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Cao T, Shi M, Zhang J, Ji H, Wang X, Sun J, Chen Z, Li Q, Song X. Nitrogen fertilization practices alter microbial communities driven by clonal integration in Moso bamboo. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171581. [PMID: 38461973 DOI: 10.1016/j.scitotenv.2024.171581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/03/2024] [Accepted: 03/06/2024] [Indexed: 03/12/2024]
Abstract
Nitrogen (N) fertilization is crucial for maintaining plant productivity. Clonal plants can share resources between connected ramets through clonal integration influencing microbial communities and regulating soil biogeochemical cycling, especially in the rhizosphere. However, the effect of various N fertilization practices on microbial communities in the rhizosphere of clonal ramets remain unknown. In this study, clonal fragments of Moso bamboo (Phyllostachys edulis), consisting of a parent ramet, an offspring ramet, and an interconnecting rhizome, were established in the field. NH4NO3 solution was applied to the parent, offspring ramets or rhizomes to investigate the effect of fertilization practices on the structure and function of rhizosphere microbial communities. The differences in N availability, microbial biomass and community composition, and abundance of nitrifying genes among rhizosphere soils of ramets gradually decreased during the rapid growth of Moso bamboo, irrespective of fertilization practice. The soil N availability variation, particularly in NO3-, caused by fertilization practices altered the rhizosphere microbial community. Soil N availability and stable microbial biomass N in parent fertilization were the highest, being 9.0 % and 18.7 %, as well as 60.8 % and 90.4 % higher than rhizome and offspring fertilizations, respectively. The microbial network nodes and links in rhizome fertilization were 1.8 and 7.5 times higher than in parent and offspring fertilization, respectively. However, the diversity of bacterial community and abundance of nitrifying and denitrifying genes were the highest in offspring fertilization among three practices, which may be associated with increased N loss. Collectively, the rhizosphere microbial community characteristics depended on fertilization practices by altering the clonal integration of N in Moso bamboo. Parent and rhizome fertilization were favorable for N retention in plant-soil system and resulted in more stable microbial functions than offspring fertilization. Our findings provide new insights into precision fertilization for the sustainable Moso bamboo forest management.
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Affiliation(s)
- Tingting Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Man Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Junbo Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Hangxiang Ji
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Jilei Sun
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhenxiong Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Quan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinzhang Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China; College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China.
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Baev V, Gecheva G, Apostolova E, Gozmanova M, Yahubyan G. Exploring the Metatranscriptome of Bacterial Communities of Two Moss Species Thriving in Different Environments-Terrestrial and Aquatic. PLANTS (BASEL, SWITZERLAND) 2024; 13:1210. [PMID: 38732425 PMCID: PMC11085137 DOI: 10.3390/plants13091210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024]
Abstract
Mosses host diverse bacterial communities essential for their fitness, nutrient acquisition, stress tolerance, and pathogen defense. Understanding the microbiome's taxonomic composition is the first step, but unraveling their functional capabilities is crucial for grasping their ecological significance. Metagenomics characterizes microbial communities by composition, while metatranscriptomics explores gene expression, providing insights into microbiome functionality beyond the structure. Here, we present for the first time a metatranscriptomic study of two moss species, Hypnum cupressiforme (Hedw.) and Platyhypnidium riparioides (Hedw.) Dixon., renowned as key biomonitors of atmospheric and water pollution. Our investigation extends beyond taxonomic profiling and offers a profound exploration of moss bacterial communities. Pseudomonadota and Actinobacteria are the dominant bacterial phyla in both moss species, but their proportions differ. In H. cupressiforme, Actinobacteria make up 62.45% and Pseudomonadota 32.48%, while in P. riparioides, Actinobacteria account for only 25.67% and Pseudomonadota 69.08%. This phylum-level contrast is reflected in genus-level differences. Our study also shows the expression of most genes related to nitrogen cycling across both microbiomes. Additionally, functional annotation highlights disparities in pathway prevalence, including carbon dioxide fixation, photosynthesis, and fatty acid biosynthesis, among others. These findings hint at potential metabolic distinctions between microbial communities associated with different moss species, influenced by their specific genotypes and habitats. The integration of metatranscriptomic data holds promise for enhancing our understanding of bryophyte-microbe partnerships, opening avenues for novel applications in conservation, bioremediation, and sustainable agriculture.
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Affiliation(s)
- Vesselin Baev
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
| | - Gana Gecheva
- Department of Ecology and Environmental Conservation, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria;
| | - Elena Apostolova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
| | - Mariyana Gozmanova
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
| | - Galina Yahubyan
- Department of Molecular Biology, Faculty of Biology, University of Plovdiv, Tzar Assen 24, 4000 Plovdiv, Bulgaria; (E.A.); (M.G.)
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Bustos-Diaz ED, Cruz-Perez A, Garfias-Gallegos D, D'Agostino PM, Gehringer MM, Cibrian-Jaramillo A, Barona-Gomez F. Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals. Microb Genom 2024; 10:001207. [PMID: 38451250 PMCID: PMC10999742 DOI: 10.1099/mgen.0.001207] [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: 09/27/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024] Open
Abstract
Cycads are known to host symbiotic cyanobacteria, including Nostocales species, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition to Nostoc spp., symbiotic cyanobacteria of the genus Aulosira were identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includes Aulosira spp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.
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Affiliation(s)
- Edder D. Bustos-Diaz
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
- Institute of Biology, Leiden University, Netherlands, 2333 BE, Leiden
| | - Arely Cruz-Perez
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
| | - Diego Garfias-Gallegos
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
| | - Paul M. D'Agostino
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069 Dresden, Germany
| | - Michelle M. Gehringer
- Department of Microbiology, University of Kaiserslautern-Landau (RPTU), 67663 Kaiserslautern, Germany
| | - Angelica Cibrian-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
- Naturalis Biodiversity Center, Leiden 2333 CR, Netherlands
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
- Institute of Biology, Leiden University, Netherlands, 2333 BE, Leiden
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Dreyling L, Penone C, Schenk NV, Schmitt I, Dal Grande F. Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in Central European forests. ISME COMMUNICATIONS 2024; 4:ycae012. [PMID: 38500703 PMCID: PMC10945369 DOI: 10.1093/ismeco/ycae012] [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: 12/15/2023] [Revised: 01/18/2024] [Indexed: 03/20/2024]
Abstract
Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal, and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central, and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occur in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.
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Affiliation(s)
- Lukas Dreyling
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Goethe University Frankfurt, Institute of Ecology, Evolution and Diversity, Frankfurt am Main 60438, Germany
| | - Caterina Penone
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | | | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Goethe University Frankfurt, Institute of Ecology, Evolution and Diversity, Frankfurt am Main 60438, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Department of Biology, University of Padova, Padua 35122, Italy
- National Biodiversity Future Center (NBFC), Palermo 90133, Italy
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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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Zhang T, Grube M, Wei X. Host selection tendency of key microbiota in arid desert lichen crusts. IMETA 2023; 2:e138. [PMID: 38868215 PMCID: PMC10989926 DOI: 10.1002/imt2.138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 09/17/2023] [Indexed: 06/14/2024]
Abstract
Lichen genus Endocarpon in biological soil crust form was chosen as a model to investigate the bacterial communities for the first time across four vertically distinct strata. Key bacterial microbiota in lichen thallus were discovered, which were gradually filtered and mainly derived from the crust soil, with clear host selection tendency. The study provided key information to better understand the homeostasis maintenance mechanism of the lichen symbiont and community assembly of desert lichen crust.
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Affiliation(s)
- Ting‐Ting Zhang
- State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Martin Grube
- Institute of BiologyUniversity of GrazGrazAustria
| | - Xin‐Li Wei
- State Key Laboratory of Mycology, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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Yang Y, Zhang W, Liu W, He D, Wan W. Irreversible community difference between bacterioplankton generalists and specialists in response to lake dredging. WATER RESEARCH 2023; 243:120344. [PMID: 37482008 DOI: 10.1016/j.watres.2023.120344] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023]
Abstract
Understanding response of bacterioplankton community responsible for maintaining ecological functions of aquatic ecosystems to environmental disturbance is an important subject. However, it remains largely unclear how bacterioplankton generalists and specialists respond to dredging disturbance. Illumina MiSeq sequencing and statistical analyses were used to evaluate landscape patterns, evolutionary potentials, environmental adaptability, and community assembly processes of generalists and specialists in response to dredging in eutrophic Lake Nanhu. The Proteobacteria and Actinobacteria dominated bacterioplankton communities of generalists and specialists, and abundances of Proteobacteria decreased and Actinobacteria increased after dredging. The generalists displayed higher phylogenetic distance, richness difference, speciation rate, extinction rate, and diversification rate as well as stronger environmental adaptation than that of specialists. In contrast, the specialists rather than generalists showed higher community diversity, taxonomic distance, and species replacement as well as closer phylogenetic clustering. Stochastic processes dominated community assemblies of generalists and specialists, and stochasticity exhibited a larger effect on community assembly of generalists rather than specialists. Our results emphasized that lake dredging could change landscape patterns of bacterioplankton generalists and specialists, whereas the short-term dredging conducted within one year was unable to reverse community difference between generalists and specialists. Our findings extend our understanding of how bacterioplankton generalists and specialists responding to dredging disturbance, and these findings might in turn call on long-term dredging for better ecological restoration of eutrophic lakes.
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Affiliation(s)
- Yuyi Yang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China
| | - Weihong Zhang
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China
| | - Donglan He
- College of Life Science, South-Central Minzu University, Wuhan 430070, China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, China.
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Lõhmus A, Motiejūnaitė J, Lõhmus P. Regionally Varying Habitat Relationships in Lichens: The Concept and Evidence with an Emphasis on North-Temperate Ecosystems. J Fungi (Basel) 2023; 9:jof9030341. [PMID: 36983509 PMCID: PMC10056719 DOI: 10.3390/jof9030341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Habitat ecology of lichens (lichen-forming fungi) involves diverse adaptations to stressful environments where lichens use specific habitat conditions. Field observations confirm that such habitat ‘preferences’ can vary significantly across species’ distribution ranges, sometimes revealing abrupt changes over short distances. We critically review and generalize such empirical evidence as broad ecological patterns, link these with the likely physiological mechanisms and evolutionary processes involved, and outline the implications for lichen conservation. Non-replicated correlative studies remain only suggestive because the data are frequently compromised by sampling bias and pervasive random errors; further noise is related to unrecognized cryptic species. Replicated evidence exists for three macroecological patterns: (a) regional limiting factors excluding a species from a part of its microhabitat range in suboptimal areas; (b) microhabitat shifts to buffer regionally adverse macroclimates; (c) substrate suitability changed by the chemical environment, notably air pollution. All these appear to be primarily buffering physiological challenges of the adverse conditions at the macrohabitat scale or, in favorable environments, coping with competition or predation. The roles of plasticity, adaptation, dispersal, and population-level stochasticity remain to be studied. Although lichens can inhabit various novel microhabitats, there is no evidence for a related adaptive change. A precautionary approach to lichen conservation is to maintain long-term structural heterogeneity in lichen habitats, and consider lichen ecotypes as potential evolutionarily significant units and a bet-hedging strategy for addressing the climate change-related challenges to biodiversity.
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Affiliation(s)
- Asko Lõhmus
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
- Correspondence:
| | - Jurga Motiejūnaitė
- Laboratory of Mycology, Institute of Botany, Nature Research Centre, Žaliųjų Ežerų 49, LT-08406 Vilnius, Lithuania
| | - Piret Lõhmus
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, 50409 Tartu, Estonia
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Hofmann B, Dreyling L, Dal Grande F, Otte J, Schmitt I. Habitat and tree species identity shape aboveground and belowground fungal communities in central European forests. Front Microbiol 2023; 14:1067906. [PMID: 36950169 PMCID: PMC10025312 DOI: 10.3389/fmicb.2023.1067906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction Trees interact with fungi in mutualistic, saprotrophic, and pathogenic relationships. With their extensive aboveground and belowground structures, trees provide diverse habitats for fungi. Thus, tree species identity is an important driver of fungal community composition in forests. Methods Here we investigate how forest habitat (bark surface vs. soil) and tree species identity (deciduous vs. coniferous) affect fungal communities in two Central European forests. We assess differences and interactions between fungal communities associated with bark surfaces and soil, in forest plots dominated either by Fagus sylvatica, Picea abies, or Pinus sylvestris in two study regions in southwestern and northeastern Germany. Results ITS metabarcoding yielded 3,357 fungal amplicon sequence variants (ASVs) in the northern and 6,088 in the southern region. Overall, soil communities were 4.7 times more diverse than bark communities. Habitat type explained 48-69% of the variation in alpha diversity, while tree species identity explained >1-3%. NMDS ordinations showed that habitat type and host tree species structured the fungal communities. Overall, few fungal taxa were shared between habitats, or between tree species, but the shared taxa were highly abundant. Network analyses, based on co-occurrence patterns, indicate that aboveground and belowground communities form distinct subnetworks. Discussion Our study suggests that habitat (bark versus soil) and tree species identity are important factors structuring fungal communities in temperate European forests. The aboveground (bark-associated) fungal community is currently poorly known, including a high proportion of reads assigned to "unknown Ascomycota" or "unknown Dothideomycetes." The role of bark as a habitat and reservoir of unique fungal diversity in forests has been underestimated.
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Affiliation(s)
- Benjamin Hofmann
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Lukas Dreyling
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
- Department of Biology, University of Padova, Padua, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Jürgen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Imke Schmitt
- Institute of Ecology, Diversity and Evolution, Goethe University Frankfurt, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
- *Correspondence: Imke Schmitt,
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He Z, Naganuma T. Chronicle of Research into Lichen-Associated Bacteria. Microorganisms 2022; 10:2111. [PMID: 36363703 PMCID: PMC9698887 DOI: 10.3390/microorganisms10112111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 02/12/2024] Open
Abstract
Lichens are mutually symbiotic systems consisting of fungal and algal symbionts. While diverse lichen-forming fungal species are known, limited species of algae form lichens. Plasticity in the combination of fungal and algal species with different eco-physiological properties may contribute to the worldwide distribution of lichens, even in extreme habitats. Lichens have been studied systematically for more than 200 years; however, plasticity in fungal-algal/cyanobacterial symbiotic combinations is still unclear. In addition, the association between non-cyanobacterial bacteria and lichens has attracted attention in recent years. The types, diversity, and functions of lichen-associated bacteria have been studied using both culture-based and culture-independent methods. This review summarizes the history of systematic research on lichens and lichen-associated bacteria and provides insights into the current status of research in this field.
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Affiliation(s)
| | - Takeshi Naganuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Japan
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Tibbs-Cortes LE, Tibbs-Cortes BW, Schmitz-Esser S. Tardigrade Community Microbiomes in North American Orchards Include Putative Endosymbionts and Plant Pathogens. Front Microbiol 2022; 13:866930. [PMID: 35923389 PMCID: PMC9340075 DOI: 10.3389/fmicb.2022.866930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/20/2022] [Indexed: 11/27/2022] Open
Abstract
The microbiome of tardigrades, a phylum of microscopic animals best known for their ability to survive extreme conditions, is poorly studied worldwide and completely unknown in North America. An improved understanding of tardigrade-associated bacteria is particularly important because tardigrades have been shown to act as vectors of the plant pathogen Xanthomonas campestris in the laboratory. However, the potential role of tardigrades as reservoirs and vectors of phytopathogens has not been investigated further. This study analyzed the microbiota of tardigrades from six apple orchards in central Iowa, United States, and is the first analysis of the microbiota of North American tardigrades. It is also the first ever study of the tardigrade microbiome in an agricultural setting. We utilized 16S rRNA gene amplicon sequencing to characterize the tardigrade community microbiome across four contrasts: location, substrate type (moss or lichen), collection year, and tardigrades vs. their substrate. Alpha diversity of the tardigrade community microbiome differed significantly by location and year of collection but not by substrate type. Our work also corroborated earlier findings, demonstrating that tardigrades harbor a distinct microbiota from their environment. We also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens (Pseudomonas, Ralstonia, and the Pantoea/Erwinia complex). Finally, we observed members of the genera Rickettsia and Wolbachia in the tardigrade microbiome; because these are obligate intracellular genera, we consider these taxa to be putative endosymbionts of tardigrades. These results suggest the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.
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Affiliation(s)
- Laura E. Tibbs-Cortes
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, United States
- *Correspondence: Laura E. Tibbs-Cortes,
| | - Bienvenido W. Tibbs-Cortes
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Stephan Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
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12
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Allen JL, Lendemer JC. A call to reconceptualize lichen symbioses. Trends Ecol Evol 2022; 37:582-589. [PMID: 35397954 DOI: 10.1016/j.tree.2022.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/23/2022]
Abstract
Several decades of research across disciplines have overturned historical perspectives of symbioses dominated by binary characterizations of highly specific species-species interactions. This paradigm shift has unlocked the previously underappreciated and overlooked dynamism of fungal mutualisms such as mycorrhizae. Lichens are another example of important fungal mutualisms where reconceptualization is urgently needed to realize their potential as model systems. This reconceptualization requires both an objective synthesis of new data and envisioning a revised integrative approach that unifies the spectrum of ecology and evolution. We propose a ten-theme framework that if pursued would propel lichens to the vanguard of symbiotic theory.
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Affiliation(s)
- Jessica L Allen
- Eastern Washington University, Biology Department, Cheney, WA 99004, USA.
| | - James C Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458-5126, USA.
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13
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The yeast lichenosphere: High diversity of basidiomycetes from the lichens Tephromela atra and Rhizoplaca melanophthalma. Fungal Biol 2022; 126:587-608. [DOI: 10.1016/j.funbio.2022.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/26/2022] [Accepted: 07/13/2022] [Indexed: 01/03/2023]
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14
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Muster C, Leiva D, Morales C, Grafe M, Schloter M, Carú M, Orlando J. Peltigera frigida Lichens and Their Substrates Reduce the Influence of Forest Cover Change on Phosphate Solubilizing Bacteria. Front Microbiol 2022; 13:843490. [PMID: 35836424 PMCID: PMC9275751 DOI: 10.3389/fmicb.2022.843490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Phosphorus (P) is one of the most critical macronutrients in forest ecosystems. More than 70 years ago, some Chilean Patagonian temperate forests suffered wildfires and the subsequent afforestation with foreign tree species such as pines. Since soil P turnover is interlinked with the tree cover, this could influence soil P content and bioavailability. Next to soil microorganisms, which are key players in P transformation processes, a vital component of Patagonian temperate forest are lichens, which represent microbial hotspots for bacterial diversity. In the present study, we explored the impact of forest cover on the abundance of phosphate solubilizing bacteria (PSB) from three microenvironments of the forest floor: Peltigera frigida lichen thallus, their underlying substrates, and the forest soil without lichen cover. We expected that the abundance of PSB in the forest soil would be strongly affected by the tree cover composition since the aboveground vegetation influences the edaphic properties; but, as P. frigida has a specific bacterial community, lichens would mitigate this impact. Our study includes five sites representing a gradient in tree cover types, from a mature forest dominated by the native species Nothofagus pumilio, to native second-growth forests with a gradual increase in the presence of Pinus contorta in the last sites. In each site, we measured edaphic parameters, P fractions, and the bacterial potential to solubilize phosphate by quantifying five specific marker genes by qPCR. The results show higher soluble P, labile mineral P, and organic matter in the soils of the sites with a higher abundance of P. contorta, while most of the molecular markers were less abundant in the soils of these sites. Contrarily, the abundance of the molecular markers in lichens and substrates was less affected by the tree cover type. Therefore, the bacterial potential to solubilize phosphate is more affected by the edaphic factors and tree cover type in soils than in substrates and thalli of P. frigida lichens. Altogether, these results indicate that the microenvironments of lichens and their substrates could act as an environmental buffer reducing the influence of forest cover composition on bacteria involved in P turnover.
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Affiliation(s)
- Cecilia Muster
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Diego Leiva
- Institute of Biology, University of Graz, Graz, Austria
| | - Camila Morales
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Martin Grafe
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Schloter
- Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München, Neuherberg, Germany
| | - Margarita Carú
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Julieta Orlando
- Laboratory of Microbial Ecology, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- *Correspondence: Julieta Orlando,
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15
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Cao PX, Liu Y, Ma HM, Zhao N, Chen ST, Xu GQ, Liu X. Fungal Diversity in the Soil of the Oxytropis glacialis Root System on the Qinghai-Tibet Plateau. Front Microbiol 2022; 13:831783. [PMID: 35283812 PMCID: PMC8907473 DOI: 10.3389/fmicb.2022.831783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/25/2022] [Indexed: 11/17/2022] Open
Abstract
Because of swainonine-producing endophytic fungal, Oxytropis glacialis is one of the main poisonous weeds in the alpine grassland and desert grassland of the Qinghai-Tibet Plateau (QTP). It has a severe impact on grassland degradation on the QTP. In this manuscript, the Internally Transcribed Spacer (ITS) region of fungal communities in the soil of the O. glacialis root system was sequenced by high-throughput sequencing and analyzed by bioinformatics methods. The physical and chemical properties of the soil samples were analyzed in combination with the fungal diversity and its relationship with the soil physical and chemical factors. The results showed that the soil fungal community in the O. glacialis root system are rich in diversity in different ecological environments and are most affected by the soil pH value and organic matter. The swainonine-producing fungal Embellisia oxytropis was first detected in the soil of the O. glacialis root system. This finding provides data to support the next step in demonstrating the horizontal spread of swainone-producing fungal from O. glacialis to soil. In addition, a stable network of core flora has a facilitating effect on the formation of O. glacialis as a dominant species in alpine ecosystems.
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Affiliation(s)
- Peng-Xi Cao
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China.,College of Life Science, Wuhan University, Wuhan, China
| | - Yixuan Liu
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China.,College of Life Science, Wuhan University, Wuhan, China
| | - Hong-Mei Ma
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China
| | - Ning Zhao
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China
| | - Shu-Ting Chen
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China
| | - Guo-Qi Xu
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China
| | - Xing Liu
- Ecological Field Station Real-Time Monitoring Center, Research Center for Ecology, Tibet University, Lhasa, China.,Laboratory of Adaptation and Evolution of Plateau Biota to Extreme Environments, Research Center for Ecology and Environment of Qinghai-Tibetan Plateau, Tibet University, Lhasa, China.,College of Life Science, Wuhan University, Wuhan, China
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16
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Likar M, Grašič M, Stres B, Regvar M, Gaberščik A. Original Leaf Colonisers Shape Fungal Decomposer Communities of Phragmites australis in Intermittent Habitats. J Fungi (Basel) 2022; 8:jof8030284. [PMID: 35330286 PMCID: PMC8951327 DOI: 10.3390/jof8030284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 01/29/2023] Open
Abstract
Common reed (Phragmites australis) has high biomass production and is primarily subjected to decomposition processes affected by multiple factors. To predict litter decomposition dynamics in intermittent lakes, it is critical to understand how communities of fungi, as the primary decomposers, form under different habitat conditions. This study reports the shotgun metagenomic sequencing of the initial fungal communities on common reed leaves decomposing under different environmental conditions. We demonstrate that a complex network of fungi forms already on the plant persists into the decomposition phase. Phragmites australis leaves contained at least five fungal phyla, with abundant Ascomycota (95.7%) and Basidiomycota (4.1%), identified as saprotrophs (48.6%), pathotrophs (22.5%), and symbiotrophs (12.6%). Most of the correlations between fungi in fresh and decomposing leaves were identified as co-occurrences (positive correlations). The geographic source of litter and leaf age did not affect the structure and diversity of fungal communities. Keystone taxa were mostly moisture-sensitive. Our results suggest that habitat has a strong effect on the formation of the fungal communities through keystone taxa. Nevertheless, it can also alter the proportions of individual fungal groups in the community through indirect effects on competition between the fungal taxa and their exploitation of favourable conditions.
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Affiliation(s)
- Matevž Likar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
- Correspondence: ; Tel.: +386-1-320-3-418
| | - Mateja Grašič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
| | - Blaž Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Marjana Regvar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
| | - Alenka Gaberščik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
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17
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Diversity and Source of Airborne Microbial Communities at Differential Polluted Sites of Rome. ATMOSPHERE 2022. [DOI: 10.3390/atmos13020224] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biogenic fraction of airborne PM10 which includes bacteria, viruses, fungi and pollens, has been proposed as one of the potential causes of the PM10 toxicity. The present study aimed to provide a comprehensive understanding of the microbial community variations associated to PM10, and their main local sources in the surrounding environment in three urban sites of Rome, characterized by differential pollution rate: green area, residential area and polluted area close to the traffic roads. We combined high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer (ITS) region, with detailed chemical analysis of particulate matter sampled from air, paved road surfaces and leaf surfaces of Quercus ilex. Our results demonstrated that bacterial and fungal airborne communities were characterized by the highest alpha-diversity and grouped separately from epiphytic and road dust communities. The reconstruction of source-sink relationships revealed that the resuspension/deposition of road dust from traffic might contribute to the maximum magnitude of microbial exchanges. The relative abundance of extremotolerant microbes was found to be enhanced in epiphytic communities and was associated to a progressively increase of pollution levels as well as opportunistic human pathogenicity in fungal communities.
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18
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Vijayakumar VR, Saravanan K, Somasundaram M, Jayaraj R, Annamalai P, Nooruddin T, Dharumadurai D. Metagenomic analysis of lichen-associated bacterial community profiling in Roccella montagnei. Arch Microbiol 2021; 204:54. [DOI: 10.1007/s00203-021-02707-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/29/2022]
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19
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Yang Y, Shi Y, Kerfahi D, Ogwu MC, Wang J, Dong K, Takahashi K, Moroenyane I, Adams JM. Elevation-related climate trends dominate fungal co-occurrence network structure and the abundance of keystone taxa on Mt. Norikura, Japan. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149368. [PMID: 34352461 DOI: 10.1016/j.scitotenv.2021.149368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/15/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Soil fungi play an important role in promoting nutrient cycling and maintaining ecosystem stability. Yet, there has been little understanding of how fungal co-occurrence networks differ along elevational climate gradients, a topic of interest to both macroecology and climate change studies. Based on high-throughput sequencing technology, we investigated the trend in co-occurrence network structure of soil fungal communities at 11 elevation levels along a 2300 m elevation gradient on Mt. Norikura, Japan, and identified the keystone taxa in the network, hypothesizing a progressive decline in network connectivity with elevation due to decreased plant diversity and enhanced environmental stress caused by changes in climate and soil characteristics. Our results demonstrated that network-level topological features such as network size, average degree, clustering coefficient, and modularity decreased significantly with increasing elevation, indicating that the fungal OTUs at low elevation were more closely associated and the network structure was more compact at low elevations. This conclusion was verified by the negative correlation between positive cohesion, negative cohesion and elevation. Moreover, the negative/positive cohesion ratio reached its peak value in mid-elevations with moderate environmental stress, indicating that the fungal community structure in mid-elevations was more stable than that at other elevations. We also found that the keystone taxa were more abundant at lower elevations. Furthermore, statistical analysis revealed that against a background of uniform geology, climate may play a dominant role in determining the properties and intensity of soil fungal networks, and significantly affect the abundance distribution of keystone taxa. These findings enhance understanding of the pattern and mechanism of the fungal community co-occurrence network along elevation, as well as the responses of microorganisms to climate change on a vertical scale in montane ecosystems. IMPORTANCE: Exploration of the elevational distribution of microbial networks and their driving factors and mechanisms may provide opportunities for predicting potential impacts of environmental changes, on ecosystem functions and biogeographic patterns at a broad scale. Although many studies have explored patterns of fungal community diversity and composition along various environmental gradients, it is unclear how the topological structure of co-occurrence networks shifts along elevational temperature gradients. In this study, we found that the connectivity of the fungal community decreased with increasing elevation and that climate was the dominant factor regulating co-occurrence patterns, apparently acting indirectly through soil characteristics. Our results also suggest that higher elevations on mountains have fewer keystone taxa than low elevations. These patterns may be related to the decrease of plant diversity and the increase of environmental stress along elevation gradients.
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Affiliation(s)
- Ying Yang
- School of Geography and Oceanography, Nanjing University, Nanjing, China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Henan, China
| | - Dorsaf Kerfahi
- School of Natural Sciences, Department of Biological Sciences, Keimyung University, Daegu, Republic of Korea
| | - Matthew C Ogwu
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Marche - Floristic Research Center of the Apennines, Gran Sasso and Monti della Laga National Park, San Colombo, Barisciano, L'Aquila, Italy
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ke Dong
- Life Science Major, Kyonggi University, Suwon, South Korea
| | - Koichi Takahashi
- Department of Biological Sciences, Shinsu University, Matsumoto, Japan
| | - Itumeleng Moroenyane
- Institut National Recherche Scientifique Centre, Institut Armand Frappier Santé Biotechnologie, Quebéc, Canada
| | - Jonathan M Adams
- School of Geography and Oceanography, Nanjing University, Nanjing, China.
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20
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Ma L, Huang S, Wu P, Xiong J, Wang H, Liao H, Liu X. The interaction of acidophiles driving community functional responses to the re-inoculated chalcopyrite bioleaching process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149186. [PMID: 34375243 DOI: 10.1016/j.scitotenv.2021.149186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
Re-inoculation was an effective way to improve bioleaching efficiency by enhancing the synergetic effects of biogenic Fe3+ coupling with S0 oxidation. However, the complex microbial interactions after re-inoculation have received far less attention, which was crucial to the bioleaching performances. Herein, the enriched ferrous oxidizers (FeO) or sulfur oxidizers (SO) were inoculated to chalcopyrite microcosm, then they were crossly re-inoculated again to characterize the interspecific interaction patterns. The results showed that the dominant species in Fe groups were Acidithiobacillus ferrooxidans, while A. thiooxidans predominated in S groups. Introducing FeO resulted in a great disturbance by shifting the community diversity and evenness significantly (p < 0.05). In comparison, the communities intensified by SO maintained the original composition and structures. Microbial networks were constructed positively and modularly. The networks intensified by FeO were less connected and complex with less nodes and edges, but showed faster responses to the re-inoculation disturbance reflected by shorter average path length. Interestingly, the genus Leptospirillum were identified as keystones in S groups, playing critical roles in iron-oxidizing with lots of sulfur oxidizers. The introduced sulfur oxidizers enhanced microbial cooperation, formed robust community with strong bio-dissolution capability, and harbored the highest bioleaching efficiency. These findings improved our understanding about the acidophiles interactions, which drive community functional responses to the re-inoculated bioleaching process.
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Affiliation(s)
- Liyuan Ma
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China; Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China.
| | - Shanshan Huang
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China; School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Peiyi Wu
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Junming Xiong
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Hongmei Wang
- School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Hehuan Liao
- Springboard, San Francisco, CA 94063, United States
| | - Xueduan Liu
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha 410083, China; School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
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21
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Wei G, Ning K, Zhang G, Yu H, Yang S, Dai F, Dong L, Chen S. Compartment Niche Shapes the Assembly and Network of Cannabis sativa-Associated Microbiome. Front Microbiol 2021; 12:714993. [PMID: 34675893 PMCID: PMC8524047 DOI: 10.3389/fmicb.2021.714993] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Interactions between plants and microbes may promote the growth of plants and regulate the production of secondary metabolites. Hemp (Cannabis sativa) is an annual herb and an important commercial crop. However, the assembly and network of hemp-associated microbiomes inhabiting in soil and plant compartments have not been comprehensively understood. This work investigated the assembly and network of bacterial and fungal communities living in soils (bulk and rhizosphere) and plant compartments (root, stem, leaf, and flower) of four hemp ecotypes cultivated in the same habitat. Microbiome assembly was predominantly shaped by compartment niche. Microbial alpha diversity was the highest in soil, continually decreased from root to flower. Core bacterial genera Pseudomonas, Bacillus, Rhizobium, Planococcus, and Sphingomonas were mostly enriched in aerial endosphere niches; Clitopilus, Plectosphaerella, and Mortierella were enriched in belowground endosphere. Microbial network complexity and connectivity decreased from root to flower. According to source tracking analysis, hemp microbiota primarily originated from soil and were subsequently filtered in different plant compartments. This work provides details on hemp-associated microbiome along the soil-plant continuum and a comprehensive understanding of the origin and transmission mode of endophytes in hemp.
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Affiliation(s)
- Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Kang Ning
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Haibin Yu
- Yunnan Industrial Investment Group, Yunnan Hemp Seed Industry Co., Ltd., Kunming, China
| | - Shuming Yang
- Yunnan Industrial Investment Group, Yunnan Hemp Seed Industry Co., Ltd., Kunming, China
| | - Fei Dai
- Yunnan Industrial Investment Group, Yunnan Hemp Seed Industry Co., Ltd., Kunming, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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22
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Lindström S, Timonen S, Sundström L. The bacterial and fungal community composition in time and space in the nest mounds of the ant Formica exsecta (Hymenoptera: Formicidae). Microbiologyopen 2021; 10:e1201. [PMID: 34459553 PMCID: PMC8289489 DOI: 10.1002/mbo3.1201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/09/2022] Open
Abstract
In a subarctic climate, the seasonal shifts in temperature, precipitation, and plant cover drive the temporal changes in the microbial communities in the topsoil, forcing soil microbes to adapt or decline. Many organisms, such as mound-building ants, survive the cold winter owing to the favorable microclimate in their nest mounds. We have previously shown that the microbial communities in the nest of the ant Formica exsecta are significantly different from those in the surrounding bulk soil. In the current study, we identified taxa, which were consistently present in the nests over a study period of three years. Some taxa were also significantly enriched in the nest samples compared with spatially corresponding reference soils. We show that the bacterial communities in ant nests are temporally stable across years, whereas the fungal communities show greater variation. It seems that the activities of the ants contribute to unique biochemical processes in the secluded nest environment, and create opportunities for symbiotic interactions between the ants and the microbes. Over time, the microbial communities may come to diverge, due to drift and selection, especially given the long lifespan (up to 30 years) of the ant colonies.
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Affiliation(s)
- Stafva Lindström
- Organismal and Evolutionary Biology Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationHankoFinland
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Sari Timonen
- Department of MicrobiologyUniversity of HelsinkiHelsinkiFinland
| | - Liselotte Sundström
- Organismal and Evolutionary Biology Research ProgrammeFaculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Tvärminne Zoological StationHankoFinland
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23
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Ceballos-González CF, Bolívar-Monsalve EJ, Quevedo-Moreno DA, Lam-Aguilar LL, Borrayo-Montaño KI, Yee-de León JF, Zhang YS, Alvarez MM, Trujillo-de Santiago G. High-Throughput and Continuous Chaotic Bioprinting of Spatially Controlled Bacterial Microcosms. ACS Biomater Sci Eng 2021; 7:2408-2419. [PMID: 33979127 DOI: 10.1021/acsbiomaterials.0c01646] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Microorganisms do not work alone but instead function as collaborative microsocieties. The spatial distribution of different bacterial strains (micro-biogeography) in a shared volumetric space and their degree of intimacy greatly influences their societal behavior. Current microbiological techniques are commonly focused on the culture of well-mixed bacterial communities and fail to reproduce the micro-biogeography of polybacterial societies. Here, we bioprinted fine-scale bacterial microcosms using chaotic flows induced by a printhead containing a static mixer. This straightforward approach (i.e., continuous chaotic bacterial bioprinting) enables the fabrication of hydrogel constructs with intercalated layers of bacterial strains. These multilayered constructs are used to analyze how the spatial distributions of bacteria affect their social behavior. For example, we show that bacteria within these biological microsystems engage in either cooperation or competition, depending on the degree of shared interface. The extent of inhibition in predator-prey scenarios (i.e., probiotic-pathogen bacteria) increases when bacteria are in greater intimacy. Furthermore, two Escherichia coli strains exhibit competitive behavior in well-mixed microenvironments, whereas stable coexistence prevails for longer times in spatially structured communities. We anticipate that chaotic bioprinting will contribute to the development of a greater complexity of polybacterial microsystems, tissue-microbiota models, and biomanufactured materials.
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Affiliation(s)
| | | | - Diego Alonso Quevedo-Moreno
- Departamento de Ingeniería Mecatrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | - Li Lu Lam-Aguilar
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | | | | | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge 02139, Massachusetts United States
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México.,Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México.,Departamento de Ingeniería Mecatrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
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24
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Leiva D, Fernández-Mendoza F, Acevedo J, Carú M, Grube M, Orlando J. The Bacterial Community of the Foliose Macro-lichen Peltigera frigida Is More than a Mere Extension of the Microbiota of the Subjacent Substrate. MICROBIAL ECOLOGY 2021; 81:965-976. [PMID: 33404820 DOI: 10.1007/s00248-020-01662-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Lichens host highly diverse microbial communities, with bacteria being one of the most explored groups in terms of their diversity and functioning. These bacteria could partly originate from symbiotic propagules developed by many lichens and, perhaps more commonly and depending on environmental conditions, from different sources of the surroundings. Using the narrowly distributed species Peltigera frigida as an object of study, we propose that bacterial communities in these lichens are different from those in their subjacent substrates, even if some taxa might be shared. Ten terricolous P. frigida lichens and their substrates were sampled from forested sites in the Coyhaique National Reserve, located in an understudied region in Chile. The mycobiont identity was confirmed using partial 28S and ITS sequences. Besides, 16S fragments revealed that mycobionts were associated with the same cyanobacterial haplotype. From both lichens and substrates, Illumina 16S amplicon sequencing was performed using primers that exclude cyanobacteria. In lichens, Proteobacteria was the most abundant phylum (37%), whereas soil substrates were dominated by Acidobacteriota (39%). At lower taxonomic levels, several bacterial groups differed in relative abundance among P. frigida lichens and their substrates, some of them being highly abundant in lichens but almost absent in substrates, like Sphingomonas (8% vs 0.2%), and others enriched in lichens, as an unassigned genus of Chitinophagaceae (10% vs 2%). These results reinforce the idea that lichens would carry some components of their microbiome when propagating, but they also could acquire part of their bacterial community from the substrates.
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Affiliation(s)
- Diego Leiva
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
- Institute of Biology, University of Graz, Graz, Austria
| | | | - José Acevedo
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
| | - Margarita Carú
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile
| | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Julieta Orlando
- Faculty of Sciences, Department of Ecological Sciences, Universidad de Chile, Santiago, Chile.
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25
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Grimm M, Grube M, Schiefelbein U, Zühlke D, Bernhardt J, Riedel K. The Lichens' Microbiota, Still a Mystery? Front Microbiol 2021; 12:623839. [PMID: 33859626 PMCID: PMC8042158 DOI: 10.3389/fmicb.2021.623839] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/10/2021] [Indexed: 01/03/2023] Open
Abstract
Lichens represent self-supporting symbioses, which occur in a wide range of terrestrial habitats and which contribute significantly to mineral cycling and energy flow at a global scale. Lichens usually grow much slower than higher plants. Nevertheless, lichens can contribute substantially to biomass production. This review focuses on the lichen symbiosis in general and especially on the model species Lobaria pulmonaria L. Hoffm., which is a large foliose lichen that occurs worldwide on tree trunks in undisturbed forests with long ecological continuity. In comparison to many other lichens, L. pulmonaria is less tolerant to desiccation and highly sensitive to air pollution. The name-giving mycobiont (belonging to the Ascomycota), provides a protective layer covering a layer of the green-algal photobiont (Dictyochloropsis reticulata) and interspersed cyanobacterial cell clusters (Nostoc spec.). Recently performed metaproteome analyses confirm the partition of functions in lichen partnerships. The ample functional diversity of the mycobiont contrasts the predominant function of the photobiont in production (and secretion) of energy-rich carbohydrates, and the cyanobiont's contribution by nitrogen fixation. In addition, high throughput and state-of-the-art metagenomics and community fingerprinting, metatranscriptomics, and MS-based metaproteomics identify the bacterial community present on L. pulmonaria as a surprisingly abundant and structurally integrated element of the lichen symbiosis. Comparative metaproteome analyses of lichens from different sampling sites suggest the presence of a relatively stable core microbiome and a sampling site-specific portion of the microbiome. Moreover, these studies indicate how the microbiota may contribute to the symbiotic system, to improve its health, growth and fitness.
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Affiliation(s)
- Maria Grimm
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University Graz, Graz, Austria
| | | | - Daniela Zühlke
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University Greifswald, Greifswald, Germany
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26
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Jauss RT, Walden S, Fiore-Donno AM, Dumack K, Schaffer S, Wolf R, Schlegel M, Bonkowski M. From Forest Soil to the Canopy: Increased Habitat Diversity Does Not Increase Species Richness of Cercozoa and Oomycota in Tree Canopies. Front Microbiol 2020; 11:592189. [PMID: 33414768 PMCID: PMC7782269 DOI: 10.3389/fmicb.2020.592189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/07/2020] [Indexed: 02/02/2023] Open
Abstract
Tree canopies provide habitats for diverse and until now, still poorly characterized communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa (Rhizaria) and Oomycota (Stramenopiles), was performed. Group specific primers were used to comprehensively analyze their diversity in various microhabitats of a floodplain forest from the forest floor to the canopy region. Beta diversity indicated highly dissimilar protistan communities in the investigated microhabitats. However, the majority of operational taxonomic units (OTUs) was present in all samples, and therefore differences in beta diversity were mainly related to species performance (i.e., relative abundance). Accordingly, habitat diversity strongly favored distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible.
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Affiliation(s)
- Robin-Tobias Jauss
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Susanne Walden
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | | | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Stefan Schaffer
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Ronny Wolf
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Martin Schlegel
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Leipzig, Germany
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
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27
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Klarenberg IJ, Keuschnig C, Warshan D, Jónsdóttir IS, Vilhelmsson O. The Total and Active Bacterial Community of the Chlorolichen Cetraria islandica and Its Response to Long-Term Warming in Sub-Arctic Tundra. Front Microbiol 2020; 11:540404. [PMID: 33391192 PMCID: PMC7775390 DOI: 10.3389/fmicb.2020.540404] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 11/30/2020] [Indexed: 01/04/2023] Open
Abstract
Lichens are traditionally defined as a symbiosis between a fungus and a green alga and or a cyanobacterium. This idea has been challenged by the discovery of bacterial communities inhabiting the lichen thalli. These bacteria are thought to contribute to the survival of lichens under extreme and changing environmental conditions. How these changing environmental conditions affect the lichen-associated bacterial community composition remains unclear. We describe the total (rDNA-based) and potentially metabolically active (rRNA-based) bacterial community of the lichen Cetaria islandica and its response to long-term warming using a 20-year warming experiment in an Icelandic sub-Arctic tundra. 16S rRNA and rDNA amplicon sequencing showed that the orders Acetobacterales (of the class Alphaproteobacteria) and Acidobacteriales (of the phylum Acidobacteria) dominated the bacterial community. Numerous amplicon sequence variants (ASVs) could only be detected in the potentially active community but not in the total community. Long-term warming led to increases in relative abundance of bacterial taxa on class, order and ASV level. Warming altered the relative abundance of ASVs of the most common bacterial genera, such as Granulicella and Endobacter. The potentially metabolically active bacterial community was also more responsive to warming than the total community. Our results suggest that the bacterial community of the lichen C. islandica is dominated by acidophilic taxa and harbors disproportionally active rare taxa. We also show for the first time that climate warming can lead to shifts in lichen-associated bacterial community composition.
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Affiliation(s)
- Ingeborg J. Klarenberg
- Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Christoph Keuschnig
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS, École Centrale de Lyon, Écully, France
| | - Denis Warshan
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Oddur Vilhelmsson
- Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
- BioMedical Center, University of Iceland, Reykjavík, Iceland
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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28
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Floral fungal-bacterial community structure and co-occurrence patterns in four sympatric island plant species. Fungal Biol 2020; 125:49-61. [PMID: 33317776 DOI: 10.1016/j.funbio.2020.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 01/30/2023]
Abstract
Flowers' fungal and bacterial communities can exert great impacts on host plant wellness and reproductive success-both directly and indirectly through species interactions. However, information about community structure and co-occurrence patterns in floral microbiome remains scarce. Here, using culture-independent methods, we investigated fungal and bacterial communities associated with stamens and pistils of four plant species (Scaevola taccada, Ipomoea cairica, Ipomoea pes-caprae, and Mussaenda kwangtungensis) growing together under the same environment conditions in an island located in South China. Plant species identity significantly influenced community composition of floral fungi but not bacteria. Stamen and pistil microbiomes did not differ in community composition, but differed in co-occurrence network topological features. Compared with the stamen network, pistil counterpart had fewer links between bacteria and fungi and showed more modular but less concentrated and connected structure. In addition, degree distribution of microbial network in each host species and each microhabitat (stamen or pistil) followed a significant power-law pattern. These results enhance our understanding in the assembly principles and ecological interactions of floral microbial communities.
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29
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Spribille T, Tagirdzhanova G, Goyette S, Tuovinen V, Case R, Zandberg WF. 3D biofilms: in search of the polysaccharides holding together lichen symbioses. FEMS Microbiol Lett 2020; 367:5731805. [PMID: 32037451 PMCID: PMC7164778 DOI: 10.1093/femsle/fnaa023] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 02/07/2020] [Indexed: 12/14/2022] Open
Abstract
Stable, long-term interactions between fungi and algae or cyanobacteria, collectively known as lichens, have repeatedly evolved complex architectures with little resemblance to their component parts. Lacking any central scaffold, the shapes they assume are casts of secreted polymers that cement cells into place, determine the angle of phototropic exposure and regulate water relations. A growing body of evidence suggests that many lichen extracellular polymer matrices harbor unicellular, non-photosynthesizing organisms (UNPOs) not traditionally recognized as lichen symbionts. Understanding organismal input and uptake in this layer is key to interpreting the role UNPOs play in lichen biology. Here, we review both polysaccharide composition determined from whole, pulverized lichens and UNPOs reported from lichens to date. Most reported polysaccharides are thought to be structural cell wall components. The composition of the extracellular matrix is not definitively known. Several lines of evidence suggest some acidic polysaccharides have evaded detection in routine analysis of neutral sugars and may be involved in the extracellular matrix. UNPOs reported from lichens include diverse bacteria and yeasts for which secreted polysaccharides play important biological roles. We conclude by proposing testable hypotheses on the role that symbiont give-and-take in this layer could play in determining or modifying lichen symbiotic outcomes.
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Affiliation(s)
- Toby Spribille
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Gulnara Tagirdzhanova
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Spencer Goyette
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Veera Tuovinen
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Rebecca Case
- Department of Biological Sciences, CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Wesley F Zandberg
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3427 University Way, Kelowna, BC V1V 1V7, Canada
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30
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Ning Y, Qi J, Dobbins MT, Liang X, Wang J, Chen S, Ma J, Jiang G. Comparative Analysis of Microbial Community Structure and Function in the Gut of Wild and Captive Amur Tiger. Front Microbiol 2020; 11:1665. [PMID: 32793154 PMCID: PMC7393233 DOI: 10.3389/fmicb.2020.01665] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/25/2020] [Indexed: 12/15/2022] Open
Abstract
It has been well acknowledged that the gut microbiome is important for host health, composition changes in these microbial communities might increase susceptibility to infections and reduce adaptability to environment. Reintroduction, as an effective strategy for wild population recovery and genetic diversity maintenance for endangered populations, usually takes captive populations as rewilding resource. While, little is known about the compositional and functional differences of gut microbiota between captive and wild populations, especially for large carnivores, like Amur tiger. In this study, high throughput sequencing of the 16S ribosomal RNA (rRNA) gene (amplicon sequencing) and metagenomics were used to analyze the composition and function variations of gut microbiota communities between captive and wild Amur tiger populations based on total 35 fecal samples (13 from captive tigers and 22 from wild tigers). Our results showed that captive Amur tigers have higher alpha diversity in gut microbiota, but that the average unweighted UniFrac distance of bacterial taxa among wild Amur tigers was much larger. The function differences involve most aspects of the body functions, especially for metabolism, environmental information processing, cellular processes, and organismal systems. It was indicated that the diet habit and environment difference between captive and wild populations lead to composition differences of gut microbiota and then resulted in significant differences in functions. These contrasts of functional and compositional variations in gut microbiota between wild and captive Amur tigers are essential insights for guiding conservation management and policy decision-making, and call for more attention on the influence of gut microbiota on the ability of captive animals to survive in the wild.
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Affiliation(s)
- Yao Ning
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jinzhe Qi
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China.,Department of Wildlife, Fish, and Conservation, University of California, Davis, Davis, CA, United States
| | - Michael T Dobbins
- Department of Wildlife, Fish, and Conservation, University of California, Davis, Davis, CA, United States
| | - Xin Liang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jingxuan Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Shiyu Chen
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Jianzhang Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
| | - Guangshun Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
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31
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Hu Y, Yao X, Wu Y, Han W, Zhou Y, Tang X, Shao K, Gao G. Contrasting Patterns of the Bacterial Communities in Melting Ponds and Periglacial Rivers of the Zhuxi glacier in the Tibet Plateau. Microorganisms 2020; 8:microorganisms8040509. [PMID: 32252494 PMCID: PMC7232332 DOI: 10.3390/microorganisms8040509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/04/2022] Open
Abstract
Since the early 21st century, global climate change has been inducing rapid glacier retreat at an unprecedented rate. In this context, the melt ponds impart increasing unique footprints on the periglacial rivers due to their hydrodynamic connection. Given that bacterial communities control numerous ecosystem processes in the glacial ecosystem, exploring the fate of bacterial communities from melt ponds to periglacial rivers yields key knowledge of the biodiversity and biogeochemistry of glacial ecosystems. Here, we analyzed the bacterial community structure, diversity, and co-occurrence network to reveal the community organization in the Zhuxi glacier in the Tibet Plateau. The results showed that the bacterial communities in melt ponds were significantly lower in alpha-diversity but were significantly higher in beta-diversity than those in periglacial rivers. The rare sub-communities significantly contributed to the stability of the bacterial communities in both habitats. The co-occurrence network inferred that the mutually beneficial relationships predominated in the two networks. Nevertheless, the lower ratio of positive to negative edges in melt ponds than periglacial rivers implicated fiercer competition in the former habitat. Based on the significantly higher value of degree, betweenness, and modules, as well as shorter average path length in melt ponds, we speculated that their bacterial communities are less resilient than those of periglacial rivers.
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Affiliation(s)
- Yang Hu
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Xin Yao
- School of Environment and Planning, Liaocheng University, Liaocheng 25200, China
| | - Yuanyuan Wu
- Sino-Japan Friendship Center for Environmental Protection, Beijing 100029, China
| | - Wei Han
- Sino-Japan Friendship Center for Environmental Protection, Beijing 100029, China
| | - Yongqiang Zhou
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Xiangming Tang
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Keqiang Shao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Guang Gao
- Taihu Laboratory for Lake Ecosystem Research, State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China;
- Correspondence: ; Tel.: (+86) 25 86882187; Fax: (+86) 25 86882187
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32
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Sierra MA, Danko DC, Sandoval TA, Pishchany G, Moncada B, Kolter R, Mason CE, Zambrano MM. The Microbiomes of Seven Lichen Genera Reveal Host Specificity, a Reduced Core Community and Potential as Source of Antimicrobials. Front Microbiol 2020; 11:398. [PMID: 32265864 PMCID: PMC7105886 DOI: 10.3389/fmicb.2020.00398] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in Colombian Paramos using 16S rRNA gene amplicon sequencing and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes varied in diversity indexes and number of OTUs, but were composed predominantly by the phyla Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria, and Verrucomicrobia. In the case of Cora and Cladonia, the microbiomes were distinguished based on the identity of the lichen host. While the majority of the lichen-associated microorganisms were not present in all lichens sampled, sixteen taxa shared among this diverse group of lichens suggest a core lichen microbiome that broadens our concept of these symbiotic structures. Additionally, we identified strains producing compounds active against clinically relevant microbial strains. These results indicate that lichen microbiomes from the Paramo ecosystem are diverse and host-specific but share a taxonomic core and can be a source of new bacterial taxa and antimicrobials.
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Affiliation(s)
- Maria A. Sierra
- Molecular Genetics, Corporación CorpoGen – Research Center, Bogotá, Colombia
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - David C. Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Tito A. Sandoval
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Gleb Pishchany
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Bibiana Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Bogotá, Colombia
| | - Roberto Kolter
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
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33
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Vesty EF, Whitbread AL, Needs S, Tanko W, Jones K, Halliday N, Ghaderiardakani F, Liu X, Cámara M, Coates JC. Cross-kingdom signalling regulates spore germination in the moss Physcomitrella patens. Sci Rep 2020; 10:2614. [PMID: 32054953 PMCID: PMC7018845 DOI: 10.1038/s41598-020-59467-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/17/2020] [Indexed: 01/10/2023] Open
Abstract
Plants live in close association with microorganisms that can have beneficial or detrimental effects. The activity of bacteria in association with flowering plants has been extensively analysed. Bacteria use quorum-sensing as a way of monitoring their population density and interacting with their environment. A key group of quorum sensing molecules in Gram-negative bacteria are the N-acylhomoserine lactones (AHLs), which are known to affect the growth and development of both flowering plants, including crops, and marine algae. Thus, AHLs have potentially important roles in agriculture and aquaculture. Nothing is known about the effects of AHLs on the earliest-diverging land plants, thus the evolution of AHL-mediated bacterial-plant/algal interactions is unknown. In this paper, we show that AHLs can affect spore germination in a representative of the earliest plants on land, the Bryophyte moss Physcomitrella patens. Furthermore, we demonstrate that sporophytes of some wild isolates of Physcomitrella patens are associated with AHL-producing bacteria.
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Affiliation(s)
- Eleanor F Vesty
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,University Centre Shrewsbury, Guildhall, Frankwell Quay, Shrewsbury, Shropshire, UK
| | - Amy L Whitbread
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,Karlsruhe Institute of Technology, Karlsruhe, Baden-Württemberg, Germany
| | - Sarah Needs
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,School of Life, Health and Chemical Sciences, Open University, Walton Hall, Kents Hill, Milton Keynes, UK
| | - Wesal Tanko
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Kirsty Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Nigel Halliday
- National Biofilm Innovations Centre, University of Nottingham Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
| | | | - Xiaoguang Liu
- National Biofilm Innovations Centre, University of Nottingham Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.,Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Miguel Cámara
- National Biofilm Innovations Centre, University of Nottingham Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
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34
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Mainland and island populations of Mussaenda kwangtungensis differ in their phyllosphere fungal community composition and network structure. Sci Rep 2020; 10:952. [PMID: 31969602 PMCID: PMC6976661 DOI: 10.1038/s41598-020-57622-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 01/03/2020] [Indexed: 01/12/2023] Open
Abstract
We compared community composition and co-occurrence patterns of phyllosphere fungi between island and mainland populations within a single plant species (Mussaenda kwangtungensis) using high-throughput sequencing technology. We then used 11 microsatellite loci for host genotyping. The island populations differed significantly from their mainland counterparts in phyllosphere fungal community structure. Topological features of co-occurrence network showed geographic patterns wherein fungal assemblages were less complex, but more modular in island regions than mainland ones. Moreover, fungal interactions and community composition were strongly influenced by the genetic differentiation of host plants. This study may advance our understanding of assembly principles and ecological interactions of phyllosphere fungal communities, as well as improve our ability to optimize fungal utilization for the benefit of people.
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35
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Kobayashi K, Aoyagi H. Microbial community structure analysis in Acer palmatum bark and isolation of novel bacteria IAD-21 of the candidate division FBP. PeerJ 2019; 7:e7876. [PMID: 31681511 PMCID: PMC6824334 DOI: 10.7717/peerj.7876] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 09/12/2019] [Indexed: 02/01/2023] Open
Abstract
Background The potential of unidentified microorganisms for academic and other applications is limitless. Plants have diverse microbial communities associated with their biomes. However, few studies have focused on the microbial community structure relevant to tree bark. Methods In this report, the microbial community structure of bark from the broad-leaved tree Acer palmatum was analyzed. Both a culture-independent approach using polymerase chain reaction (PCR) amplification and next generation sequencing, and bacterial isolation and sequence-based identification methods were used to explore the bark sample as a source of previously uncultured microorganisms. Molecular phylogenetic analyses based on PCR-amplified 16S rDNA sequences were performed. Results At the phylum level, Proteobacteria and Bacteroidetes were relatively abundant in the A. palmatum bark. In addition, microorganisms from the phyla Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Armatimonadetes, and candidate division FBP, which contain many uncultured microbial species, existed in the A. palmatum bark. Of the 30 genera present at relatively high abundance in the bark, some genera belonging to the phyla mentioned were detected. A total of 70 isolates could be isolated and cultured using the low-nutrient agar media DR2A and PE03. Strains belonging to the phylum Actinobacteria were isolated most frequently. In addition, the newly identified bacterial strain IAP-33, presumed to belong to Acidobacteria, was isolated on PE03 medium. Of the isolated bacteria, 44 strains demonstrated less than 97% 16S rDNA sequence-similarity with type strains. Molecular phylogenetic analysis of IAD-21 showed the lowest similarity (79%), and analyses suggested it belongs to candidate division FBP. Culture of the strain IAD-21 was deposited in Japan Collection of Microorganisms (JCM) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) as JCM 32665 and DSM 108248, respectively. Discussion Our results suggest that a variety of uncultured microorganisms exist in A. palmatum bark. Microorganisms acquirable from the bark may prove valuable for academic pursuits, such as studying microbial ecology, and the bark might be a promising source of uncultured bacterial isolates.
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Affiliation(s)
- Kazuki Kobayashi
- Division of Life Sciences and Bioengineering, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hideki Aoyagi
- Division of Life Sciences and Bioengineering, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Lendemer JC, Keepers KG, Tripp EA, Pogoda CS, McCain CM, Kane NC. A taxonomically broad metagenomic survey of 339 species spanning 57 families suggests cystobasidiomycete yeasts are not ubiquitous across all lichens. AMERICAN JOURNAL OF BOTANY 2019; 106:1090-1095. [PMID: 31397894 DOI: 10.1002/ajb2.1339] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/12/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and important components of lichen metacommunities. Yet, the presence of basidiomycete yeasts across a wide diversity of lichen lineages has not previously been tested. METHODS We searched for lichen-associated cystobasidiomycete yeasts in newly generated metagenomic data from 413 samples of 339 lichen species spanning 57 families and 25 orders. The data set was generated as part of a large-scale project to study lichen biodiversity gradients in the southern Appalachian Mountains Biodiversity Hotspot of southeastern North America. RESULTS Our efforts detected cystobasidiomycete yeasts in nine taxa (Bryoria nadvornikiana, Heterodermia leucomelos, Lecidea roseotincta, Opegrapha vulgata, Parmotrema hypotropum, P. subsumptum, Usnea cornuta, U. strigosa, and U. subgracilis), representing 2.7% of all species sampled. Seven of these taxa (78%) are foliose (leaf-like) or fruticose (shrubby) lichens that belong to families where basidiomycete yeasts have been previously detected. In several of the nine cases, cystobasidiomycete rDNA coverage was comparable to, or greater than, that of the primary lichen fungus single-copy nuclear genomic rDNA, suggesting sampling artifacts are unlikely to account for our results. CONCLUSIONS Studies from diverse areas of the natural sciences have led to the need to reconceptualize lichens as dynamic metacommunities. However, our failure to detect cystobasidiomycetes in 97.3% (330 species) of the sampled species suggests that basidiomycete yeasts are not ubiquitous in lichens.
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Affiliation(s)
- James C Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA
| | - Kyle G Keepers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
| | - Erin A Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
- Museum of Natural History, University of Colorado, Boulder, CO, 80302, USA
| | - Cloe S Pogoda
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
| | - Christy M McCain
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
- Museum of Natural History, University of Colorado, Boulder, CO, 80302, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80302, USA
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Qian X, Li H, Wang Y, Wu B, Wu M, Chen L, Li X, Zhang Y, Wang X, Shi M, Zheng Y, Guo L, Zhang D. Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere. Front Microbiol 2019; 10:1015. [PMID: 31143169 PMCID: PMC6521803 DOI: 10.3389/fmicb.2019.01015] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/24/2019] [Indexed: 12/21/2022] Open
Abstract
Plant-associated microbiomes are key determinants of host-plant fitness, productivity, and function. However, compared to bacterial community, we still lack fundamental knowledge concerning the variation in the fungal microbiome at the plant niche level. In this study, we quantified the fungal communities in the rhizosphere soil, as well as leaf and root endosphere compartments of a subtropical island shrub, Mussaenda kwangtungensis, using high-throughput DNA sequencing. We found that fungal microbiomes varied significantly across different plant compartments. Rhizosphere soil exhibited the highest level of fungal diversity, whereas the lowest level was found in the leaf endosphere. Further, the fungal communities inhabiting the root endosphere shared a greater proportion of fungal operational taxonomic units (OTUs) with rhizosphere communities than with leaf fungal endophyte communities, despite significant separation in community structure between the two belowground compartments. The fungal co-occurrence networks in the three compartments of M. kwangtungensis showed scale-free features and non-random co-occurrence patterns and matched the topological properties of small-world and evidently modular structure. Additionally, the rhizosphere network was more complex and showed higher centrality and connectedness than the leaf and root endosphere networks. Overall, our findings provide comprehensive insights into the structural variability, niche differentiation, and co-occurrence patterns in the plant associated fungal microbiome.
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Affiliation(s)
- Xin Qian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hanzhou Li
- Biomarker Technologies Corporation, Beijing, China
| | - Yonglong Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Binwei Wu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Mingsong Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang Chen
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingchun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ying Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiangping Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yong Zheng
- Key Laboratory of Humid Subtropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Liangdong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Almendras K, García J, Carú M, Orlando J. Nitrogen-Fixing Bacteria Associated with Peltigera Cyanolichens and Cladonia Chlorolichens. Molecules 2018; 23:E3077. [PMID: 30477264 PMCID: PMC6320784 DOI: 10.3390/molecules23123077] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/15/2018] [Accepted: 11/21/2018] [Indexed: 11/16/2022] Open
Abstract
Lichens have been extensively studied and described; however, recent evidence suggests that members of the bacterial community associated with them could contribute new functions to the symbiotic interaction. In this work, we compare the nitrogen-fixing guild associated with bipartite terricolous lichens with different types of photobiont: Peltigera cyanolichens and Cladonia chlorolichens. Since cyanobacteria contribute nitrogen to the symbiosis, we propose that chlorolichens have more diverse bacteria with the ability to fix nitrogen compared to cyanolichens. In addition, since part of these bacteria could be recruited from the substrate where lichens grow, we propose that thalli and substrates share some bacteria in common. The structure of the nitrogen-fixing guild in the lichen and substrate bacterial communities of both lichens was determined by terminal restriction fragment length polymorphism (TRFLP) of the nifH gene. Multivariate analyses showed that the nitrogen-fixing bacteria associated with both types of lichen were distinguishable from those present in their substrates. Likewise, the structure of the nitrogen-fixing bacteria present in the cyanolichens was different from that of chlorolichens. Finally, the diversity of this bacterial guild calculated using the Shannon index confirms the hypothesis that chlorolichens have a higher diversity of nitrogen-fixing bacteria than cyanolichens.
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Affiliation(s)
- Katerin Almendras
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
| | - Jaime García
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
| | - Margarita Carú
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
| | - Julieta Orlando
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago 7800003, Chile.
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Carbon Consumption Patterns of Microbial Communities Associated with Peltigera Lichens from a Chilean Temperate Forest. Molecules 2018; 23:molecules23112746. [PMID: 30355963 PMCID: PMC6278465 DOI: 10.3390/molecules23112746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/21/2018] [Accepted: 10/21/2018] [Indexed: 12/15/2022] Open
Abstract
Lichens are a symbiotic association between a fungus and a green alga or a cyanobacterium, or both. They can grow in practically any terrestrial environment and play crucial roles in ecosystems, such as assisting in soil formation and degrading soil organic matter. In their thalli, they can host a wide diversity of non-photoautotrophic microorganisms, including bacteria, which play important functions and are considered key components of the lichens. In this work, using the BioLog® EcoPlate system, we studied the consumption kinetics of different carbon-sources by microbial communities associated with the thallus and the substrate of Peltigera lichens growing in a Chilean temperate rain forest dominated by Nothofagus pumilio. Based on the similarity of the consumption of 31 carbon-sources, three groups were formed. Among them, one group clustered the microbial metabolic profiles of almost all the substrates from one of the sampling sites, which exhibited the highest levels of consumption of the carbon-sources, and another group gathered the microbial metabolic profiles from the lichen thalli with the most abundant mycobiont haplotypes. These results suggest that the lichen thallus has a higher impact on the metabolism of its microbiome than on the microbial community of its substrate, with the latter being more diverse in terms of the metabolized sources and whose activity level is probably related to the availability of soil nutrients. However, although significant differences were detected in the microbial consumption of several carbon-sources when comparing the lichen thallus and the underlying substrate, d-mannitol, l-asparagine, and l-serine were intensively metabolized by both communities, suggesting that they share some microbial groups. Likewise, some communities showed high consumption of 2-hydroxybenzoic acid, d-galacturonic acid, and itaconic acid; these could serve as suitable sources of microorganisms as bioresources of novel bioactive compounds with biotechnological applications.
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Qian X, Chen L, Guo X, He D, Shi M, Zhang D. Shifts in community composition and co-occurrence patterns of phyllosphere fungi inhabiting Mussaenda shikokiana along an elevation gradient. PeerJ 2018; 6:e5767. [PMID: 30345176 PMCID: PMC6187995 DOI: 10.7717/peerj.5767] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/17/2018] [Indexed: 02/03/2023] Open
Abstract
The altitudinal effects on the distributions of phyllosphere fungal assemblages in conspecific plants remain poorly elucidated. To address this, phyllosphere fungal communities associated with Mussaenda shikokiana were investigated at four sites across a 350 m elevation gradient in a subtropical forest by employing Illumina metabarcoding of the fungal internal transcribed spacer 2 (ITS2) region. Our results demonstrated that phyllosphere fungal assemblages with a single host possessed high taxonomic diversity and multiple trophic guilds. OTU richness was significantly influenced by elevation. The elevation gradient also entailed distinct shifts in the community composition of phyllosphere fungi, which was significantly related to geographical distance and mean annual temperature (MAT). Additionally, comparison of phyllosphere fungal networks showed reduced connectivity with increasing elevation. Our data provide insights on the distribution and interactions of the phyllosphere fungal community associated with a single host along a short elevation gradient.
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Affiliation(s)
- Xin Qian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liang Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dan He
- Center for Ecological and Environmental Sciences, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
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Hu Y, Bai C, Cai J, Dai J, Shao K, Tang X, Gao G. Co-occurrence Network Reveals the Higher Fragmentation of the Bacterial Community in Kaidu River Than Its Tributaries in Northwestern China. Microbes Environ 2018; 33:127-134. [PMID: 29794413 PMCID: PMC6031398 DOI: 10.1264/jsme2.me17170] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/12/2018] [Indexed: 12/12/2022] Open
Abstract
Rivers and their tributaries sculpt the earth's surface, and play an important role in substance circulation and energy flow. Bacteria are involved in most biogeochemical processes in the fluvial ecosystem; however, their pattern distribution in a river and its tributaries has not yet been investigated in detail. In the present study, high-throughput sequencing was employed to examine bacterial communities and their co-occurrence networks between Kaidu River and its nine tributaries in northwestern China. The results obtained demonstrated that both bacterial communities shared a similar dominant sub-community, mainly consisting of Actinobacteria, Bacteroidetes, and Proteobacteria, with Limnohabitans and Variovorax as the dominant genera. In spite of these commonalities, bacterial community structures still significantly differed between these two habitats, which may be related to the distance-related dispersal limitation. Their co-occurrence networks were generally both positively structured. The structural analysis showed that OTUs from the same phyla were more likely to co-occur. Although the keystone genera were taxonomically different between Kaidu River and its tributaries, they both shared common trophic properties in exploiting niches under oligotrophic conditions. We noted that their relative abundances were less than 1%, indicating the over-proportional roles of rare genera in the bacterial community. In addition, the inferred networks showed less nodes and edges, but higher modularity in Kaidu River than its tributaries, suggesting the higher fragmentation of the bacterial community in the mainstream.
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Affiliation(s)
- Yang Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesNanjing 210008China
- University of Chinese Academy of SciencesBeijing, 100000China
| | - Chengrong Bai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesNanjing 210008China
- University of Chinese Academy of SciencesBeijing, 100000China
| | - Jian Cai
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesNanjing 210008China
- University of Chinese Academy of SciencesBeijing, 100000China
| | - Jiangyu Dai
- State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, Nanjing Hydraulic Research InstituteNanjing, 210029P.R. China
| | - Keqiang Shao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesNanjing 210008China
| | - Xiangming Tang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesNanjing 210008China
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of SciencesNanjing 210008China
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Cernava T, Erlacher A, Aschenbrenner IA, Krug L, Lassek C, Riedel K, Grube M, Berg G. Deciphering functional diversification within the lichen microbiota by meta-omics. MICROBIOME 2017; 5:82. [PMID: 28724401 PMCID: PMC5518139 DOI: 10.1186/s40168-017-0303-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 07/06/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Recent evidence of specific bacterial communities extended the traditional concept of fungal-algal lichen symbioses by a further organismal kingdom. Although functional roles were already assigned to dominant members of the highly diversified microbiota, a substantial fraction of the ubiquitous colonizers remained unexplored. We employed a multi-omics approach to further characterize functional guilds in an unconventional model system. RESULTS The general community structure of the lichen-associated microbiota was shown to be highly similar irrespective of the employed omics approach. Five highly abundant bacterial orders-Sphingomonadales, Rhodospirillales, Myxococcales, Chthoniobacterales, and Sphingobacteriales-harbor functions that are of substantial importance for the holobiome. Identified functions range from the provision of vitamins and cofactors to the degradation of phenolic compounds like phenylpropanoid, xylenols, and cresols. CONCLUSIONS Functions that facilitate the persistence of Lobaria pulmonaria under unfavorable conditions were present in previously overlooked fractions of the microbiota. So far, unrecognized groups like Chthoniobacterales (Verrucomicrobia) emerged as functional protectors in the lichen microbiome. By combining multi-omics and imaging techniques, we highlight previously overlooked participants in the complex microenvironment of the lichens.
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Affiliation(s)
- Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnolgy GmbH, Petersgasse 14, 8010 Graz, Austria
| | - Armin Erlacher
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Ines Aline Aschenbrenner
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Lisa Krug
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Christian Lassek
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Friedrich-Ludwig-Jahn Strasse 15, 17489 Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, Ernst-Moritz-Arndt University of Greifswald, Friedrich-Ludwig-Jahn Strasse 15, 17489 Greifswald, Germany
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
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