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Wagner R, Montoya L, Head JR, Campo S, Remais J, Taylor JW. Coccidioides undetected in soils from agricultural land and uncorrelated with time or the greater soil fungal community on undeveloped land. PLoS Pathog 2023; 19:e1011391. [PMID: 37228157 PMCID: PMC10246812 DOI: 10.1371/journal.ppat.1011391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 06/07/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Coccidioidomycosis is a typically respiratory fungal disease that, in the United States, occurs primarily in Arizona and California. In California, most coccidioidomycosis cases occur in the San Joaquin Valley, a primarily agricultural region where the disease poses a risk for outdoor workers. We collected 710 soil samples and 265 settled dust samples from nine sites in the San Joaquin Valley and examined how Coccidioides detection varied by month, site, and the presence and abundance of other fungal species. We detected Coccidioides in 89 of 238 (37.4%) rodent burrow soil samples at five undeveloped sites and were unable to detect Coccidioides in any of 472 surface and subsurface soil samples at four agricultural sites. In what is the largest sampling effort undertaken on agricultural land, our results provide no evidence that agricultural soils in the San Joaquin Valley harbor Coccidioides. We found no clear association between Coccidioides and the greater soil fungal community, but we identified 19 fungal indicator species that were significantly associated with Coccidioides detection in burrows. We also did not find a seasonal pattern in Coccidioides detection in the rodent burrow soils we sampled. These findings suggest both the presence of a spore bank and that coccidioidomycosis incidence may be more strongly associated with Coccidioides dispersal than Coccidioides growth. Finally, we were able to detect Coccidioides in only five of our 265 near-surface settled dust samples, one from agricultural land, where Coccidioides was undetected in soils, and four from undeveloped land, where Coccidioides was common in the rodent burrow soils we sampled. Our ability to detect Coccidioides in few settled dust samples indicates that improved methods are likely needed moving forward, though raises questions regarding aerial dispersal in Coccidioides, whose key transmission event likely occurs over short distances in rodent burrows from soil to naïve rodent lungs.
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Affiliation(s)
- Robert Wagner
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Liliam Montoya
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Jennifer R. Head
- Division of Epidemiology, University of California Berkeley, Berkeley, California, United States of America
| | - Simon Campo
- Division of Environmental Health Sciences, University of California Berkeley, Berkeley, California, United States of America
| | - Justin Remais
- Division of Environmental Health Sciences, University of California Berkeley, Berkeley, California, United States of America
| | - John W. Taylor
- Department of Plant & Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
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A light-sensing system in the common ancestor of the fungi. Curr Biol 2022; 32:3146-3153.e3. [PMID: 35675809 PMCID: PMC9616733 DOI: 10.1016/j.cub.2022.05.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 04/04/2022] [Accepted: 05/12/2022] [Indexed: 11/25/2022]
Abstract
Diverse light-sensing organs (i.e., eyes) have evolved across animals. Interestingly, several subcellular analogs have been found in eukaryotic microbes.1 All of these systems have a common “recipe”: a light occluding or refractory surface juxtaposed to a membrane-layer enriched in type I rhodopsins.1, 2, 3, 4 In the fungi, several lineages have been shown to detect light using a diversity of non-homologous photo-responsive proteins.5, 6, 7 However, these systems are not associated with an eyespot-like organelle with one exception found in the zoosporic fungus Blastocladiella emersonii (Be).8Be possesses both elements of this recipe: an eyespot composed of lipid-filled structures (often called the side-body complex [SBC]), co-localized with a membrane enriched with a gene-fusion protein composed of a type I (microbial) rhodopsin and guanylyl cyclase enzyme domain (CyclOp-fusion protein).8,9 Here, we identify homologous pathway components in four Chytridiomycota orders (Chytridiales, Synchytriales, Rhizophydiales, and Monoblepharidiales). To further explore the architecture of the fungal zoospore and its lipid organelles, we reviewed electron microscopy data (e.g., the works of Barr and Hartmann10 and Reichle and Fuller11) and performed fluorescence-microscopy imaging of four CyclOp-carrying zoosporic fungal species, showing the presence of a variety of candidate eyespot-cytoskeletal ultrastructure systems. We then assessed the presence of canonical photoreceptors across the fungi and inferred that the last common fungal ancestor was able to sense light across a range of wavelengths using a variety of systems, including blue-green-light detection. Our data imply, independently of how the fungal tree of life is rooted, that the apparatus for a CyclOp-organelle light perception system was an ancestral feature of the fungi. A wide diversity of flagellated fungi possess the CyclOp light response circuit The same fungi possess the subcellular equipment to build lipid-based eyespots The last common ancestor of fungi possessed the CyclOp eyespot system The ancestral fungus could see a rainbow of light wavelengths
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Ilicic D, Woodhouse J, Karsten U, Zimmermann J, Wichard T, Quartino ML, Campana GL, Livenets A, Van den Wyngaert S, Grossart HP. Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones. Front Microbiol 2022; 13:805694. [PMID: 35308360 PMCID: PMC8931407 DOI: 10.3389/fmicb.2022.805694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/12/2022] [Indexed: 01/04/2023] Open
Abstract
Aquatic ecosystems are frequently overlooked as fungal habitats, although there is increasing evidence that their diversity and ecological importance are greater than previously considered. Aquatic fungi are critical and abundant components of nutrient cycling and food web dynamics, e.g., exerting top-down control on phytoplankton communities and forming symbioses with many marine microorganisms. However, their relevance for microphytobenthic communities is almost unexplored. In the light of global warming, polar regions face extreme changes in abiotic factors with a severe impact on biodiversity and ecosystem functioning. Therefore, this study aimed to describe, for the first time, fungal diversity in Antarctic benthic habitats along the salinity gradient and to determine the co-occurrence of fungal parasites with their algal hosts, which were dominated by benthic diatoms. Our results reveal that Ascomycota and Chytridiomycota are the most abundant fungal taxa in these habitats. We show that also in Antarctic waters, salinity has a major impact on shaping not just fungal but rather the whole eukaryotic community composition, with a diversity of aquatic fungi increasing as salinity decreases. Moreover, we determined correlations between putative fungal parasites and potential benthic diatom hosts, highlighting the need for further systematic analysis of fungal diversity along with studies on taxonomy and ecological roles of Chytridiomycota.
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Affiliation(s)
- Doris Ilicic
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Jason Woodhouse
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Ulf Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Jonas Zimmermann
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Jena, Germany
| | | | - Gabriela Laura Campana
- Department of Coastal Biology, Argentinean Antarctic Institute, Buenos Aires, Argentina
- Department of Basic Sciences, National University of Luján, Luján, Buenos Aires, Argentina
| | - Alexandra Livenets
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | | | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Hans-Peter Grossart,
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Rabee AE, Forster R, Elekwachi C, Sabra E, Lamara M. Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing. PeerJ 2020; 8:e10184. [PMID: 33194403 PMCID: PMC7603790 DOI: 10.7717/peerj.10184] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/23/2020] [Indexed: 11/20/2022] Open
Abstract
Breakdown of plant biomass in rumen depends on interactions between bacteria, archaea, fungi, and protozoa; however, the majority of studies of the microbiome of ruminants, including the few studies of the rumen of camels, only studied one of these microbial groups. In this study, we applied total rRNA sequencing to identify active microbial communities in 22 solid and liquid rumen samples from 11 camels. These camels were reared at three stations that use different feeding systems: clover, hay and wheat straw (G1), fresh clover (G2), and wheat straw (G3). Bacteria dominated the libraries of sequence reads generated from all rumen samples, followed by protozoa, archaea, and fungi respectively. Firmicutes, Thermoplasmatales, Diplodinium, and Neocallimastix dominated bacterial, archaeal, protozoal and fungal communities, respectively in all samples. Libraries generated from camels reared at facility G2, where they were fed fresh clover, showed the highest alpha diversity. Principal co-ordinate analysis and linear discriminate analysis showed clusters associated with facility/feed and the relative abundance of microbes varied between liquid and solid fractions. This provides preliminary evidence that bacteria dominate the microbial communities of the camel rumen and these communities differ significantly between populations of domesticated camels.
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Affiliation(s)
- Alaa Emara Rabee
- Animal and Poultry Nutrition Department, Desert Research Center, Cairo, Cairo, Egypt
| | - Robert Forster
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Chijioke Elekwachi
- Lethbridge Research and Development Centre, Agriculture and Agrifood Canada, Lethbridge, AB, Canada
| | - Ebrahim Sabra
- Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Menoufia, Egypt
| | - Mebarek Lamara
- Institut de Recherche sur les Forêts, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
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Barelli L, Waller AS, Behie SW, Bidochka MJ. Plant microbiome analysis after Metarhizium amendment reveals increases in abundance of plant growth-promoting organisms and maintenance of disease-suppressive soil. PLoS One 2020; 15:e0231150. [PMID: 32275687 PMCID: PMC7147777 DOI: 10.1371/journal.pone.0231150] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 03/17/2020] [Indexed: 12/30/2022] Open
Abstract
The microbial community in the plant rhizosphere is vital to plant productivity and disease resistance. Alterations in the composition and diversity of species within this community could be detrimental if microbes suppressing the activity of pathogens are removed. Species of the insect-pathogenic fungus, Metarhizium, commonly employed as biological control agents against crop pests, have recently been identified as plant root colonizers and provide a variety of benefits (e.g. growth promotion, drought resistance, nitrogen acquisition). However, the impact of Metarhizium amendment on the rhizosphere microbiome has yet to be elucidated. Using Illumina sequencing, we examined the community profiles (bacteria and fungi) of common bean (Phaseolus vulgaris) rhizosphere (loose soil and plant root) after amendment with M. robertsii conidia, in the presence and absence of an insect host. Although alpha diversity was not significantly affected overall, there were numerous examples of plant growth-promoting organisms that significantly increased with Metarhizium amendment (Bradyrhizobium, Flavobacterium, Chaetomium, Trichoderma). Specifically, the abundance of Bradyrhizobium, a group of nitrogen-fixing bacteria, was confirmed to be increased using a qPCR assay with genus-specific primers. In addition, the ability of the microbiome to suppress the activity of a known bean root pathogen was assessed. The development of disease symptoms after application with Fusarium solani f. sp. phaseoli was visible in the hypocotyl and upper root of plants grown in sterilized soil but was suppressed during growth in microbiome soil and soil treated with M. robertsii. Successful amendment of agricultural soils with biocontrol agents such as Metarhizium necessitates a comprehensive understanding of the effects on the diversity of the rhizosphere microbiome. Such research is fundamentally important towards sustainable agricultural practices to improve overall plant health and productivity.
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Affiliation(s)
- Larissa Barelli
- Department of Biotechnology, Brock University, St. Catharines, ON, Canada
| | - Alison S. Waller
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
| | - Scott W. Behie
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Michael J. Bidochka
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
- * E-mail:
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Zhu J, Ren Z, Huang B, Cao A, Wang Q, Yan D, Ouyang C, Wu J, Li Y. Effects of Fumigation with Allyl Isothiocyanate on Soil Microbial Diversity and Community Structure of Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1226-1236. [PMID: 31922739 DOI: 10.1021/acs.jafc.9b07292] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
As a substitute for methyl bromide, effects of allyl isothiocyanate (AITC) on nontarget microorganisms in soil are poorly understood. This study measured the half-life of AITC in the soil as well as its effects on the soil substrate-induced respiration (SIR) and on communities of soil bacteria and fungi. The results showed that AITC had a short half-life and a short-term inhibition of SIR; high-throughput sequencing analysis showed that AITC had less effect on bacterial than fungal communities. Fumigation reduced the diversity of soil bacteria temporarily, but stimulated the diversity of soil fungi in the long-term and significantly changed the structure of the fungal community. Following AITC fumigation there were significant increases in the relative abundance of probiotics such as Sphingomonas, Streptomyces, Hypocreales, Acremonium, Aspergillus, and Pseudallescheria that help to control plant diseases. Our study provided useful information for assessing the ecological safety of AITC.
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Affiliation(s)
- Jiahong Zhu
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Zongjie Ren
- National Agricultural Technology Extension Service Center , Ministry of Agriculture and Rural Affairs , Beijing 100125 , China
| | - Bin Huang
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Aocheng Cao
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Qiuxia Wang
- 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
| | - Canbin Ouyang
- Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
| | - Jiajia Wu
- 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
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7
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The disappearing periglacial ecosystem atop Mt. Kilimanjaro supports both cosmopolitan and endemic microbial communities. Sci Rep 2019; 9:10676. [PMID: 31337772 PMCID: PMC6650471 DOI: 10.1038/s41598-019-46521-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 06/18/2019] [Indexed: 11/08/2022] Open
Abstract
Microbial communities have not been studied using molecular approaches at high elevations on the African continent. Here we describe the diversity of microbial communities from ice and periglacial soils from near the summit of Mt. Kilimanjaro by using both Illumina and Sanger sequencing of 16S and 18S rRNA genes. Ice and periglacial soils contain unexpectedly diverse and rich assemblages of Bacteria and Eukarya indicating that there may be high rates of dispersal to the top of this tropical mountain and/or that the habitat is more conducive to microbial life than was previously thought. Most bacterial OTUs are cosmopolitan and an analysis of isolation by geographic distance patterns of the genus Polaromonas emphasized the importance of global Aeolian transport in the assembly of bacterial communities on Kilimanjaro. The eukaryotic communities were less diverse than the bacterial communities and showed more evidence of dispersal limitations and apparent endemism. Cercozoa dominated the 18S communities, including a high abundance of testate amoebae and a high diversity of endemic OTUs within the Vampyrellida. These results argue for more intense study of this unique high-elevation "island of the cryosphere" before the glaciers of Kilimanjaro disappear forever.
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Hahn PG, Bullington L, Larkin B, LaFlamme K, Maron JL, Lekberg Y. Effects of Short- and Long-Term Variation in Resource Conditions on Soil Fungal Communities and Plant Responses to Soil Biota. FRONTIERS IN PLANT SCIENCE 2018; 9:1605. [PMID: 30459793 DOI: 10.6084/m9.figshare.5926378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/17/2018] [Indexed: 05/23/2023]
Abstract
Soil biota can strongly influence plant performance with effects ranging from negative to positive. However, shifts in resource availability can influence plant responses, with soil pathogens having stronger negative effects in high-resource environments and soil mutualists, such as arbuscular mycorrhizal fungi (AMF), having stronger positive effects in low-resource environments. Yet the relative importance of long-term vs. short-term variation in resources on soil biota and plant responses is not well-known. To assess this, we grew the perennial herb Asclepias speciosa in a greenhouse experiment that crossed a watering treatment (wet vs. dry treatment) with a manipulation of soil biota (live vs. sterilized soil) collected from two geographic regions (Washington and Minnesota) that vary greatly in annual precipitation. Because soil biota can influence many plant functional traits, we measured biomass as well as resource acquisition (e.g., root:shoot, specific leaf area) and defense (e.g., trichome and latex production) traits. Due to their important role as mutualists and pathogens, we also characterized soil fungal communities in the field and greenhouse and used curated databases to assess fungal composition and potential function. We found that the experimental watering treatment had a greater effect than soil biota origin on plant responses; most plant traits were negatively affected by live soils under wet conditions, whereas responses were neutral or positive in live dry soil. These consistent differences in plant responses occurred despite clear differences in soil fungal community composition between inoculate origin and watering treatments, which indicates high functional redundancy among soil fungi. All plants grown in live soil were highly colonized by AMF and root colonization was higher in wet than dry soil; root colonization by other fungi was low in all treatments. The most parsimonious explanation for negative plant responses in wet soil is that AMF became parasitic under conditions that alleviated resource limitation. Thus, plant responses appeared driven by shifts within rather than between fungal guilds, which highlights the importance of coupling growth responses with characterizations of soil biota to fully understand underlying mechanisms. Collectively these results highlight how short-term changes in environmental conditions can mediate complex interactions between plants and soil biota.
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Affiliation(s)
- Philip G Hahn
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | | | | | | | - John L Maron
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Ylva Lekberg
- MPG Ranch, Missoula, MT, United States
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, United States
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9
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Hahn PG, Bullington L, Larkin B, LaFlamme K, Maron JL, Lekberg Y. Effects of Short- and Long-Term Variation in Resource Conditions on Soil Fungal Communities and Plant Responses to Soil Biota. FRONTIERS IN PLANT SCIENCE 2018; 9:1605. [PMID: 30459793 PMCID: PMC6233719 DOI: 10.3389/fpls.2018.01605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/17/2018] [Indexed: 05/07/2023]
Abstract
Soil biota can strongly influence plant performance with effects ranging from negative to positive. However, shifts in resource availability can influence plant responses, with soil pathogens having stronger negative effects in high-resource environments and soil mutualists, such as arbuscular mycorrhizal fungi (AMF), having stronger positive effects in low-resource environments. Yet the relative importance of long-term vs. short-term variation in resources on soil biota and plant responses is not well-known. To assess this, we grew the perennial herb Asclepias speciosa in a greenhouse experiment that crossed a watering treatment (wet vs. dry treatment) with a manipulation of soil biota (live vs. sterilized soil) collected from two geographic regions (Washington and Minnesota) that vary greatly in annual precipitation. Because soil biota can influence many plant functional traits, we measured biomass as well as resource acquisition (e.g., root:shoot, specific leaf area) and defense (e.g., trichome and latex production) traits. Due to their important role as mutualists and pathogens, we also characterized soil fungal communities in the field and greenhouse and used curated databases to assess fungal composition and potential function. We found that the experimental watering treatment had a greater effect than soil biota origin on plant responses; most plant traits were negatively affected by live soils under wet conditions, whereas responses were neutral or positive in live dry soil. These consistent differences in plant responses occurred despite clear differences in soil fungal community composition between inoculate origin and watering treatments, which indicates high functional redundancy among soil fungi. All plants grown in live soil were highly colonized by AMF and root colonization was higher in wet than dry soil; root colonization by other fungi was low in all treatments. The most parsimonious explanation for negative plant responses in wet soil is that AMF became parasitic under conditions that alleviated resource limitation. Thus, plant responses appeared driven by shifts within rather than between fungal guilds, which highlights the importance of coupling growth responses with characterizations of soil biota to fully understand underlying mechanisms. Collectively these results highlight how short-term changes in environmental conditions can mediate complex interactions between plants and soil biota.
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Affiliation(s)
- Philip G. Hahn
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | | | | | | | - John L. Maron
- Division of Biological Sciences, University of Montana, Missoula, MT, United States
| | - Ylva Lekberg
- MPG Ranch, Missoula, MT, United States
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, United States
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10
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Davis WJ, Picard KT, Antonetti J, Edmonds J, Fults J, Letcher PM, Powell MJ. Inventory of chytrid diversity in two temporary forest ponds using a multiphasic approach. Mycologia 2018; 110:811-821. [DOI: 10.1080/00275514.2018.1510725] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- William J. Davis
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487
| | - Kathryn T. Picard
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Jonathan Antonetti
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487
| | - Jennifer Edmonds
- Department of Physical and Life Sciences, Nevada State College, Henderson, Nevada 89002
| | - Jessica Fults
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487
| | - Peter M. Letcher
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487
| | - Martha J. Powell
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487
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11
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Chen S, Yu H, Zhou X, Wu F. Cucumber ( Cucumis sativus L.) Seedling Rhizosphere Trichoderma and Fusarium spp. Communities Altered by Vanillic Acid. Front Microbiol 2018; 9:2195. [PMID: 30283420 PMCID: PMC6157394 DOI: 10.3389/fmicb.2018.02195] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/28/2018] [Indexed: 12/20/2022] Open
Abstract
Root exudates mediate soil microbiome composition and diversity, which might further influence plant development and health. Vanillic acid from root exudates is usually referred as autotoxin of cucumber, however, how vanillic acid affect soil microbial community diversities and abundances remains unclear. In this study, vanillic acid (VA; 0.02, 0.05, 0.1, and 0.2 μmol g-1 soil) was applied to soil every other day for a total of five applications. We used Illumina MiSeq sequencing, quantitative PCR (qPCR) and PCR-denaturing gradient gel electrophoresis (PCR-DGGE) to test the effects of VA on the total fungi community composition as well as the Trichoderma and Fusarium spp. community abundances and structures in the cucumber rhizosphere. Illumina MiSeq sequencing showed that VA (0.05 μmol g-1 soil) increased the relative abundance of the fungal phylum Basidiomycota while decreasing the relative abundance of Ascomycota (P < 0.05), and not altered the diversity of the soil fungal community. VA (0.05 μmol g-1 soil) also increased the relative abundances of the fungal genera with plant pathogens, such as Conocybe and Spizellomyces spp.(P < 0.05). A qPCR analysis showed that VA (0.05 to 0.2 μmol g-1 soil) exerted promoting effects on Trichoderma spp. community abundance and stimulated Fusarium spp. abundance at low concentrations (0.02 to 0.05 μmol g-1 soil) but inhibited it at high concentrations (0.1 to 0.2 μmol g-1 soil). The PCR-DGGE analysis showed that all concentrations of VA altered the community structures of Trichoderma spp. and that the application of VA (0.02 and 0.05 μmol g-1 soil) changed the band number and the Shannon-Wiener index of the Fusarium spp. community. This study demonstrated that VA changed the total fungal community in the cucumber seedling rhizosphere and that the Trichoderma and Fusarium spp. communities showed different responses to VA.
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Affiliation(s)
- Shaocan Chen
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Hongjie Yu
- Department of Horticulture, Northeast Agricultural University, Harbin, China
| | - Xingang Zhou
- Department of Horticulture, Northeast Agricultural University, Harbin, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China
| | - Fengzhi Wu
- Department of Horticulture, Northeast Agricultural University, Harbin, China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture, Harbin, China
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12
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Wakefield WS, Powell MJ, Letcher PM, Barr DJ, Churchill PF, Longcore JE, Chen SF. A molecular phylogenetic evaluation of the Spizellomycetales. Mycologia 2017; 102:596-604. [DOI: 10.3852/09-120] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | | | - Perry F. Churchill
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487
| | - Joyce E. Longcore
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - Shu-Fen Chen
- Department of Health and Nutrition, Chia-Nan, University of Pharmacy and Science, Tainan 71710, Taiwan
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13
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Al-Sadi A, Al-Mazroui S, Phillips A. Evaluation of culture-based techniques and 454 pyrosequencing for the analysis of fungal diversity in potting media and organic fertilizers. J Appl Microbiol 2015; 119:500-9. [DOI: 10.1111/jam.12854] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/08/2015] [Accepted: 05/08/2015] [Indexed: 12/01/2022]
Affiliation(s)
- A.M. Al-Sadi
- Department of Crop Sciences; College of Agricultural and Marine Sciences; Sultan Qaboos University; Al Khoud Oman
| | | | - A.J.L. Phillips
- Department of Life Sciences; New University of Lisbon; Caparica Portugal
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Can zoosporic true fungi grow or survive in extreme or stressful environments? Extremophiles 2010; 14:417-25. [PMID: 20640865 DOI: 10.1007/s00792-010-0323-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 07/05/2010] [Indexed: 10/19/2022]
Abstract
Zoosporic true fungi are thought to be ubiquitous in many ecosystems, especially in cool, moist soils and freshwater habitats which are rich in organic matter. However, some of the habitats where these fungi are found may periodically experience extreme conditions, such as soils in extremely dry, hot and cold climates, acidic and alkaline soils, polluted rivers, anaerobic soil and water, saline soil and water, periglacial soils, oligotrophic soils, tree canopies and hydrothermal vents. It is clear that many ecotypes of zoosporic true fungi have indeed adapted to extreme or stressful environmental conditions. This conclusion is supported by studies in both the field and in the laboratory. Therefore, in our opinion, at least some true zoosporic fungi can be considered to be extremophiles.
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Lim YW, Kim BK, Kim C, Jung HS, Kim BS, Lee JH, Chun J. Assessment of soil fungal communities using pyrosequencing. J Microbiol 2010; 48:284-9. [PMID: 20571944 DOI: 10.1007/s12275-010-9369-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 01/22/2010] [Indexed: 11/24/2022]
Abstract
Pyrosequencing, a non-electrophoretic method of DNA sequencing, was used to investigate the extensive fungal community in soils of three islands in the Yellow Sea of Korea, between Korea and China. Pyrosequencing was carried out on amplicons derived from the 5' region of 18S rDNA. A total of 10,166 reads were obtained, with an average length of 103 bp. The maximum number of fungal phylotypes in soil predicted at 99% similarity was 3,334. The maximum numbers of phylotypes predicted at 97% and 95% similarities were 736 and 286, respectively. Through phylogenetic assignment using BLASTN, a total of 372 tentative taxa were identified. The majority of true fungal sequences recovered in this study belonged to the Ascomycota (182 tentative taxa in 2,708 reads) and Basidiomycota (172 tentative taxa in 6,837 reads). The predominant species of Ascomycota detected have been described as lichen-forming fungi, litter/wood decomposers, plant parasites, endophytes, and saprotrophs: Peltigera neopolydactyla (Lecanoromycetes), Paecilomyces sp. (Sordariomycetes), Phacopsis huuskonenii (Lecanoromycetes), and Raffaelea hennebertii (mitosporicAscomycota). The majority of sequences in the Basidiomycota matched ectomycorrhizal and wood rotting fungi, including species of the Agaricales and Aphyllophorales, respectively. A high number of sequences in the Thelephorales, Boletales, Stereales, Hymenochaetales, and Ceratobasidiomycetes were also detected. By applying high-throughput pyrosequencing, we observed a high diversity of soil fungi and found evidence that pyrosequencing is a reliable technique for investigating fungal communities in soils.
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Affiliation(s)
- Young Woon Lim
- National Institute of Biological Resource, Incheon, 404-708, Republic of Korea
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Evidence that chytrids dominate fungal communities in high-elevation soils. Proc Natl Acad Sci U S A 2009; 106:18315-20. [PMID: 19826082 DOI: 10.1073/pnas.0907303106] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Periglacial soils are one of the least studied ecosystems on Earth, yet they are widespread and are increasing in area due to retreat of glaciers worldwide. Soils in these environments are cold and during the brief summer are exposed to high levels of UV radiation and dramatic fluctuations in moisture and temperature. Recent research suggests that these environments harbor immense microbial diversity. Here we use sequencing of environmental DNA, culturing of isolates, and analysis of environmental variables to show that members of the Chytridiomycota (chytrids) dominate fungal biodiversity and perhaps decomposition processes in plant-free, high-elevation soils from the highest mountain ranges on Earth. The zoosporic reproduction of chytrids requires free water, yet we found that chytrids constituted over 70% of the ribosomal gene sequences of clone libraries from barren soils of the Himalayas and Rockies; by contrast, they are rare in other soil environments. Very few chytrids have been cultured, although we were successful at culturing chytrids from high-elevation sites throughout the world. In a more focused study of our sites in Colorado, we show that carbon sources that support chytrid growth (eolian deposited pollen and microbial phototrophs) are abundant and that soils are saturated with water for several months under the snow, thus creating ideal conditions for the development of a chytrid-dominated ecosystem. Our work broadens the known biodiversity of the Chytridomycota, and describes previously unsuspected links between aquatic and terrestrial ecosystems in alpine regions.
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Scupham AJ, Presley LL, Wei B, Bent E, Griffith N, McPherson M, Zhu F, Oluwadara O, Rao N, Braun J, Borneman J. Abundant and diverse fungal microbiota in the murine intestine. Appl Environ Microbiol 2006; 72:793-801. [PMID: 16391120 PMCID: PMC1352209 DOI: 10.1128/aem.72.1.793-801.2006] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4',6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions.
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MESH Headings
- Animals
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- DNA, Bacterial/analysis
- DNA, Bacterial/isolation & purification
- DNA, Fungal/analysis
- DNA, Fungal/isolation & purification
- Female
- Fungi/classification
- Fungi/genetics
- Fungi/isolation & purification
- Genes, rRNA
- In Situ Hybridization, Fluorescence
- Intestine, Large/microbiology
- Intestine, Small/microbiology
- Male
- Mice
- Mice, Inbred C57BL
- Molecular Sequence Data
- Oligonucleotide Probes
- Polymerase Chain Reaction
- RNA, Ribosomal/genetics
- Sequence Analysis, DNA
- Specific Pathogen-Free Organisms
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