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He J, Owusu-Asumeng E, Zidar K, Stolper J, Attri S, Price JR, Partridge D, Montalto F, Sales CM. Impacts of a herring gull colony on runoff water quality from an urban green roof. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174430. [PMID: 38960163 DOI: 10.1016/j.scitotenv.2024.174430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 04/02/2024] [Accepted: 06/30/2024] [Indexed: 07/05/2024]
Abstract
Green infrastructure (GI) strategies, including green roofs, have become a common, decentralized, nature-based strategy for reducing urban runoff and restoring ecosystem services to the urban environment. In this study, we examined the water quality of incident rainfall and runoff from a green roof installed on top of the Jacob K. Javits Convention Center in New York City. Since the 2014 installation of this green roof, one of the largest in North America, a colony of nesting herring gulls grew to approximately 100 nesting pairs in 2018 and 150 nesting pairs in 2019. Water quality monitoring took place between September 2018 and October 2019. Except for phosphorus on some occasions, we found concentrations of nitrate, nitrite, chlorine, sulfate to be below federal drinking water standards. Levels of the fecal indicator bacteria (FIB), total coliform, E. coli, and Enterococcus, were consistently higher in runoff samples than rainwater, ranging from 150 to over 20,000 CFU/100 mL for E. coli and 100 to over 140,000 CFU/100 mL for total coliform. Quantitative polymerase chain reaction (qPCR) methods were used to search for potential opportunistic pathogens, including Legionella spp., Mycobacterium spp., Campylobacter spp., and Salmonella spp. Discovery of the presence of Catellicoccus marimammalium, a gull-associated marker in runoff water indicates that herring gulls are the likely source of contamination. Due to habitat loss, herring gulls, and other Larus gull species are increasingly nesting on urban roofs, both green (such as at the Javits Center) and conventional (such as on Rikers and Governors Islands). Habitat creation is one of the target ecosystem services desired from GI systems. Although the discharge from the green roof of the Javits Center is directed to the city's sewer system, this study demonstrates the need to treat runoff from green roofs with nesting gull populations if its intended use involves reuse or human contact.
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Affiliation(s)
- Jinjie He
- Civil, Architectural, and Environmental Engineering, Drexel University, Philadelphia, PA 19104, USA.
| | - Elrod Owusu-Asumeng
- Civil, Architectural, and Environmental Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Kate Zidar
- Department of Geology & Planetary Science, University of Pittsburgh, 4107 O'Hara Street, Pittsburgh, PA 15260, USA
| | - Julian Stolper
- Civil, Architectural, and Environmental Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Sudipti Attri
- Civil, Architectural, and Environmental Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Jacob R Price
- Civil, Architectural, and Environmental Engineering, Drexel University, Philadelphia, PA 19104, USA
| | | | - Franco Montalto
- Civil, Architectural, and Environmental Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Christopher M Sales
- Civil, Architectural, and Environmental Engineering, Drexel University, Philadelphia, PA 19104, USA
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2
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Bouchali R, Mandon C, Danty-Berger E, Géloën A, Marjolet L, Youenou B, Pozzi ACM, Vareilles S, Galia W, Kouyi GL, Toussaint JY, Cournoyer B. Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns. Int J Hyg Environ Health 2024; 260:114391. [PMID: 38781750 DOI: 10.1016/j.ijheh.2024.114391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 03/15/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.
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Affiliation(s)
- Rayan Bouchali
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Claire Mandon
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Emmanuelle Danty-Berger
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Alain Géloën
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Laurence Marjolet
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Benjamin Youenou
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Adrien C M Pozzi
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Sophie Vareilles
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Wessam Galia
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | | | - Jean-Yves Toussaint
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Benoit Cournoyer
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France.
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3
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O'Malley K, McNamara P, Marshall C, LaMartina EL, Lam TD, Ali N, McDonald W. Environmental drivers impact the accumulation and diversity of antibiotic resistance in green stormwater infrastructure. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133923. [PMID: 38457973 DOI: 10.1016/j.jhazmat.2024.133923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/12/2024] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
Antibiotic resistance poses an urgent public health concern, with the environment playing a crucial role in the development and dissemination of resistant bacteria. There is a growing body of research indicating that stormwater is a significant source and transport vector of resistance elements. This research sought to characterize the role of green stormwater infrastructure (GSI), designed for stormwater infiltration, in accumulating and propagating antibiotic resistance in the urban water cycle. Sampling included 24 full-scale GSI systems representing three distinct types of GSI - bioswales, bioretention cells, and constructed wetlands. The results indicated that GSI soils accumulate antibiotic resistance genes (ARGs) at elevated concentrations compared to nonengineered soils. Bioretention cells specifically harbored higher abundances of ARGs, suggesting that the type of GSI influences ARG accumulation. Interestingly, ARG diversity in GSI soils was not impacted by the type of GSI design or the diversity of the microbial community and mobile genetic elements. Instead, environmental factors (catchment imperviousness, metals, nutrients, and salts) were identified as significant drivers of ARG diversity. These findings highlight how environmental selective pressures in GSI promote ARG persistence and proliferation independently of the microbial community. Therefore, GSI systems have the potential to be a substantial contributor of abundant and diverse ARGs to the urban water cycle.
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Affiliation(s)
- Kassidy O'Malley
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA
| | - Patrick McNamara
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA
| | - Christopher Marshall
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Emily Lou LaMartina
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA; Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Thuy Duyen Lam
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA
| | - Numair Ali
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Walter McDonald
- Department of Civil, Construction, and Environmental Engineering, Marquette University, Milwaukee, WI 53233, USA.
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Christel A, Dequiedt S, Chemidlin-Prevost-Bouré N, Mercier F, Tripied J, Comment G, Djemiel C, Bargeot L, Matagne E, Fougeron A, Mina Passi JB, Ranjard L, Maron PA. Urban land uses shape soil microbial abundance and diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163455. [PMID: 37062324 DOI: 10.1016/j.scitotenv.2023.163455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 06/03/2023]
Abstract
Soil microbial biodiversity provides many useful services in cities. However, the ecology of microbial communities in urban soils remains poorly documented, and studies are required to better predict the impact of urban land use. We characterized microbial communities (archea/bacteria and fungi) in urban soils in Dijon (Burgundy, France). Three main land uses were considered - public leisure, traffic, and urban agriculture - sub-categorized in sub-land uses according to urban indexes and management practices. Microbial biomass and diversity were determined by quantifying and high-throughput sequencing of soil DNA. Variation partitioning analysis was used to rank soil physicochemical characteristics and land uses according to their relative contribution to the variation of soil microbial communities. Urban soils in Dijon harbored high levels of microbial biomass and diversity that varied according to land uses. Microbial biomass was 1.8 times higher in public leisure and traffic sites than in urban agriculture sites. Fungal richness increased by 25 % in urban agriculture soils, and bacterial richness was lower (by 20 %) in public leisure soils. Partitioning models explained 25.7 %, 46.2 % and 75.6 % of the variance of fungal richness, bacterial richness and microbial biomass, respectively. The organic carbon content and the C/N ratio were the best predictors of microbial biomass, whereas soil bacterial diversity was mainly explained by soil texture and land use. Neither metal trace elements nor polycyclic aromatic hydrocarbons contents explained variations of microbial communities, probably due to their very low concentration in the soils. The microbial composition results highlighted that leisure sites represented a stabilized habitat favoring specialized microbial groups and microbial plant symbionts, as opposed to urban agriculture sites that stimulated opportunistic populations able to face the impact of agricultural practices. Altogether, our results provide evidence that there is scope for urban planners to drive soil microbial diversity through sustainable urban land use and associated management practices.
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Affiliation(s)
- Amélie Christel
- AgroParisTech, 75732 Paris, France; Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Samuel Dequiedt
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Florian Mercier
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Julie Tripied
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Gwendoline Comment
- Platforme GenoSol, INRAE-Université de Bourgogne, CMSE, 21000 Dijon, France
| | - Christophe Djemiel
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | | | - Eric Matagne
- AGARIC-IG, 144 Rue Rambuteau, 71000 Macon, France
| | - Agnès Fougeron
- Jardin de l'Arquebuse Mairie de Dijon, CS 73310, 21033 Dijon Cedex, France
| | | | - Lionel Ranjard
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, Institut Agro, INRAE, Univ. Bourgogne Franche-Comté, 21000 Dijon, France.
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Medriano CA, Chan A, De Sotto R, Bae S. Different types of land use influence soil physiochemical properties, the abundance of nitrifying bacteria, and microbial interactions in tropical urban soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161722. [PMID: 36690092 DOI: 10.1016/j.scitotenv.2023.161722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Anthropogenic activities have led to unexpected changes in microbial community composition and structure, resulting in an interruption of soil ecological roles in urban environments. We questioned the impact of the different land use (e.g., agricultural, industrial, recreational, coastal, and residential areas) on the distribution of nitrifying bacteria and microbial interaction in tropical soil. The dominant nitrifying bacteria were ammonia-oxidizing archaea (AOA) in tropical soils up to 107 copies/g of soil, while the abundance of ammonia-oxidizing bacteria (AOB) was significantly higher in agricultural soil only. Comammox (CMX) was ubiquitous up to 105 copies/g of tropical soil, indicating that CMX might share ecological niches with AOA and considerably contribute to nitrification in urban areas. The most abundant phylum is Actinobacteria, accounting for 27-34 % relative abundance among most land-use types, but Proteobacteria was observed as the most prevalent phylum in agricultural soil. The physicochemical properties (e.g., soil pH and nutrient contents) of different types of land use influenced microbial richness and diversities associated with nitrogen cycling. Multivariate analysis disclosed that agricultural soils were distinct from other land uses because of the concentrations of nutrients and heavy metals and the abundance of microorganisms associated with nitrogen cycles. Also, the microbial co-occurrence network revealed that agricultural soils were a highly interconnected network of the microbial community. In this study, C: N ratio might have a significant impact on ecological networks and the abundance of nitrogen-related taxa, which could influence microbial interactions and complexity in tropical soils. Thus, the impact of anthropogenic land use induced changes in microbial composition and diversity, co-occurrence network, and nitrifying bacteria, leading to potential transformation in ecological services of tropical soils and nitrogen cycling in urban environments.
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Affiliation(s)
- Carl Angelo Medriano
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore
| | - Amabel Chan
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore
| | - Ryan De Sotto
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore
| | - Sungwoo Bae
- Civil and Environmental Engineering Department, National University of Singapore, 1 Engineering Drive 3, Singapore 117580, Singapore.
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Xiong G, Ji L, Cheng M, Ning K. Niche-Based Microbial Community Assemblage in Urban Transit Systems and the Influence of City Characteristics. Microbiol Spectr 2023; 11:e0016723. [PMID: 36916942 PMCID: PMC10101094 DOI: 10.1128/spectrum.00167-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/10/2023] [Indexed: 03/16/2023] Open
Abstract
Microbiota residing on the urban transit systems (UTSs) can be shared by travelers and have niche-specific assemblage. However, it remains unclear how the assemblages are influenced by city characteristics, rendering city-specific and microbial-aware urban planning challenging. Here, we analyzed 3,359 UTS microbial samples collected from 16 cities around the world. We found the stochastic process dominated in all UTS microbiota assemblages, with the explanation rate (R2) of the neutral community model (NCM) higher than 0.7. Moreover, city characteristics predominantly drove such assemblage, largely responsible for the variation in the stochasticity ratio (50.1%). Furthermore, by utilizing an artificial intelligence model, we quantified the ability of UTS microbes in discriminating between cities and found that the ability was also strongly affected by city characteristics, especially climate and continent. From these, we found that although the NCM R2 of the New York City UTS microbiota was 0.831, the accuracy of the microbial-based city characteristic classifier was higher than 0.9. This is the first study to demonstrate the effects of city characteristics on the UTS microbiota assemblage, paving the way for city-specific and microbial-aware applications. IMPORTANCE We analyzed the urban transit system microbiota assemblage across 16 cities. The stochastic process was dominant in the urban transit system microbiota assemblage. The urban transit system microbe's ability in discriminating between cities was quantified using transfer learning based on random forest (RF) methods. Certain urban transit system microbes were strongly affected by city characteristics.
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Affiliation(s)
- Guangzhou Xiong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lei Ji
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mingyue Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
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7
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Native plant gardens support more microbial diversity and higher relative abundance of potentially beneficial taxa compared to adjacent turf grass lawns. Urban Ecosyst 2023. [DOI: 10.1007/s11252-022-01325-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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8
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Li L, Li S, Ma X, Yan Y. Effects of Urban Green Infrastructure Designs on Soil Bacterial Community Composition and Function. Ecosystems 2022. [DOI: 10.1007/s10021-022-00797-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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9
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Liang Z, Dong CB, Liang H, Zhen YX, Zhou RL, Han YF, Liang ZQ. A microbiome study reveals the potential relationship between the bacterial diversity of a gymnastics hall and human health. Sci Rep 2022; 12:5663. [PMID: 35383217 PMCID: PMC8983745 DOI: 10.1038/s41598-022-09355-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 03/08/2022] [Indexed: 11/09/2022] Open
Abstract
Currently, investigations on the microbiota of sports centers and related facilities have been carried out in some countries, which showed that Microsporum gypseum, Trichophyton mentagrophytes and T. tonsurans are important dermatoprotofungi. In China, some research on athletes and sports equipment between the fungal community and public health has made some interesting achievements. However, the bacterial group among them has not been reported. Therefore, The aim of this study was to uncover (I) gymnastic equipment is there potential pathogenic factors and (ii) is there any difference in the biomarker of bacterial in different types of gymnastic room? The samples were collected from the gymnastics halls of one university in western China and main sports equipment, including gymnastics carpets, moving barres, hoops and balls, as well as wall bars, parallel bars and horizontal bars. The 16S rDNA of all the samples was sequenced, and the analyses were performed using FaproTax, Bug base function prediction and Line Discriminant Analysis (LDA) Effect Size. A 16S rDNA sequence analysis revealed abundant bacterial species biodiversity on gymnasts and apparatuses from two gymnastics halls at a university in western China. An analysis using the FaproTax and Bugbase functional prediction platforms showed that there were some opportunistic pathogens on the athletes and equipment from the Rhythmic Gymnastics (RG) and Artistic Gymnastics (AG) halls, such as Staphylococcus and Corynebacteiaceae. Infectious agents associated with cancer induction and development, such as Ruminococcaceae, Veillonellaceae and Moraxellaceae, as well as microbial toxin producers with a potential impact on human health, were also detected. According to a line discriminant analysis (LDA effect size), the bacterial biomarker groups of the two gymnasiums were different at the phylum-genus level: for RG, Erysipelatoclostridium, Lachnospiraceae and Bacteroidales, while for AG, Rhizobiales. Based on the results of the investigation, we suggest that more comprehensive consideration should be given to indoor microbial biodiversity and related public health problems in school gymnasiums.
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Affiliation(s)
- Z Liang
- Gymnastics Department, Chengdu Sport University, Chengdu, 610041, Sichuan, China
| | - C B Dong
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China
| | - H Liang
- Physical Education College, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Y X Zhen
- Gymnastics Department, Chengdu Sport University, Chengdu, 610041, Sichuan, China
| | - R L Zhou
- Gymnastics Department, Chengdu Sport University, Chengdu, 610041, Sichuan, China
| | - Y F Han
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Z Q Liang
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou, China.
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10
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Biochar-Based Compost Affects Bacterial Community Structure and Induces a Priming Effect on Soil Organic Carbon Mineralization. Processes (Basel) 2022. [DOI: 10.3390/pr10040682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Urban forests are key to mitigating the Urban Heat Island Effect, which contributes to temperature increases in urban areas. However, the trees in these forests are usually under stress because urban soil is typically degraded. Biochar/compost amendments help with soil management by improving the physiochemical properties and bacterial communities of soil. Here, we compared the physiochemical properties and bacterial communities before and after (1) biochar-only and (2) biochar-based compost amendments. Our results suggested that biochar-only application did not improve soil properties after 1 year of treatment, whereas in the biochar-based compost treatment, the soil properties and bacterial communities changed after just four months. The increase in potassium and decrease in organic material, calcium, and available phosphorus in the soil of the former treatment indicated that the nutrient uptake of its trees had improved. Although there was no significant variation in the soil’s total nitrogen, the higher abundance of potential nitrogen-fixing bacteria in the biochar-based treatment suggested that the soil contained a supplement to nitrogen. Our results show that biochar-based compost amendment improves soil quality and associated bacterial communities in urban forest management.
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11
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Nugent A, Allison SD. A framework for soil microbial ecology in urban ecosystems. Ecosphere 2022. [DOI: 10.1002/ecs2.3968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Andie Nugent
- Department of Ecology and Evolutionary Biology University of California–Irvine Irvine California USA
| | - Steven D. Allison
- Department of Ecology and Evolutionary Biology University of California–Irvine Irvine California USA
- Department of Earth System Science University of California–Irvine Irvine California USA
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12
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Mills JG, Selway CA, Weyrich LS, Skelly C, Weinstein P, Thomas T, Young JM, Marczylo E, Yadav S, Yadav V, Lowe AJ, Breed MF. Rare genera differentiate urban green space soil bacterial communities in three cities across the world. Access Microbiol 2022; 4:000320. [PMID: 35252756 PMCID: PMC8895604 DOI: 10.1099/acmi.0.000320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/09/2021] [Indexed: 11/18/2022] Open
Abstract
Vegetation complexity is potentially important for urban green space designs aimed at fostering microbial biodiversity to benefit human health. Exposure to urban microbial biodiversity may influence human health outcomes via immune training and regulation. In this context, improving human exposure to microbiota via biodiversity-centric urban green space designs is an underused opportunity. There is currently little knowledge on the association between vegetation complexity (i.e. diversity and structure) and soil microbiota of urban green spaces. Here, we investigated the association between vegetation complexity and soil bacteria in urban green spaces in Bournemouth, UK; Haikou, China; and the City of Playford, Australia by sequencing the 16S rRNA V4 gene region of soil samples and assessing bacterial diversity. We characterized these green spaces as having ‘low’ or ‘high’ vegetation complexity and explored whether these two broad categories contained similar bacterial community compositions and diversity around the world. Within cities, we observed significantly different alpha and beta diversities between vegetation complexities; however, these results varied between cities. Rare genera (<1% relative abundance individually, on average 35% relative abundance when pooled) were most likely to be significantly different in sequence abundance between vegetation complexities and therefore explained much of the differences in microbial communities observed. Overall, general associations exist between soil bacterial communities and vegetation complexity, although these are not consistent between cities. Therefore, more in-depth work is required to be done locally to derive practical actions to assist the conservation and restoration of microbial communities in urban areas.
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Affiliation(s)
- Jacob G. Mills
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Caitlin A. Selway
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Laura S. Weyrich
- Department of Anthropology and Huck Institutes of the Life Sciences, Pennsylvania State University, Pennsylvania, USA
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Chris Skelly
- Research & Intelligence, Public Health Dorset, Dorset County Council, Dorset, UK
- Healthy Urban Microbiome Initiative
| | - Philip Weinstein
- School of Public Health, The University of Adelaide, Adelaide, Australia
- Environment Institute, The University of Adelaide, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Environmental and Earth Sciences, University of New South Wales, Sydney, Australia
| | - Jennifer M. Young
- College of Science and Engineering, Flinders University, Bedford Park, South Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Emma Marczylo
- Toxicology Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Oxfordshire, UK
| | - Sudesh Yadav
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vijay Yadav
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Andrew J. Lowe
- Environment Institute, The University of Adelaide, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Martin F. Breed
- Environment Institute, The University of Adelaide, Adelaide, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
- College of Science and Engineering, Flinders University, Bedford Park, South Australia
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13
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Buzzard V, Gil-Loaiza J, Graf Grachet N, Talkington H, Youngerman C, Tfaily MM, Meredith LK. Green infrastructure influences soil health: Biological divergence one year after installation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 801:149644. [PMID: 34428660 DOI: 10.1016/j.scitotenv.2021.149644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Global threats to soils remain one of the greatest concerns and challenges of the 21st century. Built landscapes have profound local and global effects because they create urban heat islands, increase habitat fragmentation, and reduce biological diversity. Additionally, impervious surfaces alter natural watersheds and reduce infiltration increasing runoff that leads to erosion and soil degradation. To combat these effects, green infrastructure (GI) practices, like water harvesting rain gardens, are implemented in the Southwest United States to restore natural ecological function, yet little is known about how GI impacts soil health. Soil health can be measured using indicators that include physical, chemical, and biological characteristics that support ecosystem processes. This study aimed to evaluate changes in water holding capacity, bulk density, pH, electrical conductivity, Gibbs free energy, species richness and Shannon diversity in response to rain gardens that received different inputs (frequency and amount) and sources of harvested water (rain, municipal, greywater) one year after installation. We hypothesized that soil health indicators in GI diverge from the unaltered control treatment one year following installation. Although physical and chemical indicators were comparatively less sensitive to GI treatments than biological indicators, they varied within treatments after one year of GI management (pH increased: H = 36.37; p-value = 0.00; electrical conductivity decreased: H = 33.94; p-value = 0.00). Overall, we observed significantly higher soil microbial diversity (F = 4.29; p-value = 0.015) and richness (F = 4.02; p-value = 0.019) in surface soils in GI treatments after one year of management. Our findings suggest GI practices enhanced soil biological health which may lead to positive feedbacks that assist gradual changes in the abiotic environment thus enhancing soil health over time. These findings have broad implications for effectively assessing the success of GI management practices over short time periods using soil biological health indicators.
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Affiliation(s)
- Vanessa Buzzard
- School of Natural Resources and the Environment, University of Arizona, United States of America.
| | - Juliana Gil-Loaiza
- School of Natural Resources and the Environment, University of Arizona, United States of America
| | - Nathalia Graf Grachet
- The Department of Environmental Science, University of Arizona, United States of America
| | - Hannah Talkington
- School of Natural Resources and the Environment, University of Arizona, United States of America
| | - Connor Youngerman
- School of Natural Resources and the Environment, University of Arizona, United States of America
| | - Malak M Tfaily
- The Department of Environmental Science, University of Arizona, United States of America
| | - Laura K Meredith
- School of Natural Resources and the Environment, University of Arizona, United States of America; BIO5 Institute, University of Arizona, United States of America
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14
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Vander Meer L, DeHeer K, Mellinger J, Gibes S, Paasch B, Wildschut J, Miller WL, He SY, DuBois KN. Indicator species characterization and removal in a detention pond in the Plaster Creek watershed. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 298:113503. [PMID: 34426212 DOI: 10.1016/j.jenvman.2021.113503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Microbial pathogen contamination is a leading cause of impairment for urban rivers and streams in Michigan. Reports on the ability of green infrastructure best management practices to remove microbial pathogens have been highly variable. This study evaluated the influence of a detention basin (Kreiser Pond) on microbial dynamics in the Plaster Creek watershed in West Michigan. High levels of fecal indicator bacteria and coliphage were documented in influent and effluent water, with significant increases in indicator microbe concentrations during storm events. In dry conditions, Kreiser Pond efficiently reduced the number of indicator microbes flowing through the basin. Rainfall volume had a greater influence on the diversity of bacteria than sampling location. Antibiotic resistance was prevalent in culturable E. coli from Kreiser Pond, demonstrating a potential public health risk and highlighting the need for identifying the ultimate sources of microbial pollution.
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Affiliation(s)
- Luke Vander Meer
- Biology Department, Calvin University, 3201 Burton St. SE, Grand Rapids, MI, 49546, USA.
| | - Katherine DeHeer
- Biology Department, Calvin University, 3201 Burton St. SE, Grand Rapids, MI, 49546, USA.
| | - Joseph Mellinger
- Biology Department, Calvin University, 3201 Burton St. SE, Grand Rapids, MI, 49546, USA.
| | - Sarah Gibes
- Biology Department, Calvin University, 3201 Burton St. SE, Grand Rapids, MI, 49546, USA.
| | - Bradley Paasch
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Biology, Duke University, Durham, NC, 27708, USA.
| | - Julie Wildschut
- Engineering Department, Calvin University, 3201 Burton St. SE, Grand Rapids, MI, 49546, USA.
| | - William L Miller
- Biology Department, Calvin University, 3201 Burton St. SE, Grand Rapids, MI, 49546, USA.
| | - Sheng-Yang He
- Department of Biology, Duke University, Durham, NC, 27708, USA; Howard Hughes Medical Institute, Durham, NC, 27708, USA.
| | - Kelly N DuBois
- Biology Department, Calvin University, 3201 Burton St. SE, Grand Rapids, MI, 49546, USA.
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15
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Biswal BK, Vijayaraghavan K, Adam MG, Lee Tsen-Tieng D, Davis AP, Balasubramanian R. Biological nitrogen removal from stormwater in bioretention cells: a critical review. Crit Rev Biotechnol 2021; 42:713-735. [PMID: 34486441 DOI: 10.1080/07388551.2021.1969888] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Excess nitrogen in stormwater degrades surface water quality via eutrophication and related processes. Bioretention has been recognized as a highly effective low-impact development (LID) technology for the management of high runoff volumes and reduction of nitrogen (N) pollutants through various mechanisms. This paper provides a comprehensive and critical review of recent developments on the biological N removal processes occurring in bioretention systems. The key plant- and microbe-mediated N transformation processes include assimilation (N uptake by plants and microbes), nitrification, denitrification, and anammox (anaerobic ammonia oxidation), but denitrification is the major pathway of permanent N removal. Overall, both laboratory- and field-scale bioretention systems have demonstrated promising N removal performance (TN: >70%). The phyla Bacteroidetes and Proteobacteria are the most abundant microbial communities found to be enriched in biofilter media. Furthermore, the denitrifying communities contain several functional genes (e.g., nirK/nirS, and nosZ), and their concentrations increase near the surface of media depth. The N removal effectiveness of bioretention systems is largely impacted by the hydraulics and environmental factors. When a bioretention system operates at: low hydraulic/N loading rate, containing a saturation zone, vegetated with native plants, having deeper and multilayer biofilter media with warm climate temperature and wet storm events periods, the N removal efficiency can be high. This review highlights shortcomings and current knowledge gaps in the area of total nitrogen removal using bioretention systems, as well as identifies future research directions on this topic.
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Affiliation(s)
- Basanta Kumar Biswal
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| | - Kuppusamy Vijayaraghavan
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| | - Max Gerrit Adam
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
| | - Daryl Lee Tsen-Tieng
- Centre for Urban Greenery and Ecology, National Parks Board, Singapore, Singapore
| | - Allen P Davis
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA
| | - Rajasekhar Balasubramanian
- Department of Civil and Environmental Engineering, National University of Singapore, Singapore, Singapore
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16
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Lammel DR, Nüsslein K, Cerri CEP, Veresoglou SD, Rillig MC. Soil biota shift with land use change from pristine rainforest and Savannah (Cerrado) to agriculture in southern Amazonia. Mol Ecol 2021; 30:4899-4912. [PMID: 34297871 DOI: 10.1111/mec.16090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
Southern Amazonia is currently experiencing extensive land use change from forests to agriculture caused by increased local and global demand for agricultural products. However, little is known about the impacts of deforestation and land use change on soil biota. We investigated two regions in southern Amazonia (rainforest and Savannah/Cerrado biomes), analysing soil biota community turnover based on 16S (Archaea and Bacteria) and 18S rRNA genes (Eukaryotes, including Fungi, Protists and Animalia) and correlating them with soil chemistry and land use intensity. We found that soil biota community structure is driven by land use change in both Cerrado and rainforest. Crop fields approximatively doubled the richness of soil Archaea, Bacteria and Protists. We propose that crop systems not only increase soil pH and fertility, but also create continued disturbance (crop seasons) that stimulates soil diversity, as predicted by the dynamic equilibrium model (DEM) and the intermediate disturbance hypothesis (IDH). Even though agricultural fields had higher soil biota richness, some taxa were suppressed by agriculture (6/31 operational taxonomic units of Archaea, 245/1790 of Bacteria, 12/74 of Animalia, 20/144 of Fungi and 25/310 of Protists). Consequently, land use change in this region should proceed with caution. In the southern Amazonia region of Brazil, current laws require farmers to keep 20%-80% pristine vegetation areas on their property. Our data support the relevance of this law: since there are unique soil taxa under native vegetation, keeping these pristine areas adjacent to the agricultural fields should maximize soil biodiversity protection in these regions.
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Affiliation(s)
- Daniel R Lammel
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany.,Department of Microbiology, University of Massachusetts, Amherst, MA, USA.,ESALQ&CENA, University of São Paulo, Piracicaba, Brazil
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | | | - Stavros D Veresoglou
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Matthias C Rillig
- Freie Universität Berlin, Institut für Biologie, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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17
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Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 2021; 184:3376-3393.e17. [PMID: 34043940 PMCID: PMC8238498 DOI: 10.1016/j.cell.2021.05.002] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 04/29/2021] [Indexed: 01/14/2023]
Abstract
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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Affiliation(s)
- David Danko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Evan E Afshin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Chandrima Bhattacharya
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniel J Butler
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Kern Rei Chng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Daisy Donnellan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Katelyn Jackson
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Katerina Kuchin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Mikhail Karasikov
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abigail Lyons
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Lauren Mak
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dmitry Meleshko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Harun Mustafa
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Beth Mutai
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Kenya Medical Research Institute - Kisumu, Kisumu, Kenya
| | - Russell Y Neches
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amanda Ng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | | | | | - Eileen Png
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Krista A Ryon
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jorge L Sanchez
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Heba Shaaban
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Maria A Sierra
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dominique Thomas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Ben Young
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Omar O Abudayyeh
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Josue Alicea
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Malay Bhattacharyya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India
| | | | - Eduardo Castro-Nallar
- Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Ana M Cañas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Aspassia D Chatziefthimiou
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Youping Deng
- University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Christelle Desnues
- Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Emmanuel Dias-Neto
- Medical Genomics group, A.C.Camargo Cancer Center, São Paulo - SP, Brazil
| | - Marius Dybwad
- Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine
| | - Dennis Gankin
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | | | - David C Green
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Iman Hajirasouliha
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jaden J A Hastings
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Santiago, Chile; Wellcome Sanger Institute, Hinxton, UK
| | | | - Andre Kahles
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; Kyiv Academic University, Kyiv, Ukraine; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Frank J Kelly
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Kaymisha Knights
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paweł P Łabaj
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Boku University Viennna, Vienna, Austria
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Per O Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Ken McGrath
- Microba, 388 Queen St, Brisbane City, QLD 4000, Australia
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Emmanuel F Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | | | - Houtan Noushmehr
- University of São Paulo, Ribeirão Preto Medical School, Ribeirão Preto - SP, Brazil
| | - Manuela Oliveira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria
| | - Orhan Özcan
- Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicolás Rascovan
- Microbial Paleogenomics Unit, Institut Pasteur, CNRS UMR2000, Paris 75015, France
| | - Hugues Richard
- Sorbonne University, Faculty of Science, Institute of Biology Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France; Robert Koch Institute, Berlin, Germany
| | - Gunnar Rätsch
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | - Leming Shi
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Rania Siam
- University of Medicine and Health Sciences, St. Kitts, West Indies and American University in Cairo, Cairo, Egypt
| | - Le Huu Song
- 108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
| | | | - Denise Syndercombe Court
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | | | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Klas I Udekwu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; SciLife EVP, Department of Aquatic Sciences Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Santiago, Chile; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Brandon Valentine
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dimitar I Vassilev
- Faculty of Mathematics and Informatics, Sofia University "St. Kliment Ohridski," Sofia, Bulgaria
| | - Elena M Vayndorf
- Institute of Arctic Biology, University of Alaska, Fairbanks, Fairbanks, AK, USA
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Univeristätsklinikum Tübingen, Tübingen, Germany; Faculty of Medicine, Duy Tan University, Da Nang, Vietnam
| | - Jun Wu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | | | - Jifeng Zhu
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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Stephanou C, Omirou M, Philippot L, Zissimos AM, Christoforou IC, Trajanoski S, Oulas A, Ioannides IM. Land use in urban areas impacts the composition of soil bacterial communities involved in nitrogen cycling. A case study from Lefkosia (Nicosia) Cyprus. Sci Rep 2021; 11:8198. [PMID: 33854127 PMCID: PMC8047022 DOI: 10.1038/s41598-021-87623-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/31/2021] [Indexed: 01/04/2023] Open
Abstract
The different types of land-use and soil lithology in urban and peri-urban areas of modern cities compose a complex mosaic of soil ecosystems. It is largely unknown how these differences result in changes in bacterial community composition and structure as well as in functional guilds involved in N cycling. To investigate the bacterial composition and the proportion of denitrifiers in agricultural, forested, schoolyard and industrial areas, 24 samples were collected from urban and peri-urban sites of Lefkosia. Bacterial diversity and the proportion of denitrifiers were assessed by NGS and qPCR, respectively. Proteobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Acidobacteria and Planctomycetes were identified as the most dominant phyla across all sites, while agricultural sites exhibited the highest bacterial diversity. Heavy metals such as Co, Pb, V and Al were identified as key factors shaping bacterial composition in industrial and schoolyard sites, while the bacterial assemblages in agricultural and forested sites were associated with Ca. Variance partitioning analysis showed that 10.2% of the bacterial community variation was explained by land use management, 5.1% by chemical elements due to soil lithology, and 1.4% by sampling location. The proportion of denitrifiers varied with land use management. In industrial and schoolyard sites, the abundance of the nosZII bacterial community increased while nirK abundance declined. Our data showed that land use and lithology have a moderate impact on the bacterial assemblages in urban and peri-urban areas of Lefkosia. As the nosZII bacterial community is important to the N2O sink capacity of soils, it would be interesting to elucidate the factors contributing to the proliferation of the nosZII clade in these soils.
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Affiliation(s)
- Coralea Stephanou
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus
| | - Michalis Omirou
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus. .,Department of Agrobiotechnology, Agricultural Microbiology Laboratory, Agricultural Research Institute, Athalassa, Cyprus.
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRA, AgroSup Dijon, Agroécologie, 21000, Dijon, France
| | - Andreas M Zissimos
- Geological Survey Department, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Irene C Christoforou
- Geological Survey Department, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Slave Trajanoski
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Anastasis Oulas
- Cyprus Institute of Neurology and Genetics, Bioinformatics Group, Engomi, Cyprus
| | - Ioannis M Ioannides
- Department of Agrobiotechnology, Agricultural Research Institute, Nicosia, Cyprus
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Tang J, Wang W, Feng J, Yang L, Ruan T, Xu Y. Urban green infrastructure features influence the type and chemical composition of soil dissolved organic matter. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 764:144240. [PMID: 33385659 DOI: 10.1016/j.scitotenv.2020.144240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
In urban areas, green infrastructure (GI) has been widely developed utilizing different types of engineered soil to enhance ecosystem functions to interact with soil dissolved organic matter (DOM). However, there remains a lack of urban studies that have examined the link between GI features and soil DOM. This study, which was conducted in a typical heavily industrialized and urbanized area (Ningbo City, East China), aimed to characterize the chemical variation and composition of DOM in the engineered soil of four GI types (enhanced tree tips, ETP; street-side infiltration swales, SSIS; vegetated swales, VS; urban forests, UF). The results showed that soil organic carbon varies among the four GI types with significantly lower content in SSIS and ETP compared to VS and UF. Smaller variation was observed in the water-soluble organic carbon (WSOC) content, with UF having significantly higher content than ETP. Three humic-like substances and one protein-like substance were derived using the parallel factor analysis (PARAFAC) model. These fluorescent compositions and their spectral parameters displayed specific distributions among GI features with VS having the highest proportion of humic-like substances (C1) and the lowest proportion of protein-like substances (C4). The distribution of spectral indices indicated terrigenous sources of DOM in these GI engineered soils. Significant positive correlations were found between protein-like substances and the population density and nightlight index, while negative correlations were found between humic-like substances (C1) and these two indices. These results demonstrate significant human disturbance of the chemical composition and characteristics of GI features. Our findings suggest that the overall design and management of GI features have a fundamental influence on soil DOM that is vital for carbon cycling in urban ecosystems.
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Affiliation(s)
- Jianfeng Tang
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, China.
| | - Wendong Wang
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, China
| | - Jiayong Feng
- Ningbo Environmental Monitoring Center, Ningbo 315012, China
| | - Lei Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Tian Ruan
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, China
| | - Yaoyang Xu
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Ningbo Urban Environment Observation and Research Station, Chinese Academy of Sciences, Ningbo 315800, China
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Gill AS, Purnell K, Palmer MI, Stein J, McGuire KL. Microbial Composition and Functional Diversity Differ Across Urban Green Infrastructure Types. Front Microbiol 2020; 11:912. [PMID: 32582043 PMCID: PMC7291602 DOI: 10.3389/fmicb.2020.00912] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/17/2020] [Indexed: 01/04/2023] Open
Abstract
Functional and biogeographical properties of soil microbial communities in urban ecosystems are poorly understood despite their role in metabolic processes underlying valuable ecosystem services. The worldwide emergence of engineered habitats in urban landscapes-green roofs, bioswales, and other types of soil-based green infrastructure-highlights the importance of understanding how environmental changes affect the community assembly processes that shape urban microbial diversity and function. In this study we investigated (1) whether engineered green roofs and bioswales in New York City had distinct microbial community composition and trait-associated diversity compared to non-engineered soils in parks and tree pits, and (2) if these patterns were consistent with divergent community assembly processes associated with engineered specifications of green infrastructure habitats not present in conventional, non-engineered green infrastructure; specifically, tree pit and park lawn soils. We found that green roofs and bioswales each had distinct bacterial and fungal communities, but that community composition and diversity were not significantly associated with geographic distance, suggesting that the processes structuring these differences are related to aspects of the habitats themselves. Bioswales, and to a lesser extent green roofs, also contained increased functional potential compared to conventional GI soils, based on the diversity and abundance of taxa associated with nitrogen cycling, biodegradation, decomposition, and traits positively associated with plant growth. We discuss these results in the context of community assembly theory, concluding that urban soil microbial community composition and diversity in engineered habitats are driven largely by environmental filtering, whereas stochastic processes are more important among non-engineered soils.
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Affiliation(s)
- Aman S. Gill
- Department of Environmental Science and Policy Management, University of California, Berkeley, Berkeley, CA, United States
| | - Kai Purnell
- Department of Biology, Barnard College, New York, NY, United States
| | - Matthew I. Palmer
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Jaime Stein
- Programs for Sustainable Planning and Development, School of Architecture, Pratt Institute, Brooklyn, NY, United States
| | - Krista L. McGuire
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
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