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Zampolli J, De Giani A, Rossi M, Finazzi M, Di Gennaro P. Who inhabits the built environment? A microbiological point of view on the principal bacteria colonizing our urban areas. Front Microbiol 2024; 15:1380953. [PMID: 38863750 PMCID: PMC11165352 DOI: 10.3389/fmicb.2024.1380953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024] Open
Abstract
Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the ever-increasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities.
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Affiliation(s)
| | | | | | | | - Patrizia Di Gennaro
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
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Zheng F, Gu J, Lu D, Yang J, Shuai X, Li C, Chen H. Mixing with native broadleaf trees modified soil microbial communities of Cunninghamia lanceolata monocultures in South China. Front Microbiol 2024; 15:1372128. [PMID: 38505544 PMCID: PMC10949948 DOI: 10.3389/fmicb.2024.1372128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Mixing with different broadleaf trees into the monocultures of Cunninghamia lanceolata is widely adopted as an efficient transformation of the pure C. lanceolata forest. However, it is unclear how native broad-leaved trees influence the belowground ecological environment of the pure C. lanceolata culture plantation in nutrient-poor soil of South China. Herein, we aimed to investigate how a long-time mixing with native broadleaf trees shape soil microbial community of the pure C. lanceolata forest across different soil depth (0-20 cm and 20-40 cm) and to clarify relationships between the modified soil microbial community and those affected soil chemical properties. Using high-throughput sequencing technology, microbial compositions from the mixed C. lanceolata-broadleaf forest and the pure C. lanceolata forest were analyzed. Network analysis was utilized to investigate correlations among microorganisms, and network robustness was assessed by calculating network natural connectivity. Results demonstrated that the content of soil microbial biomass carbon and nitrogen, total phosphorus and pH in mixed forest stand were significantly higher than those in pure forest stand, except for available phosphorus in topsoil (0-20 cm). Simultaneously, the mixed C. lanceolata-broadleaf forest has a more homogeneous bacterial and fungal communities across different soil depth compared with the pure C. lanceolata forest, wherein the mixed forest recruited more diverse bacterial community in subsoil (20-40 cm) and reduced the diversity of fungal community in topsoil. Meanwhile, the mixed forest showed higher bacterial community stability while the pure forest showed higher fungal community stability. Moreover, bacterial communities showed significant correlations with various soil chemical indicators, whereas fungal communities exhibited correlations with only TP and pH. Therefore, the mixed C. lanceolata-broadleaf forest rely on their recruiting bacterial community to enhance and maintain the higher nutrient status of soil while the pure C. lanceolata forest rely on some specific fungi to satisfy their phosphorus requirement for survive strategy.
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Affiliation(s)
| | | | | | | | | | | | - Hongyue Chen
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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Li H, Zhang G. How can plant-enriched natural environments benefit human health: a narrative review of relevant theories. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024; 34:1241-1254. [PMID: 36697394 DOI: 10.1080/09603123.2023.2170990] [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: 01/02/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Plant-enriched environments, the most common terrestrial landscapes, are usually coded as "green space" in urban studies. To understand how these natural environments can benefit human health, many theories have been developed, such as the well-known Attention Restoration Theory. Nowadays, more theories are emerging with regard to various and complex health dimensions. In this context, we searched online databases (from 2000 to 2022) and conducted a narrative review aiming to introduce relevant theories concerning psychological (e.g. Perceptual Fluency Account and Conditioned Restoration Theory), physiological (e.g. volatile organic compounds and environmental microbiomes), and behavioural (e.g. physical activity and social contact) perspectives. We also slightly mentioned some limitations and directions to be considered when using these theories. These results may offer general readers insights into the value of nature exposure and also help relevant researchers with study design and result interpretation.
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Affiliation(s)
- Hansen Li
- Key Laboratory of Physical Fitness Evaluation and Motor Function Monitoring, Institute of Sports Science, College of Physical Education, Southwest University, Chongqing, China
| | - Guodong Zhang
- Key Laboratory of Physical Fitness Evaluation and Motor Function Monitoring, Institute of Sports Science, College of Physical Education, Southwest University, Chongqing, China
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4
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Hudson JE, Levia DF, Yoshimura KM, Gottel NR, Hudson SA, Biddle JF. Mapping bark bacteria: initial insights of stemflow-induced changes in bark surface phyla. Microbiol Spectr 2023; 11:e0356223. [PMID: 37971233 PMCID: PMC10715197 DOI: 10.1128/spectrum.03562-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Compared with the phyllosphere, bacteria inhabiting bark surfaces are inadequately understood. Based on a preliminary pilot study, our work suggests that microbial populations vary across tree bark surfaces and may differ in relation to surrounding land use. Initial results suggest that stemflow, the water that flows along the bark surface, actively moves bacterial communities across a tree. These preliminary findings underscore the need for further study of niche microbial populations to determine whether there are connections between the biodiversity of microbiomes inhabiting corticular surfaces, land use, and hydrology.
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Affiliation(s)
- J. E. Hudson
- Department of Geography and Spatial Sciences, University of Delaware, Newark, Delaware, USA
| | - D. F. Levia
- Department of Geography and Spatial Sciences, University of Delaware, Newark, Delaware, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
| | - K. M. Yoshimura
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
| | - N. R. Gottel
- Argonne National Lab, University of Chicago Medicine, Chicago, Illinois, USA
| | - S. A. Hudson
- Department of Geography and Spatial Sciences, University of Delaware, Newark, Delaware, USA
| | - J. F. Biddle
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
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5
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Onouye TC, Busse HJ, Prescott RD, Darris MK, Donachie SP. Chitinophaga pendula, sp. nov., from an air conditioner condensate drain line. Int J Syst Evol Microbiol 2023; 73. [PMID: 37578826 DOI: 10.1099/ijsem.0.006008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
A Gram-negative, rod-shaped and filamentous bacterium designated MD30BT was isolated from a biofilm hanging in water flowing from an air conditioner condensate drain line in Honolulu, Hawai'i. Based on 1517 nucleotides of the strain's 16S rRNA gene, its nearest neighbours are Chitinophaga rhizosphaerae T16R-86T (96.7 %), Chitinophaga caseinilytica S-52T (96.6 %), Chitinophaga lutea ZY74T (96.6 %), Chitinophaga niabensis JS13-10T (96.6 %) and Chitinophaga ginsengisoli Gsoil 052T (96.5 %). MD30BT cells are non-motile, strictly aerobic, and catalase and oxidase positive. Growth occurs between 10 and 45 °C. Major fatty acids in whole cells of MD30BT are 13-methyl tetradecanoic acid (34.1 %), cis-11-hexadecenoic acid (30.3 %), and 3-hydroxy, 15-methyl hexadecanoic acid (13.3 %). The quinone system contains predominantly menaquinone MK-7. The polar lipid profile contains the major lipids phosphatidylethanolamine, one unidentified lipid lacking a functional group, and two unidentified aminolipids. sym-Homospermidine is the major polyamine. The G+C content of the genome is 47.58 mol%. Based on phenotypic and genotypic differences between MD30BT and extant species in the Chitinophaga, we propose that MD30BT represents a new Chitinophaga species, for which the name Chitinophaga pendula sp. nov. is proposed to accommodate strain MD30BT as the type strain (DSM 112477T=NCTC 14606T).
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Affiliation(s)
- T Chiyoko Onouye
- School of Life Sciences, University of Hawai'i at Mānoa, 1800 East-West Road, Honolulu, Hawai'i 96822, USA
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Rebecca D Prescott
- School of Life Sciences, University of Hawai'i at Mānoa, 1800 East-West Road, Honolulu, Hawai'i 96822, USA
- Astromaterials Research and Exploration Science (ARES) Division, NASA Johnson SpaceCenter, 2101 E NASA Parkway, Houston, TX 77058, USA
| | - Maxwell K Darris
- School of Life Sciences, University of Hawai'i at Mānoa, 1800 East-West Road, Honolulu, Hawai'i 96822, USA
- University of Hawai'i, 200 W. Kāwili Street. Hilo, Hawai'i 96720, USA
| | - Stuart P Donachie
- School of Life Sciences, University of Hawai'i at Mānoa, 1800 East-West Road, Honolulu, Hawai'i 96822, USA
- Advanced Studies in Genomics, Proteomics, and Bioinformatics, University of Hawai'i at Mānoa, 1800 East-West Road, Honolulu, Hawai'i 96822, USA
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Mehl C, Schoeman MC, Sanko TJ, Bezuidenhout C, Mienie CMS, Preiser W, Vosloo D. Wastewater treatment works change the intestinal microbiomes of insectivorous bats. PLoS One 2021; 16:e0247475. [PMID: 33657147 PMCID: PMC7928523 DOI: 10.1371/journal.pone.0247475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022] Open
Abstract
Mammals, born with a near-sterile intestinal tract, are inoculated with their mothers’ microbiome during birth. Thereafter, extrinsic and intrinsic factors shape their intestinal microbe assemblage. Wastewater treatment works (WWTW), sites synonymous with pollutants and pathogens, receive influent from domestic, agricultural and industrial sources. The high nutrient content of wastewater supports abundant populations of chironomid midges (Diptera), which transfer these toxicants and potential pathogens to their predators, such as the banana bat Neoromicia nana (Vespertilionidae), thereby influencing their intestinal microbial assemblages. We used next generation sequencing and 16S rRNA gene profiling to identify and compare intestinal bacteria of N. nana at two reference sites and two WWTW sites. We describe the shared intestinal microbiome of the insectivorous bat, N. nana, consisting of seven phyla and eleven classes. Further, multivariate analyses revealed that location was the most significant driver (sex, body size and condition were not significant) of intestinal microbiome diversity. Bats at WWTW sites exhibited greater intestinal microbiota diversity than those at reference sites, likely due to wastewater exposure, stress and/or altered diet. Changes in their intestinal microbiota assemblages may allow these bats to cope with concomitant stressors.
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Affiliation(s)
- Calvin Mehl
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - M. Corrie Schoeman
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tomasz J. Sanko
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Carlos Bezuidenhout
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Charlotte M. S. Mienie
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg Hospital, Tygerberg, South Africa
| | - Dalene Vosloo
- Centre for Functional Biodiversity, School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
- * E-mail:
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Abstract
Microbiome research projects are often interdisciplinary, involving fields such as microbiology, genetics, ecology, evolution, bioinformatics, and statistics. These research projects can be an excellent fit for undergraduate courses ranging from introductory biology labs to upper-level capstone courses. Microbiome research projects can attract the interest of students majoring in health and medical sciences, environmental sciences, and agriculture, and there are meaningful ties to real-world issues relating to human health, climate change, and environmental sustainability and resilience in pristine, fragile ecosystems to bustling urban centers. In this review, we will discuss the potential of microbiome research integrated into classes using a number of different modalities. Our experience scaling-up and implementing microbiome projects at a range of institutions across the US has provided us with insight and strategies for what works well and how to diminish common hurdles that are encountered when implementing undergraduate microbiome research projects. We will discuss how course-based microbiome research can be leveraged to help faculty make advances in their own research and professional development and the resources that are available to support faculty interested in integrating microbiome research into their courses.
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Affiliation(s)
- Theodore R Muth
- Department of Biology, Brooklyn College of The City University of New York, Brooklyn, NY, United States.,Molecular, Cellular, and Developmental Biology Department at The Graduate Center of The City University of New York, New York, NY, United States
| | - Avrom J Caplan
- Department of Biology, Dyson College of Arts and Sciences, Pace University, New York, NY, United States
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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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9
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Espenshade J, Thijs S, Gawronski S, Bové H, Weyens N, Vangronsveld J. Influence of Urbanization on Epiphytic Bacterial Communities of the Platanus × hispanica Tree Leaves in a Biennial Study. Front Microbiol 2019; 10:675. [PMID: 31024477 PMCID: PMC6460055 DOI: 10.3389/fmicb.2019.00675] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/18/2019] [Indexed: 12/20/2022] Open
Abstract
The aerial surfaces of plants harbor diverse communities of microorganisms. The rising awareness concerning the potential roles of these phyllosphere microbiota for airborne pollutant remediation and plant growth promotion, advocates for a better understanding of their community structure and dynamics in urban ecosystems. Here, we characterized the epiphytic microbial communities on leaves of Platanus × hispanica trees in the city centre of Hasselt (Belgium), and the nearby forest area of Bokrijk, Genk (Belgium). We compared the influences of season, site, and air pollutants concentration variations on the tree's phyllosphere microbiome by determining the intra- and inter-individual variation in leaf bacterial communities. High-throughput amplicon sequencing of the 16S rRNA gene revealed large variation in the bacterial community structure and diversity throughout the years but also allowed to discriminate an environment effect on community assembly. Partial drivers for this environment effect on composition can be correlated with the huge differences in ultrafine particulate matter (UFP) and black carbon on the leaves. A change in bacterial community composition was noted for trees growing in the city center compared to the natural site, and also more human-associated genera were found colonizing the leaves from the city center. These integrated results offer an original and first insight in the Platanus phyllomicrobiota, which can offer new opportunities to use phyllosphere microorganisms to enhance air pollution degradation.
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Affiliation(s)
- Jordan Espenshade
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Sofie Thijs
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Stanislaw Gawronski
- Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Hannelore Bové
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
- Centre for Surface Chemistry and Catalysis, KU Leuven, Leuven, Belgium
| | - Nele Weyens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- Department of Plant Physiology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Lublin, Poland
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Gerner SM, Rattei T, Graf AB. Assessment of urban microbiome assemblies with the help of targeted in silico gold standards. Biol Direct 2018; 13:22. [PMID: 30621760 PMCID: PMC6889603 DOI: 10.1186/s13062-018-0225-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/25/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metagenome samples. The only in silico approach that allows us to find unknown species, is the assembly and classification of draft genomes from a metagenomic dataset. In this study we (1) investigate the applicability of an assembly and binning approach for urban metagenome datasets, and (2) develop a new method for the generation of in silico gold standards to better understand the specific challenges of such datasets and provide a guide in the selection of available software. RESULTS We applied combinations of three assembly (Megahit, SPAdes and MetaSPAdes) and three binning tools (MaxBin, MetaBAT and CONCOCT) to whole genome shotgun datasets from the CAMDA 2017 Challenge. Complex in silico gold standards with a simulated bacterial fraction were generated for representative samples of each surface type and city. Using these gold standards, we found the combination of SPAdes and MetaBAT to be optimal for urban metagenome datasets by providing the best trade-off between the number of high-quality genome draft bins (MIMAG standards) retrieved, the least amount of misassemblies and contamination. The assembled draft genomes included known species like Propionibacterium acnes but also novel species according to respective ANI values. CONCLUSIONS In our work, we showed that, even for datasets with high diversity and low sequencing depth from urban environments, assembly and binning-based methods can provide high-quality genome drafts. Of vital importance to retrieve high-quality genome drafts is sequence depth but even more so a high proportion of the bacterial sequence fraction too achieve high coverage for bacterial genomes. In contrast to read-based methods relying on database knowledge, genome-centric methods as applied in this study can provide valuable information about unknown species and strains as well as functional contributions of single community members within a sample. Furthermore, we present a method for the generation of sample-specific highly complex in silico gold standards. REVIEWERS This article was reviewed by Craig Herbold, Serghei Mangul and Yana Bromberg.
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Affiliation(s)
- Samuel M. Gerner
- Department Bioengineering, University of Applied Sciences FH Campus Wien, Vienna, Austria
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Alexandra B. Graf
- Department Bioengineering, University of Applied Sciences FH Campus Wien, Vienna, Austria
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Jani K, Dhotre D, Bandal J, Shouche Y, Suryavanshi M, Rale V, Sharma A. World's Largest Mass Bathing Event Influences the Bacterial Communities of Godavari, a Holy River of India. MICROBIAL ECOLOGY 2018. [PMID: 29536131 DOI: 10.1007/s00248-018-1169-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Kumbh Mela is one of the largest religious mass gathering events (MGE) involving bathing in rivers. The exponential rise in the number of devotees, from around 0.4 million in 1903 to 120 million in 2013, bathing in small specified sites can have a dramatic impact on the river ecosystem. Here, we present the spatiotemporal profiling of bacterial communities in Godavari River, Nashik, India, comprising five sites during the Kumbh Mela, held in 2015. Assessment of environmental parameters indicated deterioration of water quality. Targeted amplicon sequencing demonstrates approximately 37.5% loss in microbial diversity because of anthropogenic activity during MGE. A significant decrease in phyla viz. Actinobacteria, Chloroflexi, Proteobacteria, and Bacteroidetes was observed, while we noted substantial increase in prevalence of the phylum Firmicutes (94.6%) during MGE. qPCR estimations suggested nearly 130-fold increase in bacterial load during the event. Bayesian mixing model accounted the source of enormous incorporation of bacterial load of human origin. Further, metagenomic imputations depicted increase in virulence and antibiotic resistance genes during the MGE. These observations suggest the striking impact of the mass bathing on river ecosystem. The subsequent increase in infectious diseases and drug-resistant microbes pose a critical public health concern.
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Affiliation(s)
- Kunal Jani
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
- Symbiosis School of Biological Sciences, Symbiosis International University, Pune, 412115, India
| | - Dhiraj Dhotre
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Jayashree Bandal
- Department of Microbiology, KTHM College, Nashik, Maharashtra, 422002, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Mangesh Suryavanshi
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India
| | - Vinay Rale
- Symbiosis School of Biological Sciences, Symbiosis International University, Pune, 412115, India
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Sutarwadi, Pashan, Pune, Maharashtra, 411021, India.
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12
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Zolfo M, Asnicar F, Manghi P, Pasolli E, Tett A, Segata N. Profiling microbial strains in urban environments using metagenomic sequencing data. Biol Direct 2018; 13:9. [PMID: 29743119 PMCID: PMC5944035 DOI: 10.1186/s13062-018-0211-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 04/26/2018] [Indexed: 11/10/2022] Open
Abstract
Background The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context. It is thus currently unclear whether such methods, that have proven successful at distinguishing even closely related strains in human microbiomes, are also effective in urban settings for tasks such as cultivation-free pathogen detection and microbial surveillance. Here, we aimed at a) testing the currently available metagenomic profiling tools on urban metagenomics; b) characterizing the organisms in urban environment at the resolution of single strain and c) discussing the biological insights that can be inferred from such methods. Results We applied three complementary methods on the 1614 metagenomes of the CAMDA 2017 challenge. With MetaMLST we identified 121 known sequence-types from 15 species of clinical relevance. For instance, we identified several Acinetobacter strains that were close to the nosocomial opportunistic pathogen A. nosocomialis. With StrainPhlAn, a generalized version of the MetaMLST approach, we inferred the phylogenetic structure of Pseudomonas stutzeri strains and suggested that the strain-level heterogeneity in environmental samples is higher than in the human microbiome. Finally, we also probed the functional potential of the different strains with PanPhlAn. We further showed that SNV-based and pangenome-based profiling provide complementary information that can be combined to investigate the evolutionary trajectories of microbes and to identify specific genetic determinants of virulence and antibiotic resistances within closely related strains. Conclusion We show that strain-level methods developed primarily for the analysis of human microbiomes can be effective for city-associated microbiomes. In fact, (opportunistic) pathogens can be tracked and monitored across many hundreds of urban metagenomes. However, while more effort is needed to profile strains of currently uncharacterized species, this work poses the basis for high-resolution analyses of microbiomes sampled in city and mass transportation environments. Reviewers This article was reviewed by Alexandra Bettina Graf, Daniel Huson and Trevor Cickovski. Electronic supplementary material The online version of this article (10.1186/s13062-018-0211-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Moreno Zolfo
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, TN, Italy
| | - Francesco Asnicar
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, TN, Italy
| | - Paolo Manghi
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, TN, Italy
| | - Edoardo Pasolli
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, TN, Italy
| | - Adrian Tett
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, TN, Italy
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, TN, Italy.
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Wang H, Cheng M, Dsouza M, Weisenhorn P, Zheng T, Gilbert JA. Soil Bacterial Diversity Is Associated with Human Population Density in Urban Greenspaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5115-5124. [PMID: 29624051 DOI: 10.1021/acs.est.7b06417] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Urban greenspaces provide extensive ecosystem services, including pollutant remediation, water management, carbon maintenance, and nutrient cycling. However, while the urban soil microbiota underpin these services, we still have limited understanding of the factors that influence their distribution. We characterized soil bacterial communities from turf-grasses associated with urban parks, streets, and residential sites across a major urban environment, including a gradient of human population density. Bacterial diversity was significantly positively correlated with the population density; and species diversity was greater in park and street soils, compared to residential soils. Population density and greenspace type also led to significant differences in the microbial community composition that was also significantly correlated with soil pH, moisture, and texture. Co-occurrence network analysis revealed that microbial guilds in urban soils were well correlated. Abundant soil microbes in high density population areas had fewer interactions, while abundant bacteria in high moisture soils had more interactions. These results indicate the significant influence of changes in urban demographics and land-use on soil microbial communities. As urbanization is rapidly growing across the planet, it is important to improve our understanding of the consequences of urban zoning on the soil microbiota.
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Affiliation(s)
- Haitao Wang
- The Microbiome Center, Department of Surgery , University of Chicago , Chicago , Illinois 60637 , United States
- School of Life Sciences , Xiamen University , Xiamen , Fujian Province 361102 , China
| | - Minying Cheng
- School of Architecture , South China University of Technology , Guangzhou , Guangdong Province 510641 , China
| | - Melissa Dsouza
- The Microbiome Center, Department of Surgery , University of Chicago , Chicago , Illinois 60637 , United States
- The Marine Biological Laboratory , Woods Hole , Massachusetts 02543 , United States
| | - Pamela Weisenhorn
- The Microbiome Center, Department of Surgery , University of Chicago , Chicago , Illinois 60637 , United States
- The Microbiome Center , Argonne National Laboratory , Lemont , Illinois 60439 , United States
| | - Tianling Zheng
- School of Life Sciences , Xiamen University , Xiamen , Fujian Province 361102 , China
| | - Jack A Gilbert
- The Microbiome Center, Department of Surgery , University of Chicago , Chicago , Illinois 60637 , United States
- The Marine Biological Laboratory , Woods Hole , Massachusetts 02543 , United States
- The Microbiome Center , Argonne National Laboratory , Lemont , Illinois 60439 , United States
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Hamdy AM, El-massry M, Kashef MT, Amin MA, Aziz RK. Toward the Drug Factory Microbiome: Microbial Community Variations in Antibiotic-Producing Clean Rooms. ACTA ACUST UNITED AC 2018; 22:133-144. [DOI: 10.1089/omi.2017.0091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Amal M. Hamdy
- Misr Company for Pharmaceutical Industries, Cairo, Egypt
| | - Moamen El-massry
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas
| | - Mona T. Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Magdy A. Amin
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ramy K. Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Tree Leaf Bacterial Community Structure and Diversity Differ along a Gradient of Urban Intensity. mSystems 2017; 2:mSystems00087-17. [PMID: 29238751 PMCID: PMC5715107 DOI: 10.1128/msystems.00087-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/14/2017] [Indexed: 02/01/2023] Open
Abstract
In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome. In this study, we aimed (i) to characterize phyllosphere bacterial communities of seven tree species in urban environments and (ii) to describe the changes in tree phyllosphere bacterial community structure and diversity along a gradient of increasing urban intensity and at two degrees of tree isolation. Our results indicate that, as anthropogenic pressures increase, urban leaf bacterial communities show a reduction in the abundance of the dominant class in the natural plant microbiome, the Alphaproteobacteria. Our work in the urban environment here reveals that the structures of leaf bacterial communities differ along the gradient of urban intensity. The diversity of phyllosphere microbial communities increases at higher urban intensity, also displaying a greater number and variety of associated indicator taxa than the low and medium urban gradient sites. In conclusion, we find that urban environments influence tree bacterial community composition, and our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes. IMPORTANCE In natural forests, tree leaf surfaces host diverse bacterial communities whose structure and composition are primarily driven by host species identity. Tree leaf bacterial diversity has also been shown to influence tree community productivity, a key function of terrestrial ecosystems. However, most urban microbiome studies have focused on the built environment, improving our understanding of indoor microbial communities but leaving much to be understood, especially in the nonbuilt microbiome. Here, we provide the first multiple-species comparison of tree phyllosphere bacterial structures and diversity along a gradient of urban intensity. We demonstrate that urban trees possess characteristic bacterial communities that differ from those seen with trees in nonurban environments, with microbial community structure on trees influenced by host species identity but also by the gradient of urban intensity and by the degree of isolation from other trees. Our results suggest that feedback between human activity and plant microbiomes could shape urban microbiomes.
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Gu Y, Wang Y, Lu S, Xiang Q, Yu X, Zhao K, Zou L, Chen Q, Tu S, Zhang X. Long-term Fertilization Structures Bacterial and Archaeal Communities along Soil Depth Gradient in a Paddy Soil. Front Microbiol 2017; 8:1516. [PMID: 28861048 PMCID: PMC5559540 DOI: 10.3389/fmicb.2017.01516] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/27/2017] [Indexed: 01/23/2023] Open
Abstract
Soil microbes provide important ecosystem services. Though the effects of changes in nutrient availability due to fertilization on the soil microbial communities in the topsoil (tilled layer, 0–20 cm) have been extensively explored, the effects on communities and their associations with soil nutrients in the subsoil (below 20 cm) which is rarely impacted by tillage are still unclear. 16S rRNA gene amplicon sequencing was used to investigate bacterial and archaeal communities in a Pup-Calric-Entisol soil treated for 32 years with chemical fertilizer (CF) and CF combined with farmyard manure (CFM), and to reveal links between soil properties and specific bacterial and archaeal taxa in both the top- and subsoil. The results showed that both CF and CFM treatments increased soil organic carbon (SOC), soil moisture (MO) and total nitrogen (TN) while decreased the nitrate_N content through the profile. Fertilizer applications also increased Olsen phosphorus (OP) content in most soil layers. Microbial communities in the topsoil were significantly different from those in subsoil. Compared to the CF treatment, taxa such as Nitrososphaera, Nitrospira, and several members of Acidobacteria in topsoil and Subdivision 3 genera incertae sedis, Leptolinea, and Bellilinea in subsoil were substantially more abundant in CFM. A co-occurrence based network analysis demonstrated that SOC and OP were the most important soil parameters that positively correlated with specific bacterial and archaeal taxa in topsoil and subsoil, respectively. Hydrogenophaga was identified as the keystone genus in the topsoil, while genera Phenylobacterium and Steroidobacter were identified as the keystone taxa in subsoil. The taxa identified above are involved in the decomposition of complex organic compounds and soil carbon, nitrogen, and phosphorus transformations. This study revealed that the spatial variability of soil properties due to long-term fertilization strongly shapes the bacterial and archaeal community composition and their interactions at both high and low taxonomic levels across the whole soil profile.
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Affiliation(s)
- Yunfu Gu
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Yingyan Wang
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Sheng'e Lu
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Quanju Xiang
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Xiumei Yu
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Likou Zou
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
| | - Shihua Tu
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural SciencesChengdu, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resource Science and Technology, Sichuan Agricultural UniversityChengdu, China
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Be NA, Avila-Herrera A, Allen JE, Singh N, Checinska Sielaff A, Jaing C, Venkateswaran K. Whole metagenome profiles of particulates collected from the International Space Station. MICROBIOME 2017; 5:81. [PMID: 28716113 PMCID: PMC5514531 DOI: 10.1186/s40168-017-0292-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/27/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND The built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized. METHODS This study examined the whole metagenome of ISS microbes at both species- and gene-level resolution. Air filter and dust samples from the ISS were analyzed and compared to samples collected in a terrestrial cleanroom environment. Furthermore, metagenome mining was carried out to characterize dominant, virulent, and novel microorganisms. The whole genome sequences of select cultivable strains isolated from these samples were extracted from the metagenome and compared. RESULTS Species-level composition in the ISS was found to be largely dominated by Corynebacterium ihumii GD7, with overall microbial diversity being lower in the ISS relative to the cleanroom samples. When examining detection of microbial genes relevant to human health such as antimicrobial resistance and virulence genes, it was found that a larger number of relevant gene categories were observed in the ISS relative to the cleanroom. Strain-level cross-sample comparisons were made for Corynebacterium, Bacillus, and Aspergillus showing possible distinctions in the dominant strain between samples. CONCLUSION Species-level analyses demonstrated distinct differences between the ISS and cleanroom samples, indicating that the cleanroom population is not necessarily reflective of space habitation environments. The overall population of viable microorganisms and the functional diversity inherent to this unique closed environment are of critical interest with respect to future space habitation. Observations and studies such as these will be important to evaluating the conditions required for long-term health of human occupants in such environments.
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Affiliation(s)
- Nicholas A Be
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Aram Avila-Herrera
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jonathan E Allen
- Computation Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Nitin Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Aleksandra Checinska Sielaff
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
- Present Address: Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Crystal Jaing
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA.
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Patients as Patches: Ecology and Epidemiology in Healthcare Environments. Infect Control Hosp Epidemiol 2016; 37:1507-1512. [PMID: 27760571 DOI: 10.1017/ice.2016.224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The modern healthcare system involves complex interactions among microbes, patients, providers, and the built environment. It represents a unique and challenging setting for control of the emergence and spread of infectious diseases. We examine an extension of the perspectives and methods from ecology (and especially urban ecology) to address these unique issues, and we outline 3 examples: (1) viewing patients as individual microbial ecosystems; (2) the altered ecology of infectious diseases specifically within hospitals; and (3) ecosystem management perspectives for infection surveillance and control. In each of these cases, we explore the accuracy and relevance of analogies to existing urban ecological perspectives, and we demonstrate a few of the potential direct uses of this perspective for altering research into the control of healthcare-associated infections. Infect Control Hosp Epidemiol. 2016;1507-1512.
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Abstract
Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors--miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors.
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Affiliation(s)
- Yaniv Erlich
- Department of Computer Science, Columbia University, New York, New York 10027, USA; New York Genome Center, New York, New York 10013, USA
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Newton RJ, McLellan SL. A unique assemblage of cosmopolitan freshwater bacteria and higher community diversity differentiate an urbanized estuary from oligotrophic Lake Michigan. Front Microbiol 2015; 6:1028. [PMID: 26483766 PMCID: PMC4586452 DOI: 10.3389/fmicb.2015.01028] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/10/2015] [Indexed: 12/31/2022] Open
Abstract
Water quality is impacted significantly by urbanization. The delivery of increased nutrient loads to waterways is a primary characteristic of this land use change. Despite the recognized effects of nutrient loading on aquatic systems, the influence of urbanization on the bacterial community composition of these systems is not understood. We used massively-parallel sequencing of bacterial 16S rRNA genes to examine the bacterial assemblages in transect samples spanning the heavily urbanized estuary of Milwaukee, WI to the relatively un-impacted waters of Lake Michigan. With this approach, we found that genera and lineages common to freshwater lake epilimnia were common and abundant in both the high nutrient, urban-impacted waterways, and the low nutrient Lake Michigan. Although the two environments harbored many taxa in common, we identified a significant change in the community assemblage across the urban-influence gradient, and three distinct community features drove this change. First, we found the urban-influenced waterways harbored significantly greater bacterial richness and diversity than Lake Michigan (i.e., taxa augmentation). Second, we identified a shift in the relative abundance among common freshwater lineages, where acI, acTH1, Algoriphagus and LD12, had decreased representation and Limnohabitans, Polynucleobacter, and Rhodobacter had increased representation in the urban estuary. Third, by oligotyping 18 common freshwater genera/lineages, we found that oligotypes (highly resolved sequence clusters) within many of these genera/lineages had opposite preferences for the two environments. With these data, we suggest many of the defined cosmopolitan freshwater genera/lineages contain both oligotroph and more copiotroph species or populations, promoting the idea that within-genus lifestyle specialization, in addition to shifts in the dominance among core taxa and taxa augmentation, drive bacterial community change in urbanized waters.
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Affiliation(s)
- Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee, WI, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee Milwaukee, WI, USA
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Fisher JC, Newton RJ, Dila DK, McLellan SL. Urban microbial ecology of a freshwater estuary of Lake Michigan. ELEMENTA (WASHINGTON, D.C.) 2015; 3:000064. [PMID: 26866046 PMCID: PMC4746012 DOI: 10.12952/journal.elementa.000064] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an "urban microbial signature," and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas, and Pseudomonas, which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with potential long term impacts on the function of estuarine and nearshore ecosystems.
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Affiliation(s)
- Jenny C. Fisher
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
| | - Ryan J. Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
| | - Deborah K. Dila
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
| | - Sandra L. McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States
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