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Klarenberg IJ, Keuschnig C, Salazar A, Benning LG, Vilhelmsson O. Moss and underlying soil bacterial community structures are linked to moss functional traits. Ecosphere 2023. [DOI: 10.1002/ecs2.4447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Affiliation(s)
- Ingeborg J. Klarenberg
- Natural Resource Sciences University of Akureyri Akureyri Iceland
- Faculty of Life and Environmental Sciences University of Iceland Reykjavík Iceland
- Department of Ecological Science Vrije Universiteit Amsterdam Amsterdam Netherlands
| | - Christoph Keuschnig
- Environmental Microbial Genomics Laboratoire Ampère, CNRS, École Centrale de Lyon Écully France
- German Research Centre for Geosciences (GFZ) Interface Geochemistry Potsdam Germany
| | - Alejandro Salazar
- Faculty of Environmental and Forest Sciences Agricultural University of Iceland Reykjavík Iceland
| | - Liane G. Benning
- German Research Centre for Geosciences (GFZ) Interface Geochemistry Potsdam Germany
- Department of Earth Sciences Free University of Berlin Berlin Germany
| | - Oddur Vilhelmsson
- Natural Resource Sciences University of Akureyri Akureyri Iceland
- BioMedical Center University of Iceland Reykjavík Iceland
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2
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Naz B, Liu Z, Malard LA, Ali I, Song H, Wang Y, Li X, Usman M, Ali I, Liu K, An L, Xiao S, Chen S. Dominant plant species play an important role in regulating bacterial antagonism in terrestrial Antarctica. Front Microbiol 2023; 14:1130321. [PMID: 37032907 PMCID: PMC10076557 DOI: 10.3389/fmicb.2023.1130321] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
In Antarctic terrestrial ecosystems, dominant plant species (grasses and mosses) and soil physicochemical properties have a significant influence on soil microbial communities. However, the effects of dominant plants on bacterial antagonistic interactions in Antarctica remain unclear. We hypothesized that dominant plant species can affect bacterial antagonistic interactions directly and indirectly by inducing alterations in soil physicochemical properties and bacterial abundance. We collected soil samples from two typical dominant plant species; the Antarctic grass Deschampsia antarctica and the Antarctic moss Sanionia uncinata, as well as bulk soil sample, devoid of vegetation. We evaluated bacterial antagonistic interactions, focusing on species from the genera Actinomyces, Bacillus, and Pseudomonas. We also measured soil physicochemical properties and evaluated bacterial abundance and diversity using high-throughput sequencing. Our results suggested that Antarctic dominant plants significantly influenced bacterial antagonistic interactions compared to bulk soils. Using structural equation modelling (SEM), we compared and analyzed the direct effect of grasses and mosses on bacterial antagonistic interactions and the indirect effects through changes in edaphic properties and bacterial abundance. SEMs showed that (1) grasses and mosses had a significant direct influence on bacterial antagonistic interactions; (2) grasses had a strong influence on soil water content, pH, and abundances of Actinomyces and Pseudomonas and (3) mosses influenced bacterial antagonistic interactions by impacting abundances of Actinomyces, Bacillus, and Pseudomonas. This study highlights the role of dominant plants in modulating bacterial antagonistic interactions in Antarctic terrestrial ecosystems.
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Affiliation(s)
- Beenish Naz
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Ziyang Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Lucie A. Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Izhar Ali
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Hongxian Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yajun Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Xin Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Muhammad Usman
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ikram Ali
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Kun Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Sa Xiao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Shuyan Chen
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
- *Correspondence: Shuyan Chen,
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The Study of Soil Bacterial Diversity and the Influence of Soil Physicochemical Factors in Meltwater Region of Ny-Ålesund, Arctic. Microorganisms 2022; 10:microorganisms10101913. [PMID: 36296189 PMCID: PMC9611652 DOI: 10.3390/microorganisms10101913] [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: 08/25/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Global climate change has caused the changes of the ecological environment in the Arctic region, including sea ice melting, runoff increase, glacial lake expansion, and a typical meltwater area has formed in the Arctic coastal area. In this study, the meltwater areas near six different characteristic areas of Ny-Ålesund in 2018 were taken as the research objects, and high-throughput sequencing of V3–V4 regions of all samples were performed using 16S rDNA. Among the soil samples of six glacial meltwater areas in Ny-Ålesund, Arctic, the meltwater area near the reservoir bay had the highest bacterial abundance, and the meltwater area near the sand had the lowest one. The dominant phyla in soil samples were Proteobacteria, Actinobacteria, Acidobacteria. The NH4+-N content in intertidal soil was higher than that in subtidal soil. Through WGCNA analysis and LEFSE analysis, it was found that the core bacteria significantly related to NH4+-N were basically distributed in the intertidal area. For example, Nitrosomonadaceae, Nitrospira and Sphingomonas were the core bacteria showed significant different abundance in the intertidal area, which have the ability to metabolize NH4+-N. Our findings suggest that NH4+-N plays an important role in soil bacterial community structure in the Arctic meltwater areas.
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Dong K, Yu Z, Kerfahi D, Lee SS, Li N, Yang T, Adams JM. Soil microbial co-occurrence networks become less connected with soil development in a high Arctic glacier foreland succession. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152565. [PMID: 34953844 DOI: 10.1016/j.scitotenv.2021.152565] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/30/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Classically, ecologists have considered that biota becomes more integrated and interdependent with ecosystem development in primary successional environments. However, recent work on soil microbial communities suggests that there may in fact be no change in network integration over successional time series. Here, we performed a test of this principle by identifying network-level topological features of the soil microbial co-occurrence networks in the primary successional foreland environment of the retreating high-Arctic glacier of Midtre Lovénbreen, Svalbard. Soil was sampled at sites along the foreland of inferred ages 10-90 years since deglaciation. DNA was extracted and amplicon sequenced for 16 s rRNA genes for bacteria and ITS1 region for fungi. Despite the chronologically-related soil pH decline and organic C/N accumulation, analysis on network-level topological features showed network integration did not change with inferred chronological ages, whereas network integration declined with decreasing pH and increasing total organic carbon (TOC) - both factors that can be viewed as an indicator of soil development. We also found that bacteria played a greater role in the network structure than fungi, with all keystone species in the microbial co-occurrence network being bacteria species. Both number and relative abundance of the keystone species were significantly higher when soil pH increased or TOC decreased. It appears that in the more extreme and less productive conditions of early primary succession, integration between members of soil biota into consortia may play a greater role in niche adaptation and survival. Our finding also emphasizes that ecosystem development is not simply a product of time but is influenced by locally heterogeneous factors.
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Affiliation(s)
- Ke Dong
- Life Science Major, Kyonggi University, Suwon, South Korea
| | - Zhi Yu
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, South Korea
| | - Dorsaf Kerfahi
- School of Natural Sciences, Department of Biological Sciences, Keimyung University, Daegu, South Korea
| | - Sang-Seob Lee
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, South Korea
| | - Nan Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Nanning Normal University, Nanning, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jonathan M Adams
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, China.
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5
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Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates. J Fungi (Basel) 2022; 8:jof8030226. [PMID: 35330228 PMCID: PMC8955040 DOI: 10.3390/jof8030226] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/19/2022] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.
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Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F, Human ZR, Jomura M, Kolařík M, Kvasničková J, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Meszárošová L, Michalčíková L, Michalová T, Mundra S, Navrátilová D, Odriozola I, Piché-Choquette S, Štursová M, Švec K, Tláskal V, Urbanová M, Vlk L, Voříšková J, Žifčáková L, Baldrian P. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 2020; 7:228. [PMID: 32661237 PMCID: PMC7359306 DOI: 10.1038/s41597-020-0567-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023] Open
Abstract
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Camelia Algora
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Barbara Doreen Bahnmann
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Květa Bílohnědá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Federica D'Alò
- Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Zander Rainier Human
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Kvasničková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Meszárošová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sunil Mundra
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Diana Navrátilová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Voříšková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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Zhang Q, Acuña JJ, Inostroza NG, Duran P, Mora ML, Sadowsky MJ, Jorquera MA. Niche Differentiation in the Composition, Predicted Function, and Co-occurrence Networks in Bacterial Communities Associated With Antarctic Vascular Plants. Front Microbiol 2020; 11:1036. [PMID: 32582056 PMCID: PMC7285837 DOI: 10.3389/fmicb.2020.01036] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/27/2020] [Indexed: 12/21/2022] Open
Abstract
Climate change directly affecting the Antarctic Peninsula has been reported to induce the successful colonization of ice-free lands by two Antarctic vascular plants (Deschampsia antarctica and Colobanthus quitensis). While studies have revealed the importance of microbiota for plant growth and stress tolerance in temperate climates, the role that plant-associated microbes play in the colonization of ice-free lands remains unknown. Consequently, we used high-throughput DNA sequence analyses to explore the composition, predicted functions, and interactive networks of plant-associated microbial communities among the rhizosphere, endosphere, and phyllosphere niches of D. antarctica and C. quitensis. Here we report a greater number of operational taxonomic units (OTUs), diversity, and richness in the microbial communities from the rhizosphere, relative to endosphere and phyllosphere. While taxonomic assignments showed greater relative abundances of Proteobacteria, Bacteroidetes, and Actinobacteria in plant niches, principal coordinate analysis revealed differences among the bacterial communities from the other compartments examined. More importantly, however, our results showed that most of OTUs were exclusively found in each plant niche. Major predicted functional groups of these microbiota were attributed to heterotrophy, aerobic heterotrophy, fermentation, and nitrate reduction, independent of plant niches or plant species. Co-occurrences network analyses identified 5 (e.g., Microbacteriaceae, Pseudomonaceae, Lactobacillaceae, and Corynebacteriaceae), 23 (e.g., Chitinophagaceae and Sphingomonadaceae) and 7 (e.g., Rhodospirillaceae) putative keystone taxa present in endosphere, phyllosphere, and rhizosphere, respectively. Our results revealed niche differentiation in Antarctic vascular plants, highlighting some putative microbial indicators and keystone taxa in each niche. However, more studies are required to determine the pivotal role that these microbes play in the successful colonization of ice-free lands by Antarctic plants.
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Affiliation(s)
- Qian Zhang
- The BioTechnology Institute, University of Minnesota, St Paul, MN, United States
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Nitza G Inostroza
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Paola Duran
- Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - María L Mora
- Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Michael J Sadowsky
- The BioTechnology Institute, University of Minnesota, St Paul, MN, United States.,Department of Soil, Water, and Climate, and Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada (EMALAB), Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Temuco, Chile.,Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
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Juottonen H, Männistö M, Tiirola M, Kytöviita MM. Cryptogams signify key transitions of bacteria and fungi in Arctic sand dune succession. THE NEW PHYTOLOGIST 2020; 226:1836-1849. [PMID: 32017117 DOI: 10.1111/nph.16469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/28/2020] [Indexed: 05/26/2023]
Abstract
Primary succession models focus on aboveground vascular plants. However, the prevalence of mosses and lichens, that is cryptogams, suggests they play a role in soil successions. Here, we explore whether effects of cryptogams on belowground microbes can facilitate progressive shifts in sand dune succession. We linked aboveground vegetation, belowground bacterial and fungal communities, and soil chemical properties in six successional stages in Arctic inland sand dunes: bare sand, grass, moss, lichen, ericoid heath and mountain birch forest. Compared with the bare sand and grass stages, microbial biomass and the proportion of fungi increased in the moss stage, and later stage microbial groups appeared despite the absence of their host plants. Microbial communities of the lichen stage resembled the communities in the vascular plant stages. Bacterial communities correlated better with soil chemical variables than with vegetation and vice versa for fungal communities. The correlation of fungi with vegetation increased with vascular vegetation. Distinct bacterial and fungal patterns of biomass, richness and plant-microbe interactions showed that the aboveground vegetation change structured the bacterial and fungal community differently. The asynchrony of aboveground vs belowground changes suggests that cryptogams can drive succession towards vascular plant dominance through microbially mediated facilitation in eroded Arctic soil.
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Affiliation(s)
- Heli Juottonen
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Minna Männistö
- Natural Resources Institute Finland (Luke), 96300, Rovaniemi, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Minna-Maarit Kytöviita
- Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
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Ding L, Shang Y, Zhang W, Zhang Y, Li S, Wei X, Zhang Y, Song X, Chen X, Liu J, Yang F, Yang X, Zou C, Wang P. Disentangling the effects of driving forces on soil bacterial and fungal communities under shrub encroachment on the Guizhou Plateau of China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 709:136207. [PMID: 31887509 DOI: 10.1016/j.scitotenv.2019.136207] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
Global shrub encroachment (SE) affects the structure and function of grassland ecosystem. The effects of SE on plant and soil abiotic properties have been well studied; however, little is known about the extent to which driving forces structure soil microbes under SE, especially in subalpine regions of the Guizhou Plateau of China, which is undergoing progressive SE. We investigated the plant factors (viz, plant diversity and relative shrub cover), soil physicochemical properties, enzymatic activities, and microbial communities, quantified microbial element limitations under three encroachment stages, and disentangled the effects sizes of the factors that structure the diversity and composition of soil microbial communities. Redundancy analysis showed that soil factors made a greater contribution than plant factors to shaping the diversity and composition of the soil bacterial community, soil chemical factors made a greater contribution than physical factors both to structuring the diversity and composition of the soil bacterial community and to structuring the composition of the soil fungal community; and soil nutrient stoichiometry made a greater contribution than soil nutrient content to shaping soil bacterial community's diversity and fungal community's composition. In contrast, soil nutrient content made a greater contribution than soil nutrient stoichiometry to shaping the soil bacterial community's composition. The decrease in bacterial community's diversity observed under SE was attributable to increases in the carbon and nitrogen limitations consequent to SE, and the nitrogen limitation had a greater contribution to the soil bacterial community's diversity and composition than did the carbon limitation. These findings provide updated knowledge of the driving forces shaping the diversity and composition of soil microbial communities, which could be crucial for improving microbial prediction models and revealing the element cycling that occurs in SE biomes.
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Affiliation(s)
- Leilei Ding
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
| | - Yishun Shang
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
| | - Wen Zhang
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
| | - Yu Zhang
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
| | - Shige Li
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
| | - Xin Wei
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
| | - Yujun Zhang
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
| | - Xuelian Song
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
| | - Xi Chen
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
| | - Jiajia Liu
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
| | - Fuli Yang
- College of Animal Science, Guizhou University, Guiyang 550006, Guizhou, China
| | - Xuedong Yang
- Guizhou Grassland Technology Spread Station, Guiyang 550006, Guizhou, China; College of Forestry, Guizhou University, Guiyang 550006, Guizhou, China
| | - Chao Zou
- College of Animal Science, Guizhou University, Guiyang 550006, Guizhou, China
| | - Puchang Wang
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China; College of Animal Science, Guizhou University, Guiyang 550006, Guizhou, China.
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10
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Farrer EC, Porazinska DL, Spasojevic MJ, King AJ, Bueno de Mesquita CP, Sartwell SA, Smith JG, White CT, Schmidt SK, Suding KN. Soil Microbial Networks Shift Across a High-Elevation Successional Gradient. Front Microbiol 2019; 10:2887. [PMID: 31921064 PMCID: PMC6930148 DOI: 10.3389/fmicb.2019.02887] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/29/2019] [Indexed: 01/30/2023] Open
Abstract
While it is well established that microbial composition and diversity shift along environmental gradients, how interactions among microbes change is poorly understood. Here, we tested how community structure and species interactions among diverse groups of soil microbes (bacteria, fungi, non-fungal eukaryotes) change across a fundamental ecological gradient, succession. Our study system is a high-elevation alpine ecosystem that exhibits variability in successional stage due to topography and harsh environmental conditions. We used hierarchical Bayesian joint distribution modeling to remove the influence of environmental covariates on species distributions and generated interaction networks using the residual species-to-species variance-covariance matrix. We hypothesized that as ecological succession proceeds, diversity will increase, species composition will change, and soil microbial networks will become more complex. As expected, we found that diversity of most taxonomic groups increased over succession, and species composition changed considerably. Interestingly, and contrary to our hypothesis, interaction networks became less complex over succession (fewer interactions per taxon). Interactions between photosynthetic microbes and any other organism became less frequent over the gradient, whereas interactions between plants or soil microfauna and any other organism were more abundant in late succession. Results demonstrate that patterns in diversity and composition do not necessarily relate to patterns in network complexity and suggest that network analyses provide new insight into the ecology of highly diverse, microscopic communities.
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Affiliation(s)
- Emily C. Farrer
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, United States
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
| | - Dorota L. Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - Marko J. Spasojevic
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA, United States
| | - Andrew J. King
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- King Ecological Consulting, Knoxville, TN, United States
| | - Clifton P. Bueno de Mesquita
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Samuel A. Sartwell
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Jane G. Smith
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
| | - Caitlin T. White
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Katharine N. Suding
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
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11
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Yang J, Tang Y. The increase in ecosystem services values of the sand dune succession in northeastern China. Heliyon 2019; 5:e02243. [PMID: 31453401 PMCID: PMC6700414 DOI: 10.1016/j.heliyon.2019.e02243] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/02/2019] [Accepted: 08/02/2019] [Indexed: 11/03/2022] Open
Abstract
Ecosystem services values play a vital role in evaluating the economic benefits of ecosystems and for drawing up the vegetation restoration policy. The change of ecosystem services values in sand dune succession, especially in China, is little reported. This study was conducted in the Wulanaodu region, southeastern of the Horqin Sandy Land, one of the largest sandy lands in China. Here, we used quantitative methods including marketing value method, the alternative market method, the carbon tax method, the industrial oxygen method, the opportunity cost method, the water balance method, and the shadow engineering method. We evaluated ecosystem services values in fixed sand dunes, semi-fixed sand dunes, and mobile sand dunes. These sand dunes constitute a sand dune succession. The results showed that ecosystem services values in mobile sand dunes, semi-fixed sand dunes, and fixed sand dunes were 6206.58 CNY·hm-2·a-1, 9986.28 CNY·hm-2·a-1, and 31466.56 CNY·hm-2·a-1 separately. The ecosystem services values in fixed sand dunes were five times to these in mobile sand dunes. It suggests that ecosystem services values increase along with the sand dune succession. Moreover, in fixed sand dunes, the main categories contributing to ecosystem services values were gas regulation (17748.11 CNY·hm-2·a-1), and soil formation and retention (6461.80 CNY·hm-2·a-1). Meanwhile, gas regulation (3696.61 CNY·hm-2·a-1), and soil formation and retention (3124.74 CNY·hm-2·a-1) were also the main categories contributing to ecosystem services values in semi-fixed sand dunes. The main categories contributing to ecosystem services values were gas regulation (2760.10 CNY·hm-2·a-1) and water regulation (2278.00 CNY·hm-2·a-1) in mobile sand dunes. This study provides evidence that an increase in ecosystem services values in sandy lands is consistent with the aim of the combat of desertification.
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Affiliation(s)
| | - Yi Tang
- School of Life Science, Liaoning University, Shenyang, 110036, China
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12
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Wang N, Guo Y, Li G, Xia Y, Ma M, Zang J, Ma Y, Yin X, Han W, Lv J, Cao H. Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics. Microbes Environ 2019; 34:180-190. [PMID: 31178526 PMCID: PMC6594734 DOI: 10.1264/jsme2.me18091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 02/23/2019] [Indexed: 11/27/2022] Open
Abstract
Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3-V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.
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Affiliation(s)
- Nengfei Wang
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic AdministrationQingdao 266061China
| | - Yudong Guo
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science & TechnologyQingdao 266042China
| | - Gaoyang Li
- College of Computer Science and Technology, Jilin UniversityChangchun, Jilin 100012China
| | - Yan Xia
- Jilin University First HospitalChangchun, Jilin 100012China
| | - Mingyang Ma
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic AdministrationQingdao 266061China
| | - Jiaye Zang
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic AdministrationQingdao 266061China
| | - Yue Ma
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science & TechnologyQingdao 266042China
| | - Xiaofei Yin
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic AdministrationQingdao 266061China
| | - Wenbing Han
- College of Chemistry and Chemical Engineering, Qingdao UniversityQingdao 266071China
| | - Jinjiang Lv
- College of Chemistry and Chemical Engineering, Qingdao UniversityQingdao 266071China
| | - Huansheng Cao
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State UniversityTempe, AZ 85287USA
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13
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Wang Y, Chen X, Guo W, Zhou H. Distinct bacterial and archaeal diversities and spatial distributions in surface sediments of the Arctic Ocean. FEMS Microbiol Lett 2018; 365:5184458. [DOI: 10.1093/femsle/fny273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/13/2018] [Indexed: 12/22/2022] Open
Affiliation(s)
- Yuguang Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 361005 Xiamen, P.R. China
| | - Xinhua Chen
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 361005 Xiamen, P.R. China
- College of Animal Sciences, Fujian Agriculture and Forestry University, 350002 Fuzhou, P.R. China
| | - Wenbin Guo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 361005 Xiamen, P.R. China
| | - Hongbo Zhou
- School of Minerals Processing and Bioengineering, Central South University, 410083 Changsha, P.R. China
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14
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Poosakkannu A, Nissinen R, Kytöviita MM. Native arbuscular mycorrhizal symbiosis alters foliar bacterial community composition. MYCORRHIZA 2017; 27:801-810. [PMID: 28812152 DOI: 10.1007/s00572-017-0796-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/04/2017] [Indexed: 06/07/2023]
Abstract
The effects of arbuscular mycorrhizal (AM) fungi on plant-associated microbes are poorly known. We tested the hypothesis that colonization by an AM fungus affects microbial species richness and microbial community composition of host plant tissues. We grew the grass, Deschampsia flexuosa in a greenhouse with or without the native AM fungus, Claroideoglomus etunicatum. We divided clonally produced tillers into two parts: one inoculated with AM fungus spores and one without AM fungus inoculation (non-mycorrhizal, NM). We characterized bacterial (16S rRNA gene) and fungal communities (internal transcribed spacer region) in surface-sterilized leaf and root plant compartments. AM fungus inoculation did not affect microbial species richness or diversity indices in leaves or roots, but the AM fungus inoculation significantly affected bacterial community composition in leaves. A total of three OTUs in leaves belonging to the phylum Firmicutes positively responded to the presence of the AM fungus in roots. Another six OTUs belonging to the Proteobacteria (Alpha, Beta, and Gamma) and Bacteroidetes were significantly more abundant in NM plants when compared to AM fungus-inoculated plants. Further, there was a significant correlation between plant dry weight and leaf microbial community compositional shift. Also, there was a significant correlation between leaf bacterial community compositional shift and foliar nitrogen content changes due to AM fungus inoculation. The results suggest that AM fungus colonization in roots has a profound effect on plant physiology that is reflected in leaf bacterial community composition.
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Affiliation(s)
- Anbu Poosakkannu
- Department of Biological and Environmental Science, University of Jyvaskyla, PO Box 35, FI-40014, Jyvaskyla, Finland.
| | - Riitta Nissinen
- Department of Biological and Environmental Science, University of Jyvaskyla, PO Box 35, FI-40014, Jyvaskyla, Finland
| | - Minna-Maarit Kytöviita
- Department of Biological and Environmental Science, University of Jyvaskyla, PO Box 35, FI-40014, Jyvaskyla, Finland
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15
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Fungal community assemblage of different soil compartments in mangrove ecosystem. Sci Rep 2017; 7:8560. [PMID: 28819270 PMCID: PMC5561109 DOI: 10.1038/s41598-017-09281-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/25/2017] [Indexed: 11/11/2022] Open
Abstract
The fungal communities of different soil compartments in mangrove ecosystem are poorly studied. We sequenced the internal transcribed spacer (ITS) regions to characterize the fungal communities in Avicennia marina root-associated soils (rhizosphere and pneumatophore) and bulk soil compartments. The rhizosphere but not pneumatophore soil compartment had significantly lower fungal species richness than bulk soil. However, bulk soil fungal diversity (Shannon diversity index) was significantly higher than both pneumatophore and rhizosphere soil compartments. The different soil compartments significantly affected the fungal community composition. Pairwise sample analyses showed that bulk soil microbial community composition significantly different from rhizosphere and pneumatophore soil compartments. There was, however no significant difference observed between rhizosphere and pneumatophore soil fungal community composition and they shared relatively more OTUs between them. Further, there was a significant correlation observed between fungal community compositional changes and carbon or nitrogen availability of different soil compartments. These results suggest that few characteristics such as fungal richness and taxa abundance of rhizosphere and pneumatophore soil compartments were significantly different in mangrove ecosystem.
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