401
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Indoor-air microbiome in an urban subway network: diversity and dynamics. Appl Environ Microbiol 2014; 80:6760-70. [PMID: 25172855 DOI: 10.1128/aem.02244-14] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Subway systems are indispensable for urban societies, but microbiological characteristics of subway aerosols are relatively unknown. Previous studies investigating microbial compositions in subways employed methodologies that underestimated the diversity of microbial exposure for commuters, with little focus on factors governing subway air microbiology, which may have public health implications. Here, a culture-independent approach unraveling the bacterial diversity within the urban subway network in Hong Kong is presented. Aerosol samples from multiple subway lines and outdoor locations were collected. Targeting the 16S rRNA gene V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those associated with skin. Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. Microbial diversities and assemblages also varied depending on the day sampled, as well as the time of day, and changes in microbial communities between peak and nonpeak commuting hours were attributed largely to increases in skin-associated genera in peak samples. Microbial diversities within the subway were influenced by temperature and relative humidity, while carbon dioxide levels showed a positive correlation with abundances of commuter-associated genera. This Hong Kong data set and communities from previous studies conducted in the United States formed distinct community clusters, indicating that additional work is required to unravel the mechanisms that shape subway microbiomes around the globe.
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402
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Sharpe RA, Bearman N, Thornton CR, Husk K, Osborne NJ. Indoor fungal diversity and asthma: a meta-analysis and systematic review of risk factors. J Allergy Clin Immunol 2014; 135:110-22. [PMID: 25159468 DOI: 10.1016/j.jaci.2014.07.002] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 06/06/2014] [Accepted: 07/01/2014] [Indexed: 11/30/2022]
Abstract
BACKGROUND Indoor dampness increases the risk of indoor fungal growth. A complex interaction between occupant behaviors and the built environment are thought to affect indoor fungal concentrations and species diversity, which are believed to increase the risk of having asthma, exacerbation of asthma symptoms, or both. To date, no systematic review has investigated this relationship. OBJECTIVE This review aims to assess the relationship between exposure to indoor fungi identified to the genera or species level on asthma outcomes in children and adults. METHODS Ten databases were systematically searched on April 18, 2013, and limited to articles published since 1990. Reference lists were independently screened by 2 reviewers, and authors were contacted to identify relevant articles. Data were extracted from included studies meeting our eligibility criteria by 2 reviewers and quality assessed by using the Newcastle-Ottawa scale designed for assessment of case-control and cohort studies. RESULTS Cladosporium, Alternaria, Aspergillus, and Penicillium species were found to be present in higher concentrations in homes of asthmatic participants. Exposure to Penicillium, Aspergillus, and Cladosporium species were found to be associated with increased risk of reporting asthma symptoms by a limited number of studies. The presence of Cladosporium, Alternaria, Aspergillus, and Penicillium species increased the exacerbation of current asthma symptoms by 36% to 48% compared with those exposed to lower concentrations of these fungi, as shown by using random-effect estimates. Studies were of medium quality and showed medium-high heterogeneity, but evidence concerning the specific role of fungal species was limited. CONCLUSION Longitudinal studies assessing increased exposure to indoor fungi before the development of asthma symptoms suggests that Penicillium, Aspergillus, and Cladosporium species pose a respiratory health risk in susceptible populations. Increased exacerbation of current asthma symptoms in children and adults were associated with increased levels of Penicillium, Aspergillus, Cladosporium, and Alternaria species, although further work should consider the role of fungal diversity and increased exposure to other fungal species.
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Affiliation(s)
- Richard A Sharpe
- European Centre for Environment and Human Health, University of Exeter Medical School, Truro, United Kingdom
| | - Nick Bearman
- European Centre for Environment and Human Health, University of Exeter Medical School, Truro, United Kingdom; Department of Geography and Planning, University of Liverpool, Liverpool, United Kingdom
| | - Christopher R Thornton
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Kerryn Husk
- European Centre for Environment and Human Health, University of Exeter Medical School, Truro, United Kingdom
| | - Nicholas J Osborne
- European Centre for Environment and Human Health, University of Exeter Medical School, Truro, United Kingdom; Department of Paediatrics, University of Melbourne, Melbourne, Australia.
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403
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Dannemiller KC, Mendell MJ, Macher JM, Kumagai K, Bradman A, Holland N, Harley K, Eskenazi B, Peccia J. Next-generation DNA sequencing reveals that low fungal diversity in house dust is associated with childhood asthma development. INDOOR AIR 2014; 24:236-47. [PMID: 24883433 PMCID: PMC4048861 DOI: 10.1111/ina.12072] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
UNLABELLED Dampness and visible mold in homes are associated with asthma development, but causal mechanisms remain unclear. The goal of this research was to explore associations among measured dampness, fungal exposure, and childhood asthma development without the bias of culture-based microbial analysis. In the low-income, Latino CHAMACOS birth cohort, house dust was collected at age 12 months, and asthma status was determined at age 7 years.The current analysis included 13 asthma cases and 28 controls. Next-generation DNA sequencing methods quantified fungal taxa and diversity. Lower fungal diversity (number of fungal operational taxonomic units) was significantly associated with increased risk of asthma development: unadjusted odds ratio(OR) 4.80 (95% confidence interval (CI) 1.04–22.1). Control for potential confounders strengthened this relationship. Decreased diversity within the genus Cryptococcus was significantly associated with increased asthma risk (OR 21.0, 95% CI 2.16–204). No fungal taxon (species, genus, class) was significantly positively associated with asthma development, and one was significantly negatively associated. Elevated moisture was associated with increased fungal diversity, and moisture/mold indicators were associated with four fungal taxa. Next-generation DNA sequencing provided comprehensive estimates of fungal identity and diversity, demonstrating significant associations between low fungal diversity and childhood asthma development in this community. PRACTICAL IMPLICATIONS Early life exposure to low fungal diversity in house dust was associated with increased risk for later asthma developmen tin this low-income, immigrant community. No individual fungal taxon (species, genus, or class) was associated with asthma development, although exposure to low diversity within the genus Cryptococcus was associated with asthma development. Future asthma development studies should incorporate fungal diversity measurements, in addition to measuring individual fungal taxa. These results represent a step toward identifying the aspect(s) of indoor microbial populations that are associated with asthma development and suggest that understanding the factors that control diversity in the indoor environment may lead to public health recommendations for asthma prevention in the future.
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Affiliation(s)
- Karen C. Dannemiller
- Department of Chemical and Environmental Engineering, Yale University, 9 Hillhouse Ave, PO Box 208286, New Haven, CT 06520, USA
| | - Mark J. Mendell
- Indoor Air Quality Section, Environmental Health Laboratory Branch, 850 Marina Bay Parkway, MS G365/EHLB, California Department of Public Health, Richmond, CA 94804, USA
| | - Janet M. Macher
- Indoor Air Quality Section, Environmental Health Laboratory Branch, 850 Marina Bay Parkway, MS G365/EHLB, California Department of Public Health, Richmond, CA 94804, USA
| | - Kazukiyo Kumagai
- Indoor Air Quality Section, Environmental Health Laboratory Branch, 850 Marina Bay Parkway, MS G365/EHLB, California Department of Public Health, Richmond, CA 94804, USA
| | - Asa Bradman
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, UC Berkeley, 1995 University Ave., Suite 265, Berkeley, CA 94720, USA
| | - Nina Holland
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, UC Berkeley, 1995 University Ave., Suite 265, Berkeley, CA 94720, USA
| | - Kim Harley
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, UC Berkeley, 1995 University Ave., Suite 265, Berkeley, CA 94720, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Children’s Health (CERCH), School of Public Health, UC Berkeley, 1995 University Ave., Suite 265, Berkeley, CA 94720, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, 9 Hillhouse Ave, PO Box 208286, New Haven, CT 06520, USA
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404
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Indoor-biofilter growth and exposure to airborne chemicals drive similar changes in plant root bacterial communities. Appl Environ Microbiol 2014; 80:4805-13. [PMID: 24878602 DOI: 10.1128/aem.00595-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Due to the long durations spent inside by many humans, indoor air quality has become a growing concern. Biofiltration has emerged as a potential mechanism to clean indoor air of harmful volatile organic compounds (VOCs), which are typically found at concentrations higher indoors than outdoors. Root-associated microbes are thought to drive the functioning of plant-based biofilters, or biowalls, converting VOCs into biomass, energy, and carbon dioxide, but little is known about the root microbial communities of such artificially grown plants, how or whether they differ from those of plants grown in soil, and whether any changes in composition are driven by VOCs. In this study, we investigated how bacterial communities on biofilter plant roots change over time and in response to VOC exposure. Through 16S rRNA amplicon sequencing, we compared root bacterial communities from soil-grown plants with those from two biowalls, while also comparing communities from roots exposed to clean versus VOC-laden air in a laboratory biofiltration system. The results showed differences in bacterial communities between soil-grown and biowall-grown plants and between bacterial communities from plant roots exposed to clean air and those from VOC-exposed plant roots. Both biowall-grown and VOC-exposed roots harbored enriched levels of bacteria from the genus Hyphomicrobium. Given their known capacities to break down aromatic and halogenated compounds, we hypothesize that these bacteria are important VOC degraders. While different strains of Hyphomicrobium proliferated in the two studied biowalls and our lab experiment, strains were shared across plant species, suggesting that a wide range of ornamental houseplants harbor similar microbes of potential use in living biofilters.
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405
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406
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Adams RI, Miletto M, Lindow SE, Taylor JW, Bruns TD. Airborne bacterial communities in residences: similarities and differences with fungi. PLoS One 2014; 9:e91283. [PMID: 24603548 PMCID: PMC3946336 DOI: 10.1371/journal.pone.0091283] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 02/08/2014] [Indexed: 01/31/2023] Open
Abstract
Genetic analysis of indoor air has uncovered a rich microbial presence, but rarely have both the bacterial and fungal components been examined in the same samples. Here we present a study that examined the bacterial component of passively settled microbes from both indoor and outdoor air over a discrete time period and for which the fungal component has already been reported. Dust was allowed to passively settle in five common locations around a home − living room, bedroom, bathroom, kitchen, and balcony − at different dwellings within a university-housing complex for a one-month period at two time points, once in summer and again in winter. We amplified the bacterial 16S rRNA gene in these samples and analyzed them with high-throughput sequencing. Like fungal OTU-richness, bacterial OTU-richness was higher outdoors then indoors and was invariant across different indoor room types. While fungal composition was structured largely by season and residential unit, bacterial composition varied by residential unit and room type. Bacteria from putative outdoor sources, such as Sphingomonas and Deinococcus, comprised a large percentage of the balcony samples, while human-associated taxa comprised a large percentage of the indoor samples. Abundant outdoor bacterial taxa were also observed indoors, but the reverse was not true; this is unlike fungi, in which the taxa abundant indoors were also well-represented outdoors. Moreover, there was a partial association of bacterial composition and geographic distance, such that samples separated by even a few hundred meters tended have greater compositional differences than samples closer together in space, a pattern also observed for fungi. These data show that while the outdoor source for indoor bacteria and fungi varies in both space and time, humans provide a strong and homogenizing effect on indoor bacterial bioaerosols, a pattern not observed in fungi.
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Affiliation(s)
- Rachel I. Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, California, United States of America
- * E-mail:
| | - Marzia Miletto
- Department of Plant & Microbial Biology, University of California, Berkeley, California, United States of America
| | - Steven E. Lindow
- Department of Plant & Microbial Biology, University of California, Berkeley, California, United States of America
| | - John W. Taylor
- Department of Plant & Microbial Biology, University of California, Berkeley, California, United States of America
| | - Thomas D. Bruns
- Department of Plant & Microbial Biology, University of California, Berkeley, California, United States of America
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407
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Yamamoto N, Bibby K. Clustering of fungal community internal transcribed spacer sequence data obscures taxonomic diversity. Environ Microbiol 2014; 16:2491-500. [DOI: 10.1111/1462-2920.12390] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/23/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Naomichi Yamamoto
- Department of Environmental Health; Seoul National University; Seoul Korea
| | - Kyle Bibby
- Department of Civil and Environmental Engineering; University of Pittsburgh; Pittsburgh PA USA
- Department of Computational and Systems Biology; University of Pittsburgh Medical School; Pittsburgh PA USA
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408
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Kembel SW, Meadow JF, O’Connor TK, Mhuireach G, Northcutt D, Kline J, Moriyama M, Brown GZ, Bohannan BJM, Green JL. Architectural design drives the biogeography of indoor bacterial communities. PLoS One 2014; 9:e87093. [PMID: 24489843 PMCID: PMC3906134 DOI: 10.1371/journal.pone.0087093] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/18/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined microbiological data with information on the function, form, and organization of spaces from a classroom and office building to understand how design choices influence the biogeography of the built environment microbiome. RESULTS Sequencing of the bacterial 16S gene from dust samples revealed that indoor bacterial communities were extremely diverse, containing more than 32,750 OTUs (operational taxonomic units, 97% sequence similarity cutoff), but most communities were dominated by Proteobacteria, Firmicutes, and Deinococci. Architectural design characteristics related to space type, building arrangement, human use and movement, and ventilation source had a large influence on the structure of bacterial communities. Restrooms contained bacterial communities that were highly distinct from all other rooms, and spaces with high human occupant diversity and a high degree of connectedness to other spaces via ventilation or human movement contained a distinct set of bacterial taxa when compared to spaces with low occupant diversity and low connectedness. Within offices, the source of ventilation air had the greatest effect on bacterial community structure. CONCLUSIONS Our study indicates that humans have a guiding impact on the microbial biodiversity in buildings, both indirectly through the effects of architectural design on microbial community structure, and more directly through the effects of human occupancy and use patterns on the microbes found in different spaces and space types. The impact of design decisions in structuring the indoor microbiome offers the possibility to use ecological knowledge to shape our buildings in a way that will select for an indoor microbiome that promotes our health and well-being.
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Affiliation(s)
- Steven W. Kembel
- Département des sciences biologiques, Université du Québec à Montréal, Montréal, Québec, Canada
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - James F. Meadow
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- * E-mail:
| | - Timothy K. O’Connor
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Gwynne Mhuireach
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
- Energy Studies in Buildings Laboratory, University of Oregon, Eugene, Oregon, United States of America
| | - Dale Northcutt
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
- Energy Studies in Buildings Laboratory, University of Oregon, Eugene, Oregon, United States of America
| | - Jeff Kline
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
- Energy Studies in Buildings Laboratory, University of Oregon, Eugene, Oregon, United States of America
| | - Maxwell Moriyama
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
- Energy Studies in Buildings Laboratory, University of Oregon, Eugene, Oregon, United States of America
| | - G. Z. Brown
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
- Energy Studies in Buildings Laboratory, University of Oregon, Eugene, Oregon, United States of America
- Department of Architecture, University of Oregon, Eugene, Oregon, United States of America
| | - Brendan J. M. Bohannan
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Jessica L. Green
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, United States of America
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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409
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Bokulich NA, Thorngate JH, Richardson PM, Mills DA. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. Proc Natl Acad Sci U S A 2014; 111:E139-48. [PMID: 24277822 PMCID: PMC3890796 DOI: 10.1073/pnas.1317377110] [Citation(s) in RCA: 535] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.
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Affiliation(s)
- Nicholas A. Bokulich
- Departments of aViticulture and Enology and
- bFood Science and Technology, and
- cFoods for Health Institute, University of California, Davis, CA 95616
| | | | | | - David A. Mills
- Departments of aViticulture and Enology and
- bFood Science and Technology, and
- cFoods for Health Institute, University of California, Davis, CA 95616
- 1To whom correspondence should be addressed. E-mail:
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410
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Rittenour WR, Ciaccio CE, Barnes CS, Kashon ML, Lemons AR, Beezhold DH, Green BJ. Internal transcribed spacer rRNA gene sequencing analysis of fungal diversity in Kansas City indoor environments. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2014; 16:33-43. [PMID: 24258337 PMCID: PMC3966654 DOI: 10.1039/c3em00441d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Compared to traditional methods of fungal exposure assessment, molecular methods have provided new insight into the richness of fungal communities present in both indoor and outdoor environments. In this study, we describe the diversity of fungi in the homes of asthmatic children located in Kansas City. Fungal diversity was determined by sequencing the internal transcribed spacer (ITS) regions of ribosomal RNA derived from fungi collected in air and dust samples from 31 homes participating in the Kansas City Safe and Healthy Homes Program (KCSHHP). Sequencing results were then compared to data obtained using viable and non-viable fungal exposure assessment methods. ITS clone libraries were predominantly derived from the phylum Ascomycota in both air (68%) and dust (92%) samples and followed by the Basidiomycota and Zygomycota. The majority of Ascomycota clones belonged to four orders including the Pleosporales, Eurotiales, Capnodiales, and Dothideales. ITS sequencing revealed the presence of a number of rarely documented fungal species placed in the Pleosporales. Several species placed in the Basidiomycota were detected in ITS clone libraries but not by viable or non-viable methods. The prevalence of organizational taxonomic units (OTUs) was significantly higher in air than in dust samples (p < 0.0001); however, no differences between OTUs in air samples collected in the subjects' room and basement were observed. These sequencing results demonstrate a much broader diversity of Ascomycota and Basidiomycota communities in KCSHHP indoor environments than previously estimated using traditional methods of assessment.
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Affiliation(s)
- William R Rittenour
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV 26505, USA.
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411
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Yamamoto N, Dannemiller KC, Bibby K, Peccia J. Identification accuracy and diversity reproducibility associated with internal transcribed spacer-based fungal taxonomic library preparation. Environ Microbiol 2013; 16:2764-76. [DOI: 10.1111/1462-2920.12338] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/19/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Naomichi Yamamoto
- Department of Environmental Health; Seoul National University; 1 Gwanak-ro Gwanak-gu Seoul 151-742 Korea
| | - Karen C. Dannemiller
- Department of Chemical and Environmental Engineering; Yale University; New Haven CT 06520 USA
| | - Kyle Bibby
- Department of Civil and Environmental Engineering; University of Pittsburgh; Pittsburgh PA 15261 USA
- Department of Computational and Systems Biology; University of Pittsburgh School of Medicine; Pittsburgh PA 15260 USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering; Yale University; New Haven CT 06520 USA
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412
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Adams RI, Miletto M, Taylor JW, Bruns TD. The diversity and distribution of fungi on residential surfaces. PLoS One 2013; 8:e78866. [PMID: 24223861 PMCID: PMC3815347 DOI: 10.1371/journal.pone.0078866] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/23/2013] [Indexed: 01/29/2023] Open
Abstract
The predominant hypothesis regarding the composition of microbial assemblages in indoor environments is that fungal assemblages are structured by outdoor air with a moderate contribution by surface growth, whereas indoor bacterial assemblages represent a mixture of bacteria entered from outdoor air, shed by building inhabitants, and grown on surfaces. To test the fungal aspect of this hypothesis, we sampled fungi from three surface types likely to support growth and therefore possible contributors of fungi to indoor air: drains in kitchens and bathrooms, sills beneath condensation-prone windows, and skin of human inhabitants. Sampling was done in replicated units of a university-housing complex without reported mold problems, and sequences were analyzed using both QIIME and the new UPARSE approach to OTU-binning, to the same result. Surfaces demonstrated a mycological profile similar to that of outdoor air from the same locality, and assemblages clustered by surface type. "Weedy" genera typical of indoor air, such as Cladosporium and Cryptococcus, were abundant on sills, as were a diverse set of fungi of likely outdoor origin. Drains supported more depauperate assemblages than the other surfaces and contained thermotolerant genera such as Exophiala, Candida, and Fusarium. Most surprising was the composition detected on residents' foreheads. In addition to harboring Malassezia, a known human commensal, skin also possessed a surprising richness of non-resident fungi, including plant pathogens such as ergot (Claviceps purperea). Overall, fungal richness across indoor surfaces was high, but based on known autecologies, most of these fungi were unlikely to be growing on surfaces. We conclude that while some endogenous fungal growth on typical household surfaces does occur, particularly on drains and skin, all residential surfaces appear - to varying degrees - to be passive collectors of airborne fungi of putative outdoor origin, a view of the origins of the indoor microbiome quite different from bacteria.
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Affiliation(s)
- Rachel I. Adams
- Plant & Microbial Biology, University of California, Berkeley, California, United States of America
| | - Marzia Miletto
- Plant & Microbial Biology, University of California, Berkeley, California, United States of America
| | - John W. Taylor
- Plant & Microbial Biology, University of California, Berkeley, California, United States of America
| | - Thomas D. Bruns
- Plant & Microbial Biology, University of California, Berkeley, California, United States of America
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413
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Adams RI, Amend AS, Taylor JW, Bruns TD. A unique signal distorts the perception of species richness and composition in high-throughput sequencing surveys of microbial communities: a case study of fungi in indoor dust. MICROBIAL ECOLOGY 2013; 66:735-41. [PMID: 23880792 PMCID: PMC3824195 DOI: 10.1007/s00248-013-0266-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 07/08/2013] [Indexed: 05/07/2023]
Abstract
Sequence-based surveys of microorganisms in varied environments have found extremely diverse assemblages. A standard practice in current high-throughput sequence (HTS) approaches in microbial ecology is to sequence the composition of many environmental samples at once by pooling amplicon libraries at a common concentration before processing on one run of a sequencing platform. Biomass of the target taxa, however, is not typically determined prior to HTS, and here, we show that when abundances of the samples differ to a large degree, this standard practice can lead to a perceived bias in community richness and composition. Fungal signal in settled dust of five university teaching laboratory classrooms, one of which was used for a mycology course, was surveyed. The fungal richness and composition in the dust of the nonmycology classrooms were remarkably similar to each other, while the mycology classroom was dominated by abundantly sporulating specimen fungi, particularly puffballs, and appeared to have a lower overall richness based on rarefaction curves and richness estimators. The fungal biomass was three to five times higher in the mycology classroom than the other classrooms, indicating that fungi added to the mycology classroom swamped the background fungi present in indoor air. Thus, the high abundance of a few taxa can skew the perception of richness and composition when samples are sequenced to an even depth. Next, we used in silico manipulations of the observed data to confirm that a unique signature can be identified with HTS approaches when the source is abundant, whether or not the taxon identity is distinct. Lastly, aerobiology of indoor fungi is discussed.
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Affiliation(s)
- Rachel I Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720, USA,
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