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Baba T, Hirose D. Two novel Archaeorhizomyces species isolated from ericoid mycorrhizal roots and their association with ericaceous plants in vitro. Fungal Biol 2024; 128:1939-1953. [PMID: 39059849 DOI: 10.1016/j.funbio.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 07/28/2024]
Abstract
Archaeorhizomyces is a diverse and ubiquitous genus of the subphylum Taphrinomycotina, which contains soil-inhabiting/root-associated fungi. Although ecological importance and root-associating lifestyles of Archaeorhizomyces can be postulated, morphological aspects of fungal body and root colonization are largely unknown due to the scarcity of cultures. We obtained three unidentified Archaeorhizomyces isolates from ericoid mycorrhizal (ErM) roots of Rhododendron scabrum and Rhododendron × obtusum collected in Japan. To advance our understanding of lifestyle of the genus, we investigated their general morphology, phylogeny, and in vitro root-colonizing ability in ericoid mycorrhizal hosts, Vaccinium virgatum and Rhododendron kaempferi. Some morphological characteristics, such as slow glowing white-to-creamy-colored colonies and formation of yeast-like or chlamydospore-like cells, were shared between our strains and two described species, Archaeorhizomycesfinlayi and Archaeorhizomyces borealis, but they were phylogenetically distant. Our strains were clearly distinguished as two undescribed species based on morphology and phylogenetic relationship. As seen in typical ErM fungi, both species frequently formed hyphal coils within vital rhizodermal cells of ErM plants in vitro. The morphology of hyphal coils was also different between species. Consequently, two novel species, Archaeorhizomyces notokirishimae sp. nov. and Archaeorhizomyces ryukyuensis sp. nov., were described.
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Affiliation(s)
- Takashi Baba
- Division of Fruit Tree Production Research, Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa, Morioka, Iwate 020-0123, Japan
| | - Dai Hirose
- School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555, Japan.
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Vélez-Martínez GA, Reyes-Ardila WL, Duque-Zapata JD, Rugeles-Silva PA, Muñoz Flórez JE, López-Álvarez D. Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems. Int Microbiol 2024; 27:377-391. [PMID: 37458953 PMCID: PMC10991037 DOI: 10.1007/s10123-023-00392-8] [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: 06/08/2023] [Accepted: 06/15/2023] [Indexed: 04/05/2024]
Abstract
The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.
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Affiliation(s)
- Glever Alexander Vélez-Martínez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia.
| | - Wendy Lorena Reyes-Ardila
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Juan Diego Duque-Zapata
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Paula Andrea Rugeles-Silva
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Jaime Eduardo Muñoz Flórez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia
| | - Diana López-Álvarez
- Grupo de Investigación en Diversidad Biológica, Departamento de Ciencias Biológicas, Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia-Sede Palmira, Carrera, 32 No. 12-00, 763536, Palmira, Valle del Cauca, Colombia.
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3
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Wang Y, Xu J, Yuan Q, Guo L, Xiao C, Yang C, Li L, Jiang W, Zhou T. Effect of symbiotic fungi- Armillaria gallica on the yield of Gastrodia elata Bl. and insight into the response of soil microbial community. Front Microbiol 2023; 14:1233555. [PMID: 37744896 PMCID: PMC10512952 DOI: 10.3389/fmicb.2023.1233555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Armillaria members play important roles in the nutrient supply and growth modulation of Gastrodia elata Bl., and they will undergo severe competition with native soil organisms before colonization and become symbiotic with G. elata. Unraveling the response of soil microbial organisms to symbiotic fungi will open up new avenues to illustrate the biological mechanisms driving G. elata's benefit from Armillaria. For this purpose, Armillaria strains from four main G. elata production areas in China were collected, identified, and co-planted with G. elata in Guizhou Province. The result of the phylogenetic tree indicated that the four Armillaria strains shared the shortest clade with Armillaria gallica. The yields of G. elata were compared to uncover the potential role of these A. gallica strains. Soil microbial DNA was extracted and sequenced using Illumina sequencing of 16S and ITS rRNA gene amplicons to decipher the changes of soil bacterial and fungal communities arising from A. gallica strains. The yield of G. elata symbiosis with the YN strain (A. gallica collected from Yunnan) was four times higher than that of the GZ strain (A. gallica collected from Guizhou) and nearly two times higher than that of the AH and SX strains (A. gallica collected from Shanxi and Anhui). We found that the GZ strain induced changes in the bacterial community, while the YN strain mainly caused changes in the fungal community. Similar patterns were identified in non-metric multidimensional scaling analysis, in which the GZ strain greatly separated from others in bacterial structure, while the YN strain caused significant separation from other strains in fungal structure. This current study revealed the assembly and response of the soil microbial community to A. gallica strains and suggested that exotic strains of A. gallica might be helpful in improving the yield of G. elata by inducing changes in the soil fungal community.
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Affiliation(s)
- Yanhong Wang
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jiao Xu
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qingsong Yuan
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chenghong Xiao
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Changgui Yang
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Liangyuan Li
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Weike Jiang
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Tao Zhou
- Resource Institute for Chinese & Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
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Cheng F, Li M, Ren Y, Hou L, Gao T, He P, Deng X, Lu J. Soil Fungal Community Characteristics at Timberlines of Sejila Mountain in Southeast Tibet, China. J Fungi (Basel) 2023; 9:jof9050596. [PMID: 37233307 DOI: 10.3390/jof9050596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/08/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023] Open
Abstract
Soil fungal community characteristics of alpine timberlines are unclear. In this study, soil fungal communities in five vegetation zones across timberlines on the south and north slopes of Sejila Mountain in Tibet, China were investigated. The results show that the alpha diversity of soil fungi was not different between the north- and south-facing timberlines or among the five vegetation zones. Archaeorhizomyces (Ascomycota) was a dominant genus at the south-facing timberline, whereas the ectomycorrhizal genus Russula (Basidiomycota) decreased with decreasing Abies georgei coverage and density at the north-facing timberline. Saprotrophic soil fungi were dominant, but their relative abundance changed little among the vegetation zones at the south timberline, whereas ectomycorrhizal fungi decreased with tree hosts at the north timberline. Soil fungal community characteristics were related to coverage and density, soil pH and ammonium nitrogen at the north timberline, whereas they had no associations with the vegetation and soil factors at the south timberline. In conclusion, timberline and A. georgei presence exerted apparent influences on the soil fungal community structure and function in this study. The findings may enhance our understanding of the distribution of soil fungal communities at the timberlines of Sejila Mountain.
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Affiliation(s)
- Fei Cheng
- Institute of Tibet Plateau Ecology, Tibet Agricultural & Animal Husbandry University, Nyingchi 860000, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Tibet Agricultural & Animal Husbandry University, Nyingchi 860000, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, Forestry College, Guangxi University, Nanning 530004, China
| | - Mingman Li
- Guangxi Key Laboratory of Forest Ecology and Conservation, Forestry College, Guangxi University, Nanning 530004, China
| | - Yihua Ren
- Institute of Tibet Plateau Ecology, Tibet Agricultural & Animal Husbandry University, Nyingchi 860000, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Tibet Agricultural & Animal Husbandry University, Nyingchi 860000, China
| | - Lei Hou
- Institute of Tibet Plateau Ecology, Tibet Agricultural & Animal Husbandry University, Nyingchi 860000, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Tibet Agricultural & Animal Husbandry University, Nyingchi 860000, China
| | - Tan Gao
- Institute of Tibet Plateau Ecology, Tibet Agricultural & Animal Husbandry University, Nyingchi 860000, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Tibet Agricultural & Animal Husbandry University, Nyingchi 860000, China
| | - Peng He
- Guangxi Key Laboratory of Forest Ecology and Conservation, Forestry College, Guangxi University, Nanning 530004, China
| | - Xiangsheng Deng
- Guangxi Key Laboratory of Forest Ecology and Conservation, Forestry College, Guangxi University, Nanning 530004, China
| | - Jie Lu
- Institute of Tibet Plateau Ecology, Tibet Agricultural & Animal Husbandry University, Nyingchi 860000, China
- Key Laboratory of Forest Ecology in Tibet Plateau, Tibet Agricultural & Animal Husbandry University, Nyingchi 860000, China
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5
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Giorgio M, Niccolò BGM, Benedetta T, Luisa M, Leonardo BF, Gregory B, Pietro B, Alberto A, Domizia D, Emidio A. Fungal and Bacterial Diversity in the Tuber magnatum Ecosystem and Microbiome. MICROBIAL ECOLOGY 2023; 85:508-521. [PMID: 35237850 DOI: 10.1007/s00248-021-01950-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Fungi belonging to the genus Tuber produce edible ascocarps known as truffles. Tuber magnatum Picco may be the most appreciated truffle species given its peculiar aroma. While its life cycle is not yet fully elucidated, some studies demonstrated an active role of microorganisms. The main goal of this study was to determine how the T. magnatum microbiome varies across space and time. To address this, we characterized microbial communities associated with T. magnatum through high-throughput amplicon sequencing of internal transcribed spacer (ITS) and 16S rDNAs in three productive natural sites in Italy across 2 years. At each site, four truffles were sampled as well as the soil underneath and at 40, 100, and 200 cm from the harvesting points, to assess for microbial variation between substrates, years, and sites. A statistically significant site-related effect on microbial communities was identified, whereas only the prokaryotic community was significantly affected by the distance of soil from the truffle. Significant differences between sampling years were also found, demonstrating a possible relation among rainfall precipitation and Firmicutes and Actinobacteria. Thirty-six bacterial OTUs in truffles and 11 bacterial OTUs in soils beneath truffles were identified as indicator taxa. As shown for other truffle species, the dominance of Bradyrhizobium, Rhizobium, and Ensifer spp. within the truffle fruiting body suggests an evolutionary adaptation of this microorganism to the genus Tuber. The present work offers novel and relevant insights into the microbial ecology of T. magnatum ecosystems and fruiting bodies. The function and role of these bacteria in the truffle microbiome and life cycle are in need of further investigation.
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Affiliation(s)
- Marozzi Giorgio
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Benucci Gian Maria Niccolò
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA.
| | - Turchetti Benedetta
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Massaccesi Luisa
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, 01100, Viterbo, Italy
| | - Baciarelli Falini Leonardo
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Bonito Gregory
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Buzzini Pietro
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Agnelli Alberto
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Donnini Domizia
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
| | - Albertini Emidio
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121, Perugia, Italy
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6
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DNA metabarcoding reveals compositional and functional differences in fungal communities among Amazonian canga formations. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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He D, Guo Z, Shen W, Ren L, Sun D, Yao Q, Zhu H. Fungal Communities Are More Sensitive to the Simulated Environmental Changes than Bacterial Communities in a Subtropical Forest: the Single and Interactive Effects of Nitrogen Addition and Precipitation Seasonality Change. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02092-8. [PMID: 35927588 DOI: 10.1007/s00248-022-02092-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Increased nitrogen deposition (N factor) and changes in precipitation patterns (W factor) can greatly impact soil microbial communities in tropical/subtropical forests. Although knowledge about the effects of a single factor on soil microbial communities is growing rapidly, little is understood about the interactive effects of these two environmental change factors. In this study, we investigated the responses of soil bacterial and fungal communities to the short-term simulated environmental changes (nitrogen addition, precipitation seasonality change, and their combination) in a subtropical forest in South China. The interaction between N and W factors was detected significant for affecting some soil physicochemical properties (such as pH, soil water, and NO3- contents). Fungi were more susceptible to treatment than bacteria in a variety of community traits (alpha, beta diversity, and network topological features). The N and W factors act antagonistically to affect fungal alpha diversity, and the interaction effect was detected significant for the dry season. The topological features of the meta-community (containing both bacteria and fungi) network overrode the alpha and beta diversity of bacterial or fungal communities in explaining the variation of soil enzyme activities. The associations between Ascomycota fungi and Gammaproteobacteria or Alphaproteobacteria might be important in mediating the inter-kingdom interactions. In summary, our results suggested that fungal communities were more sensitive to N and W factors (and their interaction) than bacterial communities, and the treatments' effects were more prominent in the dry season, which may have great consequences in soil processes and ecosystem functions in subtropical forests.
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Affiliation(s)
- Dan He
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Xianlie Road 100#, Guangzhou, 510070, China
| | - Zhiming Guo
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Weijun Shen
- College of Forestry, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Daxue Road 100#, Nanning, 530004, China.
| | - Lijuan Ren
- Department of Ecology, Institute of Hydrobiology, Jinan University, Guangzhou, 510632, China
| | - Dan Sun
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Honghui Zhu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Institute of Microbiology, Guangdong Academy of Sciences, Xianlie Road 100#, Guangzhou, 510070, China.
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Mafa‐Attoye TG, Borden KA, Alvarez DO, Thevathasan N, Isaac ME, Dunfield KE. Roots alter soil microbial diversity and interkingdom interactions in diversified agricultural landscapes. OIKOS 2022. [DOI: 10.1111/oik.08717] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
| | - Kira A. Borden
- Faculty of Land and Food Systems, Univ. of British Columbia Vancouver BC Canada
| | | | | | - Marney E. Isaac
- Dept of Physical&Environmental Sciences, Univ. of Toronto Scarborough Toronto ON Canada
| | - Kari E. Dunfield
- School of Environmental Sciences, Univ. of Guelph Guelph ON Canada
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Kui L, Xiang G, Wang Y, Wang Z, Li G, Li D, Yan J, Ye S, Wang C, Yang L, Zhang S, Zhang S, Zhou L, Gui H, Xu J, Chen W, Zhang J, Huang T, Majeed A, Sheng J, Dong Y. Large-Scale Characterization of the Soil Microbiome in Ancient Tea Plantations Using High-Throughput 16S rRNA and Internal Transcribed Spacer Amplicon Sequencing. Front Microbiol 2021; 12:745225. [PMID: 34721345 PMCID: PMC8555698 DOI: 10.3389/fmicb.2021.745225] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022] Open
Abstract
There is a special interaction between the environment, soil microorganisms, and tea plants, which constitute the ecosystem of tea plantations. Influenced by environmental factors and human management, the changes in soil microbial community affected the growth, quality, and yield of tea plants. However, little is known about the composition and structure of soil bacterial and fungal communities in 100-year-old tea plantations and the mechanisms by which they are affected. In this regard, we characterized the microbiome of tea plantation soils by considering the bacterial and fungal communities in 448 soil samples from 101 ancient tea plantations in eight counties of Lincang city, which is one of the tea domestication centers in the world. 16S and Internal Transcribed Spacer (ITS) rRNA high-throughput amplicon sequencing techniques were applied in this study. The results showed that the abundance, diversity, and composition of the bacterial and fungal communities have different sensitivity with varying pH, altitude, and latitude. pH and altitude affect soil microbial communities, and bacterial communities are more sensitive than fungi in terms of abundance and diversity to pH. The highest α-diversity of bacterial communities is shown in the pH 4.50–5.00 and 2,200-m group, and fungi peaked in the pH 5.00–5.50 and 900-m group. Because of environmental and geographical factors, all microbes are similarly changing, and further correlations showed that the composition and structure of bacterial communities are more sensitive than fungal communities, which were affected by latitude and altitude. In conclusion, the interference of anthropogenic activities plays a more important role in governing fungal community selection than environmental or geographical factors, whereas for the bacterial community, it is more selective to environment adaptation than to adaptation to human activities.
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Affiliation(s)
- Ling Kui
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Guisheng Xiang
- Yunnan Agricultural University Applied Genomics Technology Laboratory, School of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Ya Wang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zijun Wang
- Yunnan Agricultural University Applied Genomics Technology Laboratory, School of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Guorong Li
- Lincang Tea Research Institute, Lincang, China
| | - Dawei Li
- Yunnan Agricultural University Applied Genomics Technology Laboratory, School of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Jing Yan
- Yunnan Agricultural University Applied Genomics Technology Laboratory, School of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Shuang Ye
- Yunnan Agricultural University Applied Genomics Technology Laboratory, School of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Chunping Wang
- Yunnan Agricultural University Applied Genomics Technology Laboratory, School of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Ling Yang
- Yunnan Agricultural University Applied Genomics Technology Laboratory, School of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Shiyu Zhang
- Yunnan Agricultural University Applied Genomics Technology Laboratory, School of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Shuangyan Zhang
- Yunnan Agricultural University Applied Genomics Technology Laboratory, School of Biological Big Data, Yunnan Agricultural University, Kunming, China
| | - Ling Zhou
- Yunnan Agricultural University Applied Genomics Technology Laboratory, School of Biological Big Data, Yunnan Agricultural University, Kunming, China.,Longrun Pu'er Tea College of Yunnan Agricultural University, Kunming, China
| | - Heng Gui
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jianchu Xu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,Centre for Mountain Futures, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Wei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Jun Zhang
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Tingyuan Huang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Aasim Majeed
- Molecular Genetics Laboratory, Central University of Punjab, Lahore, India
| | - Jun Sheng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China.,Key Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Yunnan Research Institute for Local Plateau Agriculture and Industry, Kunming, China
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10
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Mikryukov VS, Dulya OV, Bergman IE, Lihodeevskiy GA, Loginova AD, Tedersoo L. Sheltering Role of Well-Decayed Conifer Logs for Forest Floor Fungi in Long-Term Polluted Boreal Forests. Front Microbiol 2021; 12:729244. [PMID: 34690970 PMCID: PMC8527098 DOI: 10.3389/fmicb.2021.729244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/14/2021] [Indexed: 01/04/2023] Open
Abstract
Coarse woody debris (CWD) provides food and shelter to a large proportion of forest biota and is considered vital for biodiversity during periods of harsh weather. However, its importance in long-term stressed ecosystems remains largely unknown. In this work, we explored the contribution of CWD to fungal diversity along the gradient of boreal forest degradation caused by 77 years of heavy industrial emissions. We analyzed the diversity and composition of fungi in 270 samples of well-decayed Picea abies and Abies sibirica logs, as well as forest litter both adjacent to and distant from the logs. Compared with forest litter, the wood had higher water content and possessed substantially lower concentrations of heavy metals, which suggests its potential favorability for biota in polluted areas. The pollution-induced loss of fungal diversity in forest litter reached 34% and was stronger in the microhabitats not influenced by CWD. Meanwhile, wood fungal communities lost less than 10% of their total richness and even increased in alpha diversity. These processes led to the diversity and compositional convergence of fungal communities from different microhabitats and substrates in polluted areas. Despite this, the importance of wood and CWD-influenced microhabitats for fungal diversity maintenance was low. Apart from wood-associated fungi, the taxa whose diversity increased in the wood of polluted areas were ectomycorrhizal fungi and eurytopic soil saprotrophs (Mucoromycota, Mortierellomycota, Eurotiomycetes, and Helotiales) that easily tolerate highly toxic litter. Within the majority of pollution-sensitive soil saprotrophic groups, only terricolous Tricholomataceae benefit from CWD as microrefugia. Upon considering the ecological variability within low-rank taxa, the importance of decayed logs as safe sites can be high for certain soil-inhabiting fungal groups in polluted areas.
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Affiliation(s)
- Vladimir S. Mikryukov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- Department of Botany, Chair of Mycology, Institute of Ecology and Earth Sciences, Tartu, Estonia
| | - Olesya V. Dulya
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- Department of Botany, Chair of Mycology, Institute of Ecology and Earth Sciences, Tartu, Estonia
| | - Igor E. Bergman
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | | | - Anzhelika D. Loginova
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
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11
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Mod HK, Buri A, Yashiro E, Guex N, Malard L, Pinto-Figueroa E, Pagni M, Niculita-Hirzel H, van der Meer JR, Guisan A. Predicting spatial patterns of soil bacteria under current and future environmental conditions. THE ISME JOURNAL 2021; 15:2547-2560. [PMID: 33712699 PMCID: PMC8397778 DOI: 10.1038/s41396-021-00947-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 02/01/2023]
Abstract
Soil bacteria are largely missing from future biodiversity assessments hindering comprehensive forecasts of ecosystem changes. Soil bacterial communities are expected to be more strongly driven by pH and less by other edaphic and climatic factors. Thus, alkalinisation or acidification along with climate change may influence soil bacteria, with subsequent influences for example on nutrient cycling and vegetation. Future forecasts of soil bacteria are therefore needed. We applied species distribution modelling (SDM) to quantify the roles of environmental factors in governing spatial abundance distribution of soil bacterial OTUs and to predict how future changes in these factors may change bacterial communities in a temperate mountain area. Models indicated that factors related to soil (especially pH), climate and/or topography explain and predict part of the abundance distribution of most OTUs. This supports the expectations that microorganisms have specific environmental requirements (i.e., niches/envelopes) and that they should accordingly respond to environmental changes. Our predictions indicate a stronger role of pH over other predictors (e.g. climate) in governing distributions of bacteria, yet the predicted future changes in bacteria communities are smaller than their current variation across space. The extent of bacterial community change predictions varies as a function of elevation, but in general, deviations from neutral soil pH are expected to decrease abundances and diversity of bacteria. Our findings highlight the need to account for edaphic changes, along with climate changes, in future forecasts of soil bacteria.
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Affiliation(s)
- Heidi K Mod
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland.
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Erika Yashiro
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lucie Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Marco Pagni
- Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hélène Niculita-Hirzel
- Department of Occupational Health and Environment, Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | | | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
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12
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Velez P, Tapia-Torres Y, García-Oliva F, Gasca-Pineda J. Small-scale variation in a pristine montane cloud forest: evidence on high soil fungal diversity and biogeochemical heterogeneity. PeerJ 2021; 9:e11956. [PMID: 34447634 PMCID: PMC8364316 DOI: 10.7717/peerj.11956] [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: 03/12/2021] [Accepted: 07/21/2021] [Indexed: 12/04/2022] Open
Abstract
Montane cloud forests are fragile biodiversity hotspots. To attain their conservation, disentangling diversity patterns at all levels of ecosystem organization is mandatory. Biotic communities are regularly structured by environmental factors even at small spatial scales. However, studies at this scale have received less attention with respect to larger macroscale explorations, hampering the robust view of ecosystem functioning. In this sense, fungal small-scale processes remain poorly understood in montane cloud forests, despite their relevance. Herein, we analyzed soil fungal diversity and ecological patterns at the small-scale (within a 10 m triangular transect) in a pristine montane cloud forest of Mexico, using ITS rRNA gene amplicon Illumina sequencing and biogeochemical profiling. We detected a taxonomically and functionally diverse fungal community, dominated by few taxa and a large majority of rare species (81%). Undefined saprotrophs represented the most abundant trophic guild. Moreover, soil biogeochemical data showed an environmentally heterogeneous setting with patchy clustering, where enzymatic activities suggest distinctive small-scale soil patterns. Our results revealed that in this system, deterministic processes largely drive the assemblage of fungal communities at the small-scale, through multifactorial environmental filtering.
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Affiliation(s)
- Patricia Velez
- Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Yunuen Tapia-Torres
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Morelia, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
| | - Jaime Gasca-Pineda
- UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Estado de México, Mexico
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13
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Tonjer LR, Thoen E, Morgado L, Botnen S, Mundra S, Nybakken L, Bryn A, Kauserud H. Fungal community dynamics across a forest-alpine ecotone. Mol Ecol 2021; 30:4926-4938. [PMID: 34314543 DOI: 10.1111/mec.16095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 07/15/2021] [Accepted: 07/23/2021] [Indexed: 12/30/2022]
Abstract
Climate change is causing upward shift of forest lines worldwide, with consequences for soil biota and carbon (C) sequestration. We here analyse compositional changes in the soil biota across the forest line ecotone, an important transition zone between different ecosystems. We collected soil samples along transects stretching from subalpine mountain birch forests to alpine heath. Soil fungi and micro-eukaryotes were surveyed using DNA metabarcoding of the ITS2 and 18S markers, while ergosterol was used to quantify fungal biomass. We observed a strong shift in the soil biota across the forest line ecotone: Below the forest line, there were higher proportions of basidiomycetes and mucoromycetes, including ectomycorrhizal and saprotrophic fungi. Above it, we observed relatively more root-associated ascomycetes, including Archaeorhizomycetes, ericoid mycorrhizal fungi and dark septate endophytes. Ergosterol and percentage C content in soil correlated strongly and positively with the abundance of root-associated ascomycetes. The predominance of ectomycorrhizal and saprotrophic fungi below the forest line probably promote high C turnover, while root-associated ascomycetes above the forest line may enhance C sequestration. With further rise in forest lines, there will be a corresponding shift in the below-ground biota, probably leading to enhanced release of soil C.
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Affiliation(s)
- Lea-Rebekka Tonjer
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
| | - Ella Thoen
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
| | - Luis Morgado
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway.,Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Synnøve Botnen
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
| | - Sunil Mundra
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway.,Department of Biology, College of Science, United Arab Emirates University, Abu Dhabi, UAE
| | - Line Nybakken
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Anders Bryn
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), University of Oslo, Oslo, Norway
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14
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Similarities and Differences among Soil Fungal Assemblages in Managed Forests and Formerly Managed Forest Reserves. FORESTS 2021. [DOI: 10.3390/f12030353] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Unlike the numerous works concerning the effect of management on the forest mycobiome, only a few studies have addressed how fungi from different trophic groups recover from natural and anthropogenic disturbances and develop structural features typical of unmanaged old-growth forests. Our objective is to compare the soil fungal assemblages represented by different functional/trophic groups in protected and managed stands located in European mixed forests dominated by Scots pine. Fungal communities were analyzed using high-throughput Illumina MiSeq sequencing of fungal internal transcribed spacer 1 (ITS1) amplicons. Formerly managed forest reserves (established around 50 years ago) and forests under standard forest management appeared to be similar in terms of total and mean species richness of all fungal operational taxonomic units (OTUs), as well as OTUs assigned to different functional trophic groups. Among the 599 recorded OTUs, 497 (83%) were shared between both management types, whereas 9.5% of taxa were unique to forest reserves and 7.5% were unique to managed stands. Ascomycota and Basidiomycota were the predominant phyla, comprising 88% of all identified fungi. The main functional components of soil fungal assemblages consisted of saprotrophic (42% fungal OTUs; 27% reads) and ectomycorrhizal fungi (16%; 47%). Two-way analysis of similarities (ANOSIM) revealed that both site and management strategy influenced the species composition of soil fungal communities, with site being a primary effect for saprotrophic and ectomycorrhizal fungi. Volume of coarse and very fine woody debris and soil pH significantly influenced the ectomycorrhizal fungal community, whereas saprotrophic fungi were influenced primarily by volume of coarse woody debris and soil nitrate concentration. Among the identified fungal OTUs, 18 red-listed fungal species were identified from both forest reserves and managed forests, comprising two ECM fungi and four saprotrophs from the category of endangered species. Our results suggest that the transformation of fungal diversity after cessation of forest management is rather slow, and that both forest reserves and managed forests help uphold fungal diversity.
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15
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Mundra S, Kjønaas OJ, Morgado LN, Krabberød AK, Ransedokken Y, Kauserud H. Soil depth matters: shift in composition and inter-kingdom co-occurrence patterns of microorganisms in forest soils. FEMS Microbiol Ecol 2021; 97:fiab022. [PMID: 33547899 PMCID: PMC7948073 DOI: 10.1093/femsec/fiab022] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/04/2021] [Indexed: 02/01/2023] Open
Abstract
Soil depth represents a strong physiochemical gradient that greatly affects soil-dwelling microorganisms. Fungal communities are typically structured by soil depth, but how other microorganisms are structured is less known. Here, we tested whether depth-dependent variation in soil chemistry affects the distribution and co-occurrence patterns of soil microbial communities. This was investigated by DNA metabarcoding in conjunction with network analyses of bacteria, fungi, as well as other micro-eukaryotes, sampled in four different soil depths in Norwegian birch forests. Strong compositional turnover in microbial assemblages with soil depth was detected for all organismal groups. Significantly greater microbial diversity and fungal biomass appeared in the nutrient-rich organic layer, with sharp decrease towards the less nutrient-rich mineral zones. The proportions of copiotrophic bacteria, Arthropoda and Apicomplexa were markedly higher in the organic layer, while patterns were opposite for oligotrophic bacteria, Cercozoa, Ascomycota and ectomycorrhizal fungi. Network analyses indicated more intensive inter-kingdom co-occurrence patterns in the upper mineral layer (0-5 cm) compared to the above organic and the lower mineral soil, signifying substantial influence of soil depth on biotic interactions. This study supports the view that different microbial groups are adapted to different forest soil strata, with varying level of interactions along the depth gradient.
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Affiliation(s)
- Sunil Mundra
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, Abu-Dhabi, UAE
| | - O Janne Kjønaas
- NIBIO, Department of Terrestrial Ecology, NO-1431 Ås, Norway
| | - Luis N Morgado
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
- Naturalis Biodiversity Center, 2300 RA Leiden, the Netherlands
| | - Anders Kristian Krabberød
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Yngvild Ransedokken
- Faculty of Environmental and Natural Resource Management, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EvoGene), Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
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16
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Chevalier M, Mod H, Broennimann O, Di Cola V, Schmid S, Niculita‐Hirzel H, Pradervand J, Schmidt BR, Ursenbacher S, Pellissier L, Guisan A. Low spatial autocorrelation in mountain biodiversity data and model residuals. Ecosphere 2021. [DOI: 10.1002/ecs2.3403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Mathieu Chevalier
- Department of Ecology and Evolution University of Lausanne Biophore LausanneCH‐1015Switzerland
| | - Heidi Mod
- Department of Ecology and Evolution University of Lausanne Biophore LausanneCH‐1015Switzerland
- Department of Geosciences and Geography University of Helsinki HelsinkiFI‐00014Finland
| | - Olivier Broennimann
- Department of Ecology and Evolution University of Lausanne Biophore LausanneCH‐1015Switzerland
- Institute of Earth Surface Dynamics University of Lausanne Géopolis LausanneCH‐1015Switzerland
| | - Valeria Di Cola
- Department of Ecology and Evolution University of Lausanne Biophore LausanneCH‐1015Switzerland
| | - Sarah Schmid
- Department of Ecology and Evolution University of Lausanne Biophore LausanneCH‐1015Switzerland
| | - Hélène Niculita‐Hirzel
- Department Health, Work and Environment Center for Primary Care and Public Health (Unisanté) University of Lausanne EpalingesCH‐1066Switzerland
| | | | - Benedikt R. Schmidt
- Info Fauna ‐ Karch UniMail, Bâtiment G, Bellevaux 51 Neuchâtel2000Switzerland
- Institut für Evolutionsbiologie und Umweltwissenschaften Universität Zürich Winterthurerstrasse 190 Zürich8057Switzerland
| | - Sylvain Ursenbacher
- Info Fauna ‐ Karch UniMail, Bâtiment G, Bellevaux 51 Neuchâtel2000Switzerland
- Department of Environmental Science Section of Conservation Biology University of Basel BaselCH‐4056Switzerland
| | - Loïc Pellissier
- Landscape Ecology Institute of Terrestrial Ecosystems Department of Environmental Systems Science ETH Zürich Zürich Switzerland
- Unit of Land Change Science Swiss Federal Research Institute WSL Birmensdorf Switzerland
| | - Antoine Guisan
- Department of Ecology and Evolution University of Lausanne Biophore LausanneCH‐1015Switzerland
- Institute of Earth Surface Dynamics University of Lausanne Géopolis LausanneCH‐1015Switzerland
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17
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Mod HK, Scherrer D, Di Cola V, Broennimann O, Blandenier Q, Breiner FT, Buri A, Goudet J, Guex N, Lara E, Mitchell EAD, Niculita‐Hirzel H, Pagni M, Pellissier L, Pinto‐Figueroa E, Sanders IR, Schmidt BR, Seppey CVW, Singer D, Ursenbacher S, Yashiro E, van der Meer JR, Guisan A. Greater topoclimatic control of above- versus below-ground communities. GLOBAL CHANGE BIOLOGY 2020; 26:6715-6728. [PMID: 32866994 PMCID: PMC7756268 DOI: 10.1111/gcb.15330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/04/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
Assessing the degree to which climate explains the spatial distributions of different taxonomic and functional groups is essential for anticipating the effects of climate change on ecosystems. Most effort so far has focused on above-ground organisms, which offer only a partial view on the response of biodiversity to environmental gradients. Here including both above- and below-ground organisms, we quantified the degree of topoclimatic control on the occurrence patterns of >1,500 taxa and phylotypes along a c. 3,000 m elevation gradient, by fitting species distribution models. Higher model performances for animals and plants than for soil microbes (fungi, bacteria and protists) suggest that the direct influence of topoclimate is stronger on above-ground species than on below-ground microorganisms. Accordingly, direct climate change effects are predicted to be stronger for above-ground than for below-ground taxa, whereas factors expressing local soil microclimate and geochemistry are likely more important to explain and forecast the occurrence patterns of soil microbiota. Detailed mapping and future scenarios of soil microclimate and microhabitats, together with comparative studies of interacting and ecologically dependent above- and below-ground biota, are thus needed to understand and realistically forecast the future distribution of ecosystems.
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Affiliation(s)
- Heidi K. Mod
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of Geosciences and GeographyUniversity of HelsinkiHelsinkiFinland
| | - Daniel Scherrer
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Valeria Di Cola
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Olivier Broennimann
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Institute of Earth Surface DynamicsUniversity of LausanneLausanneSwitzerland
| | - Quentin Blandenier
- Laboratory of Soil BiodiversityInstitute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
- Real Jardín BotánicoCSICMadridSpain
| | - Frank T. Breiner
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Aline Buri
- Institute of Earth Surface DynamicsUniversity of LausanneLausanneSwitzerland
| | - Jérôme Goudet
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Swiss Institute of BioinformaticsUniversity of LausanneLausanneSwitzerland
| | - Nicolas Guex
- Bioinformatics Competence CenterUniversity of LausanneLausanneSwitzerland
- Vital‐IT GroupSwiss Institute of BioinformaticsLausanneSwitzerland
| | | | - Edward A. D. Mitchell
- Laboratory of Soil BiodiversityInstitute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
- Jardin Botanique de NeuchâtelNeuchâtelSwitzerland
| | - Hélène Niculita‐Hirzel
- Department of Occupational Health and EnvironmentCenter for Primary Care and Public Health (Unisanté)University of LausanneLausanneSwitzerland
| | - Marco Pagni
- Vital‐IT GroupSwiss Institute of BioinformaticsLausanneSwitzerland
| | - Loïc Pellissier
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
- Landscape EcologyDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | | | - Ian R. Sanders
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
| | - Benedikt R. Schmidt
- Info Fauna KarchNeuchâtelSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | | | - David Singer
- Laboratory of Soil BiodiversityInstitute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
- Department of ZoologyInstitute of BiosciencesUniversity of São PauloSão PauloBrazil
| | - Sylvain Ursenbacher
- Info Fauna KarchNeuchâtelSwitzerland
- Department of Environmental SciencesSection of Conservation BiologyUniversity of BaselBaselSwitzerland
| | - Erika Yashiro
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| | - Jan R. van der Meer
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| | - Antoine Guisan
- Department of Ecology and EvolutionUniversity of LausanneLausanneSwitzerland
- Institute of Earth Surface DynamicsUniversity of LausanneLausanneSwitzerland
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18
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Kalsoom Khan F, Kluting K, Tångrot J, Urbina H, Ammunet T, Eshghi Sahraei S, Rydén M, Ryberg M, Rosling A. Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi. IMA Fungus 2020; 11:23. [PMID: 33292867 PMCID: PMC7607712 DOI: 10.1186/s43008-020-00045-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/14/2020] [Indexed: 01/04/2023] Open
Abstract
Due to their submerged and cryptic lifestyle, the vast majority of fungal species are difficult to observe and describe morphologically, and many remain known to science only from sequences detected in environmental samples. The lack of practices to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here, we use environmental sequence data as taxonomical evidence and combine phylogenetic and ecological data to generate and test species hypotheses in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing from a well-studied Swedish pine forest podzol soil, we generate 68 distinct species hypotheses of Archaeorhizomycetes, of which two correspond to the only described species in the class. Nine of the species hypotheses represent 78% of the sequenced Archaeorhizomycetes community, and are supported by long read data that form the backbone for delimiting species hypothesis based on phylogenetic branch lengths. Soil fungal communities are shaped by environmental filtering and competitive exclusion so that closely related species are less likely to co-occur in a niche if adaptive traits are evolutionarily conserved. In soil profiles, distinct vertical horizons represent a testable niche dimension, and we found significantly differential distribution across samples for a well-supported pair of sister species hypotheses. Based on the combination of phylogenetic and ecological evidence, we identify two novel species for which we provide molecular diagnostics and propose names. While environmental sequences cannot be automatically translated to species, they can be used to generate phylogenetically distinct species hypotheses that can be further tested using sequences as ecological evidence. We conclude that in the case of abundantly and frequently observed species, environmental sequences can support species recognition in the absences of physical specimens, while rare taxa remain uncaptured at our sampling and sequencing intensity.
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Affiliation(s)
- Faheema Kalsoom Khan
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.,Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Kerri Kluting
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Jeanette Tångrot
- Department of Molecular Biology, National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Umeå University, Umeå, Sweden
| | - Hector Urbina
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.,Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Gainesville, Florida, 32608, USA
| | - Tea Ammunet
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Shadi Eshghi Sahraei
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Martin Rydén
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Martin Ryberg
- Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
| | - Anna Rosling
- Department of Ecology and Genetics, Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
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19
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Gilbert KJ, Bittleston LS, Naive MAK, Kiszewski AE, Buenavente PAC, Lohman DJ, Pierce NE. Investigation of an Elevational Gradient Reveals Strong Differences Between Bacterial and Eukaryotic Communities Coinhabiting Nepenthes Phytotelmata. MICROBIAL ECOLOGY 2020; 80:334-349. [PMID: 32291478 PMCID: PMC7371667 DOI: 10.1007/s00248-020-01503-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
Elevation is an important determinant of ecological community composition. It integrates several abiotic features and leads to strong, repeatable patterns of community structure, including changes in the abundance and richness of numerous taxa. However, the influence of elevational gradients on microbes is understudied relative to plants and animals. To compare the influence of elevation on multiple taxa simultaneously, we sampled phytotelm communities within a tropical pitcher plant (Nepenthes mindanaoensis) along a gradient from 400 to 1200 m a.s.l. We use a combination of metabarcoding and physical counts to assess diversity and richness of bacteria, micro-eukaryotes, and arthropods, and compare the effect of elevation on community structure to that of regulation by a number of plant factors. Patterns of community structure differed between bacteria and eukaryotes, despite their living together in the same aquatic microhabitats. Elevation influences community composition of eukaryotes to a significantly greater degree than it does bacteria. When examining pitcher characteristics, pitcher dimorphism has an effect on eukaryotes but not bacteria, while variation in pH levels strongly influences both taxa. Consistent with previous ecological studies, arthropod abundance in phytotelmata decreases with elevation, but some patterns of abundance differ between living inquilines and prey.
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Affiliation(s)
- Kadeem J Gilbert
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA.
- Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, PA, 16802, USA.
| | - Leonora S Bittleston
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 1-290, Cambridge, MA, 02139, USA
- Department of Biological Sciences, Boise State University, 1910 W University Dr, Boise, ID, 83725, USA
| | - Mark Arcebal K Naive
- Department of Biological Sciences, College of Science and Mathematics, Mindanao State University-Iligan Institute of Technology, Andres Bonifacio Ave, 9200, Iligan, Lanao del Norte, Philippines
| | - Anthony E Kiszewski
- Department of Natural and Applied Sciences, Bentley University, 175 Forest Street, Waltham, MA, 02452, USA
| | | | - David J Lohman
- Entomology Section, National Museum of Natural History, Manila, Philippines
- Biology Department, City College of New York, City University of New York, New York, NY, USA
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY, USA
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
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20
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R. Carrino-Kyker S, P. Coyle K, A. Kluber L, J. Burke D. Fungal and Bacterial Communities Exhibit Consistent Responses to Reversal of Soil Acidification and Phosphorus Limitation over Time. Microorganisms 2019; 8:E1. [PMID: 31861322 PMCID: PMC7022789 DOI: 10.3390/microorganisms8010001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 01/16/2023] Open
Abstract
Chronic acid deposition affects many temperate hardwood forests of the northeastern United States, reduces soil pH and phosphorus (P) availability, and can alter the structure and function of soil microbial communities. The strategies that microorganisms possess for survival in acidic, low P soil come at a carbon (C) cost. Thus, how microbial communities respond to soil acidification in forests may be influenced by plant phenological stage as C allocation belowground varies; however, this remains largely unexplored. In this study, we examined microbial communities in an ecosystem level manipulative experiment where pH and/or P availability were elevated in three separate forests in Northeastern Ohio. Tag-encoded pyrosequencing was used to examine bacterial and fungal community structure at five time points across one year corresponding to plant phenological stages. We found significant effects of pH treatment and time on fungal and bacterial communities in soil. However, we found no interaction between pH treatment and time of sampling for fungal communities and only a weak interaction between pH elevation and time for bacterial communities, suggesting that microbial community responses to soil pH are largely independent of plant phenological stage. In addition, fungal communities were structured largely by site, suggesting that fungi were responding to differences between the forests, such as plant community differences.
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Affiliation(s)
- Sarah R. Carrino-Kyker
- The Holden Arboretum, Kirtland, OH 44094, USA; (L.A.K.); (D.J.B.)
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Kaitlin P. Coyle
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA;
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Laurel A. Kluber
- The Holden Arboretum, Kirtland, OH 44094, USA; (L.A.K.); (D.J.B.)
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - David J. Burke
- The Holden Arboretum, Kirtland, OH 44094, USA; (L.A.K.); (D.J.B.)
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA;
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