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Li SP, Wang P, Chen Y, Wilson MC, Yang X, Ma C, Lu J, Chen XY, Wu J, Shu WS, Jiang L. Island biogeography of soil bacteria and fungi: similar patterns, but different mechanisms. ISME JOURNAL 2020; 14:1886-1896. [PMID: 32341471 PMCID: PMC7305213 DOI: 10.1038/s41396-020-0657-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/27/2020] [Accepted: 04/02/2020] [Indexed: 11/27/2022]
Abstract
Microbes, similar to plants and animals, exhibit biogeographic patterns. However, in contrast with the considerable knowledge on the island biogeography of higher organisms, we know little about the distribution of microorganisms within and among islands. Here, we explored insular soil bacterial and fungal biogeography and underlying mechanisms, using soil microbiota from a group of land-bridge islands as a model system. Similar to island species-area relationships observed for many macroorganisms, both island-scale bacterial and fungal diversity increased with island area; neither diversity, however, was affected by island isolation. By contrast, bacterial and fungal communities exhibited strikingly different assembly patterns within islands. The loss of bacterial diversity on smaller islands was driven primarily by the systematic decline of diversity within samples, whereas the loss of fungal diversity on smaller islands was driven primarily by the homogenization of community composition among samples. Lower soil moisture limited within-sample bacterial diversity, whereas smaller spatial distances among samples restricted among-sample fungal diversity, on smaller islands. These results indicate that among-island differences in habitat quality generate the bacterial island species-area relationship, whereas within-island dispersal limitation generates the fungal island species-area relationship. Together, our study suggests that different mechanisms underlie similar island biogeography patterns of soil bacteria and fungi.
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Affiliation(s)
- Shao-Peng Li
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China.,Institute of Eco-Chongming (IEC), Shanghai, 202162, China
| | - Pandeng Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,School of Life Sciences & School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yongjian Chen
- School of Life Sciences & School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Maxwell C Wilson
- School of Life Sciences & School of Sustainability, Arizona State University, Tempe, AZ, 85287, USA
| | - Xian Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Chao Ma
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Enviro\nment, Anhui Agricultural University, Hefei, 230036, China
| | - Jianbo Lu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Xiao-Yong Chen
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China.,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Jianguo Wu
- School of Life Sciences & School of Sustainability, Arizona State University, Tempe, AZ, 85287, USA
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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252
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Guo J, Xiong Y, Kang T, Xiang Z, Qin C. Bacterial community analysis of floor dust and HEPA filters in air purifiers used in office rooms in ILAS, Beijing. Sci Rep 2020; 10:6417. [PMID: 32286482 PMCID: PMC7156680 DOI: 10.1038/s41598-020-63543-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/01/2020] [Indexed: 01/08/2023] Open
Abstract
Air purifiers with high-efficiency particulate air (HEPA) filters remove not only particulate matter but also airborne microorganisms in indoor environments. We investigated the bacterial community in HEPA filters (used for 1 year) and that in the floor dust of 12 office rooms in Beijing. We found that the viable bacteria proportion in the filter was significantly higher than that in the floor dust (p < 0.001). The Non-Metric Multi-Dimensional Scaling analysis showed that the bacterial communities in the filters and dust were significantly different (p = 0.001). The Chao1, Shannon-Wiener and phylogenetic diversity values in the filter were significantly higher than those in the dust (p < 0.001). The predominant bacterial classes in the filter were Alphaproteobacteria and Actinobacteria, whereas those in the dust were Bacteroidia, Clostridia and Bacilli. Human occupancy contributed more to the bacterial community in the filter than that in the dust. Klebsiella and Alloprevotella in the dust and filters positively correlated with the occupancy density. Soil bacteria contributed to a significantly higher proportion of the bacteria in the HEPA filter (p < 0.001). In contrast, human oral, indoor air and outdoor haze contributed to a higher proportion of the bacteria in the dust samples (p < 0.001, p < 0.01 and p < 0.05, respectively). As HEPA filters serve as an ecological niche for indoor bacteria, they should be carefully investigated during the assessment of indoor environmental health.
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Affiliation(s)
- Jianguo Guo
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, CAMS&PUMC, Beijing, 100021, China
- Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese Medicine, Beijing, 100021, China
| | - Yi Xiong
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Taisheng Kang
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, CAMS&PUMC, Beijing, 100021, China
- Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese Medicine, Beijing, 100021, China
| | - Zhiguang Xiang
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, CAMS&PUMC, Beijing, 100021, China
- Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese Medicine, Beijing, 100021, China
| | - Chuan Qin
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, CAMS&PUMC, Beijing, 100021, China.
- Key Laboratory of Human Diseases Animal Model, State Administration of Traditional Chinese Medicine, Beijing, 100021, China.
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253
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Huang B, Yan D, Ouyang C, Zhang D, Zhu J, Liu J, Li Y, Wang Q, Han Q, Cao A. Chloropicrin fumigation alters the soil phosphorus and the composition of the encoding alkaline phosphatase PhoD gene microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:135080. [PMID: 31818557 DOI: 10.1016/j.scitotenv.2019.135080] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
The transformation of phosphorus (P) compounds in soil depends largely on soil microbial communities and is sensitive to agricultural practices. However, the effects of soil fumigation on soil P, and microbes involved in P transformation, are unknown. Our results showed that chloropicrin (CP) fumigation significantly increased the available-P, Leached-P and active-P fractionation (inorganic P extracted from H2O, NaHCO3 and NaOH) in Shangdong and Miyun soils in the early stages of culture, while soil alkaline phosphatase (ALP) activity and phoD gene abundance decreased significantly. Leached-P in fumigated soil was positively correlated with increased active-P fractionation, indicating that it was an important source of soil Leached-P after fumigation. The changes in P-fractionation, Leached-P and ALP after fumigation were also significantly correlated with the composition of the microbial communities. CP fumigation briefly stimulated an increase in the abundance and diversity of phoD-harboring microbial communities and promoted the mineralization process of soil P. PICRUSt metagenomic analysis showed an increase in the relative abundance of microorganisms with involved in carbohydrate/lipid transport and metabolism functions after fumigation. These results suggest CP fumigation altered soil P transformation and phoD-harboring microbes that might lead to an increased risk of P enrichment in waterways.
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Affiliation(s)
- Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Canbin Ouyang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiahong Zhu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China
| | - Qingli Han
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing 100193, China.
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254
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Fungal bio-aerosol in multiple micro-environments from eastern India: source, distribution, and health hazards. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2323-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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255
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Abstract
Atopy and fungi have a long associative history. Fungal spores were among the first substances to which humans were noted to be sensitized. Humans contact fungal spores in the outdoor, indoor, and occupational environments. As organisms, fungi have their own kingdom and are found in all environmental niches on earth. Currently, fungal exposure in the indoor environment especially related to wet housing conditions is of particular concern. Sensitization rates to fungi typically exceed 5% of the general public with higher rates among the atopic population. Alternaria is the best studied of the allergic fungi; however, cross sensitization to multiple fungi is well documented. Recent advances in understanding mechanisms of the innate immune system are beginning to explain why the fungal atopy relationship is unique and why fungal sensitivity seems to extend to many non-atopic individuals. Evidence has been accumulated that indicates fungal allergen exposure can be via intact spores as well as spore and mycelial fragments. Germinating spores produce a different and often increased allergen picture. Much evidence has been developed through animal studies that extends the mechanisms surrounding long-term low-level fungal exposure. However, it should be emphasized that the presence of fungi in the air does not necessarily equate with illness. Indeed, in the absence of an atopic individual and/or a significant immune response against fungi, there is little evidence suggesting pathology. Allergists frequently deal with patients who have concerns about indoor fungal exposure and respiratory disease in those patients with an allergic response.
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Fakunle AG, Olusola B, Jafta N, Faneye A, Heederik D, Smit LA, Naidoo RN. Home Assessment of Indoor Microbiome (HAIM) in Relation to Lower Respiratory Tract Infections among Under-Five Children in Ibadan, Nigeria: The Study Protocol. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17061857. [PMID: 32183028 PMCID: PMC7143126 DOI: 10.3390/ijerph17061857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/22/2020] [Accepted: 03/03/2020] [Indexed: 12/15/2022]
Abstract
The association between household air pollution and lower respiratory tract infections (LRTI) among children under five years of age has been well documented; however, the extent to which the microbiome within the indoor environment contributes to this association is uncertain. The home assessment of indoor microbiome (HAIM) study seeks to assess the abundance of indoor microbiota (IM) in the homes of under-five children (U-5Cs) with and without LRTI. HAIM is a hospital- and community-based study involving 200 cases and 200 controls recruited from three children’s hospitals in Ibadan, Nigeria. Cases will be hospital-based patients with LRTI confirmed by a pediatrician, while controls will be community-based participants, matched to cases on the basis of sex, geographical location, and age (±3 months) without LRTI. The abundance of IM in houses of cases and controls will be investigated using active and passive air sampling techniques and analyzed by qualitative detection of bacterial 16SrRNA gene (V3–V4), fungal ITS1 region, and viral RNA sequencing. HAIM is expected to elucidate the relationship between exposure to IM and incidence of LRTI among U-5Cs and ultimately provide evidence base for strategic interventions to curtail the burgeoning burden of LRTI on the subcontinent.
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Affiliation(s)
- Adekunle G. Fakunle
- Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban 4041, South Africa;
- Department of Environmental Health Sciences, Faculty of Public Health, University of Ibadan, Ibadan 200212, Nigeria
- Correspondence: (A.G.F.); (R.N.N.); Tel.: +234-90-9395-6165 (A.G.F.); +27-824-379-333 (R.N.N.)
| | - Babatunde Olusola
- Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria; (B.O.); (A.F.)
| | - Nkosana Jafta
- Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban 4041, South Africa;
| | - Adedayo Faneye
- Department of Virology, College of Medicine, University of Ibadan, Ibadan 200212, Nigeria; (B.O.); (A.F.)
| | - Dick Heederik
- Institute for Risk Assessment Sciences, Environmental Epidemiology Division (IRAS-EEPI), Utrecht University, 80177 Utrecht, The Netherlands; (D.H.)
| | - Lidwien A.M. Smit
- Institute for Risk Assessment Sciences, Environmental Epidemiology Division (IRAS-EEPI), Utrecht University, 80177 Utrecht, The Netherlands; (D.H.)
| | - Rajen N. Naidoo
- Discipline of Occupational and Environmental Health, University of KwaZulu-Natal, 321 George Campbell Building Howard College Campus, Durban 4041, South Africa;
- Correspondence: (A.G.F.); (R.N.N.); Tel.: +234-90-9395-6165 (A.G.F.); +27-824-379-333 (R.N.N.)
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257
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Horve PF, Lloyd S, Mhuireach GA, Dietz L, Fretz M, MacCrone G, Van Den Wymelenberg K, Ishaq SL. Building upon current knowledge and techniques of indoor microbiology to construct the next era of theory into microorganisms, health, and the built environment. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2020; 30:219-235. [PMID: 31308484 PMCID: PMC7100162 DOI: 10.1038/s41370-019-0157-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/23/2019] [Accepted: 06/30/2019] [Indexed: 05/06/2023]
Abstract
In the constructed habitat in which we spend up to 90% of our time, architectural design influences occupants' behavioral patterns, interactions with objects, surfaces, rituals, the outside environment, and each other. Within this built environment, human behavior and building design contribute to the accrual and dispersal of microorganisms; it is a collection of fomites that transfer microorganisms; reservoirs that collect biomass; structures that induce human or air movement patterns; and space types that encourage proximity or isolation between humans whose personal microbial clouds disperse cells into buildings. There have been recent calls to incorporate building microbiology into occupant health and exposure research and standards, yet the built environment is largely viewed as a repository for microorganisms which are to be eliminated, instead of a habitat which is inexorably linked to the microbial influences of building inhabitants. Health sectors have re-evaluated the role of microorganisms in health, incorporating microorganisms into prevention and treatment protocols, yet no paradigm shift has occurred with respect to microbiology of the built environment, despite calls to do so. Technological and logistical constraints often preclude our ability to link health outcomes to indoor microbiology, yet sufficient study exists to inform the theory and implementation of the next era of research and intervention in the built environment. This review presents built environment characteristics in relation to human health and disease, explores some of the current experimental strategies and interventions which explore health in the built environment, and discusses an emerging model for fostering indoor microbiology rather than fearing it.
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Affiliation(s)
- Patrick F Horve
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Savanna Lloyd
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Gwynne A Mhuireach
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Leslie Dietz
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Mark Fretz
- Institute for Health and the Built Environment, University of Oregon, Portland, OR, 97209, USA
| | - Georgia MacCrone
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Kevin Van Den Wymelenberg
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
- Institute for Health and the Built Environment, University of Oregon, Portland, OR, 97209, USA
| | - Suzanne L Ishaq
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA.
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258
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Indoor Microbiome: Quantification of Exposure and Association with Geographical Location, Meteorological Factors, and Land Use in France. Microorganisms 2020; 8:microorganisms8030341. [PMID: 32121209 PMCID: PMC7143953 DOI: 10.3390/microorganisms8030341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 02/25/2020] [Indexed: 12/28/2022] Open
Abstract
The indoor microbial community is a mixture of microorganisms resulting from outdoor ecosystems that seed the built environment. However, the biogeography of the indoor microbial community is still inadequately studied. Dust from more than 3000 dwellings across France was analyzed by qPCR using 17 targets: 10 molds, 3 bacteria groups, and 4 mites. Thus, the first spatial description of the main indoor microbial allergens on the French territory, in relation with biogeographical factors influencing the distribution of microorganisms, was realized in this study. Ten microorganisms out of 17 exhibited increasing abundance profiles across the country: Five microorganisms (Dermatophagoïdes pteronyssinus, Dermatophagoïdes spp., Streptomyces spp., Cladosporium sphaerospermum, Epicoccum nigrum) from northeast to southwest, two (Cryptococcus spp., Alternaria alternata) from northwest to southeast, Mycobacteria from east to west, Aspergillus fumigatus from south to north, and Penicillium chrysogenum from south to northeast. These geographical patterns were partly linked to climate and land cover. Multivariate analysis showed that composition of communities seemed to depend on landscapes, with species related to closed and rather cold and humid landscapes (forests, located in the northeast) and others to more open, hot, and dry landscapes (herbaceous and coastal regions, located in the west). This study highlights the importance of geographical location and outdoor factors that shape communities. In order to study the effect of microorganisms on human health (allergic diseases in particular), it is important to identify biogeographic factors that structure microbial communities on large spatial scales and to quantify the exposure with quantitative tools, such as the multi-qPCR approach.
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259
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Xu W, Liu B, Wang C, Kong X. Organic cultivation of grape affects yeast succession and wine sensory quality during spontaneous fermentation. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2019.108894] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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260
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Langda S, Zhang C, Zhang K, Gui B, Ji D, Deji C, Cuoji A, Wang X, Wu Y. Diversity and Composition of Rumen Bacteria, Fungi, and Protozoa in Goats and Sheep Living in the Same High-Altitude Pasture. Animals (Basel) 2020; 10:ani10020186. [PMID: 31978949 PMCID: PMC7070549 DOI: 10.3390/ani10020186] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/14/2020] [Accepted: 01/20/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Tibetan goats and sheep graze together but have different growth performances, immune responses, and feeding preferences in the Tibetan pasture. Rumen microbiota composed of bacteria, fungi, and protozoa are necessary for a healthy ruminant. Therefore, in this study, we comprehensively describe composition and diversity of bacteria, fungi, and protozoa in the high- altitude rumen. Compared with sheep, the bacteria that degrade crude protein and produce volatile fatty acids (VFA) were increased in the rumen of goats (Saccharofermentans and Lachnospiraceae_XPB1014) (p < 0.05). In addition, when compared with goats, the fungi and protozoa that degrade fiber were increased in rumen of sheep (Neocallimastigaceae and Metadinium) (p < 0.05). Furthermore, VFA were significantly increased in the rumen of goats compared with sheep (p < 0.05). The VFA level was consistent with differences in the microbiota composition in the rumen between goats and sheep. Under mixed grazing conditions, goats tend to select a high-crude protein diet that is good for growth, whereas sheep tend to select a high-lignin diet that is difficult to digest. Therefore, the different microbiota in the rumen of goats and sheep may be explained by dietary preference. Abstract Environmental adaptation of ruminants was highly related to microbiota in the rumen. To investigate the diversity and composition of bacteria, fungi, and protozoa in the rumen of high-altitude animals, amplicon gene sequencing was performed using rumen fluid samples derived from both Tibetan goats and sheep at the same pasture in a highland (altitude > 4800 m). Between these two species, the ruminal bacteria and fungi were significantly different at multiple taxonomic levels. The alpha diversity of bacteria was significantly high in goats (p < 0.05). One hundred and sixty-four and 29 Operational Taxonomy Units (OTUs) with significant differences were detected in bacteria and fungi, respectively. The abundance of bacteria, fungi, and protozoa in the rumen was characterized at multiple taxonomic levels, and we determined that Firmicutes, Bacteroidetes, Neocallimastigomycota, and Ciliophora were the most abundant bacteria, fungi, and protozoa. The family Neocallimastigaceae and the genus Metadinium had cellulose degradation capacity in the rumen with high abundance, thereby, suggesting that fungi and protozoa played an essential role in rumen fermentation. In addition, by comparing microbiota in the rumen of goats and sheep it was found, that the fiber-degrading fungi genus (Cyllamyces) was increased in the rumen of sheep (p < 0.05) whereas VFA-producing bacteria (Saccharofermentans and Lachnospiraceae_XPB1014) were increased in the rumen of goats (p < 0.05). Interestingly, in the rumen, no differences in protozoa were observed between goats and sheep (p > 0.05). Furthermore, when compared to sheep, level of acetic acid, propionic acid, and total volatile fatty acid (TVFA) were significantly increased in the rumen of goats (p < 0.05). Taken together, these results suggested microbiota in the rumen drive goats to better adapt to high-altitude grazing conditions.
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Affiliation(s)
- Suo Langda
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
| | - Chenguang Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (C.Z.); (K.Z.)
| | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (C.Z.); (K.Z.)
| | - Ba Gui
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
| | - De Ji
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
| | - Ciren Deji
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
| | - Awang Cuoji
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (C.Z.); (K.Z.)
- Correspondence: (X.W.); (Y.W.)
| | - Yujiang Wu
- Institute of Animal Sciences, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850009, China; (S.L.); (B.G.); (D.J.); (C.D.); (A.C.)
- Correspondence: (X.W.); (Y.W.)
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261
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Simons A, Bertron A, Aubert JE, Roux C, Roques C. Characterization of the microbiome associated with in situ earthen materials. ENVIRONMENTAL MICROBIOME 2020; 15:4. [PMID: 33902730 PMCID: PMC8066951 DOI: 10.1186/s40793-019-0350-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 12/07/2019] [Indexed: 06/12/2023]
Abstract
BACKGROUND The current increase in public awareness of environmental risks is giving rise to a growth of interest in the microbiological safety of buildings. In particular, microbial proliferation on construction materials can be responsible for the degradation of indoor air quality that can increase health-risk to occupants. Raw earth materials are still widely used throughout the world and, in some cases, are linked to heritage habitats, as in the southwest of France. Moreover, these building materials are currently the subject of renewed interest for ecological and economic reasons. However, the microbial status of earthen materials raises major concerns: could the microbiome associated with such natural materials cause disease in building occupants? Very few analyses have been performed on the microbial communities present on these supports. Characterizing the raw earth material microbiome is also important for a better evaluation and understanding of the susceptibility of such materials to microbial development. This study presents the distribution of in situ bacterial and fungal communities on different raw earth materials used in construction. Various buildings were sampled in France and the microbial communities present were characterized by amplicon high-throughput sequencing (bacterial 16S rRNA gene and fungal ITS1 region). Bacterial culture isolates were identified at the species level by MALDI-TOF mass spectrometry. RESULTS The major fungal and bacterial genera identified were mainly associated with conventional outdoor and indoor environmental communities, and no specific harmful bacterial species were detected on earthen materials. However, contrary to expectations, few human-associated genera were detected in dwellings. We found lower microbial alpha-diversity in earthen material than is usually found in soil, suggesting a loss of diversity during the use of these materials in buildings. Interestingly enough, the main features influencing microbial communities were building history and room use, rather than material composition. CONCLUSIONS These results constitute a first in-depth analysis of microbial communities present on earthen materials in situ and may be considered as a first referential to investigate microbial communities on such materials according to environmental conditions and their potential health impact. The bacterial and fungal flora detected were similar to those found in conventional habitats and are thought to be mainly impacted by specific events in the building's life, such as water damage.
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Affiliation(s)
- Alexis Simons
- Laboratoire de Génie Chimique, Université de Toulouse, UMR 5503 UPS - CNRS - INPT, Toulouse, France.
- Laboratoire Matériaux et Durabilité des Constructions, Université de Toulouse, UPS - INSA, Toulouse, France.
| | - Alexandra Bertron
- Laboratoire Matériaux et Durabilité des Constructions, Université de Toulouse, UPS - INSA, Toulouse, France
| | - Jean-Emmanuel Aubert
- Laboratoire Matériaux et Durabilité des Constructions, Université de Toulouse, UPS - INSA, Toulouse, France
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, UMR 5546 UPS - CNRS, Castanet-Tolosan, France
| | - Christine Roques
- Laboratoire de Génie Chimique, Université de Toulouse, UMR 5503 UPS - CNRS - INPT, Toulouse, France
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Niu H, Leng Y, Ran S, Amee M, Du D, Sun J, Chen K, Hong S. Toxicity of soil labile aluminum fractions and aluminum species in soil water extracts on the rhizosphere bacterial community of tall fescue. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 187:109828. [PMID: 31639644 DOI: 10.1016/j.ecoenv.2019.109828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
Different forms of aluminum (Al) in soil can be toxic to plants and the bacterial community. In our previous study, the distribution and toxicity to plants of soil Al species and soil labile Al fractions were examined. However, the toxicity of different forms of Al on the bacterial community has not been completely studied. In this study, five soil samples (pH: 4.92, 6.17, 6.62, 6.70, 8.51) were collected from Lichuan, China. Tall fescue was planted in rhizosphere boxes with those soils for 120 days. The toxicity of soil Al species and soil labile Al fractions on the bacterial community of near-rhizosphere (NR) soils and far-rhizosphere (FR) soils were analyzed. The effect of different forms of Al on bacterial community between NR and FR soils was small, but the difference was obvious according to the different spatial distribution of samples. An individual bacterial community has eosinophilia, and most bacterial communities are tolerant of heavy metals (e.g., Cu, Zn, Cd). The toxicity of exchangeable Al has a strong effect on the bacterial community. Meanwhile, the toxicity of Al3+ to the bacterial community is strong. In this study, the key finding was that the toxicity of the Al-F- complex toward the bacterial community and plants was different. AlF2+, AlF2+, AlF3, and AlF4- are toxic for the bacterial community, and the correlation decreases with the addition of F-. This finding is of considerable significance to the treatment of acid-contaminated soil and the study of the tolerance mechanism of plants toward Al.
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Affiliation(s)
- Hong Niu
- College of Resources and Environmental Science, Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan, PR China
| | - Yifei Leng
- Key Laboratory of Aquatic Botany and Watershed Ecology & CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Shangmin Ran
- College of Resources and Environmental Science, Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan, PR China
| | - Maurice Amee
- Key Laboratory of Aquatic Botany and Watershed Ecology & CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Dongyun Du
- College of Resources and Environmental Science, Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan, PR China
| | - Jie Sun
- College of Resources and Environmental Science, Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan, PR China
| | - Ke Chen
- College of Resources and Environmental Science, Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan, PR China.
| | - Song Hong
- School of Resource and Environmental Sciences, Wuhan University, Wuhan, 430079, China.
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263
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Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics. Nat Commun 2020; 11:34. [PMID: 31911594 PMCID: PMC6946711 DOI: 10.1038/s41467-019-13913-9] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 11/28/2019] [Indexed: 11/16/2022] Open
Abstract
Community assembly of crop-associated fungi is thought to be strongly influenced by deterministic selection exerted by the plant host, rather than stochastic processes. Here we use a simple, sorghum system with abundant sampling to show that stochastic forces (drift or stochastic dispersal) act on fungal community assembly in leaves and roots early in host development and when sorghum is drought stressed, conditions when mycobiomes are small. Unexpectedly, we find no signal for stochasticity when drought stress is relieved, likely due to renewed selection by the host. In our experimental system, the host compartment exerts the strongest effects on mycobiome assembly, followed by the timing of plant development and lastly by plant genotype. Using a dissimilarity-overlap approach, we find a universality in the forces of community assembly of the mycobiomes of the different sorghum compartments and in functional guilds of fungi. Fungal community assembly on crop plants is thought to be driven by deterministic selection exerted by the host. Here Gao et al. use a sorghum system to show that stochastic forces act on fungal community assembly in leaves and roots early in host development and when sorghum is drought stressed.
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264
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Tiew PY, Mac Aogain M, Ali NABM, Thng KX, Goh K, Lau KJX, Chotirmall SH. The Mycobiome in Health and Disease: Emerging Concepts, Methodologies and Challenges. Mycopathologia 2020; 185:207-231. [PMID: 31894501 PMCID: PMC7223441 DOI: 10.1007/s11046-019-00413-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023]
Abstract
Fungal disease is an increasingly recognised global clinical challenge associated with high mortality. Early diagnosis of fungal infection remains problematic due to the poor sensitivity and specificity of current diagnostic modalities. Advances in sequencing technologies hold promise in addressing these shortcomings and for improved fungal detection and identification. To translate such emerging approaches into mainstream clinical care will require refinement of current sequencing and analytical platforms, ensuring standardisation and consistency through robust clinical benchmarking and its validation across a range of patient populations. In this state-of-the-art review, we discuss current diagnostic and therapeutic challenges associated with fungal disease and provide key examples where the application of sequencing technologies has potential diagnostic application in assessing the human ‘mycobiome’. We assess how ready access to fungal sequencing may be exploited in broadening our insight into host–fungal interaction, providing scope for clinical diagnostics and the translation of emerging mycobiome research into clinical practice.
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Micheál Mac Aogain
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | | | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
| | - Karlyn Goh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kenny J X Lau
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Singapore.
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265
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Ben Maamar S, Hu J, Hartmann EM. Implications of indoor microbial ecology and evolution on antibiotic resistance. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2020; 30:1-15. [PMID: 31591493 PMCID: PMC8075925 DOI: 10.1038/s41370-019-0171-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/17/2019] [Accepted: 08/18/2019] [Indexed: 05/19/2023]
Abstract
The indoor environment is an important source of microbial exposures for its human occupants. While we naturally want to favor positive health outcomes, built environment design and operation may counter-intuitively favor negative health outcomes, particularly with regard to antibiotic resistance. Indoor environments contain microbes from both human and non-human origins, providing a unique venue for microbial interactions, including horizontal gene transfer. Furthermore, stressors present in the built environment could favor the exchange of genetic material in general and the retention of antibiotic resistance genes in particular. Intrinsic and acquired antibiotic resistance both pose a potential threat to human health; these phenomena need to be considered and controlled separately. The presence of both environmental and human-associated microbes, along with their associated antibiotic resistance genes, in the face of stressors, including antimicrobial chemicals, creates a unique opportunity for the undesirable spread of antibiotic resistance. In this review, we summarize studies and findings related to various interactions between human-associated bacteria, environmental bacteria, and built environment conditions, and particularly their relation to antibiotic resistance, aiming to guide "healthy" building design.
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Affiliation(s)
- Sarah Ben Maamar
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Jinglin Hu
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA.
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266
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Zhang D, Yan D, Cheng H, Fang W, Huang B, Wang X, Wang X, Yan Y, Ouyang C, Li Y, Wang Q, Cao A. Effects of multi-year biofumigation on soil bacterial and fungal communities and strawberry yield. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 256:113415. [PMID: 31672346 DOI: 10.1016/j.envpol.2019.113415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/31/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Biofumigation is an effective, non-chemical method to control soil-borne pests and diseases and to maximize crop yield. We studied the responses of soil bacterial and fungal communities, the soil's nutritional state and strawberry yield, when the soil was biofumigated each year for five consecutive years using fresh chicken manure (BioFum). BioFum significantly increased the soil's NH4+-N, NO3--N, available P and K and organic matter. Fusarium spp. and Phytophthora spp. which are known to cause plant disease, were significantly decreased after BioFum. In addition, Biofum increased the soil's temperature, enhanced chlorophyll levels in the leaves of strawberry plants, and the soluble sugar and ascorbic acid content in strawberry fruit. We used high-throughput gene sequencing to monitor changes in the soil's bacterial and fungal communities. Although BioFum significantly decreased the diversity of these communities, it increased the relative abundance of some biological control agents in the phylum Actinobacteria and the genera Pseudomonas, Bacillus and Chaetomium. An increase in these biological control agents would reduce the incidence of soil-borne pathogens and plant disease. Although strawberry marketable yield using BioFum was higher in the first three years, the decline in the final two years could be due to the accumulation of P and K which may have delayed flowering and fruiting. Methods to overcome yield losses using BioFum need to be developed in the future. Our research, however, showed that BioFum enhanced soil fertility, reduced the presence of soil pathogens, increased the relative abundance of beneficial bacteria and fungi and improved strawberry quality. Unlike chemical soil treatments that can cause pest and disease resistance when used continuously over many years, our multi-year research program on BioFum showed that this treatment provided significant benefits to the soil, plant and strawberry fruit.
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Affiliation(s)
- Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing, 100193, China
| | - Hongyan Cheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xianli Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoning Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yue Yan
- Agricultural Environmental Protection and Rural Energy Principal Station of Shandong Province, Shandong, 250014, China
| | - Canbin Ouyang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing, 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing, 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing, 100193, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Beijing Innovation Consortium of Agriculture Research System, Beijing, 100193, China.
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267
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Libert X, Chasseur C, Packeu A, Bureau F, Roosens NH, De Keersmaecker SCJ. Exploiting the Advantages of Molecular Tools for the Monitoring of Fungal Indoor Air Contamination: First Detection of Exophiala jeanselmei in Indoor Air of Air-Conditioned Offices. Microorganisms 2019; 7:microorganisms7120674. [PMID: 31835614 PMCID: PMC6955718 DOI: 10.3390/microorganisms7120674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 11/16/2022] Open
Abstract
Today, indoor air pollution is considered a public health issue. Among the impacting pollutants, indoor airborne fungi are increasingly highlighted. Most of the monitoring protocols are culture-based, but these are unable to detect the uncultivable and/or dead fraction or species suppressed by fast-growing fungi, even though this fraction could impact health. Among the contaminants suspected to be part of this fraction, Exophiala jeanselmei is an interesting case study. Known to be pathogenic, this black yeast grows in humid environments such as air-conditioning systems, where it has been previously detected using classical culture-based methods. However, until now, this fungus was never detected in indoor air in contact with these air-conditioning systems. This study shows the first detection of E. jeanselmei in indoor air collected from offices in contact with contaminated air-conditioning reservoirs. While its presence in indoor air could not be demonstrated with culture-based methods, it was found by real-time PCR and massive parallel sequencing. The latter also allowed obtaining a broader view on the fungal diversity in the tested samples. Similar approaches were applied on water samples collected from the conditioning reservoirs to trace the source of contamination. The comparison of results obtained with both methods confirmed that the molecular tools could improve indoor air monitoring, especially of dead and/or uncultivable contaminants or when competition between species could occur.
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Affiliation(s)
- Xavier Libert
- Transversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Cellular and Molecular Immunology, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA), Université de Liège (ULg), Avenue de l′Hôpital, 1 (B34), 4000 Sart-Tilman, Belgium
| | - Camille Chasseur
- Mycology and Aerobiology, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Ann Packeu
- Mycology and Aerobiology, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Fabrice Bureau
- Cellular and Molecular Immunology, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA), Université de Liège (ULg), Avenue de l′Hôpital, 1 (B34), 4000 Sart-Tilman, Belgium
| | - Nancy H. Roosens
- Transversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Sigrid C. J. De Keersmaecker
- Transversal activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Correspondence: ; Tel.: +32-2-642-5257
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268
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Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment. DIVERSITY 2019. [DOI: 10.3390/d11120234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.
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269
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Fungal aerobiota are not affected by time nor environment over a 13-y time series at the Mauna Loa Observatory. Proc Natl Acad Sci U S A 2019; 116:25728-25733. [PMID: 31801876 PMCID: PMC6926071 DOI: 10.1073/pnas.1907414116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Although fungi in the air make up a disproportionately large part of particulate matter and affect both local and global biogeochemical cycles, the factors influencing their composition and diversity are less clear, especially over relatively long timescales. Here we leverage the longest time series of aerobiota to date from a remote sampling location on Hawaii Island to examine changes in fungi over time and in response to environmental conditions. Our results provide evidence for a relatively unstable fungal aerobiota, whose composition is likely influenced by the ability to disperse into the system, rather than season or climate. Our finding of core taxa throughout the sampling period indicates resistance among some fungi to natural environmental fluctuations and human-associated global change. Fungi are ubiquitous and often abundant components of virtually all ecosystems on Earth, serving a diversity of functions. While there is clear evidence that fungal-mediated processes can influence environmental conditions, and in turn select for specific fungi, it is less clear how fungi respond to environmental fluxes over relatively long time frames. Here we set out to examine changes in airborne fungi collected over the course of 13 y, which is the longest sampling time to date. Air filter samples were collected from the Mauna Loa Observatory (MLO) on Hawaii Island, and analyzed using Illumina amplicon sequencing. As a study site, MLO is unique because of its geographic isolation and high elevation, making it an ideal place to capture global trends in climate and aerobiota. We found that the fungal aerobiota sampled at MLO had high species turnover, but compositional similarity did not decrease as a function of time between samples. We attribute these patterns to neutral processes such as idiosyncratic dispersal timing and trajectories. Furthermore, the composition of fungi at any given point was not significantly influenced by any local or global environmental variables we examined. This, and our additional finding of a core set of persistent fungi during our entire sampling period, indicates some degree of stability among fungi in the face of natural environmental fluctuations and human-associated global change. We conclude that the movement of fungi through the atmosphere is a relatively stochastic process.
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270
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Wang P, Li S, Yang X, Zhou J, Shu W, Jiang L. Mechanisms of soil bacterial and fungal community assembly differ among and within islands. Environ Microbiol 2019; 22:1559-1571. [DOI: 10.1111/1462-2920.14864] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 11/10/2019] [Accepted: 11/14/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Conservation of Guangdong Higher Education Institutes, School of Life Sciences Sun Yat‐sen University Guangzhou 510275 People's Republic of China
- School of Biological Sciences, Georgia Institute of Technology Atlanta GA 30332 USA
| | - Shao‐Peng Li
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences East China Normal University Shanghai 200241 China
- Institute of Eco‐Chongming (IEC) Shanghai 200062 China
| | - Xian Yang
- School of Biological Sciences, Georgia Institute of Technology Atlanta GA 30332 USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, and School of Civil Engineering and Environmental Sciences University of Oklahoma Norman OK 73019 USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing 100084 People's Republic of China
| | - Wensheng Shu
- School of Life Sciences, South China Normal University Guangzhou 510631 People's Republic of China
| | - Lin Jiang
- School of Biological Sciences, Georgia Institute of Technology Atlanta GA 30332 USA
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271
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Beng KC, Corlett RT. Identifying the mechanisms that shape fungal community and metacommunity patterns in Yunnan, China. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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272
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Zhang M, Riaz M, Zhang L, Xia H, El-Desouki Z, Jiang C. Response of fungal communities in different soils to biochar and chemical fertilizers under simulated rainfall conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 691:654-663. [PMID: 31325864 DOI: 10.1016/j.scitotenv.2019.07.151] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Biochar is a good soil additive, which cannot only effectively store carbon, but also improve soil fertility and crop yield. However, the specific response of fungal communities to biochar and chemical fertilizers are still relatively lacking. In addition, most studies do not take into account rainfall factors when conducting culture experiments. In the case of simulated rainfall, we investigated the response of fungal communities in different soils to biochar and fertilizers in China and analyzed the correlation between chemical properties and different fungal species. The tested soils were yellow-brown soil, fluvo-aquic soil, lou soil and black soil, and the simulated daily rainfall was 25 mm. The results indicated that the application of biochar and chemical fertilizers had a greater impact on the alpha diversity of acidic soils (yellow-brown soil, fluvo-aquic soil), but less on alkaline soils (lou soil, black soil). The relative abundance of Ascomycetes was most affected by biochar and fertilizer in any soil. From the point of view of the fungal community, yellow-brown soil was more suitable for single application of biochar, because it not only improved the ability of the soil to degrade persistent organic matter but also inhibited the spread of soil pathogens. In black soil, the relative abundance of Fusarium was significantly reduced by the combined application of biochar and chemical fertilizers (FC), and the decline was much higher than several other bacteria. However, FC caused the greatest changes in the structure of all soil fungal communities. Moreover, there was a significant correlation between the content of available nutrients and composition of fungal community in fluvo-aquic soil. In summary, it can be explained that the effects of biochar and chemical fertilizers on soil fungi may vary depending on the soil type, so it is very urgent to conduct long-term research on different typical soils.
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Affiliation(s)
- Mengyang Zhang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei Province 430070, PR China
| | - Muhammad Riaz
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei Province 430070, PR China
| | - Lin Zhang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei Province 430070, PR China
| | - Hao Xia
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei Province 430070, PR China
| | - Zeinab El-Desouki
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei Province 430070, PR China; Department of Soil Sciences, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Cuncang Jiang
- Microelement Research Center, College of Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei Province 430070, PR China.
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273
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Liu X, Ge W, Zhang X, Chai C, Wu J, Xiang D, Chen X. Biodegradation of aged polycyclic aromatic hydrocarbons in agricultural soil by Paracoccus sp. LXC combined with humic acid and spent mushroom substrate. JOURNAL OF HAZARDOUS MATERIALS 2019; 379:120820. [PMID: 31271936 DOI: 10.1016/j.jhazmat.2019.120820] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/30/2019] [Accepted: 06/24/2019] [Indexed: 06/09/2023]
Abstract
Paracoccus sp. LXC combined with humic acid (HA) and spent mushroom substrate (SMS) obtained from Auricularia auricular and Sarcomyxa edulis was tested for the remediation of agricultural soil contaminated with aged polycyclic aromatic hydrocarbons (PAHs). The biomass and diversity of bacteria and fungi and the soil enzyme activity were analyzed. PAH removal and dissipation kinetics were examined. The highest degradation rate of PAHs was 56.5% when soil was amended with Paracoccus sp. LXC combined with HA and unsterilized SMS from A. auricular. The half-life of PAHs decreased from 2323.3 days in natural attenuation to 66.6-277.2 days in amended treatments. Soil treated with Paracoccus sp. LXC combined with HA and SMS from A. auricular acquired high contents of organic matter and nutrients. HA and SMS aided the growth of PAH-degrading bacteria and promoted the diversity of bacteria but not of fungi. The degradation rate of PAHs was mainly correlated positively with soil laccase activity. Low- and middle-molecular-weight PAHs were significantly removed by Paracoccus sp. LXC, HA and SMS. High-molecular-weight PAHs were removed by SMS but not by Paracoccus sp. LXC. Biodegradation by Paracoccus sp. LXC combined with HA and SMS is a promising choice for remediating aged PAH-contaminated agricultural soils.
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Affiliation(s)
- Xiuchu Liu
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wei Ge
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaomei Zhang
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Chai
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Juan Wu
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Dan Xiang
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiaoyu Chen
- Qingdao Engineering Research Center for Rural Environment, Qingdao Agricultural University, Qingdao, 266109, China
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274
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Su Y, Lv JL, Yu M, Ma ZH, Xi H, Kou CL, He ZC, Shen AL. Long-term decomposed straw return positively affects the soil microbial community. J Appl Microbiol 2019; 128:138-150. [PMID: 31495045 DOI: 10.1111/jam.14435] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 07/24/2019] [Accepted: 08/21/2019] [Indexed: 01/12/2023]
Abstract
AIMS In order to understand the response of soil microbial communities to the long-term of decomposed straw return, the modifications of soil microbial community structure and composition induced by more than 10 years of fresh and decomposed straw return was investigated and the key environmental factors were analysed. METHODS AND RESULTS Phospholipid fatty acid analysis and high-through sequencing technique were applied to analyse the structure and composition of the soil microbial communities. Compared with fresh straw, returning decomposed straw increased the relative abundance of bacteria and fungi by 1·9 and 7·7% at a rate of ~3750 kg ha-1 , and increased by 23·1 and 5·7%, at a rate of ~7500 kg ha-1 respectively. The relative abundance of the bacteria related to soil nitrification increased, but the ones related to soil denitrification decreased with decomposed straw return, which led to higher total nitrogen contents in soils. Moreover, returning decomposed straw reduced pathogenic fungal populations (genus of Alternara), which had significantly positive correlation with soil electric conductivity. It indicated that the long-term of decomposed straw return might have lower risk of soil-borne disease mainly for the reasonable soil salinity. CONCLUSIONS Long-term of decomposed straw return could provide suitable nutrient and salinity for healthier development of soil microbial community, both in abundance and structure, compared with fresh straw return. SIGNIFICANCE AND IMPACT OF THE STUDY The results of the study helps to better understand how the microbial community modifications induced by decomposed straw return benefit on soil health. The obtained key factors impacting soil microbial community variations is meaningful in soil health management under conditions of straw return.
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Affiliation(s)
- Y Su
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - J L Lv
- Institute of Plant Nutrient, Environment and Resource, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - M Yu
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Z H Ma
- Institute of Plant Nutrient, Environment and Resource, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - H Xi
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - C L Kou
- Institute of Plant Nutrient, Environment and Resource, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Z C He
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - A L Shen
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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275
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Hu D, Lin W, Zeng J, Wu P, Zhang M, Guo L, Ye C, Wan K, Yu X. Profiling the microbial contamination in aviation fuel from an airport. BIOFOULING 2019; 35:856-869. [PMID: 31603000 DOI: 10.1080/08927014.2019.1671977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 09/14/2019] [Accepted: 09/16/2019] [Indexed: 06/10/2023]
Abstract
Microbial contamination during fuel storage can cause fuel system fouling and corrosion. Characterizing microbial contamination is critical for preventing and solving these problems. In this study, culture-based combing with the culture-independent methods, were used to profile the microbial contamination in aviation fuel. High-throughput sequencing (HTS) modified by propidium monoazide (PMA) revealed a higher diversity of contaminating microorganisms in samples than the culture method. Proteobacteria (47%), Actinobacteria (21%) and Ascomycota (>99%, fungi) were the most abundant phyla, and the neglected archaea was also detected. Additionally, qPCR-based methods revealed all samples contained a heavy level of microbial contamination, which was more accurate than its culturable counterparts, and fungal contamination was still a problem in aviation fuel. The application of a PCR-based method gives deeper insight into microbial contamination in aviation fuel than the conventional culture method, thus using it for regular detection and accurate description of fuel contamination is strongly recommended in the case of explosive microbial growth.
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Affiliation(s)
- Dong Hu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Wenfang Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
| | - Jie Zeng
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Peng Wu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
| | - Menglu Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Lizheng Guo
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Chengsong Ye
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
| | - Kun Wan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xin Yu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, People's Republic of China
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276
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Kazemian N, Pakpour S, Milani AS, Klironomos J. Environmental factors influencing fungal growth on gypsum boards and their structural biodeterioration: A university campus case study. PLoS One 2019; 14:e0220556. [PMID: 31374095 PMCID: PMC6677307 DOI: 10.1371/journal.pone.0220556] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 07/18/2019] [Indexed: 12/19/2022] Open
Abstract
The new era in the design of modern healthy buildings necessitates multidisciplinary research efforts that link principles of engineering and material sciences with those of building biology, in order to better comprehend and apply underlying interactions among design criteria. As part of this effort, there have been an array of studies in relation to the effects of building characteristics on indoor microbiota and their propensity to cause health issues. Despite the abundance of scientific inquiries, limited studies have been dedicated to concomitantly link these effects to the deterioration of 'structural integrity' in the building materials. This study focuses on the observed biodeteriorative capabilities of indoor fungi upon the ubiquitous gypsum board material as a function of building age and room functionality within a university campus. We observed that the fungal growth significantly affected the physical (weight loss) and mechanical (tensile strength) properties of moisture-exposed gypsum board samples; in some cases, tensile strength and weight decreased by more than 80%. Such intertwined associations between the biodeterioration of building material properties due to viable indoor fungi, and as a function of building characteristics, would suggest a critical need towards multi-criteria design and optimization of next-generation healthy buildings. Next to structural integrity measures, with a better understanding of what factors and environmental conditions trigger fungal growth in built environment materials, we can also optimize the design of indoor living spaces, cleaning strategies, as well as emergency management measures during probable events such as flooding or water damage.
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Affiliation(s)
- Negin Kazemian
- Department of Biology, University of British Columbia, Kelowna, Canada
- School of Engineering, University of British Columbia, Kelowna, Canada
| | - Sepideh Pakpour
- School of Engineering, University of British Columbia, Kelowna, Canada
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, United States of America
- * E-mail: (SP); (ASM); (JK)
| | - Abbas S. Milani
- School of Engineering, University of British Columbia, Kelowna, Canada
- Composites Research Network, Okanagan Node, Kelowna, Canada
- * E-mail: (SP); (ASM); (JK)
| | - John Klironomos
- Department of Biology, University of British Columbia, Kelowna, Canada
- * E-mail: (SP); (ASM); (JK)
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277
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Zhang D, Yan D, Fang W, Huang B, Wang X, Wang X, Zhu J, Liu J, Ouyang C, Li Y, Wang Q, Cao A. Chloropicrin alternated with biofumigation increases crop yield and modifies soil bacterial and fungal communities in strawberry production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 675:615-622. [PMID: 31035200 DOI: 10.1016/j.scitotenv.2019.04.222] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/12/2019] [Accepted: 04/14/2019] [Indexed: 06/09/2023]
Abstract
Chloropicrin (Pic) and biofumigation are both considered effective chemical and non-chemical alternatives to methyl bromide, respectively, for controlling crop-limiting soil-borne pests and diseases. In this study, we evaluated the effects of Pic alone and 'chloropicrin alternated with biofumigation' (CAB) on the soil's physico-chemical properties and strawberry yield, as well as their effects on soil bacterial and fungal communities. The contents of NO3--N, available phosphorus and potassium, and electrical conductivity were all significantly increased when CAB was used. In addition, CAB also significantly increased the strawberry marketable yield. High-throughput gene sequencing showed the species abundance of some soil bacteria and fungi was significantly increased such as the phyla Proteobacteria, Bacteroidetes, Actinobacteria and Ascomycota when CAB was used. However, CAB decreased the relative abundance of the phyla Firmicutes, Chloroflexi, Gemmatimonadete and Zygomycota. These results indicated that CAB could improve the physico-chemical properties of soil for strawberry production, increase the genetic diversity of microbes in the soil and enhance marketable fruit yield.
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Affiliation(s)
- Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xianli Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoning Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiahong Zhu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Canbin Ouyang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China.
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278
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Wu D, Zhang M, Peng M, Sui X, Li W, Sun G. Variations in Soil Functional Fungal Community Structure Associated With Pure and Mixed Plantations in Typical Temperate Forests of China. Front Microbiol 2019; 10:1636. [PMID: 31379786 PMCID: PMC6646410 DOI: 10.3389/fmicb.2019.01636] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 07/02/2019] [Indexed: 12/31/2022] Open
Abstract
Forest plants are in constant contact with the soil fungal community, which plays an important role in the circulation of nutrients through forest ecosystems. The objective of this study was to evaluate the fungal diversity in soil and elucidate the ecological role of functional fungal communities in forest ecosystems using soil samples from seven different plantations in northeastern China. Our results showed that the fungal communities were dominated by the phyla Ascomycota, Basidiomycota, and Mortierellomycota, and the mixed plantation of Fraxinus mandshurica and Pinus koraiensis had a soil fungal population clearly divergent from those in the other plantations. Additionally, the mixed plantation of F. mandshurica and P. koraiensis, which was low in soil nutrients, contained a highly diverse and abundant population of ectomycorrhizal fungi, whereas saprophytic fungi were more abundant in plantations with high soil nutrients. Redundancy analysis demonstrated a strong correlation between saprophytic fungi and the level of soil nutrients, whereas ectomycorrhizal fungi were mainly distributed in soils with low nutrient. Our findings provide insights into the importance of functional fungi and the mediation of soil nutrients in mixed plantations and reveal the effect of biodiversity on temperate forests.
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Affiliation(s)
- Di Wu
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Mengmeng Zhang
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Mu Peng
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Xin Sui
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Wei Li
- College of Resources and Environmental Science, Northeast Agricultural University, Harbin, China
| | - Guangyu Sun
- College of Life Science, Northeast Forestry University, Harbin, China
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279
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Establishment Limitation Constrains the Abundance of Lactic Acid Bacteria in the Napa Cabbage Phyllosphere. Appl Environ Microbiol 2019; 85:AEM.00269-19. [PMID: 31003989 DOI: 10.1128/aem.00269-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/14/2019] [Indexed: 12/15/2022] Open
Abstract
Patterns of phyllosphere diversity have become increasingly clear with high-throughput sequencing surveys, but the processes that control phyllosphere diversity are still emerging. Through a combination of lab and field experiments using Napa cabbage and lactic acid bacteria (LAB), we examined how dispersal and establishment processes shape the ecological distributions of phyllosphere bacteria. We first determined the abundance and diversity of LAB on Napa cabbage grown at three sites using both culture-based approaches and 16S rRNA gene amplicon sequencing. Across all sites, LAB made up less than 0.9% of the total bacterial community abundance. To assess whether LAB were low in abundance in the Napa cabbage phyllosphere due to a limited abundance in local species pools (source limitation), we quantified LAB in leaf and soil samples across 51 vegetable farms and gardens throughout the northeastern United States. Across all sites, LAB comprised less than 3.2% of the soil bacterial communities and less than 1.6% of phyllosphere bacterial communities. To assess whether LAB are unable to grow in the phyllosphere even if they dispersed at high rates (establishment limitation), we used a gnotobiotic Napa cabbage system in the lab with experimental communities mimicking various dispersal rates of LAB. Even at high dispersal rates, LAB became rare or completely undetectable in experimental communities, suggesting that they are also establishment limited. Collectively, our data demonstrate that the low abundance of LAB in phyllosphere communities may be explained by establishment limitation.IMPORTANCE The quality and safety of vegetable fermentations are dependent on the activities of LAB naturally present in the phyllosphere. Despite their critical role in determining the success of fermentation, the processes that determine the abundance and diversity of LAB in vegetables used for fermentation are poorly characterized. Our work demonstrates that the limited ability of LAB to grow in the cabbage phyllosphere environment may constrain their abundance on cabbage leaves. These results suggest that commercial fermentation of Napa cabbage proceeds despite low and variable abundances of LAB across different growing regions. Propagule limitation may also explain ecological distributions of other rare members of phyllosphere microbes.
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280
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Abstract
Airborne microorganisms are very difficult to assess accurately under field conditions owing to differences in the sample collection efficiency of the selected sampler and variations in DNA extraction efficiencies. Consequently, bioaerosol abundance and biodiversity can be underestimated, making it more difficult to link specific bioaerosol components to diseases and human health risk. Owing to the low biomass in air samples, it remains a challenge to obtain a representative microbiological sample to recover sufficient DNA for downstream analyses. Improved sampling methods are particularly crucial, especially for investigating viral communities, owing to the extremely low biomass of viral particles in the air compared with other environments. Without detailed information about sampling, characterization and enumeration techniques, interpretation of exposure level is very difficult. Despite this, bioaerosol research has been enhanced by molecular tools, especially next-generation sequencing approaches that have allowed faster and more detailed characterization of air samples.
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281
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Tian X, Wang D, Mao Z, Pan L, Liao J, Cai Z. Infection of Plasmodiophora brassicae changes the fungal endophyte community of tumourous stem mustard roots as revealed by high-throughput sequencing and culture-dependent methods. PLoS One 2019; 14:e0214975. [PMID: 31188828 PMCID: PMC6561537 DOI: 10.1371/journal.pone.0214975] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/28/2019] [Indexed: 01/12/2023] Open
Abstract
Diverse fungal endophytes live in plants and are shaped by some abiotic and biotic stresses. Plant disease as particular biotic stress possibly gives an impact on the communities of fungal endophytes. In this study, clubroot disease caused by an obligate biotroph protist, Plasmodiophora brassicae, was considered to analyze its influence on the fungal endophyte community using an internal transcribed spacer (ITS) through high-throughput sequencing and culture-dependent methods. The results showed that the diversity of the endophyte community in the healthy roots was much higher than the clubroots. Ascomycota was the dominant group of endophytes (Phoma, Mortierella, Penicillium, etc.) in the healthy roots while P. brassicae was the dominant taxon in the clubroots. Hierarchical clustering, principal component analysis (PCA), principal coordinates analysis (PCoA) and analysis of similarities (ANOSIM) indicated significant differences between the endophyte communities in the healthy roots and clubroots. Linear discriminant analysis effect size (LefSe) analysis showed that the dominant genera could be regarded as potential biomarkers. The endophyte community in the healthy roots had a more complex network compared with the clubroots. Also, many plant pathogenic Fusarium were isolated from the clubroots by the culture-dependent method. The outcome of this study illustrates that P. brassicae infection may change the fungal endophyte community associated with the roots of tumourous stem mustard and facilitates the entry of soil pathogen into the roots.
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Affiliation(s)
- Xueliang Tian
- Henan institute of science and technology, Xinxiang, Henan, China
| | | | - Zhenchuan Mao
- Institute of Vegetable and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Limei Pan
- Yangtze Normal University, Fuling, Chongqing, China
| | | | - Zhaoming Cai
- Yangtze Normal University, Fuling, Chongqing, China
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282
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The developing relationship between the study of fungal communities and community ecology theory. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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283
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Egidi E, Delgado-Baquerizo M, Plett JM, Wang J, Eldridge DJ, Bardgett RD, Maestre FT, Singh BK. A few Ascomycota taxa dominate soil fungal communities worldwide. Nat Commun 2019; 10:2369. [PMID: 31147554 PMCID: PMC6542806 DOI: 10.1038/s41467-019-10373-z] [Citation(s) in RCA: 215] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/30/2019] [Indexed: 12/22/2022] Open
Abstract
Despite having key functions in terrestrial ecosystems, information on the dominant soil fungi and their ecological preferences at the global scale is lacking. To fill this knowledge gap, we surveyed 235 soils from across the globe. Our findings indicate that 83 phylotypes (<0.1% of the retrieved fungi), mostly belonging to wind dispersed, generalist Ascomycota, dominate soils globally. We identify patterns and ecological drivers of dominant soil fungal taxa occurrence, and present a map of their distribution in soils worldwide. Whole-genome comparisons with less dominant, generalist fungi point at a significantly higher number of genes related to stress-tolerance and resource uptake in the dominant fungi, suggesting that they might be better in colonising a wide range of environments. Our findings constitute a major advance in our understanding of the ecology of fungi, and have implications for the development of strategies to preserve them and the ecosystem functions they provide. Soil fungi play essential roles in ecosystems worldwide. Here, the authors sequence and analyze 235 soil samples collected from across the globe, and identify dominant fungal taxa and their associated environmental attributes.
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Affiliation(s)
- Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.
| | - Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia. .,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA. .,Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología. Universidad Rey Juan Carlos, c/Tulipán s/n, 28933, Móstoles, Spain.
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Richard D Bardgett
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Fernando T Maestre
- Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología. Universidad Rey Juan Carlos, c/Tulipán s/n, 28933, Móstoles, Spain.,Departamento de Ecología and Instituto Multidisciplinar para el Estudio del Medio "Ramon Margalef", Universidad de Alicante, Alicante, Spain
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia. .,Global Centre for Land-Based Innovation, Western Sydney University, Penrith South DC, NSW, 2751, Australia.
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284
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Wu B, Hussain M, Zhang W, Stadler M, Liu X, Xiang M. Current insights into fungal species diversity and perspective on naming the environmental DNA sequences of fungi. Mycology 2019; 10:127-140. [PMID: 31448147 PMCID: PMC6691916 DOI: 10.1080/21501203.2019.1614106] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/22/2019] [Indexed: 01/09/2023] Open
Abstract
The global bio-diversity of fungi has been extensively investigated and their species number has been estimated. Notably, the development of molecular phylogeny has revealed an unexpected fungal diversity and utilisation of culture-independent approaches including high-throughput amplicon sequencing has dramatically increased number of fungal operational taxonomic units. A number of novel taxa including new divisions, classes, orders and new families have been established in last decade. Many cryptic species were identified by molecular phylogeny. Based on recently generated data from culture-dependent and -independent survey on same samples, the fungal species on the earth were estimated to be 12 (11.7-13.2) million compared to 2.2-3.8 million species recently estimated by a variety of the estimation techniques. Moreover, it has been speculated that the current use of high-throughput sequencing techniques would reveal an even higher diversity than our current estimation. Recently, the formal classification of environmental sequences and permission of DNA sequence data as fungal names' type were proposed but strongly objected by the mycologist community. Surveys on fungi in unusual niches have indicated that many previously regarded "unculturable fungi" could be cultured on certain substrates under specific conditions. Moreover, the high-throughput amplicon sequencing, shotgun metagenomics and a single-cell genomics could be a powerful means to detect novel taxa. Here, we propose to separate the fungal types into physical type based on specimen, genome DNA (gDNA) type based on complete genome sequence of culturable and uncluturable fungal specimen and digital type based on environmental DNA sequence data. The physical and gDNA type should have priority, while the digital type can be temporal supplementary before the physical type and gDNA type being available. The fungal name based on the "digital type" could be assigned as the "clade" name + species name. The "clade" name could be the name of genus, family or order, etc. which the sequence of digital type affiliates to. Facilitating future cultivation efforts should be encouraged. Also, with the advancement in knowledge of fungi inhabiting various environments mostly because of rapid development of new detection technologies, more information should be expected for fungal diversity on our planet.
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Affiliation(s)
- Bing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Muzammil Hussain
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Weiwei Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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285
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Ferguson RMW, Garcia‐Alcega S, Coulon F, Dumbrell AJ, Whitby C, Colbeck I. Bioaerosol biomonitoring: Sampling optimization for molecular microbial ecology. Mol Ecol Resour 2019; 19:672-690. [PMID: 30735594 PMCID: PMC6850074 DOI: 10.1111/1755-0998.13002] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 12/31/2022]
Abstract
Bioaerosols (or biogenic aerosols) have largely been overlooked by molecular ecologists. However, this is rapidly changing as bioaerosols play key roles in public health, environmental chemistry and the dispersal ecology of microbes. Due to the low environmental concentrations of bioaerosols, collecting sufficient biomass for molecular methods is challenging. Currently, no standardized methods for bioaerosol collection for molecular ecology research exist. Each study requires a process of optimization, which greatly slows the advance of bioaerosol science. Here, we evaluated air filtration and liquid impingement for bioaerosol sampling across a range of environmental conditions. We also investigated the effect of sampling matrices, sample concentration strategies and sampling duration on DNA yield. Air filtration using polycarbonate filters gave the highest recovery, but due to the faster sampling rates possible with impingement, we recommend this method for fine -scale temporal/spatial ecological studies. To prevent bias for the recovery of Gram-positive bacteria, we found that the matrix for impingement should be phosphate-buffered saline. The optimal method for bioaerosol concentration from the liquid matrix was centrifugation. However, we also present a method using syringe filters for rapid in-field recovery of bioaerosols from impingement samples, without compromising microbial diversity for high -throughput sequencing approaches. Finally, we provide a resource that enables molecular ecologists to select the most appropriate sampling strategy for their specific research question.
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Affiliation(s)
| | | | - Frederic Coulon
- School of Water, Energy and EnvironmentCranfield UniversityCranfieldUK
| | | | - Corinne Whitby
- School of Biological SciencesUniversity of EssexColchesterUK
| | - Ian Colbeck
- School of Biological SciencesUniversity of EssexColchesterUK
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286
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Microbial and metabolic succession on common building materials under high humidity conditions. Nat Commun 2019; 10:1767. [PMID: 30992445 PMCID: PMC6467912 DOI: 10.1038/s41467-019-09764-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/27/2019] [Indexed: 02/06/2023] Open
Abstract
Despite considerable efforts to characterize the microbial ecology of the built environment, the metabolic mechanisms underpinning microbial colonization and successional dynamics remain unclear, particularly at high moisture conditions. Here, we applied bacterial/viral particle counting, qPCR, amplicon sequencing of the genes encoding 16S and ITS rRNA, and metabolomics to longitudinally characterize the ecological dynamics of four common building materials maintained at high humidity. We varied the natural inoculum provided to each material and wet half of the samples to simulate a potable water leak. Wetted materials had higher growth rates and lower alpha diversity compared to non-wetted materials, and wetting described the majority of the variance in bacterial, fungal, and metabolite structure. Inoculation location was weakly associated with bacterial and fungal beta diversity. Material type influenced bacterial and viral particle abundance and bacterial and metabolic (but not fungal) diversity. Metabolites indicative of microbial activity were identified, and they too differed by material. Microbes inhabit built environments and could contribute to degradation of surfaces especially in damp conditions. Here the authors explore how communities of microbes and their metabolites affect four types of built surfaces under varying environmental conditions.
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287
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Checinska Sielaff A, Urbaniak C, Mohan GBM, Stepanov VG, Tran Q, Wood JM, Minich J, McDonald D, Mayer T, Knight R, Karouia F, Fox GE, Venkateswaran K. Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces. MICROBIOME 2019; 7:50. [PMID: 30955503 PMCID: PMC6452512 DOI: 10.1186/s40168-019-0666-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 03/14/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND The International Space Station (ISS) is a closed system inhabited by microorganisms originating from life support systems, cargo, and crew that are exposed to unique selective pressures such as microgravity. To date, mandatory microbial monitoring and observational studies of spacecraft and space stations have been conducted by traditional culture methods, although it is known that many microbes cannot be cultured with standard techniques. To fully appreciate the true number and diversity of microbes that survive in the ISS, molecular and culture-based methods were used to assess microbial communities on ISS surfaces. Samples were taken at eight pre-defined locations during three flight missions spanning 14 months and analyzed upon return to Earth. RESULTS The cultivable bacterial and fungal population ranged from 104 to 109 CFU/m2 depending on location and consisted of various bacterial (Actinobacteria, Firmicutes, and Proteobacteria) and fungal (Ascomycota and Basidiomycota) phyla. Amplicon sequencing detected more bacterial phyla when compared to the culture-based analyses, but both methods identified similar numbers of fungal phyla. Changes in bacterial and fungal load (by culture and qPCR) were observed over time but not across locations. Bacterial community composition changed over time, but not across locations, while fungal community remained the same between samplings and locations. There were no significant differences in community composition and richness after propidium monoazide sample treatment, suggesting that the analyzed DNA was extracted from intact/viable organisms. Moreover, approximately 46% of intact/viable bacteria and 40% of intact/viable fungi could be cultured. CONCLUSIONS The results reveal a diverse population of bacteria and fungi on ISS environmental surfaces that changed over time but remained similar between locations. The dominant organisms are associated with the human microbiome and may include opportunistic pathogens. This study provides the first comprehensive catalog of both total and intact/viable bacteria and fungi found on surfaces in closed space systems and can be used to help develop safety measures that meet NASA requirements for deep space human habitation. The results of this study can have significant impact on our understanding of other confined built environments on the Earth such as clean rooms used in the pharmaceutical and medical industries.
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Affiliation(s)
- Aleksandra Checinska Sielaff
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA
- Washington State University Extension - Youth and Families Program Unit, Washington State University, Pullman, WA, USA
| | - Camilla Urbaniak
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA
| | - Ganesh Babu Malli Mohan
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA
| | - Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Quyen Tran
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Jason M Wood
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA
| | - Jeremiah Minich
- Marine Biology Research Division, Scripps Institute of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Teresa Mayer
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Fathi Karouia
- NASA Ames Research Center, Space Bioscience Division, Moffett Field, Mountain View, CA, USA
- Research Center, Moffett Field, Mountain View, CA, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group,, Pasadena, CA, USA.
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288
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Prussin AJ, Torres PJ, Shimashita J, Head SR, Bibby KJ, Kelley ST, Marr LC. Seasonal dynamics of DNA and RNA viral bioaerosol communities in a daycare center. MICROBIOME 2019; 7:53. [PMID: 30935423 PMCID: PMC6444849 DOI: 10.1186/s40168-019-0672-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/22/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiome (virome). Longitudinal microbiome studies provide insight into the stability and dynamics of microbial communities; however, few such studies exist for the microbiome of the BE, and most have focused on bacteria. Here, we present a longitudinal, metagenomic-based analysis of the airborne DNA and RNA virome of a children's daycare center. Specifically, we investigate how the airborne virome varies as a function of season and human occupancy, and we identify possible sources of the viruses and their hosts, mainly humans, animals, plants, and insects. RESULTS Season strongly influenced the airborne viral community composition, and a single sample collected when the daycare center was unoccupied suggested that occupancy also influenced the community. The pattern of influence differed between DNA and RNA viromes. Human-associated viruses were much more diverse and dominant in the winter, while the summertime virome contained a high relative proportion and diversity of plant-associated viruses. CONCLUSIONS This airborne microbiome in this building exhibited seasonality in its viral community but not its bacterial community. Human occupancy influenced both types of communities. By adding new data about the viral microbiome to complement burgeoning information about the bacterial and fungal microbiomes, this study contributes to a more complete understanding of the airborne microbiome.
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Affiliation(s)
- Aaron J. Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Pedro J. Torres
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - John Shimashita
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Steven R. Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Kyle J. Bibby
- Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - Linsey C. Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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289
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Richardson M, Bowyer P, Sabino R. The human lung and Aspergillus: You are what you breathe in? Med Mycol 2019; 57:S145-S154. [PMID: 30816978 PMCID: PMC6394755 DOI: 10.1093/mmy/myy149] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/01/2018] [Accepted: 12/10/2018] [Indexed: 12/14/2022] Open
Abstract
The diversity of fungal species comprising the lung mycobiome is a reflection of exposure to environmental and endogenous filamentous fungi and yeasts. Most lung mycobiome studies have been culture-based. A few have utilized next generation sequencing (NGS). Despite the low number of published NGS studies, several themes emerge from the literature: (1) moulds and yeasts are present in the human respiratory tract, even during health; (2) the fungi present in the respiratory tract are highly variable between individuals; and (3) many diseases are accompanied by decreased diversity of fungi in the lungs. Even in patients with the same disease, different patients have been shown to harbor distinct fungal communities. Those fungal species present in any one individual may represent a patient's unique environmental exposure(s), either to species restricted to the indoor environment, for example, Penicillium, or species found in the outdoor environment such as Aspergillus, wood and vegetation colonizing fungi and plant pathogens. In addition to causing clinical fungal infections, the lung mycobiome may have inflammatory effects that can cause or worsen lung disease. Most respiratory diseases that have been studied, have been associated with decreases in fungal diversity. However, none of these diversity studies distinguish between accidental, transient fungal colonizers and true residents of the respiratory tract. Where does Aspergillus feature in the mycobiomes of the respiratory tract? Do these mycobiomes reflect the diversity of fungi in outdoor and internal environments? These intriguing questions are explored here.
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Affiliation(s)
- Malcolm Richardson
- Mycology Reference Centre Manchester, ECMM Centre of Excellence, Manchester University NHS Foundation Trust, Manchester, UK.,Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul Bowyer
- Division of Infection, Immunity & Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Raquel Sabino
- Nacional Institute of Health Dr. Ricardo Jorge - URSZ- Infectious Diseases Department, Lisbon, Portugal
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290
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Sylvain IA, Adams RI, Taylor JW. A different suite: The assemblage of distinct fungal communities in water-damaged units of a poorly-maintained public housing building. PLoS One 2019; 14:e0213355. [PMID: 30883565 PMCID: PMC6422403 DOI: 10.1371/journal.pone.0213355] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/19/2019] [Indexed: 11/19/2022] Open
Abstract
Water-damaged housing has been associated with a number of negative health outcomes, principally respiratory disease and asthma. Much of what we know about fungi associated with water-damaged buildings has come from culture-based and immunochemical methods. Few studies have used high-throughput sequencing technologies to assess the impact of water-damage on microbial communities in residential buildings. In this study we used amplicon sequencing and quantitative-PCR to evaluate fungal communities on surfaces and in airborne dust in multiple units of a condemned public housing project located in the San Francisco Bay Area. We recruited 21 households to participate in this study and characterized their apartments as either a unit with visible mold or no visible mold. We sampled airborne fungi from dust settled over a month-long time period from the outdoors, in units with no visible mold, and units with visible mold. In units with visible mold we additionally sampled the visible fungal colonies from bathrooms, kitchens, bedrooms, and living rooms. We found that fungal biomass in settled dust was greater outdoors compared to indoors, but there was no significant difference of fungal biomass in units with visible mold and no visible mold. Interestingly, we found that fungal diversity was reduced in units with visible mold compared to units with no visible mold and the outdoors. Units with visible mold harbored fungal communities distinct from units with no visible mold and the outdoors. Units with visible mold had a greater abundance of taxa within the classes Eurotiomycetes, Saccharomycetes, and Wallemiomycetes. Colonies of fungi collected from units with visible mold were dominated by two Cladosporium species, C. sphaerospermum and C halotolerans. This study demonstrates that high-throughput sequencing of fungi indoors can be a useful strategy for distinguishing distinct microbial exposures in water-damaged homes with visible and nonvisible mold growth, and may provide a microbial means for identifying water damaged housing.
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Affiliation(s)
- Iman A. Sylvain
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Rachel I. Adams
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
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291
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Sheng R, Li K, Zhang W, Wang H, Liu H, Zhu X, Wu H, Zhang X, Lin Q, Sun X, Tang Y, A L, Wei W. Differentiations of determinants for the community compositions of bacteria, fungi, and nitrogen fixers in various steppes. Ecol Evol 2019; 9:3239-3250. [PMID: 30962889 PMCID: PMC6434564 DOI: 10.1002/ece3.4940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/01/2019] [Accepted: 01/07/2019] [Indexed: 11/07/2022] Open
Abstract
Different types of steppes could provide heterogeneous habitat environments for underground microorganisms, but much less is known about how soil microbes fit the distinct habitats and what are the underlying mechanisms in shaping their community patterns.We simultaneously examined the community compositions and structures of soil bacteria, fungi, and diazotrophs across desert, typical, and meadow steppes in Inner Mongolia using high-throughput sequencing.The results showed that soil bacteria, fungi, and diazotrophs exhibited different distribution patterns across steppe types. Although different steppes displayed obvious differences in climate conditions, plant traits, and soil properties, most of bacterial species were shared by all the steppes while only a few species were unique, indicating that the soil bacterial compositions were hardly influenced by the steppe types. Nevertheless, the habitat heterogeneity could cause shifts in the relative abundance of some bacterial groups, which resulted in significant changes in the community structure of soil bacteria across steppes. However, the fungal community compositions and structures were similar in typical and meadow steppes but that in desert steppe were significantly different. Whereas, the community compositions and structures of diazotrophs were strongly related to the steppe types. In this study, the similar parent material backgrounds of the steppe soils might be the important factor in shaping the homologous bacterial compositions. However, the variations in soil fertility, soil water repellency, and plant species across steppes would be the major driving forces in regulating the compositions and structures of fungal communities, while the diazotrophic communities would be more closely related to the changes in plant traits and soil fertility among steppes.Our results provided evidence of habitat specificity for different microbial groups and their underlying drivers.
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Affiliation(s)
- Rong Sheng
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Ke Li
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Wenzhao Zhang
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Hai Wang
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Honglin Liu
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Xiaoya Zhu
- College of Resources and Environmental SciencesChina Agricultural UniversityBeijingChina
| | - Hongxin Wu
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Xiaoqing Zhang
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Qimei Lin
- College of Resources and Environmental SciencesChina Agricultural UniversityBeijingChina
| | - Xuecheng Sun
- College of Resources and Environmental SciencesHuazhong Agricultural UniversityWuhanChina
| | - Yafang Tang
- Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, College of Life Science and TechnologyHubei Engineering UniversityXiaoganChina
| | - Lamus A
- Institute of Grassland ScienceChinese Academy of Agricultural SciencesHuhehaoteChina
| | - Wenxue Wei
- Key Laboratory of Agro‐ecological Processes in Subtropical Regions and Taoyuan Agro‐ecosystem Research Station, Soil Molecular Ecology Section, Institute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
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292
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Wei M, Xu C, Xu X, Zhu C, Li J, Lv G. Characteristics of atmospheric bacterial and fungal communities in PM 2.5 following biomass burning disturbance in a rural area of North China Plain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:2727-2739. [PMID: 30463127 DOI: 10.1016/j.scitotenv.2018.09.399] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/29/2018] [Accepted: 09/30/2018] [Indexed: 05/23/2023]
Abstract
Biomass burning (BB) in North China Plain has been urgent issue in recent years due to the severe environmental impaction. Bacteria and fungi are ubiquitous in particulate matter. Their taxonomic composition, concentration, ecophysiological functions have potentially important implications in atmospheric biochemical cycle and human health. However, current knowledge about airborne microbes during biomass burning period is scant. Here we investigated bacterial and fungal community composition, abundance and potential function in Yucheng, the center of the North China Plain during summer harvest season in 2014. Monthly field observation suggested serious pollution with high concentration of PM2.5 and water-soluble ions during biomass burning period. Elevated total bacterial and fungal concentration determined by real-time quantitative PCR was observed for samples during burning events. The predominant bacterial taxa were gram-negative, e.g. Acinetobacter, Cyanobacterium, Janthinobacterium, Massilia, Pseudomonas, accounted for 70.9% of total bacteria. The filamentous fungi Alternaria, Aspergillus, Cladosporium and Penicillium were predominant fungal genera. Metastats analysis showed significant disparity in terms of carbohydrate, amino acids metabolism, human and plant disease predicted by PICRUSt analysis between BB and non-BB events. Microbial community structure were mainly influenced by organic carbon and water-soluble ions (magnesium and potassium) suggested by redundancy analysis (RDA) and co-occurrence analysis. Our data yielded insights into microbial community dynamics following biomass burning disturbance. This study may provide potentially important reference for environmental, agricultural and health management.
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Affiliation(s)
- Min Wei
- College of Geography and Environment, Shandong Normal University, Ji'nan 250014, China; Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China.
| | - Caihong Xu
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Xianmang Xu
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Chao Zhu
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Jiarong Li
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
| | - Ganglin Lv
- Environment Research Institute, School of Environmental Science and Engineering, Shandong University, Ji'nan 250100, China
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293
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Carpagnano GE, Susca A, Scioscia G, Lacedonia D, Cotugno G, Soccio P, Santamaria S, Resta O, Logrieco G, Foschino Barbaro MP. A survey of fungal microbiota in airways of healthy volunteer subjects from Puglia (Apulia), Italy. BMC Infect Dis 2019; 19:78. [PMID: 30669978 PMCID: PMC6341515 DOI: 10.1186/s12879-019-3718-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/11/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The human respiratory tract represents the major portal of entry for numerous microorganisms, primarily those occurring as airborne particles such as viral and bacterial entities, or fungal spores. Microorganism characteristics coupled with the local host immune response will determine whether they will be cleared or adhere and colonize the airways leading to acute or chronic pulmonary disease. Like bacteria, fungi can cause severe lung diseases, but their infection rates are much lower. The lung microbiota is commonly sampled using relatively invasive bronchoscopic procedures. Exhaled breath condensate (EBC) collection offers a potentially less invasive alternative for lung microbiota sampling. This study tries to determine the composition of fungal communities in a cohort of healthy adult volunteer subjects from Puglia (Apulia), Italy. METHODS Fungi diversity in 27 EBC samples collected from Italian adult volunteers was investigated using conventional microbiological culturing and DNA sequencing approach. RESULTS Ten tested subjects (37,03%) turned out to present fungi in the EBC. We observed complex fungal communities, in which more than 10% of the isolated species are represented by Aspergillus sydowii (14,8%) and Cladosporium spp (11,11%). Three subjects that showed fungal presence in EBC have been diagnosed with a respiratory disease. CONCLUSIONS We present a survey of an important scientific field in its early stages that is fungal contamination of airways of healthy subjects in a small geographic area. Furthermore, we interpreted our results to highlight the potential role of fungi in the context of respiratory diseases.
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Affiliation(s)
- Giovanna Elisiana Carpagnano
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy.
| | - Antonia Susca
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Giulia Scioscia
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy
| | - Donato Lacedonia
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy
| | - Grazia Cotugno
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy
| | - Piera Soccio
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy
| | - Sonia Santamaria
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy
| | - Onofrio Resta
- Department of Respiratory Diseases, University of Bari, Bari, Italy
| | | | - Maria Pia Foschino Barbaro
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Foggia, Italy
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294
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Shan Y, Wu W, Fan W, Haahtela T, Zhang G. House dust microbiome and human health risks. Int Microbiol 2019; 22:297-304. [DOI: 10.1007/s10123-019-00057-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 12/30/2022]
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295
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Liu H, Pan F, Han X, Song F, Zhang Z, Yan J, Xu Y. Response of Soil Fungal Community Structure to Long-Term Continuous Soybean Cropping. Front Microbiol 2019; 9:3316. [PMID: 30687292 PMCID: PMC6333693 DOI: 10.3389/fmicb.2018.03316] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/20/2018] [Indexed: 11/23/2022] Open
Abstract
Long-term continuous soybean cropping can lead to the aggravation of soil fungal disease. However, the manner in which the fungal community and functional groups of fungi are affected by continuous soybean cropping remains unclear. We investigated the fungal abundance, composition and diversity during soybean rotation (RS), 2-year (SS) and long-term (CS) continuous soybean cropping systems using quantitative real-time PCR and high-throughput sequencing. The results showed that the fungal abundance was significantly higher in CS than in SS and RS. CS altered the fungal composition. Compared with RS, SS had an increase of 29 and a decrease of 12 genera in fungal relative abundance, and CS increased 38 and decreased 17 genera. The Shannon index was significantly higher in CS and SS than in RS. The result of principal coordinate analysis (PCoA) showed that CS and SS grouped together and were clearly separated from RS on the PCoA1. A total of 32 features accounted for the differences in fungal composition across RS, SS, and CS. The relative abundance of 10 potentially pathogenic and 10 potentially beneficial fungi changed, and most of their relative abundances dramatically increased in SS and CS compared with RS. Our study indicated that CS results in selective stress on pathogenic and beneficial fungi and causes the development of the fungal community structure that is antagonistic to plant health.
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Affiliation(s)
- Hang Liu
- National Observation Station of Hailun Agro-ecology System, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fengjuan Pan
- National Observation Station of Hailun Agro-ecology System, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaozeng Han
- National Observation Station of Hailun Agro-ecology System, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Fengbin Song
- National Observation Station of Hailun Agro-ecology System, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhiming Zhang
- National Observation Station of Hailun Agro-ecology System, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Jun Yan
- National Observation Station of Hailun Agro-ecology System, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yanli Xu
- National Observation Station of Hailun Agro-ecology System, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
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296
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Stephens B, Azimi P, Thoemmes MS, Heidarinejad M, Allen JG, Gilbert JA. Microbial Exchange via Fomites and Implications for Human Health. CURRENT POLLUTION REPORTS 2019; 5:198-213. [PMID: 34171005 PMCID: PMC7149182 DOI: 10.1007/s40726-019-00123-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
PURPOSE OF REVIEW Fomites are inanimate objects that become colonized with microbes and serve as potential intermediaries for transmission to/from humans. This review summarizes recent literature on fomite contamination and microbial survival in the built environment, transmission between fomites and humans, and implications for human health. RECENT FINDINGS Applications of molecular sequencing techniques to analyze microbial samples have increased our understanding of the microbial diversity that exists in the built environment. This growing body of research has established that microbial communities on surfaces include substantial diversity, with considerable dynamics. While many microbial taxa likely die or lay dormant, some organisms survive, including those that are potentially beneficial, benign, or pathogenic. Surface characteristics also influence microbial survival and rates of transfer to and from humans. Recent research has combined experimental data, mechanistic modeling, and epidemiological approaches to shed light on the likely contributors to microbial exchange between fomites and humans and their contributions to adverse (and even potentially beneficial) human health outcomes. SUMMARY In addition to concerns for fomite transmission of potential pathogens, new analytical tools have uncovered other microbial matters that can be transmitted indirectly via fomites, including entire microbial communities and antibiotic-resistant bacteria. Mathematical models and epidemiological approaches can provide insight on human health implications. However, both are subject to limitations associated with study design, and there is a need to better understand appropriate input model parameters. Fomites remain an important mechanism of transmission of many microbes, along with direct contact and short- and long-range aerosols.
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Affiliation(s)
- Brent Stephens
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Alumni Memorial Hall 228E, 3201 South Dearborn Street, Chicago, IL 60616 USA
| | - Parham Azimi
- Environmental Health Department, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Megan S. Thoemmes
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA USA
| | - Mohammad Heidarinejad
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Alumni Memorial Hall 228E, 3201 South Dearborn Street, Chicago, IL 60616 USA
| | - Joseph G. Allen
- Environmental Health Department, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA USA
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Habtom H, Pasternak Z, Matan O, Azulay C, Gafny R, Jurkevitch E. Applying microbial biogeography in soil forensics. Forensic Sci Int Genet 2018; 38:195-203. [PMID: 30447564 DOI: 10.1016/j.fsigen.2018.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 10/10/2018] [Accepted: 11/07/2018] [Indexed: 11/28/2022]
Abstract
The ubiquity, heterogeneity and transferability of soil makes it useful as evidence in criminal investigations, especially using new methods that survey the microbial DNA it contains. However, to be used effectively and reliably, more needs to be learned about the natural distribution patterns of microbial communities in soil. In this study we examine these patterns in detail, at local to regional scales (2 m-260 km), across an environmental gradient in three different soil types. Geographic location was found to be more important than soil type in determining the microbial community composition: communities from the same site but different soil types, although significantly different from each other, were still much more similar to each other than were communities from the same soil type but from different sites. At a local scale (25-1000 m), distance-decay relationships were observed in all soil types: the farther apart two soil communities were located, even in the same soil type, the more they differed. At regional-scale distances (1-260 km), differences between communities did not increase with increased geographic distance between them, and the dominant factor determining the community profile was the physico-chemical environment, most notably annual precipitation (R2 = 0.69), soil sodium (R2 = 0.49) and soil ammonium (R2 = 0.47) levels. We introduce a likelihood-ratio framework for quantitative evaluation of soil microbial DNA profile evidence in casework. In conclusion, these profiles, along with detailed knowledge of natural soil microbial biogeography, provide valuable forensic information on soil sample comparison and allow the determination of approximate source location on large (hundreds of km) spatial scales. Moreover, at small spatial scales it may enable pinpointing the source location of a sample to within at least 25 m, regardless of soil type and environmental conditions.
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Affiliation(s)
- Habteab Habtom
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Ofra Matan
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Chen Azulay
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ron Gafny
- Forensic Biology Laboratory, Division of Identification and Forensic Science, Israel Police, National Headquarters, Haim Bar-Lev Road, Jerusalem, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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298
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Mahnert A, Ortega RA, Berg C, Grube M, Berg G. Leaves of Indoor Ornamentals Are Biodiversity and Functional Hotspots for Fungi. Front Microbiol 2018; 9:2343. [PMID: 30327646 PMCID: PMC6174238 DOI: 10.3389/fmicb.2018.02343] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/12/2018] [Indexed: 12/18/2022] Open
Abstract
Leaf-inhabiting fungi are an important, but often overlooked component of molecular biodiversity studies. To understand their diversity and function in relation to plant species and climate, the phyllospheres of 14 phylogenetically diverse ornamental plant species were analyzed under different controlled greenhouse conditions. We found unexpectedly high fungal diversity (H' = 2.8-6.5), OTU numbers (449-1050) and abundances (103-106 CFU cm-2 leaf surface) associated with all plants studied indoors. Despite experimental limitations, the composition of fungal communities were inclined toward a plant species-dependent pattern compared to the ambient climatic variables. Most detected fungi were patho- and saprotrophs showing a yeast-like growth morphology and were associated to the groups of endophytes and potential plant pathogens in a plant species-specific manner. A representative strain collection showed that 1/3 of the tested fungi (mainly Penicillium, Cladosporium, and Cryptococcus spp.) were able to inhibit mycelial growth and 2/3 inhibit sporulation of the plant pathogen Botrytis cinerea by the production of antifungal volatile organic compounds (VOCs) completely. This study indicates that plant leaves harbor a stable phyllosphere fungal diversity in diverse microclimates and enrich distinctive functional guilds.
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Affiliation(s)
- Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Rocel Amor Ortega
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Department of Biology, College of Science, University of the Philippines Baguio, Baguio, Philippines
| | - Christian Berg
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria
| | - Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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299
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Nygaard AB, Charnock C. Longitudinal development of the dust microbiome in a newly opened Norwegian kindergarten. MICROBIOME 2018; 6:159. [PMID: 30219104 PMCID: PMC6138906 DOI: 10.1186/s40168-018-0553-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 09/05/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND In Norway, 91% of children aged 1-5 attend kindergarten where they are exposed to indoor microbiomes which can have relevance for development and health. In order to gain a better understanding of the composition of the indoor microbiome and how it is affected by occupancy over time, floor dust samples from a newly opened kindergarten were investigated. Samples were collected during an 11-month period. Samples were analyzed for bacterial composition using 16S rRNA gene sequencing. Samples were also screened for four clinically relevant antibiotic resistance genes. In addition, Petrifilm analyses were used to evaluate surface hygiene. RESULTS Significant changes in the microbial community composition were observed over time (PERMANOVA, P < 0.05). Particularly, changes in the abundance and the proportions of human associated bacteria were found. A decrease in the prevalence of Propionibacterium from over 16% abundance to less than 1% and an increase in Streptococcus from 10 to 16% were the most significant findings. Four classes of clinically relevant antibiotic resistance genes were tested for; three were detected in the dust, indicating the presence of resistant bacteria and a potential for resistance spread. Petrifilm analysis showed that some surfaces in the kindergarten were of consistent poor hygienic quality, and new hygienic routines are required. CONCLUSIONS This study, which is the first of its kind performed at a newly opened kindergarten, reveals changes in the microbiome over time as well as the presence of antibiotic resistance genes and hygiene issues which are of relevance for occupant health.
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Affiliation(s)
- Anders B Nygaard
- Disease and Environmental Exposures Research Group, Department of Life Sciences and Health, OsloMet - Oslo Metropolitan University (OsloMet), Oslo, Norway.
- Department of Civil Engineering and Energy Technology, OsloMet, Oslo, Norway.
| | - Colin Charnock
- Disease and Environmental Exposures Research Group, Department of Life Sciences and Health, OsloMet - Oslo Metropolitan University (OsloMet), Oslo, Norway
- Department of Life Sciences and Health, OsloMet, Oslo, Norway
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