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Touchette D, Gostinčar C, Whyte LG, Altshuler I. Lichen-associated microbial members are prevalent in the snow microbiome of a sub-arctic alpine tundra. FEMS Microbiol Ecol 2023; 99:fiad151. [PMID: 37977855 DOI: 10.1093/femsec/fiad151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/27/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023] Open
Abstract
Snow is the largest component of the cryosphere, with its cover and distribution rapidly decreasing over the last decade due to climate warming. It is imperative to characterize the snow (nival) microbial communities to better understand the role of microorganisms inhabiting these rapidly changing environments. Here, we investigated the core nival microbiome, the cultivable microbial members, and the microbial functional diversity of the remote Uapishka mountain range, a massif of alpine sub-arctic tundra and boreal forest. Snow samples were taken over a two-month interval along an altitude gradient with varying degree of anthropogenic traffic and vegetation cover. The core snow alpine tundra/boreal microbiome, which was present across all samples, constituted of Acetobacterales, Rhizobiales and Acidobacteriales bacterial orders, and of Mycosphaerellales and Lecanorales fungal orders, with the dominant fungal taxa being associated with lichens. The snow samples had low active functional diversity, with Richness values ranging from 0 to 19.5. The culture-based viable microbial enumeration ranged from 0 to 8.05 × 103 CFUs/mL. We isolated and whole-genome sequenced five microorganisms which included three fungi, one alga, and one potentially novel bacterium of the Lichenihabitans genus; all of which appear to be part of lichen-associated taxonomic clades.
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Affiliation(s)
- D Touchette
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, H9X 3V9, Canada
- River Ecosystems Laboratory, ALPOLE, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, CH-1950, Sion, Switzerland
| | - C Gostinčar
- University of Ljubljana, Department of Biology, Biotechnical Faculty, Ljubljana 1000, Slovenia
| | - L G Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, H9X 3V9, Canada
| | - I Altshuler
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, H9X 3V9, Canada
- MACE Laboratory, ALPOLE, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, CH-1950, Sion, Switzerland
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Haq IU, Hillmann B, Moran M, Willard S, Knights D, Fixen KR, Schilling JS. Bacterial communities associated with wood rot fungi that use distinct decomposition mechanisms. ISME COMMUNICATIONS 2022; 2:26. [PMID: 37938255 PMCID: PMC9723729 DOI: 10.1038/s43705-022-00108-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 05/11/2023]
Abstract
Wood decomposer fungi are grouped by how they extract sugars from lignocellulose. Brown rot fungi selectively degrade cellulose and hemicellulose, leaving lignin intact, and white rot fungi degrade all components. Many trees are susceptible to both rot types, giving carbon in Earth's woody biomass, specifically lignin, a flexible fate that is affected not only by the fungal decomposition mechanism but also the associated microbial community. However, little is understood about how rot type may influence the microbial community in decaying wood. In this study, we quantified bacterial communities associated with Fomes fomentarius (white rot) and Fomitopsis betulina (brown rot) found on a shared tree host species, birch (Betula papyrifera). We collected 25 wood samples beneath sporocarps of F. fomentarius (n = 13) and F. betulina (n = 12) on standing dead trees, and coupled microbial DNA sequencing with chemical signatures of rot type (pH and lignin removal). We found that bacterial communities for both fungi were dominated by Proteobacteria, a commonly reported association. However, rot type exerted significant influence on less abundant taxa in ways that align logically with fungal traits. Amplicon sequence variants (ASVs) were enriched in Firmicutes in white-rotted wood, and were enriched in Alphaproteobacteria, Actinobacteria and Acidobacteria in lower pH brown rot. Our results suggest that wood decomposer strategies may exert significant selection effects on bacteria, or vice versa, among less-abundant taxa that have been overlooked when using abundance as the only measure of influence.
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Affiliation(s)
- Irshad Ul Haq
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Molly Moran
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
| | - Samuel Willard
- Department of Life Sciences, Imperial College London, London, UK
| | - Dan Knights
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Kathryn R Fixen
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Jonathan S Schilling
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, St. Paul, MN, USA.
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA.
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Mhuireach GÁ, Wilson H, Johnson BR. Urban Aerobiomes are Influenced by Season, Vegetation, and Individual Site Characteristics. ECOHEALTH 2021; 18:331-344. [PMID: 33170406 DOI: 10.1007/s10393-020-01493-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 10/02/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
Exposure to biodiverse environments such as forests can benefit human well-being, and evidence suggests exposure to high microbial diversity may improve mental and immune health. However, the factors that drive microbial community assembly are poorly understood, as is the relationship between exposure to these communities and human health. We characterized airborne bacterial communities in two disparate types of urban greenspace (forest and grass) in late-spring 2017 at sites previously sampled in late-summer 2015 in Eugene-Springfield, Oregon, using high-throughput metabarcode sequencing. While all sites shared a core aerobiome in late-spring consisting of plant- and soil-associated genera, forests had significantly higher diversity than grass sites (F = 12, P = 0.004). Vegetation type explained 14% of the difference between forest and grass aerobiomes, yet individual site location explained 41% of the variation. These results were similar to but amplified over those from late summer, suggesting that both aerobiome diversity and vegetation-driven effects are higher when deciduous foliage is fresher and more active, temperatures cooler, and humidity higher. Continued exploration and hypothesis-driven research will enable development of mechanistic theory describing key drivers of urban aerobiome assembly and its relationship to human health, which, in turn, will help urban designers and planners create evidence-based salutogenic cities for future generations.
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Affiliation(s)
- Gwynne Á Mhuireach
- Department of Landscape Architecture, University of Oregon, 5250 University of Oregon, Eugene, OR, 97403, USA.
- Biology and the Built Environment (BioBE) Center, University of Oregon, Eugene, OR, USA.
- Institute for Health in the Built Environment, University of Oregon, Eugene, OR, USA.
| | - Hannah Wilson
- Biology and the Built Environment (BioBE) Center, University of Oregon, Eugene, OR, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Bart R Johnson
- Department of Landscape Architecture, University of Oregon, 5250 University of Oregon, Eugene, OR, 97403, USA
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Saini MK, Sebastian A, Shirotori Y, Soulier NT, Garcia Costas AM, Drautz-Moses DI, Schuster SC, Albert I, Haruta S, Hanada S, Thiel V, Tank M, Bryant DA. Genomic and Phenotypic Characterization of Chloracidobacterium Isolates Provides Evidence for Multiple Species. Front Microbiol 2021; 12:704168. [PMID: 34220789 PMCID: PMC8245765 DOI: 10.3389/fmicb.2021.704168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Chloracidobacterium is the first and until now the sole genus in the phylum Acidobacteriota (formerly Acidobacteria) whose members perform chlorophyll-dependent phototrophy (i.e., chlorophototrophy). An axenic isolate of Chloracidobacterium thermophilum (strain B T ) was previously obtained by using the inferred genome sequence from an enrichment culture and diel metatranscriptomic profiling analyses in situ to direct adjustments to the growth medium and incubation conditions, and thereby a defined growth medium for Chloracidobacterium thermophilum was developed. These advances allowed eight additional strains of Chloracidobacterium spp. to be isolated from microbial mat samples collected from Mushroom Spring, Yellowstone National Park, United States, at temperatures of 41, 52, and 60°C; an axenic strain was also isolated from Rupite hot spring in Bulgaria. All isolates are obligately photoheterotrophic, microaerophilic, non-motile, thermophilic, rod-shaped bacteria. Chloracidobacterium spp. synthesize multiple types of (bacterio-)chlorophylls and have type-1 reaction centers like those of green sulfur bacteria. Light harvesting is accomplished by the bacteriochlorophyll a-binding, Fenna-Matthews-Olson protein and chlorosomes containing bacteriochlorophyll c. Their genomes are approximately 3.7 Mbp in size and comprise two circular chromosomes with sizes of approximately 2.7 Mbp and 1.0 Mbp. Comparative genomic studies and phenotypic properties indicate that the nine isolates represent three species within the genus Chloracidobacterium. In addition to C. thermophilum, the microbial mats at Mushroom Spring contain a second species, tentatively named Chloracidobacterium aggregatum, which grows as aggregates in liquid cultures. The Bulgarian isolate, tentatively named Chloracidobacterium validum, will be proposed as the type species of the genus, Chloracidobacterium. Additionally, Chloracidobacterium will be proposed as the type genus of a new family, Chloracidobacteriaceae, within the order Blastocatellales, the class Blastocatellia, and the phylum Acidobacteriota.
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Affiliation(s)
- Mohit Kumar Saini
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Aswathy Sebastian
- The Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Yoshiki Shirotori
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Nathan T. Soulier
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Amaya M. Garcia Costas
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Department of Biology, Colorado State University-Pueblo, Pueblo, CO, United States
| | - Daniela I. Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Stephan C. Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Istvan Albert
- The Huck Institutes for the Life Sciences, The Pennsylvania State University, University Park, PA, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Satoshi Hanada
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - Vera Thiel
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- DSMZ – German Culture Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany
| | - Marcus Tank
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- DSMZ – German Culture Collection of Microorganisms and Cell Cultures, GmbH, Braunschweig, Germany
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
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Naumoff DG, Dedysh SN. Chitinases Encoded in the Genomes of Acidobacteria: Origin and Evolution. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils. PLoS One 2020; 15:e0230157. [PMID: 32182280 PMCID: PMC7077872 DOI: 10.1371/journal.pone.0230157] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/22/2020] [Indexed: 12/26/2022] Open
Abstract
The Acidobacteria is one of the major bacterial phyla in soils and peatlands. The currently explored diversity within this phylum is assigned to 15 class-level units, five of which contain described members. The ecologically relevant traits of acidobacteria from different classes remain poorly understood. Here, we compared the patterns of acidobacterial diversity in sandy soils of tundra, along a gradient of increasing vegetation–unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. The Acidobacteria-affiliated 16S rRNA gene sequences retrieved from these soils comprised 11 to 33% of total bacterial reads and belonged mostly to members of the classes Acidobacteriia and Blastocatellia, which displayed opposite habitat preferences. The relative abundance of the Blastocatellia was maximal in unfixed sands and declined in soils of vegetated plots, showing positive correlation with soil pH and negative correlation with carbon and nitrogen availability. An opposite tendency was characteristic for the Acidobacteriia. Most Blastocatellia-affiliated reads belonged to as-yet-undescribed members of the family Arenimicrobiaceae, which appears to be characteristic for dry, depleted in organic matter soil habitats. The pool of Acidobacteriia-affiliated sequences, apart from Acidobacteriaceae- and Bryobacteraceae-related reads, had a large proportion of sequences from as-yet-undescribed families, which seem to specialize in degrading plant-derived organic matter. This analysis reveals sandy soils of tundra as a source of novel acidobacterial diversity and provides an insight into the ecological preferences of different taxonomic groups within this phylum.
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