 DOI: 10.3389/fmicb.2019.02330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 09/24/2019] [Indexed: 01/13/2023] Open
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.
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Affiliation(s)
- Dietrich J. Epp Schmidt
- Department of Environmental Science and Technology, University of Maryland, College Park, College Park, MD, United States
| | - David Johan Kotze
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Erzsébet Hornung
- Department of Ecology, University of Veterinary Science, Budapest, Hungary
| | - Heikki Setälä
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Ian Yesilonis
- Baltimore Ecosystem Study, USDA Forest Service, Baltimore, MD, United States
| | - Katalin Szlavecz
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, United States
| | - Miklós Dombos
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Richard Pouyat
- Northern Research Station, University of Delaware, Newark, DE, United States
| | - Sarel Cilliers
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Zsolt Tóth
- Department of Ecology, University of Veterinary Science, Budapest, Hungary
| | - Stephanie Yarwood
- Department of Environmental Science and Technology, University of Maryland, College Park, College Park, MD, United States
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Epp Schmidt DJ, Pouyat R, Szlavecz K, Setälä H, Kotze DJ, Yesilonis I, Cilliers S, Hornung E, Dombos M, Yarwood SA. Urbanization erodes ectomycorrhizal fungal diversity and may cause microbial communities to converge. Nat Ecol Evol 2017; 1:123. [PMID: 28812698 DOI: 10.1038/s41559-017-0123] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/23/2017] [Indexed: 11/09/2022]
Abstract
Urbanization alters the physicochemical environment, introduces non-native species and causes ecosystem characteristics to converge. It has been speculated that these alterations contribute to loss of regional and global biodiversity, but so far most urban studies have assessed macro-organisms and reported mixed evidence for biodiversity loss. We studied five cities on three continents to assess the global convergence of urban soil microbial communities. We determined the extent to which communities of bacteria, archaea and fungi are geographically distributed, and to what extent urbanization acts as a filter on species diversity. We discovered that microbial communities in general converge, but the response differed among microbial domains; soil archaeal communities showed the strongest convergence, followed by fungi, while soil bacterial communities did not converge. Our data suggest that urban soil archaeal and bacterial communities are not vulnerable to biodiversity loss, whereas urbanization may be contributing to the global diversity loss of ectomycorrhizal fungi. Ectomycorrhizae decreased in both abundance and species richness under turf and ruderal land-uses. These data add to an emerging pattern of widespread suppression of ectomycorrhizal fungi by human land-uses that involve physical disruption of the soil, management of the plant community, or nutrient enrichment.
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Affiliation(s)
- Dietrich J Epp Schmidt
- Environmental Science and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - Richard Pouyat
- USDA Forest Service, Research &Development, Washington, District of Columbia 20250, USA
| | - Katalin Szlavecz
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Heikki Setälä
- Department of Environmental Sciences, University of Helsinki, FIN-15140, Lahti, Finland
| | - D Johan Kotze
- Department of Environmental Sciences, University of Helsinki, FIN-15140, Lahti, Finland
| | - Ian Yesilonis
- USDA Forest Service, c/o Baltimore Ecosystem Study, Baltimore, Maryland 21228, USA
| | - Sarel Cilliers
- Unit of Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Erzsébet Hornung
- Department of Ecology, University of Veterinary Science, Budapest Pf. 2, Hungary
| | - Miklós Dombos
- Institute for Soil Sciences and Agricultural Chemistry, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest Pf. 102, Hungary
| | - Stephanie A Yarwood
- Environmental Science and Technology, University of Maryland, College Park, Maryland 20742, USA
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Aronson MFJ, La Sorte FA, Nilon CH, Katti M, Goddard MA, Lepczyk CA, Warren PS, Williams NSG, Cilliers S, Clarkson B, Dobbs C, Dolan R, Hedblom M, Klotz S, Kooijmans JL, Kühn I, Macgregor-Fors I, McDonnell M, Mörtberg U, Pysek P, Siebert S, Sushinsky J, Werner P, Winter M. A global analysis of the impacts of urbanization on bird and plant diversity reveals key anthropogenic drivers. Proc Biol Sci 2014; 281:20133330. [PMID: 24523278 DOI: 10.1098/rspb.2013.3330] [Citation(s) in RCA: 478] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Urbanization contributes to the loss of the world's biodiversity and the homogenization of its biota. However, comparative studies of urban biodiversity leading to robust generalities of the status and drivers of biodiversity in cities at the global scale are lacking. Here, we compiled the largest global dataset to date of two diverse taxa in cities: birds (54 cities) and plants (110 cities). We found that the majority of urban bird and plant species are native in the world's cities. Few plants and birds are cosmopolitan, the most common being Columba livia and Poa annua. The density of bird and plant species (the number of species per km(2)) has declined substantially: only 8% of native bird and 25% of native plant species are currently present compared with estimates of non-urban density of species. The current density of species in cities and the loss in density of species was best explained by anthropogenic features (landcover, city age) rather than by non-anthropogenic factors (geography, climate, topography). As urbanization continues to expand, efforts directed towards the conservation of intact vegetation within urban landscapes could support higher concentrations of both bird and plant species. Despite declines in the density of species, cities still retain endemic native species, thus providing opportunities for regional and global biodiversity conservation, restoration and education.
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Affiliation(s)
- Myla F J Aronson
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, , New Brunswick, NJ 08901, USA, Cornell Laboratory of Ornithology, , Ithaca, NY 14850, USA, Department of Fisheries and Wildlife Sciences, University of Missouri, , Columbia, MO 65211, USA, Department of Biology, California State University, , Fresno, CA 93740, USA, School of Biology, University of Leeds, , Leeds LS2 9JT, UK, Department of Natural Resources and Environmental Management, University of Hawai'i at Mānoa, , Honolulu, HI 96822, USA, Department of Environmental Conservation, University of Massachusetts at Amherst, , Amherst, MA 01003, USA, School of Land and Environment, Department of Resource Management and Geography, The University of Melbourne, , 500 Yarra Boulevard, Richmond, Victoria 3070, Australia, Australian Research Centre for Urban Ecology, Royal Botanic Gardens Melbourne, c/o School of Botany, The University of Melbourne, , Melbourne, Victoria 3010, Australia, Unit of Environmental Sciences and Management, North-West University, , Private Bag X6001, Potchefstroom 2520, South Africa, Environmental Research Institute, University of Waikato, , Private Bag 3105, Hamilton 3240, New Zealand, School of Botany and School of Land and Environment, The University of Melbourne, , Parkville, Victoria 3010, Australia, Friesner Herbarium, Butler University, , 4600 Sunset Avenue, Indianapolis, IN 46208, USA, Department of Forest Resource Management, Swedish University of Agricultural Sciences, , Umeå 901 83, Sweden, Department Community Ecology, Helmholtz Centre of Environmental Research-UFZ, , Theodor-Lieser-Strasse 4, Halle 06120, Germany, Vogelbescherming Nederland, , Boulevard 12, B3707 BM, Zeist, The Netherlands, Red de Ambiente y Sustentabilidad, Instituto de Ecología, , A.C. Antigua carretera a Coatepec 351, El Haya, Xalapa 91070, México, Environmental Management and Assessment Research Group, KTH Royal Institute of Technology, , Stockholm 100 44, Sw
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