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Yabuki A, Hoshino T, Nakamura T, Mizuno K. The copy number of the eukaryotic rRNA gene can be counted comprehensively. Microbiologyopen 2024; 13:e1399. [PMID: 38436548 PMCID: PMC10910464 DOI: 10.1002/mbo3.1399] [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: 11/20/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 03/05/2024] Open
Abstract
Gene sequence has been widely used in molecular ecology. For instance, the ribosomal RNA (rRNA) gene has been widely used as a biological marker to understand microbial communities. The variety of the detected rRNA gene sequences reflects the diversity of the microorganisms existing in the analyzed sample. Their biomass can also be estimated by applying quantitative sequencing with information on rRNA gene copy numbers in genomes; however, information on rRNA gene copy numbers is still limited. Especially, the copy number in microbial eukaryotes is much less understood than that of prokaryotes, possibly because of the large and complex structure of eukaryotic genomes. In this study, we report an alternative approach that is more appropriate than the existing method of quantitative sequencing and demonstrate that the copy number of eukaryotic rRNA can be measured efficiently and comprehensively. By applying this approach widely, information on the eukaryotic rRNA copy number can be determined, and their community structures can be depicted and compared more efficiently.
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Affiliation(s)
- Akinori Yabuki
- Research Institute for Global ChangeJapan Agency for Marine‐Earth Science and TechnologyYokosukaKanagawaJapan
- Advanced Institute for Marine Ecosystem Change (WPI‐AIMEC)YokosukaKanagawaJapan
| | - Tatsuhiko Hoshino
- Advanced Institute for Marine Ecosystem Change (WPI‐AIMEC)YokosukaKanagawaJapan
- Institute for Extra‐cutting‐edge Science and Technology Avant‐garde ResearchJapan Agency for Marine‐Earth Science and TechnologyNankokuKochiJapan
| | - Tamiko Nakamura
- Research Institute for Global ChangeJapan Agency for Marine‐Earth Science and TechnologyYokosukaKanagawaJapan
| | - Keiko Mizuno
- Research Institute for Global ChangeJapan Agency for Marine‐Earth Science and TechnologyYokosukaKanagawaJapan
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2
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Lourenço L, Ellegaard Bager S, Ng DYK, Sheikh S, Lunding Kindtler N, Broman Nielsen I, Guldberg Frøslev T, Ekelund F. DNA metabarcoding reveals the impact of Cu 2+ on soil cercozoan diversity. Protist 2024; 175:126016. [PMID: 38350284 DOI: 10.1016/j.protis.2024.126016] [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: 02/12/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 02/15/2024]
Abstract
Although copper (Cu2+) is a micronutrient, the metal may be toxic if present in high concentrations in soil ecosystems and subsequently affect various organisms, ranging from microorganisms to earthworms. We performed a microcosm study with an array of Cu2+ concentrations, with a specific focus on Cercozoa, an important protozoan group in most soil food webs. Research on Cercozoa is still scarce in terms of both diversity and ecology; hence, to explore this group in more depth, we used high-throughput sequencing to detect Cu2+ induced community changes. Increased levels of Cu2+ caused a shift in the cercozoan community, and we observed decreased cercozoan relative abundance across the majority of orders, families and genera. Due to their key role in soil food webs, especially as bacterial predators and providers of nutrients to plants, the reduction of cercozoan abundance and diversity may seriously affect soil functionality. Our results indicate that the increase of Cu2+ concentrations in the soil could potentially have this effect and the consequences need exploration.
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Affiliation(s)
- Leah Lourenço
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark.
| | - Sara Ellegaard Bager
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Duncan Y K Ng
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sanea Sheikh
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Nikolaj Lunding Kindtler
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Ida Broman Nielsen
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 Copenhagen K, Denmark
| | - Tobias Guldberg Frøslev
- Section for Geogenetics, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Flemming Ekelund
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
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3
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Ferlian O, Goldmann K, Bonkowski M, Dumack K, Wubet T, Eisenhauer N. Invasive earthworms shift soil microbial community structure in northern North American forest ecosystems. iScience 2024; 27:108889. [PMID: 38322986 PMCID: PMC10844042 DOI: 10.1016/j.isci.2024.108889] [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: 08/18/2023] [Revised: 11/20/2023] [Accepted: 01/09/2024] [Indexed: 02/08/2024] Open
Abstract
Invasive earthworms colonize ecosystems around the globe. Compared to other species' invasions, earthworm invasions have received little attention. Previous studies indicated their tremendous effects on resident soil biota representing a major part of the terrestrial biodiversity. We investigated effects of earthworm invasion on soil microbial communities in three forests in North America by conducting DNA sequencing of soil bacteria, fungi, and protists in two soil depths. Our study shows that microbial diversity was lower in highly invaded forest areas. While bacterial diversity was strongly affected compared to fungi and protists, fungal community composition and family dominance were strongly affected compared to bacteria and protists. We found most species specialized on invasion in fungi, mainly represented by saprotrophs. Comparably, few protist species, mostly bacterivorous, were specialized on invasion. As one of the first observational studies, we investigated earthworm invasion on three kingdoms showing distinct taxa- and trophic level-specific responses to earthworm invasion.
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Affiliation(s)
- Olga Ferlian
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
| | - Kezia Goldmann
- UFZ-Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- UFZ-Helmholtz Centre for Environmental Research, Department of Community Ecology, Theodor-Lieser-Str. 4, 06120 Halle (Saale), Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Puschstrasse 4, 04103 Leipzig, Germany
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4
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Zhu L, Luan L, Chen Y, Wang X, Zhou S, Zou W, Han X, Duan Y, Zhu B, Li Y, Liu W, Zhou J, Zhang J, Jiang Y, Sun B. Community assembly of organisms regulates soil microbial functional potential through dual mechanisms. GLOBAL CHANGE BIOLOGY 2024; 30:e17160. [PMID: 38379454 DOI: 10.1111/gcb.17160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/22/2024]
Abstract
Unraveling the influence of community assembly processes on soil ecosystem functioning presents a major challenge in the field of theoretical ecology, as it has received limited attention. Here, we used a series of long-term experiments spanning over 25 years to explore the assembly processes of bacterial, fungal, protist, and nematode communities using high-throughput sequencing. We characterized the soil microbial functional potential by the abundance of microbial genes associated with carbon, nitrogen, phosphorus, and sulfur cycling using GeoChip-based functional gene profiling, and determined how the assembly processes of organism groups regulate soil microbial functional potential through community diversity and network stability. Our results indicated that balanced fertilization (NPK) treatment improved the stochastic assembly of bacterial, fungal, and protist communities compared to phosphorus-deficient fertilization (NK) treatment. However, there was a nonsignificant increase in the normalized stochasticity ratio of the nematode community in response to fertilization across sites. Our findings emphasized that soil environmental factors influenced the assembly processes of the biotic community, which regulated soil microbial functional potential through dual mechanisms. One mechanism indicated that the high phosphorus levels and low soil nutrient stoichiometry may increase the stochasticity of bacterial, fungal, and protist communities and the determinism of the nematode community under NPK treatment, ultimately enhancing soil microbial functional potential by reinforcing the network stability of the biotic community. The other mechanism indicated that the low phosphorus levels and high soil nutrient stoichiometry may increase the stochastic process of the bacterial community and the determinism of the fungal, protist, and nematode communities under NK treatment, thereby enhancing soil microbial functional potential by improving the β-diversity of the biotic community. Taken together, these results provide valuable insights into the mechanisms underlying the assembly processes of the biotic community that regulate ecosystem functioning.
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Affiliation(s)
- Lingyue Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, China
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yan Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoyue Wang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiu Zou
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Xiaori Han
- College of Land and Environment, Shenyang Agricultural University, Shengyang, China
| | - Yinghua Duan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bo Zhu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Yan Li
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wenzhao Liu
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Bo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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Sachs M, Dünn M, Arndt H. Benthic Heterotrophic Protist Communities of the Southern Baltic Analyzed with the Help of Curated Metabarcoding Studies. BIOLOGY 2023; 12:1010. [PMID: 37508439 PMCID: PMC10376117 DOI: 10.3390/biology12071010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023]
Abstract
Heterotrophic protists are key components of marine ecosystems. They act as controllers of bacterial and microphytobenthos production and contribute significantly to the carbon flux to higher trophic levels. Still, metabarcoding studies on benthic protist communities are much less frequent than for planktonic organisms. Especially in the Baltic Sea, representing the largest brackish water environment on earth, so far, no extensive metabarcoding studies have been conducted to assess the diversity of benthic protists in this unique and diverse habitat. This study aims to give first insights into the diversity of benthic protist communities in two different regions of the Baltic Sea, Fehmarnbelt, and Oderbank. Using amplicon sequencing of the 18S rDNA V9 region of over 100 individual sediment samples, we were able to show significant differences in the community composition between the two regions and to give insights into the vertical distribution of protists within the sediment (0-20 cm). The results indicate that the differences in community composition in the different regions might be explained by several abiotic factors such as salinity and water depth, but are also influenced by methodological aspects such as differences between DNA and RNA results.
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Affiliation(s)
- Maria Sachs
- Institute of Zoology, General Ecology, Biocenter Cologne, University of Cologne, Zuelpicherstr. 47b, 51069 Cologne, Germany
| | - Manon Dünn
- Institute of Zoology, General Ecology, Biocenter Cologne, University of Cologne, Zuelpicherstr. 47b, 51069 Cologne, Germany
| | - Hartmut Arndt
- Institute of Zoology, General Ecology, Biocenter Cologne, University of Cologne, Zuelpicherstr. 47b, 51069 Cologne, Germany
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6
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Dünn M, Arndt H. Distribution Patterns of Benthic Protist Communities Depending on Depth Revealed by Environmental Sequencing-From the Sublittoral to the Deep Sea. Microorganisms 2023; 11:1664. [PMID: 37512837 PMCID: PMC10385078 DOI: 10.3390/microorganisms11071664] [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: 05/22/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Protists are key components of the microbial food web in marine pelagic systems because they link algal and bacterial production to higher trophic levels. However, their functioning and bathymetric distribution in benthic deep-sea ecosystems are still only poorly understood. However, biogeographical patterns of communities can be coupled to the functioning of ecosystems and are therefore important to understand ecological and evolutionary processes. In this study, we investigated the diversity and distribution of benthic protist communities from the sublittoral down to the deep seafloor (50-2000 m) around three islands of the Azores in the North Atlantic Ocean. Using amplicon sequencing of the V9 region (18S rDNA) of 21 samples, we found that protist community compositions from different depths were significantly different. Three assemblages were separated along the following depths: 50 m, 150-500 m and 1000-2000 m, which indicate that deep-sea areas surrounding islands might act as isolating barriers for benthic protist species. A limited gene flow between the communities could favor speciation processes, leading to the unique protist communities found at the different investigated islands.
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Affiliation(s)
- Manon Dünn
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - Hartmut Arndt
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
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7
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Lennartz Née Rybarski AE, Nitsche F, Schoenle A, Voigt C, Staubwasser M, Arndt H. High diversity and isolated distribution of aquatic heterotrophic protists in salars of the Atacama Desert at different salinities. Eur J Protistol 2023; 89:125987. [PMID: 37245304 DOI: 10.1016/j.ejop.2023.125987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/24/2023] [Accepted: 04/11/2023] [Indexed: 05/30/2023]
Abstract
The species richness of eukaryotes in the hypersaline environment is generally thought to be low. However, recent studies showed a high degree of phylogenetic novelty at these extreme conditions with variable chemical parameters. These findings call for a more thorough look into the species richness of hypersaline environments. In this study, various hypersaline lakes (salars, 1-348 PSU) as well as further aquatic ecosystems of northern Chile were investigated regarding diversity of heterotrophic protists by metabarcoding studies of surface water samples. Investigations of genotypes of 18S rRNA genes showed a unique community composition in nearly each salar and even among different microhabitats within one salar. The genotype distribution showed no clear connection to the composition of main ions at the sampling sites, but protist communities from similar salinity ranges (either hypersaline, hyposaline or mesosaline) clustered together regarding their OTU composition. Salars appeared to be fairly isolated systems with only little exchange of protist communities where evolutionary lineages could separately evolve.
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Affiliation(s)
- Alexandra E Lennartz Née Rybarski
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Frank Nitsche
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Alexandra Schoenle
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany
| | - Claudia Voigt
- Department of Geosciences, Institute of Geology and Mineralogy, University of Cologne, Zuelpicher Straße 49b, D-50674 Cologne, Germany; Department of Biology and Geology, Universidad de Almería, Carretera de Sacramento s.n, La Cañada de San Urbano, Almería 04120, Spain
| | - Michael Staubwasser
- Department of Geosciences, Institute of Geology and Mineralogy, University of Cologne, Zuelpicher Straße 49b, D-50674 Cologne, Germany
| | - Hartmut Arndt
- Department of General Ecology, Institute of Zoology, Biocenter Cologne, University of Cologne, Zuelpicher Straße 47b, D-50674 Cologne, Germany.
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8
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Zhou T, Zhao F, Xu K. Information Scale Correction for Varying Length Amplicons Improves Eukaryotic Microbiome Data Integration. Microorganisms 2023; 11:microorganisms11040949. [PMID: 37110372 PMCID: PMC10146031 DOI: 10.3390/microorganisms11040949] [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: 03/28/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
The integration and reanalysis of big data provide valuable insights into microbiome studies. However, the significant difference in information scale between amplicon data poses a key challenge in data analysis. Therefore, reducing batch effects is crucial to enhance data integration for large-scale molecular ecology data. To achieve this, the information scale correction (ISC) step, involving cutting different length amplicons into the same sub-region, is essential. In this study, we used the Hidden Markov model (HMM) method to extract 11 different 18S rRNA gene v4 region amplicon datasets with 578 samples in total. The length of the amplicons ranged from 344 bp to 720 bp, depending on the primer position. By comparing the information scale correction of amplicons with varying lengths, we explored the extent to which the comparability between samples decreases with increasing amplicon length. Our method was shown to be more sensitive than V-Xtractor, the most popular tool for performing ISC. We found that near-scale amplicons exhibited no significant change after ISC, while larger-scale amplicons exhibited significant changes. After the ISC treatment, the similarity among the data sets improved, especially for long amplicons. Therefore, we recommend adding ISC processing when integrating big data, which is crucial for unlocking the full potential of microbial community studies and advancing our knowledge of microbial ecology.
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Affiliation(s)
- Tong Zhou
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feng Zhao
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Becker B, Pushkareva E. Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding. Genes (Basel) 2023; 14:genes14040812. [PMID: 37107570 PMCID: PMC10138292 DOI: 10.3390/genes14040812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/23/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
The diversity of soil bacteria was analyzed via metabarcoding and metagenomic approaches using DNA samples isolated from the biocrusts of 12 different Arctic and Antarctic sites. For the metabarcoding approach, the V3-4 region of the 16S rRNA was targeted. Our results showed that nearly all operational taxonomic units (OTUs = taxa) found in metabarcoding analyses were recovered in metagenomic analyses. In contrast, metagenomics identified a large number of additional OTUs absent in metabarcoding analyses. In addition, we found huge differences in the abundance of OTUs between the two methods. The reasons for these differences seem to be (1) the higher sequencing depth in metagenomics studies, which allows the detection of low-abundance community members in metagenomics, and (2) bias of primer pairs used to amplify the targeted sequence in metabarcoding, which can change the community composition dramatically even at the lower taxonomic levels. We strongly recommend using only metagenomic approaches when establishing the taxonomic profiles of whole biological communities.
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Wang L, Zhao M, Du X, Feng K, Gu S, Zhou Y, Yang X, Zhang Z, Wang Y, Zhang Z, Zhang Q, Xie B, Han G, Deng Y. Fungi and cercozoa regulate methane-associated prokaryotes in wetland methane emissions. Front Microbiol 2023; 13:1076610. [PMID: 36687630 PMCID: PMC9853292 DOI: 10.3389/fmicb.2022.1076610] [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: 10/21/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023] Open
Abstract
Wetlands are natural sources of methane (CH4) emissions, providing the largest contribution to the atmospheric CH4 pool. Changes in the ecohydrological environment of coastal salt marshes, especially the surface inundation level, cause instability in the CH4 emission levels of coastal ecosystems. Although soil methane-associated microorganisms play key roles in both CH4 generation and metabolism, how other microorganisms regulate methane emission and their responses to inundation has not been investigated. Here, we studied the responses of prokaryotic, fungal and cercozoan communities following 5 years of inundation treatments in a wetland experimental site, and molecular ecological networks analysis (MENs) was constructed to characterize the interdomain relationship. The result showed that the degree of inundation significantly altered the CH4 emissions, and the abundance of the pmoA gene for methanotrophs shifted more significantly than the mcrA gene for methanogens, and they both showed significant positive correlations to methane flux. Additionally, we found inundation significantly altered the diversity of the prokaryotic and fungal communities, as well as the composition of key species in interactions within prokaryotic, fungal, and cercozoan communities. Mantel tests indicated that the structure of the three communities showed significant correlations to methane emissions (p < 0.05), suggesting that all three microbial communities directly or indirectly contributed to the methane emissions of this ecosystem. Correspondingly, the interdomain networks among microbial communities revealed that methane-associated prokaryotic and cercozoan OTUs were all keystone taxa. Methane-associated OTUs were more likely to interact in pairs and correlated negatively with the fungal and cercozoan communities. In addition, the modules significantly positively correlated with methane flux were affected by environmental stress (i.e., pH) and soil nutrients (i.e., total nitrogen, total phosphorus and organic matter), suggesting that these factors tend to positively regulate methane flux by regulating microbial relationships under inundation. Our findings demonstrated that the inundation altered microbial communities in coastal wetlands, and the fungal and cercozoan communities played vital roles in regulating methane emission through microbial interactions with the methane-associated community.
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Affiliation(s)
- Linlin Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Mingliang Zhao
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Songsong Gu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yuqi Zhou
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China,Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Yingcheng Wang
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Zheng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qi Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Baohua Xie
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China,Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Guangxuan Han
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China,Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Ye Deng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China,CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Ye Deng,
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11
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Zhang S, Zhang H, Liu H, Wang H, Xiu W, Li G, Zhang G, Zhou Z, Jiang N, Zhang H, Zhao J, Yang D. Fertilization drives distinct biotic and abiotic factors in regulating functional groups of protists in a 5-year fertilization system. Front Microbiol 2022; 13:1036362. [PMID: 36545203 PMCID: PMC9760849 DOI: 10.3389/fmicb.2022.1036362] [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: 09/04/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Protists play an important role in nutrient cycling, microbiome stability and soil fertility maintenance. However, the driving force of protistan functional groups remains poorly understood in agricultural ecosystems. Methods We investigated the impacts of fertilization regimes on the diversity, composition and functional groups of protists and further disentangled the effects of multiple factors shaping the community composition of functional groups in a 5-year fertilization regime (CK, no fertilization; M, organic fertilization; MNPK, combined inorganic and organic fertilization; NPK, inorganic fertilization). Results Fertilization significantly changed the community composition of protists rather than diversity. The MNPK treatment significantly increased the relative abundance of phototrophs and decreased that of the parasites and consumers. Partial least squares path modeling indicated that fertilization indirectly regulated protistan consumers via changes in the P content, which affected the composition of consumers mainly by regulating fungal community composition. Soil moisture (SM) and available phosphorus (AP) were identified as the top predictors for the composition of parasites, and the composition of phototrophs was mainly affected by SM, indicating that parasites and phototrophs were more sensitive to abiotic factors in the fertilization system. Discussion Taken together, our findings highlight that fertilization significantly affects the composition of functional groups of protists and their biotic or abiotic regulatory processes, which have implications for the potential changes in their ecosystem functions for soil management systems.
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12
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Dumack K, Feng K, Flues S, Sapp M, Schreiter S, Grosch R, Rose LE, Deng Y, Smalla K, Bonkowski M. What Drives the Assembly of Plant-associated Protist Microbiomes? Investigating the Effects of Crop Species, Soil Type and Bacterial Microbiomes. Protist 2022; 173:125913. [PMID: 36257252 DOI: 10.1016/j.protis.2022.125913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/24/2022] [Accepted: 09/22/2022] [Indexed: 12/30/2022]
Abstract
In a field experiment we investigated the influence of the environmental filters soil type (i.e. three contrasting soils) and plant species (i.e. lettuce and potato) identity on rhizosphere community assembly of Cercozoa, a dominant group of mostly bacterivorous soil protists. Plant species (14%) and rhizosphere origin (vs bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as 'protist microbiomes' in analogy to 'bacterial microbiomes'.
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Affiliation(s)
- Kenneth Dumack
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany.
| | - Kai Feng
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Sebastian Flues
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
| | - Melanie Sapp
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Population Genetics, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Susanne Schreiter
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany; Helmholtz Centre for Environmental Research GmbH (UFZ), Deptartment Soil System Science, Theodor-Lieser-Str.4, 06120 Halle, Germany
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Laura E Rose
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Population Genetics, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Michael Bonkowski
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Str. 47b, 50674 Köln, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Germany
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13
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Pescador DS, Delgado-Baquerizo M, Fiore-Donno AM, Singh BK, Bonkowski M, Maestre FT. Ecological clusters of soil taxa within bipartite networks are highly sensitive to climatic conditions in global drylands. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210387. [PMID: 35757878 PMCID: PMC9234812 DOI: 10.1098/rstb.2021.0387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/19/2022] [Indexed: 12/18/2022] Open
Abstract
Determining the influence of climate in driving the global distribution of soil microbial communities is fundamental to help predict potential shifts in soil food webs and ecosystem functioning under global change scenarios. Herein, we used a global survey including 80 dryland ecosystems from six continents, and found that the relative abundance of ecological clusters formed by taxa involved in bacteria-fungi and bacteria-cercozoa bipartite networks was highly sensitive to changes in temperature and aridity. Importantly, such a result was maintained when controlling for soil, geographical location and vegetation attributes, being pH and soil organic carbon important determinants of the relative abundance of the ecological clusters. We also identified potential global associations between important soil microbial taxa, which can be useful to support the conservation of terrestrial ecosystems under global change scenarios. Our results suggest that increases in temperature and aridity such as those forecasted for the next decades in drylands could potentially lead to drastic changes in the community composition of functionally important bipartite networks within soil food webs. This could have important but unknown implications for the provision of key ecosystem functions and associated services driven by the organisms forming these networks if other taxa cannot cope with them. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.
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Affiliation(s)
- David S. Pescador
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Anna Maria Fiore-Donno
- Department of Biology, Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Michael Bonkowski
- Department of Biology, Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | - Fernando T. Maestre
- Instituto Multidisciplinar para el Estudio del Medio ‘Ramón Margalef’, Universidad de Alicante, San Vicente del Raspeig, Spain
- Departamento de Ecología, Universidad de Alicante, San Vicente del Raspeig, Spain
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14
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Whitehead J, Roy J, Hempel S, Rillig MC. Soil microbial communities shift along an urban gradient in Berlin, Germany. Front Microbiol 2022; 13:972052. [PMID: 36033838 PMCID: PMC9412169 DOI: 10.3389/fmicb.2022.972052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
The microbial communities inhabiting urban soils determine the functioning of these soils, in regards to their ability to cycle nutrients and support plant communities. In an increasingly urbanized world these properties are of the utmost importance, and the microbial communities responsible are worthy of exploration. We used 53 grassland sites spread across Berlin to describe and explain the impacts of urbanity and other environmental parameters upon the diversity and community composition of four microbial groups. These groups were (i) the Fungi, with a separate dataset for (ii) the Glomeromycota, (iii) the Bacteria, and (iv) the protist phylum Cercozoa. We found that urbanity had distinct impacts on fungal richness, which tended to increase. Geographic distance between sites and soil chemistry, in addition to urbanity, drove microbial community composition, with site connectivity being important for Glomeromycotan communities, potentially due to plant host communities. Our findings suggest that many microbial species are well adapted to urban soils, as supported by an increase in diversity being a far more common result of urbanity than the reverse. However, we also found distinctly separate distributions of operational taxonomic unit (OTU)s from the same species, shedding doubt of the reliability of indicator species, and the use of taxonomy to draw conclusion on functionality. Our observational study employed an extensive set of sites across an urbanity gradient, in the region of the German capital, to produce a rich microbial dataset; as such it can serve as a blueprint for other such investigations.
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Affiliation(s)
- James Whitehead
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Julien Roy
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stefan Hempel
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Matthias C. Rillig
- Ecology of Plants, Institut für Biologie, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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15
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Roy J, Mazel F, Dumack K, Bonkowski M, Rillig MC. Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field. Environ Microbiol 2022; 24:5498-5508. [PMID: 35837871 DOI: 10.1111/1462-2920.16134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/27/2022] [Accepted: 07/09/2022] [Indexed: 11/27/2022]
Abstract
Protists are abundant, diverse and perform essential functions in soils. Protistan community structure and its change across time or space are traditionally studied at the species-level but the relative importance of the processes shaping these patterns depends on the taxon phylogenetic resolution. Using 18S rDNA amplicon data of the Cercozoa, a group of dominant soil protists, from an agricultural field in western Germany, we observed a turnover of relatively closely related taxa (from sequence variants to genus-level clades) across soil depth; while across soil habitats (rhizosphere, bulk soil, drilosphere) we observed turnover of relatively distantly related taxa, confirming Paracercomonadidae as a rhizosphere-associated clade. We extended our approach to show that closely related Cercozoa encounter divergent AM fungi across soil depth and that distantly related Cercozoa encounter closely related AM fungi across soil compartments. This study suggests that soil Cercozoa community assembly at the field-scale is driven by niche-based processes shaped by evolutionary legacy of adaptation to conditions primarily related to soil compartment, followed by soil layer, giving a deeper understanding on the selection pressures that shaped their evolution.
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Affiliation(s)
- Julien Roy
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Kennet Dumack
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Michael Bonkowski
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Matthias C Rillig
- Institut für Biologie, Ökologie der Pflanzen, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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16
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Agricultural management and pesticide use reduce the functioning of beneficial plant symbionts. Nat Ecol Evol 2022; 6:1145-1154. [PMID: 35798840 PMCID: PMC7613230 DOI: 10.1038/s41559-022-01799-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 05/11/2022] [Indexed: 01/04/2023]
Abstract
Phosphorus (P) acquisition is key for plant growth. Arbuscular mycorrhizal fungi (AMF) help plants acquire P from soil. Understanding which factors drive AMF-supported nutrient uptake is essential to develop more sustainable agroecosystems. Here we collected soils from 150 cereal fields and 60 non-cropped grassland sites across a 3,000 km trans-European gradient. In a greenhouse experiment, we tested the ability of AMF in these soils to forage for the radioisotope 33P from a hyphal compartment. AMF communities in grassland soils were much more efficient in acquiring 33P and transferred 64% more 33P to plants compared with AMF in cropland soils. Fungicide application best explained hyphal 33P transfer in cropland soils. The use of fungicides and subsequent decline in AMF richness in croplands reduced 33P uptake by 43%. Our results suggest that land-use intensity and fungicide use are major deterrents to the functioning and natural nutrient uptake capacity of AMF in agroecosystems.
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17
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Dumack K, Gerdzhikov D, Klisarova D. Phylogenetic analysis confirms the taxonomic placement of the marine flagellate Hermesinum adriaticum (Thecofilosea, Cercozoa, Rhizaria). J Eukaryot Microbiol 2022; 69:e12905. [PMID: 35303760 DOI: 10.1111/jeu.12905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hermesinum adriaticum is a rare marine and brackish flagellate that is of considerable interest due to its markable and fossilizable siliceous skeleton. Based on this skeleton, Hermesinum was initially considered a microalga of the Dictyochophyceae (Ochrophyta, Stramenopiles). Later on, it was assigned to the Ebriida due to its similarity to Ebria tripartita. The taxonomic assignment of the Ebriida however changed several times until it was placed within the Thecofilosea (Cercozoa, Rhizaria), based on genetic data of Ebria tripartita. We sequenced the 18S marker gene sequence of Hermesinum and confirm the close relationship of Ebria and Hermesinum.
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Affiliation(s)
- Kenneth Dumack
- University of Cologne, Terrestrial Ecology, Institute of Zoology, Zülpicher Str. 47b, 50674, Köln, Germany
| | - Dimitar Gerdzhikov
- Institute of Fish Resources, Agricultural Academy, Varna, 9000, Bulgaria
| | - Daniela Klisarova
- Institute of Fish Resources, Agricultural Academy, Varna, 9000, Bulgaria.,Medical University, Department of Anatomy, Histology, Cytology and Biology, Pleven, 5800, Bulgaria
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18
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Hess S, Suthaus A. The Vampyrellid Amoebae (Vampyrellida, Rhizaria). Protist 2022; 173:125854. [DOI: 10.1016/j.protis.2021.125854] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/25/2021] [Accepted: 12/13/2021] [Indexed: 11/29/2022]
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19
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Dumack K, Ferlian O, Morselli Gysi D, Degrune F, Jauss RT, Walden S, Öztoprak H, Wubet T, Bonkowski M, Eisenhauer N. Contrasting protist communities (Cercozoa: Rhizaria) in pristine and earthworm-invaded North American deciduous forests. Biol Invasions 2022. [DOI: 10.1007/s10530-021-02726-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractEarthworms are considered ecosystem engineers due to their fundamental impact on soil structure, soil processes and on other soil biota. An invasion of non-native earthworm species has altered soils of North America since European settlement, a process currently expanding into still earthworm-free forest ecosystems due to continuous spread and increasing soil temperatures owing to climate change. Although earthworms are known to modify soil microbial diversity and activity, it is as yet unclear how eukaryote consumers in soil microbial food webs will be affected. Here, we investigated how earthworm invasion affects the diversity of Cercozoa, one of the most dominant protist taxa in soils. Although the composition of the native cercozoan community clearly shifted in response to earthworm invasion, the communities of the different forests showed distinct responses. We identified 39 operational taxonomic units (OTUs) exclusively indicating earthworm invasion, hinting at an earthworm-associated community of Cercozoa. In particular, Woronina pythii, a hyper-parasite of plant-parasitic Oomycota in American forests, increased strongly in the presence of invasive earthworms, indicating an influence of invasive earthworms on oomycete communities and potentially on forest health, which requires further research.
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20
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Zhou Y, Sun B, Xie B, Feng K, Zhang Z, Zhang Z, Li S, Du X, Zhang Q, Gu S, Song W, Wang L, Xia J, Han G, Deng Y. Warming reshaped the microbial hierarchical interactions. GLOBAL CHANGE BIOLOGY 2021; 27:6331-6347. [PMID: 34544207 DOI: 10.1111/gcb.15891] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Global warming may alter microbially mediated ecosystem functions through reshaping of microbial diversity and modified microbial interactions. Here, we examined the effects of 5-year experimental warming on different microbial hierarchical groups in a coastal nontidal soil ecosystem, including prokaryotes (i.e., bacteria and archaea), fungi, and Cercozoa, which is a widespread phylum of protists. Warming significantly altered the diversity and structure of prokaryotic and fungal communities in soil and additionally decreased the complexity of the prokaryotic network and fragmented the cercozoan network. By using the Inter-Domain Ecological Network approach, the cross-trophic interactions among prokaryotes, fungi, and Cercozoa were further investigated. Under warming, cercozoan-prokaryotic and fungal-prokaryotic bipartite networks were simplified, whereas the cercozoan-fungal network became slightly more complex. Despite simplification of the fungal-prokaryotic network, the strengthened synergistic interactions between saprotrophic fungi and certain prokaryotic groups, such as the Bacteroidetes, retained these phyla within the network under warming. In addition, the interactions within the fungal community were quite stable under warming conditions, which stabilized the interactions between fungi and prokaryotes or protists. Additionally, we found the microbial hierarchical interactions were affected by environmental stress (i.e., salinity and pH) and soil nutrients. Interestingly, the relevant microbial groups could respond to different soil properties under ambient conditions, whereas under warming these two groups tended to respond to similar soil properties, suggesting network hub species responded to certain environmental changes related to warming, and then transferred this response to their partners through trophic interactions. Finally, warming strengthened the network modules' negative association with soil organic matters through some fungal hub species, which might trigger soil carbon loss in this ecosystem. Our study provides new insights into the response and feedback of microbial hierarchical interactions under warming scenario.
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Affiliation(s)
- Yuqi Zhou
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Baoyu Sun
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- State Key Laboratory of Estuarine and Coastal Research, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China
| | - Baohua Xie
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China
| | - Kai Feng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Zheng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Shuzhen Li
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Xiongfeng Du
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Qi Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Songsong Gu
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wen Song
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Linlin Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Jianyang Xia
- State Key Laboratory of Estuarine and Coastal Research, Shanghai Key Lab for Urban Ecological Processes and Eco-Restoration, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Guangxuan Han
- Key Laboratory of Coastal Zone Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- Yellow River Delta Field Observation and Research Station of Coastal Wetland Ecosystem, Chinese Academy of Sciences, Yantai, China
| | - Ye Deng
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
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21
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Dumack K, Siemensma F, Clauß S. Transfer of the thecate amoebae Lecythium spinosum and Pamphagus armatus to Rhizaspis (Thecofilosea, Cercozoa, Rhizaria). Eur J Protistol 2021; 83:125843. [PMID: 34920934 DOI: 10.1016/j.ejop.2021.125843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/17/2021] [Accepted: 09/21/2021] [Indexed: 11/03/2022]
Abstract
Thecofilosea is a class in Cercozoa (Rhizaria) comprising mainly freshwater-inhabiting algivores. Recently, numerous isolates of thecofilosean amoebae have been cultured and were characterized by an integrated morphological and molecular approach. The captivating spine-bearing taxa in Thecofilosea were not yet molecularly characterized due to being very rare. There are only two known spine-bearing species, Pamphagus armatus and Lecythium spinosum, which were synonymized by Penard in 1902. Due to a morphological difference of those taxa, we discuss here that we disagree with this taxonomical act. We further isolated single cells of Pamphagus armatus directly from their habitat and successfully sequenced their SSU rDNA, which we subjected to phylogenetic analyses. We show that Pamphagus armatus branches within the Rhizaspididae (Tectofilosida, Thecofilosea). Accordingly, we transfer Pamphagus armatus and the assumingly closely related species Lecythium spinosum to Rhizaspis.
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Affiliation(s)
- Kenneth Dumack
- University of Cologne, Terrestrial Ecology, Institute of Zoology, Zülpicher Str. 47b, 50674 Köln, Germany.
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22
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Vaulot D, Geisen S, Mahé F, Bass D. pr2-primers: An 18S rRNA primer database for protists. Mol Ecol Resour 2021; 22:168-179. [PMID: 34251760 DOI: 10.1111/1755-0998.13465] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/31/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023]
Abstract
Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost solely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, an informed primer choice is necessary, as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few online resources available to list existing primers. We built a database listing 285 primers and 83 unique primer pairs that have been used for eukaryotic 18S rRNA gene metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR2 version 4.12.0 for eukaryotes and a subset of silva version 132 for bacteria and archaea. We developed an R-based web application enabling browsing of the database, visualization of the taxonomic distribution of the amplified sequences with the number of mismatches, and testing any user-defined primer or primer set (https://app.pr2-primers.org). Taxonomic specificity of primer pairs, amplicon size and location of mismatches can also be determined. We identified universal primer sets that matched the largest number of sequences and analysed the specificity of some primer sets designed to target certain groups. This tool enables guided primer choices that will help a wide range of researchers to include protists as part of their investigations.
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Affiliation(s)
- Daniel Vaulot
- UMR 7144, ECOMAP, Station Biologique de Roscoff, CNRS, Sorbonne Université, Roscoff, France.,Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands.,Nanjing Agricultural University, Nanjing, China
| | - Frédéric Mahé
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, UK.,Department of Life Sciences, The Natural History Museum, London, UK
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Walden S, Jauss RT, Feng K, Fiore-Donno AM, Dumack K, Schaffer S, Wolf R, Schlegel M, Bonkowski M. On the phenology of protists: recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa and Endomyxa) communities in tree canopies. FEMS Microbiol Ecol 2021; 97:fiab081. [PMID: 34117748 PMCID: PMC8213970 DOI: 10.1093/femsec/fiab081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/10/2021] [Indexed: 11/23/2022] Open
Abstract
Tree canopies are colonized by billions of highly specialized microorganisms that are well adapted to the highly variable microclimatic conditions, caused by diurnal fluctuations and seasonal changes. In this study, we investigated seasonality patterns of protists in the tree canopies of a temperate floodplain forest via high-throughput sequencing with group-specific primers for the phyla Cercozoa and Endomyxa. We observed consistent seasonality, and identified divergent spring and autumn taxa. Tree crowns were characterized by a dominance of bacterivores and omnivores, while eukaryvores gained a distinctly larger share in litter and soil communities on the ground. In the canopy seasonality was largest among communities detected on the foliar surface: In spring, higher variance within alpha diversity of foliar samples indicated greater heterogeneity during initial colonization. However, communities underwent compositional changes during the aging of leaves in autumn, highly reflecting recurring phenological changes during protistan colonization. Surprisingly, endomyxan root pathogens appeared to be exceptionally abundant across tree canopies during autumn, demonstrating a potential role of the canopy surface as a physical filter for air-dispersed propagules. Overall, about 80% of detected OTUs could not be assigned to known species-representing dozens of microeukaryotic taxa whose canopy inhabitants are waiting to be discovered.
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Affiliation(s)
- Susanne Walden
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Robin-Tobias Jauss
- Institute of Biology, Biodiversity and Evolution, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, No. 18 Shuangqing Road, 100085 Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, 100049 Beijing, China
| | - Anna Maria Fiore-Donno
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Kenneth Dumack
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Stefan Schaffer
- Institute of Biology, Molecular Evolution and Animal Systematics, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Ronny Wolf
- Institute of Biology, Molecular Evolution and Animal Systematics, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Martin Schlegel
- Institute of Biology, Biodiversity and Evolution, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
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Solbach MD, Bonkowski M, Dumack K. Novel Endosymbionts in Rhizarian Amoebae Imply Universal Infection of Unrelated Free-Living Amoebae by Legionellales. Front Cell Infect Microbiol 2021; 11:642216. [PMID: 33763389 PMCID: PMC7982676 DOI: 10.3389/fcimb.2021.642216] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022] Open
Abstract
Legionellales-infected water is a frequent cause of local outbreaks of Legionnaires’ disease and Pontiac fever. Decontaminations are difficult because Legionellales reproduce in eukaryotic microorganisms (protists). Most often, Legionellales have been isolated from amoebae; however, the culture-based sampling methods are taxonomically biased. Sequencing studies show that amoebae in the cercozoan class Thecofilosea are dominant in soils and wastewater treatment plants, prompting us to screen their capability to serve as potential hosts of endosymbiotic bacteria. Environmental isolates of Thecofilosea contained a surprising richness of endosymbiotic Legionellales, including Legionella. Considering the widespread dispersal of Legionellales in apparently unrelated amoeboid protist taxa, it appears that the morphotype and not the evolutionary origin of amoebae determines their suitability as hosts for Legionellales. We further provide a protocol for gnotobiotic cultivation of Legionellales and their respective hosts, facilitating future genomic and transcriptomic research of host–symbiont relationships.
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Affiliation(s)
- Marcel Dominik Solbach
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Michael Bonkowski
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Kenneth Dumack
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
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25
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Rüger L, Feng K, Dumack K, Freudenthal J, Chen Y, Sun R, Wilson M, Yu P, Sun B, Deng Y, Hochholdinger F, Vetterlein D, Bonkowski M. Assembly Patterns of the Rhizosphere Microbiome Along the Longitudinal Root Axis of Maize ( Zea mays L.). Front Microbiol 2021; 12:614501. [PMID: 33643242 PMCID: PMC7906986 DOI: 10.3389/fmicb.2021.614501] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/25/2021] [Indexed: 02/02/2023] Open
Abstract
It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil - their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly of communities of prokaryotes (archaea and bacteria) and their protistan predators (Cercozoa, Rhizaria) along the longitudinal root axis of maize (Zea mays L.). We grew maize plants in an agricultural loamy soil and sampled rhizosphere soil at distinct locations along maize roots. We applied high-throughput sequencing, followed by diversity and network analyses in order to track changes in relative abundances, diversity and co-occurrence of rhizosphere microbiota along the root axis. Apart from a reduction of operational taxonomic unit (OTU) richness and a strong shift in community composition between bulk soil and root tips, patterns of microbial community assembly along maize-roots were more complex than expected. High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Root hair zone communities were characterized by massive co-occurrence of microbial taxa, likely fueled by abundant resource supply from rhizodeposition. Further up the root where lateral roots emerged processes of community assembly appeared to be more deterministic (e.g., through competition and predation). This shift toward significance of deterministic processes was revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their potential protistan predators. Such patterns were strongest in regions with fully developed laterals, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial variability is crucially important.
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Affiliation(s)
- Lioba Rüger
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Jule Freudenthal
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Yan Chen
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ruibo Sun
- Microbial Ecology Lab, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Monica Wilson
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Peng Yu
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Bo Sun
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
- Soil Science, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
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26
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Francioli D, Lentendu G, Lewin S, Kolb S. DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions. Microorganisms 2021; 9:361. [PMID: 33673098 PMCID: PMC7918050 DOI: 10.3390/microorganisms9020361] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
| | - Guillaume Lentendu
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland;
| | - Simon Lewin
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
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27
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Khanipour Roshan S, Dumack K, Bonkowski M, Leinweber P, Karsten U, Glaser K. Taxonomic and Functional Diversity of Heterotrophic Protists (Cercozoa and Endomyxa) from Biological Soil Crusts. Microorganisms 2021; 9:205. [PMID: 33498223 PMCID: PMC7908994 DOI: 10.3390/microorganisms9020205] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/25/2022] Open
Abstract
Biological soil crusts (biocrusts) accommodate diverse communities of phototrophic and heterotrophic microorganisms. Heterotrophic protists have critical roles in the microbial food webs of soils, with Cercozoa and Endomyxa often being dominant groups. Still, the diversity, community composition, and functions of Cercozoa and Endomyxa in biocrusts have been little explored. In this study, using a high-throughput sequencing method with taxon-specific barcoded primers, we studied cercozoan and endomyxan communities in biocrusts from two unique habitats (subarctic grassland and temperate dunes). The communities differed strongly, with the grassland and dunes being dominated by Sarcomonadea (69%) and Thecofilosea (43%), respectively. Endomyxa and Phytomyxea were the minor components in dunes. Sandonidae, Allapsidae, and Rhogostomidae were the most abundant taxa in both habitats. In terms of functionality, up to 69% of the grassland community was constituted by bacterivorous Cercozoa. In contrast, cercozoan and endomyxan communities in dunes consisted of 31% bacterivores, 25% omnivores, and 20% eukaryvores. Facultative and obligate eukaryvores mostly belonged to the families Rhogostomidae, Fiscullidae, Euglyphidae, Leptophryidae, and Cercomonadidae, most of which are known to feed mainly on algae. Biocrust edaphic parameters such as pH, total organic carbon, nitrogen, and phosphorus did not have any significant influence on shaping cercozoan communities within each habitat, which confirms previous results from dunes.
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Affiliation(s)
- Samira Khanipour Roshan
- Institute for Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (U.K.); (K.G.)
| | - Kenneth Dumack
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany; (K.D.); (M.B.)
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany; (K.D.); (M.B.)
| | - Peter Leinweber
- Faculty of Agriculture and Environmental Sciences, Soil Science, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany;
| | - Ulf Karsten
- Institute for Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (U.K.); (K.G.)
| | - Karin Glaser
- Institute for Biological Sciences, Applied Ecology and Phycology, University of Rostock, Albert-Einstein-Str. 3, 18059 Rostock, Germany; (U.K.); (K.G.)
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28
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Crop cover is more important than rotational diversity for soil multifunctionality and cereal yields in European cropping systems. ACTA ACUST UNITED AC 2021; 2:28-37. [PMID: 37117662 DOI: 10.1038/s43016-020-00210-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 12/03/2020] [Indexed: 01/01/2023]
Abstract
In natural ecosystems, positive effects of plant diversity on ecosystem functioning have been widely observed, yet whether this is true in cropping systems remains unclear. Here we assessed the impact of crop diversification on soil microbial diversity, soil multifunctionality (SMF) and crop yields in 155 cereal fields across a 3,000 km north-south European gradient. Overall, crop diversity showed a relatively minor effect on soil microbial diversity, SMF and yields. In contrast, the proportion of time with crop cover (including cash crops, cover crops or forage leys) during the past ten-year crop rotation had a much stronger impact. This suggests that increasing crop cover can enhance both yields and soil functioning, while also providing habitat for soil microorganisms. We found that SMF did not positively contribute to crop yields, highlighting that care must be taken to balance the provision of food with environmentally beneficial functions and services, since they do not always go hand in hand.
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29
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Sun A, Jiao XY, Chen Q, Trivedi P, Li Z, Li F, Zheng Y, Lin Y, Hu HW, He JZ. Fertilization alters protistan consumers and parasites in crop-associated microbiomes. Environ Microbiol 2021; 23:2169-2183. [PMID: 33400366 DOI: 10.1111/1462-2920.15385] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/03/2021] [Indexed: 12/12/2022]
Abstract
Crop plants carry an enormous diversity of microbiota that provide massive benefits to hosts. Protists, as the main microbial consumers and a pivotal driver of biogeochemical cycling processes, remain largely understudied in the plant microbiome. Here, we characterized the diversity and composition of protists in sorghum leaf phyllosphere, and rhizosphere and bulk soils, collected from an 8-year field experiment with multiple fertilization regimes. Phyllosphere was an important habitat for protists, dominated by Rhizaria, Alveolata and Amoebozoa. Rhizosphere and bulk soils had a significantly higher diversity of protists than the phyllosphere, and the protistan community structure significantly differed among the three plant-soil compartments. Fertilization significantly altered specific functional groups of protistan consumers and parasites. Variation partitioning models revealed that soil properties, bacteria and fungi predicted a significant proportion of the variation in the protistan communities. Changes in protists may in turn significantly alter the compositions of bacterial and fungal communities from the top-down control in food webs. Altogether, we provide novel evidence that fertilization significantly affects the functional groups of protistan consumers and parasites in crop-associated microbiomes, which have implications for the potential changes in their ecological functions under intensive agricultural managements.
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Affiliation(s)
- Anqi Sun
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Xiao-Yan Jiao
- College of Resource and Environment, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Qinglin Chen
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Zixin Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Fangfang Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Yong Zheng
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Yongxin Lin
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Hang-Wei Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China.,School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Ji-Zheng He
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China.,School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic., 3010, Australia
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30
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Abstract
Protists are mostly unicellular eukaryotes. Some protists are beneficial for plants, while others live as endosymbionts and can cause severe plant diseases. More detailed studies on plant-protist interactions exist only for plant pathogens and parasites. A number of protists live as inconspicuous endophytes and cause no visible disease symptoms, while others appear closely associated with the rhizosphere or phyllosphere of plants, but we still have only a vague understanding on their identities and functions. Here, we provide a protocol on how to assess the plant-associated protist community via Illumina-sequencing of ribosomal marker-amplicons and describe how to assign taxonomic affiliation to the obtained sequences.
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Affiliation(s)
- Kenneth Dumack
- Cluster of Excellence on Plant Sciences (CEPLAS), Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Köln, Germany.
| | - Michael Bonkowski
- Cluster of Excellence on Plant Sciences (CEPLAS), Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Köln, Germany
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31
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Jauss RT, Walden S, Fiore-Donno AM, Dumack K, Schaffer S, Wolf R, Schlegel M, Bonkowski M. From Forest Soil to the Canopy: Increased Habitat Diversity Does Not Increase Species Richness of Cercozoa and Oomycota in Tree Canopies. Front Microbiol 2020; 11:592189. [PMID: 33414768 PMCID: PMC7782269 DOI: 10.3389/fmicb.2020.592189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/07/2020] [Indexed: 02/02/2023] Open
Abstract
Tree canopies provide habitats for diverse and until now, still poorly characterized communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa (Rhizaria) and Oomycota (Stramenopiles), was performed. Group specific primers were used to comprehensively analyze their diversity in various microhabitats of a floodplain forest from the forest floor to the canopy region. Beta diversity indicated highly dissimilar protistan communities in the investigated microhabitats. However, the majority of operational taxonomic units (OTUs) was present in all samples, and therefore differences in beta diversity were mainly related to species performance (i.e., relative abundance). Accordingly, habitat diversity strongly favored distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible.
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Affiliation(s)
- Robin-Tobias Jauss
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Susanne Walden
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | | | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Stefan Schaffer
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Ronny Wolf
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Martin Schlegel
- Molecular Evolution and Animal Systematics, Institute of Biology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Leipzig, Germany
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
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32
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Rossmann M, Pérez-Jaramillo JE, Kavamura VN, Chiaramonte JB, Dumack K, Fiore-Donno AM, Mendes LW, Ferreira MMC, Bonkowski M, Raaijmakers JM, Mauchline TH, Mendes R. Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists. FEMS Microbiol Ecol 2020; 96:5775476. [PMID: 32124916 DOI: 10.1093/femsec/fiaa032] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/28/2020] [Indexed: 11/14/2022] Open
Abstract
Plants modulate the soil microbiota by root exudation assembling a complex rhizosphere microbiome with organisms spanning different trophic levels. Here, we assessed the diversity of bacterial, fungal and cercozoan communities in landraces and modern varieties of wheat. The dominant taxa within each group were the bacterial phyla Proteobacteria, Actinobacteria and Acidobacteria; the fungi phyla Ascomycota, Chytridiomycota and Basidiomycota; and the Cercozoa classes Sarcomonadea, Thecofilosea and Imbricatea. We showed that microbial networks of the wheat landraces formed a more intricate network topology than that of modern wheat cultivars, suggesting that breeding selection resulted in a reduced ability to recruit specific microbes in the rhizosphere. The high connectedness of certain cercozoan taxa to bacteria and fungi indicated trophic network hierarchies where certain predators gain predominance over others. Positive correlations between protists and bacteria in landraces were preserved as a subset in cultivars as was the case for the Sarcomonadea class with Actinobacteria. The correlations between the microbiome structure and plant genotype observed in our results suggest the importance of top-down control by organisms of higher trophic levels as a key factor for understanding the drivers of microbiome community assembly in the rhizosphere.
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Affiliation(s)
- Maike Rossmann
- Laboratory of Environmental Microbiology, Embrapa Environment, Rodovia SP 340 km 125.5, 13918-110, Jaguariúna SP, Brazil
| | - Juan E Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW); Institute of Biology, Leiden University, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Vanessa N Kavamura
- Sustainable Agriculture Sciences, West Common, AL5 2JQ, Harpenden, Rothamsted Research, UK
| | - Josiane B Chiaramonte
- Laboratory of Environmental Microbiology, Embrapa Environment, Rodovia SP 340 km 125.5, 13918-110, Jaguariúna SP, Brazil
| | - Kenneth Dumack
- Institute of Zoology & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Anna Maria Fiore-Donno
- Institute of Zoology & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Lucas W Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo, Av. Centenário, 303, 13416-000, Piracicaba SP, Brazil
| | - Márcia M C Ferreira
- Laboratory of Theoretical and Applied Chemometrics, Department of Chemistry, State University of Campinas (UNICAMP), Rua Josué de Castro, s/n, 13083-970, Campinas SP, Brazil
| | - Michael Bonkowski
- Institute of Zoology & Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW); Institute of Biology, Leiden University, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Tim H Mauchline
- Sustainable Agriculture Sciences, West Common, AL5 2JQ, Harpenden, Rothamsted Research, UK
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Rodovia SP 340 km 125.5, 13918-110, Jaguariúna SP, Brazil
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33
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Fiore-Donno AM, Richter-Heitmann T, Bonkowski M. Contrasting Responses of Protistan Plant Parasites and Phagotrophs to Ecosystems, Land Management and Soil Properties. Front Microbiol 2020; 11:1823. [PMID: 32849427 PMCID: PMC7422690 DOI: 10.3389/fmicb.2020.01823] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/10/2020] [Indexed: 11/13/2022] Open
Abstract
Functional traits are increasingly used in ecology to link the structure of microbial communities to ecosystem processes. We investigated two important protistan lineages, Cercozoa and Endomyxa (Rhizaria) in soil using Illumina sequencing and analyzed their diversity and functional traits along with their responses to environmental factors in grassland and forest across Germany. From 600 soil samples, we obtained 2,101 Operational Taxonomic Units representing ∼18 million Illumina reads (region V4, 18S rRNA gene). All major taxonomic and functional groups were present, dominated by small bacterivorous flagellates (Glissomonadida). Endomyxan plant parasites were absent from forests. In grassland, Cercozoa and Endomyxa were promoted by more intensive land use management. Grassland and forest strikingly differed in community composition. Relative abundances of bacterivores and eukaryvores were inversely influenced by environmental factors. These patterns provide new insights into the functional organization of soil biota and indications for a more sustainable land-use management.
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Affiliation(s)
- Anna Maria Fiore-Donno
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Michael Bonkowski
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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Öztoprak H, Walden S, Heger T, Bonkowski M, Dumack K. What Drives the Diversity of the Most Abundant Terrestrial Cercozoan Family (Rhogostomidae, Cercozoa, Rhizaria)? Microorganisms 2020; 8:E1123. [PMID: 32722603 PMCID: PMC7463998 DOI: 10.3390/microorganisms8081123] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/25/2022] Open
Abstract
Environmental sequencing surveys of soils and freshwaters revealed high abundance and diversity of the Rhogostomidae, a group of omnivorous thecate amoebae. This is puzzling since only a few Rhogostomidae species have yet been described and only a handful of reports mention them in field surveys. We investigated the putative cryptic diversity of the Rhogostomidae by a critical re-evaluation of published environmental sequencing data and in-depth ecological and morphological trait analyses. The Rhogostomidae exhibit an amazing diversity of genetically distinct clades that occur in a variety of different environments. We further broadly sampled for Rhogostomidae species; based on these isolates, we describe eleven new species and highlight important morphological traits for species delimitation. The most important environmental drivers that shape the Rhogostomidae community were soil moisture, soil pH, and total plant biomass. The length/width ratio of the theca was a morphological trait related to the colonized habitats, but not the shape and size of the aperture that is often linked to moisture adaption in testate and thecate amoebae.
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Affiliation(s)
- Hüsna Öztoprak
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany; (H.Ö.); (S.W.); (M.B.)
| | - Susanne Walden
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany; (H.Ö.); (S.W.); (M.B.)
| | - Thierry Heger
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260 Nyon, Switzerland;
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany; (H.Ö.); (S.W.); (M.B.)
| | - Kenneth Dumack
- Institute of Zoology, Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany; (H.Ö.); (S.W.); (M.B.)
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Velasco-González I, Sanchez-Jimenez A, Singer D, Murciano A, Díez-Hermano S, Lara E, Martín-Cereceda M. Rain-Fed Granite Rock Basins Accumulate a High Diversity of Dormant Microbial Eukaryotes. MICROBIAL ECOLOGY 2020; 79:882-897. [PMID: 31796996 DOI: 10.1007/s00248-019-01463-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
Rain fed granite rock basins are ancient geological landforms of worldwide distribution and structural simplicity. They support habitats that can switch quickly from terrestrial to aquatic along the year. Diversity of animals and plants, and the connexion between communities in different basins have been widely explored in these habitats, but hardly any research has been carried out on microorganisms. The aim of this study is to provide the first insights on the diversity of eukaryotic microbial communities from these environments. Due to the ephemeral nature of these aquatic environments, we predict that the granitic basins should host a high proportion of dormant microeukaryotes. Based on an environmental DNA diversity survey, we reveal diverse communities with representatives of all major eukaryotic taxonomic supergroups, mainly composed of a diverse pool of low abundance OTUs. Basin communities were very distinctive, with alpha and beta diversity patterns non-related to basin size or spatial distance respectively. Dissimilarity between basins was mainly characterised by turnover of OTUs. The strong microbial eukaryotic heterogeneity observed among the basins may be explained by a complex combination of deterministic factors (diverging environment in the basins), spatial constraints, and randomness including founder effects. Most interestingly, communities contain organisms that cannot coexist at the same time because of incompatible metabolic requirements, thus suggesting the existence of a pool of dormant organisms whose activity varies along with the changing environment. These organisms accumulate in the pools, which turns granitic rock into high biodiversity microbial islands whose conservation and study deserve further attention.
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Affiliation(s)
- Ismael Velasco-González
- Departamento de Genética, Fisiología y Microbiología. Facultad de Ciencias Biológicas, Universidad Complutense de Madrid (UCM), C/ José Antonio Novais 12, 28040, Madrid, Spain
| | - Abel Sanchez-Jimenez
- Departamento de Biodiversidad, Ecología y Evolución. Facultad de Ciencias Biológicas, UCM, Madrid, Spain
| | - David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000, Neuchâtel, Switzerland
- Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, 05508-090, Brazil
| | - Antonio Murciano
- Departamento de Biodiversidad, Ecología y Evolución. Facultad de Ciencias Biológicas, UCM, Madrid, Spain
| | - Sergio Díez-Hermano
- Departamento de Biodiversidad, Ecología y Evolución. Facultad de Ciencias Biológicas, UCM, Madrid, Spain
| | - Enrique Lara
- Real Jardín Botánico, CSIC Plaza de Murillo 2, 28014, Madrid, Spain
| | - Mercedes Martín-Cereceda
- Departamento de Genética, Fisiología y Microbiología. Facultad de Ciencias Biológicas, Universidad Complutense de Madrid (UCM), C/ José Antonio Novais 12, 28040, Madrid, Spain.
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Siemensma F, Dumack K. SSU rDNA Phylogeny Indicates the Scale-lacking Trivalvulariida ord. nov. as a Sister Group to the Euglyphida (Cercozoa, Rhizaria). Protist 2020; 171:125701. [DOI: 10.1016/j.protis.2019.125701] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 01/21/2023]
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Ren X, Tang J, Liu X, Liu Q. Effects of microplastics on greenhouse gas emissions and the microbial community in fertilized soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 256:113347. [PMID: 31672352 DOI: 10.1016/j.envpol.2019.113347] [Citation(s) in RCA: 176] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 05/09/2023]
Abstract
Microplastics (MPs) are characterized by small particle sizes (<5 mm) and are widely distributed in the soil environment. To date, little research has been conducted on investigating the effects of MPs on the soil microbial community, which plays a vital role in biogeochemical cycling. In the present study, we investigate the influence of two particle sizes of MPs on dissolved organic carbon (DOC) and its relative functional groups, fluxes of greenhouse gases (GHGs), and the bacterial and fungal communities in fertilized soil. The results showed that a 5% concentration of MPs had no significant effect on soil DOC, whereas the formation of aromatic functional groups was accelerated. In fertilized soil, the existence of MPs decreased the global warming potential (GWP) as a result of a reduction in N2O emissions during the first three days. A potential mechanism for this reduction in N2O emissions might be that MPs inhibited the phylum Chloroflexi, Rhodoplanes genera, and increased the abundance of Thermoleophilia on day 3. An increase in N2O emissions was observed on day 30, mainly due to the acceleration of the NO3- reduction and a decrease in the abundance of Gemmatimonadacea. The CH4 uptake was significantly correlated with Hyphomicrobiaceae on day 3 and Rhodomicrobium on day 30. In soil with MPs, Actinobacteria replaced Proteobacteria as the dominant phylum. Larger MPs increased the richness (Chao1) and abundance-based coverage estimators (ACE) and diversity (Shannon) of the bacterial community on day 3, whereas these decreased on day 30. The richness and diversity of the fungal community were also reduced on days 3 and 30. Smaller MPs increased the community richness and diversity of both bacterial and fungal communities in fertilized soil. Our findings suggest that MPs have selective effects on microbes and can potentially have a serious impact on terrestrial biogeochemical cycles.
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Affiliation(s)
- Xinwei Ren
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jingchun Tang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| | - Xiaomei Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Qinglong Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
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Dumack K, Fiore‐Donno AM, Bass D, Bonkowski M. Making sense of environmental sequencing data: Ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria). Mol Ecol Resour 2019; 20:398-403. [DOI: 10.1111/1755-0998.13112] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Kenneth Dumack
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
| | - Anna Maria Fiore‐Donno
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
| | - David Bass
- Centre for Environment Fisheries and Aquaculture Science (Cefas) Weymouth UK
- Department of Life Sciences The Natural History Museum London UK
| | - Michael Bonkowski
- Institute of Zoology Terrestrial Ecology Cluster of Excellence on Plant Sciences (CEPLAS) University of Cologne Cologne Germany
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Voss C, Fiore-Donno AM, Guerreiro MA, Peršoh D, Bonkowski M. Metatranscriptomics reveals unsuspected protistan diversity in leaf litter across temperate beech forests, with Amoebozoa the dominating lineage. FEMS Microbiol Ecol 2019; 95:5565044. [DOI: 10.1093/femsec/fiz142] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022] Open
Abstract
ABSTRACTForest litter harbors complex networks of microorganisms whose major components are bacteria, fungi and protists. Protists, being highly selective consumers of bacteria and fungi could influence decomposition processes by shifting competitive microbial interactions. We investigated the eukaryotic diversity from 18 samples of one-year beech (Fagus sylvatica) leaf litter by RNA-based high-throughput sequencing of the small-subunit ribosomal RNA gene. By applying a metatranscriptomics approach, we avoided biases inherent to PCR-based methods, and could therefore focus on elusive protistan groups. We obtained 14 589 eukaryotic assembled sequences (contigs) representing 2223 unique taxa. Fungi dominated the eukaryotic assemblage, followed by an equal proportion of protists and plants. Among protists, the phylum Amoebozoa clearly dominated, representing more than twice the proportion of Alveolata (mostly ciliates) and Rhizaria (mostly Cercozoa), which are often retrieved as the dominant protistan groups in soils, revealing potential primer biases. By assigning functional traits to protists, we could assess that the proportion of free-living and heterotrophs was much higher than that of parasites and autotrophs, opening the way to a better understanding of the role played by the protistan communities and how biodiversity interacts with decomposition processes.
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Affiliation(s)
- Christian Voss
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - Anna Maria Fiore-Donno
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Zuelpicher Str. 47b, 50674 Cologne, Germany
| | - Marco Alexandre Guerreiro
- Department of Geobotany, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitaetstr. 150, 44801 Bochum, Germany
| | - Derek Peršoh
- Department of Geobotany, Faculty of Biology and Biotechnology, Ruhr-University of Bochum, Universitaetstr. 150, 44801 Bochum, Germany
| | - Michael Bonkowski
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Zuelpicher Str. 47b, 50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Zuelpicher Str. 47b, 50674 Cologne, Germany
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Inkinen J, Jayaprakash B, Siponen S, Hokajärvi AM, Pursiainen A, Ikonen J, Ryzhikov I, Täubel M, Kauppinen A, Paananen J, Miettinen IT, Torvinen E, Kolehmainen M, Pitkänen T. Active eukaryotes in drinking water distribution systems of ground and surface waterworks. MICROBIOME 2019; 7:99. [PMID: 31269979 PMCID: PMC6610866 DOI: 10.1186/s40168-019-0715-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/20/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Eukaryotes are ubiquitous in natural environments such as soil and freshwater. Little is known of their presence in drinking water distribution systems (DWDSs) or of the environmental conditions that affect their activity and survival. METHODS Eukaryotes were characterized by Illumina high-throughput sequencing targeting 18S rRNA gene (DNA) that estimates the total community and the 18S rRNA gene transcript (RNA) that is more representative of the active part of the community. DWDS cold water (N = 124), hot water (N = 40), and biofilm (N = 16) samples were collected from four cities in Finland. The sampled DWDSs were from two waterworks A-B with non-disinfected, recharged groundwater as source water and from three waterworks utilizing chlorinated water (two DWDSs of surface waterworks C-D and one of ground waterworks E). In each DWDS, samples were collected from three locations during four seasons of 1 year. RESULTS A beta-diversity analysis revealed that the main driver shaping the eukaryotic communities was the DWDS (A-E) (R = 0.73, P < 0.001, ANOSIM). The kingdoms Chloroplastida (green plants and algae), Metazoa (animals: rotifers, nematodes), Fungi (e.g., Cryptomycota), Alveolata (ciliates, dinoflagellates), and Stramenopiles (algae Ochrophyta) were well represented and active-judging based on the rRNA gene transcripts-depending on the surrounding conditions. The unchlorinated cold water of systems (A-B) contained a higher estimated total number of taxa (Chao1, average 380-480) than chlorinated cold water in systems C-E (Chao1 ≤ 210). Within each DWDS, unique eukaryotic communities were identified at different locations as was the case also for cold water, hot water, and biofilms. A season did not have a consistent impact on the eukaryotic community among DWDSs. CONCLUSIONS This study comprehensively characterized the eukaryotic community members within the DWDS of well-maintained ground and surface waterworks providing good quality water. The study gives an indication that each DWDS houses a unique eukaryotic community, mainly dependent on the raw water source and water treatment processes in place at the corresponding waterworks. In particular, disinfection as well as hot water temperature seemed to represent a strong selection pressure that controlled the number of active eukaryotic species.
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Affiliation(s)
- Jenni Inkinen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | | | - Sallamaari Siponen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box, 1627, FI-70211 Kuopio, Finland
| | - Anna-Maria Hokajärvi
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Anna Pursiainen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Jenni Ikonen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Ivan Ryzhikov
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box, 1627, FI-70211 Kuopio, Finland
| | - Martin Täubel
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Ari Kauppinen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Ilkka T. Miettinen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
| | - Eila Torvinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box, 1627, FI-70211 Kuopio, Finland
| | - Mikko Kolehmainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box, 1627, FI-70211 Kuopio, Finland
| | - Tarja Pitkänen
- Department of Health Security, National Institute for Health and Welfare, P.O. Box 95, FI-70701 Kuopio, Finland
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Fiore-Donno AM, Richter-Heitmann T, Degrune F, Dumack K, Regan KM, Marhan S, Boeddinghaus RS, Rillig MC, Friedrich MW, Kandeler E, Bonkowski M. Functional Traits and Spatio-Temporal Structure of a Major Group of Soil Protists (Rhizaria: Cercozoa) in a Temperate Grassland. Front Microbiol 2019; 10:1332. [PMID: 31244819 PMCID: PMC6579879 DOI: 10.3389/fmicb.2019.01332] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 05/28/2019] [Indexed: 12/27/2022] Open
Abstract
Soil protists are increasingly appreciated as essential components of soil foodwebs; however, there is a dearth of information on the factors structuring their communities. Here we investigate the importance of different biotic and abiotic factors as key drivers of spatial and seasonal distribution of protistan communities. We conducted an intensive survey of a 10 m2 grassland plot in Germany, focusing on a major group of protists, the Cercozoa. From 177 soil samples, collected from April to November, we obtained 694 Operational Taxonomy Units representing >6 million Illumina reads. All major cercozoan taxonomic and functional groups were present, dominated by the small flagellates of the Glissomonadida. We found evidence of environmental selection structuring the cercozoan communities both spatially and seasonally. Spatial analyses indicated that communities were correlated within a range of 3.5 m. Seasonal variations in the abundance of bacterivores and bacteria, followed by that of omnivores suggested a dynamic prey-predator succession. The most influential edaphic properties were moisture and clay content, which differentially affected each functional group. Our study is based on an intense sampling of protists at a small scale, thus providing a detailed description of the biodiversity of different taxa/functional groups and the ecological processes involved in shaping their distribution.
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Affiliation(s)
- Anna Maria Fiore-Donno
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Florine Degrune
- Institute of Biology, Plant Ecology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Kenneth Dumack
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Kathleen M. Regan
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Sven Marhan
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Runa S. Boeddinghaus
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Matthias C. Rillig
- Institute of Biology, Plant Ecology, Freie Universität Berlin, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ellen Kandeler
- Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Michael Bonkowski
- Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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Pochon X, Wecker P, Stat M, Berteaux-Lecellier V, Lecellier G. Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons. PeerJ 2019; 7:e6898. [PMID: 31139503 PMCID: PMC6521813 DOI: 10.7717/peerj.6898] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/02/2019] [Indexed: 11/20/2022] Open
Abstract
High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and tested a dual-index sequence library preparation method that pools and simultaneously sequences multiple Symbiodiniaceae gene amplicons per sample for in-depth biodiversity assessments. The rationale for this approach was to allow the metabarcoding of multiple genes without extra costs associated with additional single amplicon dual indexing and library preparations. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three pooled gene amplicons investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. The pooled Symbiodiniaceae multi-gene metabarcoding approach described here is readily scalable, offering considerable analytical cost savings while providing sufficient phylogenetic information and sequence coverage.
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Affiliation(s)
- Xavier Pochon
- Coastal & Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | | | - Michael Stat
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | | | - Gaël Lecellier
- UMR250/9220 ENTROPIE, IRD-CNRS-UR, LabEx CORAIL, Nouméa, New-Caledonia.,Université Paris-Saclay, UVSQ, Versailles Cedex, France
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43
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Degrune F, Dumack K, Fiore-Donno AM, Bonkowski M, Sosa-Hernández MA, Schloter M, Kautz T, Fischer D, Rillig MC. Distinct communities of Cercozoa at different soil depths in a temperate agricultural field. FEMS Microbiol Ecol 2019; 95:5420472. [DOI: 10.1093/femsec/fiz041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/21/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Florine Degrune
- Freie Universität Berlin, Institut für Biologie, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195 Berlin, Germany
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Anna Maria Fiore-Donno
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Moisés A Sosa-Hernández
- Freie Universität Berlin, Institut für Biologie, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195 Berlin, Germany
| | - Michael Schloter
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Timo Kautz
- Humboldt-Universität zu Berlin. Albrecht Daniel Thaer-Institut für Agrar- und Gartenbauwissenschaften, Albrecht-Thaer-Weg 5, 14195 Berlin, Germany
| | - Doreen Fischer
- Research Unit for Environmental Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Matthias C Rillig
- Freie Universität Berlin, Institut für Biologie, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstr. 34, 14195 Berlin, Germany
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Rippin M, Lange S, Sausen N, Becker B. Biodiversity of biological soil crusts from the Polar Regions revealed by metabarcoding. FEMS Microbiol Ecol 2019. [PMID: 29514253 DOI: 10.1093/femsec/fiy036] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Biological soil crusts (BSCs) are amalgamations of autotrophic, heterotrophic and saprotrophic organisms. In the Polar Regions, these unique communities occupy essential ecological functions such as primary production, nitrogen fixation and ecosystem engineering. Here, we present the first molecular survey of BSCs from the Arctic and Antarctica focused on both eukaryotes and prokaryotes as well as passive and active biodiversity. Considering sequence abundance, Bryophyta is among the most abundant taxa in all analyzed BSCs suggesting that they were in a late successional stage. In terms of algal and cyanobacterial biodiversity, the genera Chloromonas, Coccomyxa, Elliptochloris and Nostoc were identified in all samples regardless of origin confirming their ubiquitous distribution. For the first time, we found the chrysophyte Spumella to be common in polar BSCs as it was present in all analyzed samples. Co-occurrence analysis revealed the presence of sulfur metabolizing microbes indicating that BSCs also play an important role for the sulfur cycle. In general, phototrophs were most abundant within the BSCs but there was also a diverse community of heterotrophs and saprotrophs. Our results show that BSCs are unique microecosystems in polar environments with an unexpectedly high biodiversity.
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Affiliation(s)
- Martin Rippin
- University of Cologne, Botanical Institute, Zülpicher Str. 47B, 50674 Cologne, Germany
| | - Sebastian Lange
- University of Cologne, Botanical Institute, Zülpicher Str. 47B, 50674 Cologne, Germany
| | - Nicole Sausen
- University of Cologne, Botanical Institute, Zülpicher Str. 47B, 50674 Cologne, Germany
| | - Burkhard Becker
- University of Cologne, Botanical Institute, Zülpicher Str. 47B, 50674 Cologne, Germany
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Usual alga from unusual habitats: Biodiversity of Klebsormidium (Klebsormidiophyceae, Streptophyta) from the phylogenetic superclade G isolated from biological soil crusts. Mol Phylogenet Evol 2018; 133:236-255. [PMID: 30576758 DOI: 10.1016/j.ympev.2018.12.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 12/10/2018] [Accepted: 12/13/2018] [Indexed: 01/13/2023]
Abstract
Seven new species and two varieties of Klebsormidium were described using an integrative approach on the base of 28 strains from the poorly studied phylogenetic superclade G. These strains originated from the unusual and exotic habitats (semi-deserts, semi-arid shrublands, Mediterranean shrub and deciduous vegetation, temperate Araucaria forests, peat bogs, dumps after coal mining, maritime sand dunes etc.) of four continents (Africa, South and North America, and Europe). Molecular phylogenies based on ITS-1,2, rbcL gene and concatenated dataset of ITS-1,2-rbcL, secondary structure of ITS-2, morphology, ecology and biogeography, micrographs and drawings of the investigated strains were assessed. Additionally, phylogeny and morphology of 18 Klebsormidium strains from other lineages isolated from the same localities (different vegetation types of Chile and maritime sand dunes of Germany) were investigated for the comparison with representatives of clade G. Clade G Klebsormidium is characterized by distant phylogenetic position from the other Klebsormidium lineages and prominent morphology: four-lobed chloroplasts and mostly short swollen cells in young culture, compact small pyrenoids, curved or disintegrated filaments, unusual elongation of cells in old culture, formation of specific cluster- and knot-like colonies on agar surface, especially prominent in strains isolated from desert regions, from which the group probably originated. Comparison of Klebsormidium diversity from different biogeographic regions showed that the representatives of clade G are common algae in regions of the southern hemisphere (South Africa and Chile) and rare representatives in terrestrial ecosystems of the northern hemisphere. Further investigation of mostly unstudied territories of the southern hemisphere could bring many surprises and discoveries, leading to a change of the present concept that Klebsormidium is cosmopolitan in distribution.
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Phylogeny and Classification of Novel Diversity in Sainouroidea (Cercozoa, Rhizaria) Sheds Light on a Highly Diverse and Divergent Clade. Protist 2018; 169:853-874. [DOI: 10.1016/j.protis.2018.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 01/08/2023]
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