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Yu M, Li W, He X, He G, Yao Y, Wang Y, Shao M, Xiong T, Xu H, Zhao J. Metabarcoding of protozoa and helminth in black-necked cranes: a high prevalence of parasites and free-living amoebae. Parasite 2024; 31:28. [PMID: 38819296 PMCID: PMC11141520 DOI: 10.1051/parasite/2024028] [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: 11/27/2023] [Accepted: 05/04/2024] [Indexed: 06/01/2024] Open
Abstract
Parasites and free-living amoebae (FLA) are common pathogens that pose threats to wildlife and humans. The black-necked crane (Grus nigricollis) is a near-threatened species and there is a shortage of research on its parasite diversity. Our study aimed to use noninvasive methods to detect intestinal parasites and pathogenic FLA in G. nigricollis using high-throughput sequencing (HTS) based on the 18S rDNA V9 region. A total of 38 fresh fecal samples were collected in Dashanbao, China, during the overwintering period (early-, middle I-, middle II-, and late-winter). Based on the 18S data, eight genera of parasites were identified, including three protozoan parasites: Eimeria sp. (92.1%) was the dominant parasite, followed by Tetratrichomonas sp. (36.8%) and Theileria sp. (2.6%). Five genera of helminths were found: Echinostoma sp. (100%), Posthodiplostomum sp. (50.0%), Euryhelmis sp. (26.3%), Eucoleus sp. (50.0%), and Halomonhystera sp. (2.6%). Additionally, eight genera of FLA were detected, including the known pathogens Acanthamoeba spp. (n = 13) and Allovahlkampfia spp. (n = 3). Specific PCRs were used to further identify the species of some parasites and FLA. Furthermore, the 18S data indicated significant changes in the relative abundance and genus diversity of the protozoan parasites and FLA among the four periods. These results underscore the importance of long-term monitoring of pathogens in black-necked cranes to protect this near-endangered species.
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Affiliation(s)
- Mengshi Yu
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Wenhao Li
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Xin He
- Sichuan Academy of Grassland Sciences Chengdu 610000 PR China
| | - Guiwen He
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University Zhaotong 657000 PR China
| | - Yonfang Yao
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Yuanjian Wang
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province Zhaotong 657000 Yunnan PR China
| | - Mingcui Shao
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province Zhaotong 657000 Yunnan PR China
| | - Tingsong Xiong
- Management Bureau of Dashanbao Black-Necked Crane National Nature Reserve, Yunnan Province Zhaotong 657000 Yunnan PR China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University Ya’an 625014 PR China
| | - Junsong Zhao
- College of Agronomy and Life Sciences, Zhaotong University Zhaotong 657000 PR China
- Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University Zhaotong 657000 PR China
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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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Wang Y, Kong J, Gu S, Huang B, Sun P. Dynamics of benthic microeukaryotic communities in a mangrove wetland invaded by Spartina alterniflora: Effects of vegetation, seasonality, and sediment depth. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170231. [PMID: 38246384 DOI: 10.1016/j.scitotenv.2024.170231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Benthic microeukaryotes are crucial mediators of biogeochemical cycles in coastal wetland ecosystems, yet their spatial and temporal variability remains poorly understood. This study delineates the diversity patterns of benthic microeukaryotes in a Spartina alterniflora-invaded mangrove ecosystem in Fujian, China. Using high-throughput sequencing of 18S rRNA gene transcripts, we identified the influences of vegetation, seasonality, and sediment depth on microeukaryotic communities. We discovered that vegetation cover significantly affects community composition, primarily driven by nutrient concentrations and pH. The community structure of microeukaryotes varied seasonally and vertically, correlating with changes in sediment temperature, pH, salinity, and fucoxanthin concentration. Notably, invasive Spartina alterniflora habitats showed enhanced heterotrophic interactions, suggesting that invasive species can reshape benthic microeukaryotic co-occurrence patterns. Seasonal co-occurrence patterns revealed dominant Bacillariophyta assemblages exhibited distinct network modules enriched in the cold (spring) and warm (summer and fall) seasons, respectively, which indicated potential ecological niche differentiation. Our findings reveal the complex relationships between environmental factors and benthic microeukaryotic diversity, offering insights into microbial responses to natural and invasive vegetation influences.
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Affiliation(s)
- Ying Wang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Jie Kong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Songsong Gu
- Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China
| | - Bangqin Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
| | - Ping Sun
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China.
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Fu Q, Qiu Y, Zhao J, Li J, Xie S, Liao Q, Fu X, Huang Y, Yao Z, Dai Z, Qiu Y, Yang Y, Li F, Chen H. Monotonic trends of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169351. [PMID: 38123079 DOI: 10.1016/j.scitotenv.2023.169351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Thus, we conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO), and marsh (MA) in the Altai region of Xinjiang, China. Our results showed that soil total carbon (TC), total nitrogen, NH4+, and NO3- increased, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. A shift in microbial community composition is evident along the soil moisture gradient, with Proteobacteria, Basidiomycota, and Evosea proliferating but a decline in Actinobacteria and Cercozoa. The β-diversity of microbiomes, metagenomic, and metabolomic functioning were correlated with soil moisture gradients and have significant associations with specific soil factors of TC, NH4+, and pH. Metagenomic functions associated with carbohydrate and DNA metabolisms, as well as phages, prophages, TE, plasmids functions diminished with moisture, whereas the genes involved in nitrogen and potassium metabolism, along with certain biological interactions and environmental information processing functions, demonstrated an augmentation. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules and organic oxygen compounds, except certain metabolites showing decline trends along water gradients, such as N'-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Thus, our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential, and metabolite fractions.
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Affiliation(s)
- Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiaxin Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Siqi Xie
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Qiuchang Liao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yu Huang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Furong Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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5
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Du J, Jia T, Liu J, Chai B. Relationships among protozoa, bacteria and fungi in polycyclic aromatic hydrocarbon-contaminated soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 270:115904. [PMID: 38181605 DOI: 10.1016/j.ecoenv.2023.115904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/16/2023] [Accepted: 12/27/2023] [Indexed: 01/07/2024]
Abstract
Soil bacterial and fungal communities play key roles in the degradation of organic contaminants, and their structure and function are regulated by bottom-up and top-down factors. Microbial ecological effects of polycyclic aromatic hydrocarbons (PAHs) and trophic interactions among protozoa and bacteria/fungi in PAH-polluted soils have yet to be determined. We investigated the trophic interactions and structure of the microbiome in PAH-contaminated wasteland and farmland soils. The results indicated that the total concentration of the 16 PAHs (∑PAHs) was significantly correlated with the Shannon index, NMDS1 and the relative abundances of bacteria, fungi and protozoa (e.g., Pseudofungi) in the microbiome. Structural equation modelling and linear fitting demonstrated cascading relationships among PAHs, protozoan and bacterial/fungal communities in terms of abundance and diversity. Notably, individual PAHs were significantly correlated with microbe-grazing protozoa at the genus level, and the abundances of these organisms were significantly correlated with those of PAH-degrading bacteria and fungi. Bipartite networks and linear fitting indicated that protozoa indirectly modulate PAH degradation by regulating PAH-degrading bacterial and fungal communities. Therefore, protozoa might be involved in regulating the microbial degradation of PAHs by predation in contaminated soil.
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Affiliation(s)
- Jingqi Du
- Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Institute of the Loess Plateau, Shanxi University, Taiyuan, China; Department of Life Sciences, Lyuliang University, Lyuliang, China
| | - Tong Jia
- Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Institute of the Loess Plateau, Shanxi University, Taiyuan, China
| | - Jinxian Liu
- Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Institute of the Loess Plateau, Shanxi University, Taiyuan, China
| | - Baofeng Chai
- Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Institute of the Loess Plateau, Shanxi University, Taiyuan, China.
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6
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Scheel M, Zervas A, Rijkers R, Tveit AT, Ekelund F, Campuzano Jiménez F, Christensen TR, Jacobsen CS. Abrupt permafrost thaw triggers activity of copiotrophs and microbiome predators. FEMS Microbiol Ecol 2023; 99:fiad123. [PMID: 37796894 PMCID: PMC10599396 DOI: 10.1093/femsec/fiad123] [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: 03/01/2023] [Revised: 08/31/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023] Open
Abstract
Permafrost soils store a substantial part of the global soil carbon and nitrogen. However, global warming causes abrupt erosion and gradual thaw, which make these stocks vulnerable to microbial decomposition into greenhouse gases. Here, we investigated the microbial response to abrupt in situ permafrost thaw. We sequenced the total RNA of a 1 m deep soil core consisting of up to 26 500-year-old permafrost material from an active abrupt erosion site. We analysed the microbial community in the active layer soil, the recently thawed, and the intact permafrost, and found maximum RNA:DNA ratios in recently thawed permafrost indicating a high microbial activity. In thawed permafrost, potentially copiotrophic Burkholderiales and Sphingobacteriales, but also microbiome predators dominated the community. Overall, both thaw-dependent and long-term soil properties significantly correlated with changes in community composition, as did microbiome predator abundance. Bacterial predators were dominated in shallower depths by Myxococcota, while protozoa, especially Cercozoa and Ciliophora, almost tripled in relative abundance in thawed layers. Our findings highlight the ecological importance of a diverse interkingdom and active microbial community highly abundant in abruptly thawing permafrost, as well as predation as potential biological control mechanism.
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Affiliation(s)
- Maria Scheel
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
- Department of Ecoscience, Aarhus University, Roskilde 4000, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
| | - Ruud Rijkers
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø 9019, Norway
| | - Flemming Ekelund
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
- Department of Biology, Copenhagen University, DK-2200 Copenhagen, Denmark
| | | | - Torben R Christensen
- Department of Ecoscience, Aarhus University, Roskilde 4000, Denmark
- Water, Energy and Environmental Engineering Research Unit, University of Oulu, FI-90014 Oulu, Finland
| | - Carsten S Jacobsen
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
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Topalović O, Bak F, Santos S, Sikder MM, Sapkota R, Ekelund F, Nicolaisen MH, Vestergård M. Activity of root-knot nematodes associated with composition of a nematode-attached microbiome and the surrounding soil microbiota. FEMS Microbiol Ecol 2023; 99:fiad091. [PMID: 37553158 DOI: 10.1093/femsec/fiad091] [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: 04/03/2023] [Revised: 06/20/2023] [Accepted: 08/07/2023] [Indexed: 08/10/2023] Open
Abstract
We investigated if activity of the pre-infective juveniles (J2s) of root-knot nematodes is linked to the recruitment of a specific microbiome on the nematode surface and/or to the composition of the surrounding microbiota. For this, we determined the J2 activity (active vs. non-motile, which referred to dead and immobile J2s) upon a 3-day incubation in soil suspensions and studied the composition of bacteria, protists, and fungi present on the nematode surface and in the suspensions using amplicon sequencing of the 16S/18S rRNA genes, and ITS region. We also amended suspensions with Pseudomonas protegens strain CHA0 to study its effects on J2 activity and microbial composition. The J2 activity was suppressed in soil suspensions, but increased when suspensions were amended with P. protegens CHA0. The active and non-motile J2s differed in the composition of surface-attached bacteria, which was altered by the presence of P. protegens CHA0 in the soil suspensions. The bacterial genera Algoriphagus, Pedobacter, and Bdellovibrio were enriched on active J2s and may have protected the J2s against antagonists. The incubation time appeared short for attachment of fungi and protists. Altogether, our study is a step forward in disentangling the complex nematode-microbe interactions in soil for more successful nematode control.
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Affiliation(s)
- Olivera Topalović
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark
- Department of Terrestrial Ecology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Frederik Bak
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Susana Santos
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark
| | - Md Maniruzzaman Sikder
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark
- Department of Botany, Faculty of Biological Sciences, Jahangirnagar University, 1342 Savar, Dhaka, Bangladesh
| | - Rumakanta Sapkota
- Department of Environmental Science, Faculty of Technical Sciences, Aarhus University, 4000 Roskilde, Denmark
| | - Flemming Ekelund
- Department of Terrestrial Ecology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Mette Haubjerg Nicolaisen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Mette Vestergård
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, 4200 Slagelse, Denmark
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Li S, Ren K, Yan X, Tsyganov AN, Mazei Y, Smirnov A, Mazei N, Zhang Y, Rensing C, Yang J. Linking biodiversity and ecological function through extensive microeukaryotic movement across different habitats in six urban parks. IMETA 2023; 2:e103. [PMID: 38868434 PMCID: PMC10989963 DOI: 10.1002/imt2.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/08/2023] [Accepted: 03/22/2023] [Indexed: 06/14/2024]
Abstract
Highly diverse but divergent microeukaryotes dwell in all types of habitats in urban park ecosystems. Extensive microbial migration occurs between both terrestrial and aquatic habitats. Microbial movement is beneficial to the maintenance of biodiversity and the exchange of functional guilds.
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Affiliation(s)
- Shuzhen Li
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
| | - Kexin Ren
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
| | - Xue Yan
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Yuri Mazei
- Lomonosov Moscow State UniversityMoscowRussia
- Faculty of BiologyShenzhen MSU‐BIT UniversityShenzhenChina
- A. N. Severtsov Institute of Ecology and EvolutionRussian Academy of SciencesMoscowRussia
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of BiologySt. Petersburg UniversitySt. PetersburgRussia
| | | | - Yiyue Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
| | - Christopher Rensing
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
- Institute of Environmental Microbiology, College of Resources and the EnvironmentFujian Agriculture & Forestry UniversityFuzhouChina
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed EcologyInstitute of Urban Environment, Chinese Academy of SciencesXiamenChina
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9
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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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Kalu EI, Reyes-Prieto A, Barbeau MA. Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy. ISME COMMUNICATIONS 2023; 3:21. [PMID: 36918616 PMCID: PMC10014957 DOI: 10.1038/s43705-023-00226-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
Protists (microbial eukaryotes) are a critically important but understudied group of microorganisms. They are ubiquitous, represent most of the genetic and functional diversity among eukaryotes, and play essential roles in nutrient and energy cycling. Yet, protists remain a black box in marine sedimentary ecosystems like the intertidal mudflats in the Bay of Fundy. The harsh conditions of the intertidal zone and high energy nature of tides in the Bay of Fundy provide an ideal system for gaining insights into the major food web players, diversity patterns and potential structuring influences of protist communities. Our 18S rDNA metabarcoding study quantified seasonal variations and vertical stratification of protist communities in Bay of Fundy mudflat sediments. Three 'SAR' lineages were consistently dominant (in terms of abundance, richness, and prevalence), drove overall community dynamics and formed the core microbiome in sediments. They are Cercozoa (specifically thecate, benthic gliding forms), Bacillariophyta (mainly cosmopolitan, typically planktonic diatoms), and Dinophyceae (dominated by a toxigenic, bloom-forming species). Consumers were the dominant trophic functional group and were comprised mostly of eukaryvorous and bacterivorous Cercozoa, and omnivorous Ciliophora, while phototrophs were dominated by Bacillariophyta. The codominance of Apicomplexa (invertebrate parasites) and Syndiniales (protist parasites) in parasite assemblages, coupled with broader diversity patterns, highlighted the combined marine and terrestrial influences on microbial communities inhabiting intertidal sediments. Our findings, the most comprehensive in a hypertidal benthic system, suggest that synergistic interactions of both local and regional processes (notably benthic-pelagic coupling) may drive heterogenous microbial distribution in high-energy coastal systems.
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Affiliation(s)
- Eke I Kalu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada.
| | | | - Myriam A Barbeau
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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11
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Lv Z, Xu M, Liu Y, Rønn R, Rensing C, Liu S, Gao S, Liao H, Liu YR, Chen W, Zhu YG, Huang Q, Hao X. Phagotrophic Protists Modulate Copper Resistance of the Bacterial Community in Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:3590-3601. [PMID: 36811608 DOI: 10.1021/acs.est.2c07136] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Protist predation is a crucial biotic driver modulating bacterial populations and functional traits. Previous studies using pure cultures have demonstrated that bacteria with copper (Cu) resistance exhibited fitness advantages over Cu-sensitive bacteria under the pressure of protist predation. However, the impact of diverse natural communities of protist grazers on bacterial Cu resistance in natural environments remains unknown. Here, we characterized the communities of phagotrophic protists in long-term Cu-contaminated soils and deciphered their potential ecological impacts on bacterial Cu resistance. Long-term field Cu pollution increased the relative abundances of most of the phagotrophic lineages in Cercozoa and Amoebozoa but reduced the relative abundance of Ciliophora. After accounting for soil properties and Cu pollution, phagotrophs were consistently identified as the most important predictor of the Cu-resistant (CuR) bacterial community. Phagotrophs positively contributed to the abundance of a Cu resistance gene (copA) through influencing the cumulative relative abundance of Cu-resistant and -sensitive ecological clusters. Microcosm experiments further confirmed the promotion effect of protist predation on bacterial Cu resistance. Our results indicate that the selection by protist predation can have a strong impact on the CuR bacterial community, which broadens our understanding of the ecological function of soil phagotrophic protists.
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Affiliation(s)
- Zhenguang Lv
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Regin Rønn
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Song Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shenghan Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Liao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan 430070, China
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12
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About the Analysis of 18S rDNA Sequence Data from Trypanosomes in Barcoding and Phylogenetics: Tracing a Continuation Error Occurring in the Literature. BIOLOGY 2022; 11:biology11111612. [DOI: 10.3390/biology11111612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
The variable regions (V1–V9) of the 18S rDNA are routinely used in barcoding and phylogenetics. In handling these data for trypanosomes, we have noticed a misunderstanding that has apparently taken a life of its own in the literature over the years. In particular, in recent years, when studying the phylogenetic relationship of trypanosomes, the use of V7/V8 was systematically established. However, considering the current numbering system for all other organisms (including other Euglenozoa), V7/V8 was never used. In Maia da Silva et al. [Parasitology 2004, 129, 549–561], V7/V8 was promoted for the first time for trypanosome phylogenetics, and since then, more than 70 publications have replicated this nomenclature and even discussed the benefits of the use of this region in comparison to V4. However, the primers used to amplify the variable region of trypanosomes have actually amplified V4 (concerning the current 18S rDNA numbering system).
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13
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Lee HB, Jeong DH, Cho BC, Park JS. The Diversity Patterns of Rare to Abundant Microbial Eukaryotes Across a Broad Range of Salinities in a Solar Saltern. MICROBIAL ECOLOGY 2022; 84:1103-1121. [PMID: 34779881 PMCID: PMC9747883 DOI: 10.1007/s00248-021-01918-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Solar salterns are excellent artificial systems for examining species diversity and succession along salinity gradients. Here, the eukaryotic community in surface water of a Korean solar saltern (30 to 380 practical salinity units) was investigated from April 2019 to October 2020 using Illumina sequencing targeting the V4 and V9 regions of 18S rDNA. A total of 926 operational taxonomic units (OTUs) and 1,999 OTUs were obtained with the V4 and V9 regions, respectively. Notably, most of the OTUs were microbial eukaryotes, and the high-abundance groups (> 5% relative abundance (RA), Alveolata, Stramenopila, Archaeplastida, and Opisthokonta) usually accounted for > 90% of the total cumulative read counts and > 80% of all OTUs. Moreover, the high-abundance Alveolata (larger forms) and Stramenopila (smaller forms) groups displayed a significant inverse relationship, probably due to predator-prey interactions. Most of the low-abundance (0.1-5% RA) and rare (< 0.1% RA) groups remained small portion during the field surveys. Taxonomic novelty (at < 90% sequence identity) was high in the Amoebozoa, Cryptista, Haptista, Rhizaria, and Stramenopila groups (69.8% of all novel OTUs), suggesting the presence of a large number of hidden species in hypersaline environments. Remarkably, the high-abundance groups had little overlap with the other groups, implying the weakness of rare-to-prevalent community dynamics. The low-abundance Discoba group alone temporarily became the high-abundance group, suggesting that it is an opportunistic group. Overall, the composition and diversity of the eukaryotic community in hypersaline environments may be persistently stabilized, despite diverse disturbance events.
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Affiliation(s)
- Hyeon Been Lee
- Department of Oceanography, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Dong Hyuk Jeong
- Department of Oceanography, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Byung Cheol Cho
- School of Earth and Environmental Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Saemangeum Environmental Research Center, Kunsan National University, Kunsan, 54150, Republic of Korea
| | - Jong Soo Park
- Department of Oceanography, Kyungpook National University, Daegu, 41566, Republic of Korea.
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14
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Briddon CL, Szekeres E, Hegedüs A, Nicoară M, Chiriac C, Stockenreiter M, Drugă B. The combined impact of low temperatures and shifting phosphorus availability on the competitive ability of cyanobacteria. Sci Rep 2022; 12:16409. [PMID: 36180771 PMCID: PMC9525609 DOI: 10.1038/s41598-022-20580-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
In freshwater systems, cyanobacteria are strong competitors under enhanced temperature and eutrophic conditions. Understanding their adaptive and evolutionary potential to multiple environmental states allows us to accurately predict their response to future conditions. To better understand if the combined impacts of temperature and nutrient limitation could suppress the cyanobacterial blooms, a single strain of Microcystis aeruginosa was inoculated into natural phytoplankton communities with different nutrient conditions: oligotrophic, eutrophic and eutrophic with the addition of bentophos. We found that the use of the bentophos treatment causes significant differences in prokaryotic and eukaryotic communities. This resulted in reduced biodiversity among the eukaryotes and a decline in cyanobacterial abundance suggesting phosphorus limitation had a strong impact on the community structure. The low temperature during the experiment lead to the disappearance of M. aeruginosa in all treatments and gave other phytoplankton groups a competitive advantage leading to the dominance of the eukaryotic families that have diverse morphologies and nutritional modes. These results show cyanobacteria have a reduced competitive advantage under certain temperature and nutrient limiting conditions and therefore, controlling phosphorus concentrations could be a possible mitigation strategy for managing harmful cyanobacterial blooms in a future warmer climate.
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Affiliation(s)
- Charlotte L Briddon
- Institute of Biological Research (NIRDBS), 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Edina Szekeres
- Institute of Biological Research (NIRDBS), 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Adriana Hegedüs
- Institute of Biological Research (NIRDBS), 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Maria Nicoară
- Institute of Biological Research (NIRDBS), 48 Republicii Street, 400015, Cluj-Napoca, Romania
| | - Cecilia Chiriac
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, 37005, České Budějovice, Czech Republic
| | - Maria Stockenreiter
- Department of Biology II, Experimental Aquatic Ecology, Ludwig-Maximilians-Universitӓt Müchen, Groβhaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Bogdan Drugă
- Institute of Biological Research (NIRDBS), 48 Republicii Street, 400015, Cluj-Napoca, Romania.
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15
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Ma G, Logares R, Xue Y, Yang J. Does filter pore size introduce bias in DNA sequence-based plankton community studies? Front Microbiol 2022; 13:969799. [PMID: 36225356 PMCID: PMC9549009 DOI: 10.3389/fmicb.2022.969799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
The cell size of microbial eukaryotic plankton normally ranges from 0.2 to 200 μm. During the past decade, high-throughput sequencing of DNA has been revolutionizing their study on an unprecedented scale. Nonetheless, it is currently unclear whether we can accurately, effectively, and quantitatively depict the microbial eukaryotic plankton community using size-fractionated filtration combined with environmental DNA (eDNA) molecular methods. Here we assessed the microbial eukaryotic plankton communities with two filtering strategies from two subtropical reservoirs, that is one-step filtration (0.2–200 μm) and size-fractionated filtration (0.2–3 and 3–200 μm). The difference of 18S rRNA gene copy abundance between the two filtering treatments was less than 50% of the 0.2–200 μm microbial eukaryotic community for 95% of the total samples. Although the microbial eukaryotic plankton communities within the 0.2–200 μm and the 0.2–3 and 3–200 μm size fractions had approximately identical 18S rRNA gene copies, there were significant differences in their community composition. Furthermore, our results demonstrate that the systemic bias introduced by size-fractionation filtration has more influence on unique OTUs than shared OTUs, and the significant differences in abundance between the two eukaryotic plankton communities largely occurred in low-abundance OTUs in specific seasons. This work provides new insights into the use of size-fractionation in molecular studies of microbial eukaryotes populating the plankton.
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Affiliation(s)
- Guolin Ma
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Ningbo Observation and Research Station, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Yuanyuan Xue
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Ningbo Observation and Research Station, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
- *Correspondence: Yuanyuan Xue,
| | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Ningbo Observation and Research Station, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo, China
- Jun Yang,
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16
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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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17
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Bazany KE, Wang JT, Delgado-Baquerizo M, Singh BK, Trivedi P. Water deficit affects inter-kingdom microbial connections in plant rhizosphere. Environ Microbiol 2022; 24:3722-3734. [PMID: 35582745 PMCID: PMC9545320 DOI: 10.1111/1462-2920.16031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/03/2022]
Abstract
The frequency and severity of drought are increasing due to anthropogenic climate change and are already limiting cropping system productivity in many regions around the world. Few microbial groups within plant microbiomes can potentially contribute towards the fitness and productivity of their hosts under abiotic stress events including water deficits. However, microbial communities are complex and integrative work considering the multiple co-existing groups of organisms is needed to better understand how the entire microbiome responds to environmental stresses. We hypothesize that water deficit stress will differentially shape bacterial, fungal, and protistan microbiome composition and influence inter-kingdom microbial interactions in the rhizospheres of corn and sugar beet. We used amplicon sequencing to profile bacterial, fungal, and protistan communities in corn and sugar beet rhizospheres grown under irrigated and water deficit conditions. The water deficit treatment had a stronger influence than host species on bacterial composition, whereas the opposite was true for protists. These results indicate that different microbial kingdoms have variable responses to environmental stress and host factors. Water deficit also influenced intra- and inter-kingdom microbial associations, wherein the protist taxa formed a separate cluster under water deficit conditions. Our findings help elucidate the influence of environmental and host drivers of bacterial, fungal, and protistan community assembly and co-occurrence in agricultural rhizosphere environments.
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Affiliation(s)
- Kathryn E Bazany
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Jun-Tao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia.,State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - 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
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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18
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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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19
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Jauss RT, Nowack A, Walden S, Wolf R, Schaffer S, Schellbach B, Bonkowski M, Schlegel M. To the canopy and beyond: Air dispersal as a mechanism of ubiquitous protistan pathogen assembly in tree canopies. Eur J Protistol 2021; 80:125805. [PMID: 34090087 DOI: 10.1016/j.ejop.2021.125805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 01/19/2023]
Abstract
Cercozoa and Oomycota contain a huge biodiversity and important pathogens of forest trees and other vegetation. We analyzed air dispersal of these protistan phyla with an air sampler near-ground (~2 m) and in tree crowns (~25 m) of three tree species (oak, linden and ash) in a temperate floodplain forest in March (before leafing) and May (after leaf unfolding) 2019 with a cultivation-independent high-throughput metabarcoding approach. We found a high diversity of Cercozoa and Oomycota in air samples with 122 and 81 OTUs, respectively. Especially oomycetes showed a significant difference in community composition between both sampling dates. Differences in community composition between air samples in tree canopies and close to the ground were however negligible, and also tree species identity did not affect communities in air samples, indicating that the distribution of protistan propagules through the air was not spatially restricted in the forest ecosystem. OTUs of plant pathogens, whose host species did not occur in the forest, demonstrate dispersal of propagules from outside the forest biome. Overall, our results lead to a better understanding of the stochastic processes of air dispersal of protists and protistan pathogens, a prerequisite to understand the mechanisms of their community assembly in forest ecosystems.
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Affiliation(s)
- Robin-Tobias Jauss
- University of Leipzig, Institute of Biology, Biodiversity and Evolution, Talstraße 33, 04103 Leipzig, Germany.
| | - Anne Nowack
- University of Leipzig, Institute of Biology, Biodiversity and Evolution, Talstraße 33, 04103 Leipzig, Germany
| | - Susanne Walden
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Ronny Wolf
- University of Leipzig, Institute of Biology, Molecular Evolution & Animal Systematics, Talstraße 33, 04103 Leipzig, Germany
| | - Stefan Schaffer
- University of Leipzig, Institute of Biology, Molecular Evolution & Animal Systematics, Talstraße 33, 04103 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
| | - Barbara Schellbach
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Michael Bonkowski
- University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Martin Schlegel
- University of Leipzig, Institute of Biology, Biodiversity and Evolution, Talstraße 33, 04103 Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
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20
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Meisner A, Snoek BL, Nesme J, Dent E, Jacquiod S, Classen AT, Priemé A. Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles. THE ISME JOURNAL 2021; 15:1207-1221. [PMID: 33408369 PMCID: PMC8115648 DOI: 10.1038/s41396-020-00844-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.
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Affiliation(s)
- Annelein Meisner
- grid.4514.40000 0001 0930 2361Microbial Ecology, Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden ,grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.418375.c0000 0001 1013 0288Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Present Address: Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, The Netherlands
| | - Basten L. Snoek
- grid.5477.10000000120346234Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Joseph Nesme
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Elizabeth Dent
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Samuel Jacquiod
- grid.5613.10000 0001 2298 9313Agroécologie, AgroSup Dijon, INRAE Centre Dijon, Université de Bourgogne Franche-Comté, Dijon, France
| | - Aimée T. Classen
- grid.214458.e0000000086837370Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, MI 48109 USA ,grid.59062.380000 0004 1936 7689The Gund Institute for Environment, University of Vermont, Burlington, VT USA ,grid.5254.60000 0001 0674 042XThe Center for Macroecology, Evolution and Climate, The University of Copenhagen, Copenhagen Ø, Denmark
| | - Anders Priemé
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, 1350 Copenhagen, Denmark
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21
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Ohore OE, Zhang S, Guo S, Addo FG, Manirakiza B, Zhang W. Ciprofloxacin increased abundance of antibiotic resistance genes and shaped microbial community in epiphytic biofilm on Vallisneria spiralis in mesocosmic wetland. BIORESOURCE TECHNOLOGY 2021; 323:124574. [PMID: 33412499 DOI: 10.1016/j.biortech.2020.124574] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
This study investigated the fate of ciprofloxacin (CIP) in wetlands dominated by Vallisneria spiralis. About 99% of CIP was degraded from overlaying water within 4 days of treatment but significantly inhibited the nutrient removal capacity (TN, TP, and COD) by causing a drastic reduction in microbial aggregation in epiphytic biofilm and bacterial biodiversity. CIP triggered resistance mechanisms among dominant bacteria phyla such as Proteobacteria, Actinobacteria, and Planctomycetes causing their increased relative abundance. Additionally, the relative abundances of eukaryotic microorganisms (including; Chloroplastida, Metazoa, and Rhizaria) and 13 ARGs subtypes (including; Efflux pump, Tetracycline, Multi-drug, Rifampin, Beta-lactam, Peptide, Trimethoprim) were significantly increased. While dominant metabolic pathways such as Carbohydrate, amino acid, energy and nucleotide metabolism were inhibited. This study revealed that V. spiralis has great sorption capacity for CIP than sediment and though CIP was effectively removed from the overlying water, it caused a prolonged effect on the epiphytic biofilm microbial communities.
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Affiliation(s)
- Okugbe Ebiotubo Ohore
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China.
| | - Shaozhuang Guo
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Felix Gyawu Addo
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Benjamin Manirakiza
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China; University of Rwanda (UR), College of Science and Technology (CST), Department of Biology, P.O. Box 3900, Kigali, Rwanda
| | - Wenjun Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
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22
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Liu Y, Li Y, Pan B, Zhang X, Zhang H, Steinberg CEW, Qiu H, Vijver MG, Peijnenburg WJGM. Application of low dosage of copper oxide and zinc oxide nanoparticles boosts bacterial and fungal communities in soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 757:143807. [PMID: 33288254 DOI: 10.1016/j.scitotenv.2020.143807] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 06/12/2023]
Abstract
With the expanding nanotechnology, nanoparticles (NPs) embedded products are used in the agricultural sector to improve soil fertility. Thus, two typical metal oxides NPs and their mixtures were applied in different doses to evaluate the impacts on soil microbes. CuO and ZnO NPs boosted soil microbial communities as reflected by the increased number of extractable bacterial or fungal groups and the enlarged values of Chao 1, ACE, and Shannon indices. Relative abundance of some susceptible taxa such as Sphingomonadales increased with increasing concentrations of ZnO NPs, while IMCC26256 decreased with increasing concentrations of CuO NPs. The mixture of CuO and ZnO NPs did not show more promotional effects on the soil bacterial community than the sum of individual effects. Increased soil organic carbon mitigated the impacts on soil bacteria for CuO NPs, but not for ZnO NPs. As micro-nutrients, the ions released from CuO and ZnO NPs had the potential to promote soil microbial community richness and diversity. However, the positive impacts of MNPs were impaired at dosage higher than 250 mg kg-1 soil (213.08 mg kg-1 soil of Cu, 162.73 mg kg-1 soil of Zn). Thus, the application dose and soil type other than the coexistence of MNPs should be considered before the wide use in increasing agricultural productivity.
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Affiliation(s)
- Yang Liu
- Yunnan Provincial Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Yang Li
- Yunnan Provincial Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Bo Pan
- Yunnan Provincial Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China.
| | - Xinyue Zhang
- Yunnan Provincial Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China
| | - Huang Zhang
- Faculty of Agriculture and Food, Kunming University of Science and Technology, Kunming 650500, China
| | - Christian E W Steinberg
- Yunnan Provincial Key Laboratory of Soil Carbon Sequestration and Pollution Control, Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; Institute of Biology, Freshwater & Stress Ecology, Humboldt University, Berlin 12437, Germany
| | - Hao Qiu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Martina G Vijver
- Institute of Environmental Sciences (CML), Leiden University, Leiden 2300, RA, the Netherlands
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, Leiden 2300, RA, the Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, Bilthoven 3720 BA, the Netherlands
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23
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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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24
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Choe YH, Kim M, Lee YK. Distinct Microbial Communities in Adjacent Rock and Soil Substrates on a High Arctic Polar Desert. Front Microbiol 2021; 11:607396. [PMID: 33488547 PMCID: PMC7819959 DOI: 10.3389/fmicb.2020.607396] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/08/2020] [Indexed: 01/04/2023] Open
Abstract
Understanding microbial niche variability in polar regions can provide insights into the adaptive diversification of microbial lineages in extreme environments. Compositions of microbial communities in Arctic soils are well documented but a comprehensive multidomain diversity assessment of rocks remains insufficiently studied. In this study, we obtained two types of rocks (sandstone and limestone) and soils around the rocks in a high Arctic polar desert (Svalbard), and examined the compositions of archaeal, bacterial, fungal, and protistan communities in the rocks and soils. The microbial community structure differed significantly between rocks and soils across all microbial groups at higher taxonomic levels, indicating that Acidobacteria, Gemmatimonadetes, Latescibacteria, Rokubacteria, Leotiomycetes, Pezizomycetes, Mortierellomycetes, Sarcomonadea, and Spirotrichea were more abundant in soils, whereas Cyanobacteria, Deinococcus-Thermus, FBP, Lecanoromycetes, Eurotiomycetes, Trebouxiophyceae, and Ulvophyceae were more abundant in rocks. Interestingly, fungal communities differed markedly between two different rock types, which is likely to be ascribed to the predominance of distinct lichen-forming fungal taxa (Verrucariales in limestone, and Lecanorales in sandstone). This suggests that the physical or chemical properties of rocks could be a major determinant in the successful establishment of lichens in lithic environments. Furthermore, the biotic interactions among microorganisms based on co-occurrence network analysis revealed that Polyblastia and Verrucaria in limestone, and Atla, Porpidia, and Candelariella in sandstone play an important role as keystone taxa in the lithic communities. Our study shows that even in niches with the same climate regime and proximity to each other, heterogeneity of edaphic and lithic niches can affect microbial community assembly, which could be helpful in comprehensively understanding the effects of niche on microbial assembly in Arctic terrestrial ecosystems.
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Affiliation(s)
- Yong-Hoe Choe
- Korea Polar Research Institute, Incheon, South Korea
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon, South Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon, South Korea
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25
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Gu R, Sun P, Wang Y, Yu F, Jiao N, Xu D. Genetic Diversity, Community Assembly, and Shaping Factors of Benthic Microbial Eukaryotes in Dongshan Bay, Southeast China. Front Microbiol 2020; 11:592489. [PMID: 33424795 PMCID: PMC7785585 DOI: 10.3389/fmicb.2020.592489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/27/2020] [Indexed: 11/28/2022] Open
Abstract
Microbial eukaryotes are pivotal components of marine ecosystems. However, compared with the pelagic environments, the diversity distribution and the driving mechanisms of microbial eukaryotes in the marine sediments have rarely been explored. In this study, sediment cores were collected along a transect from inner to outer Dongshan Bay, Southeast China. By combining high throughput sequencing of small-subunit (SSU) rRNA gene with measurements on multiple environmental variables, the genetic diversity, community structure and assembly processes, and environmental shaping factors were investigated. Alveolata (mainly Ciliophora and Dinophyceae), Rhizaria (mainly Cercozoa), and Stramenopiles (mainly Bacillariophyta) were the most dominant groups in terms of both relative sequence abundance and operational taxonomic unit (OTU) richness. Grain size composition of the sediment was the primary factor determining the alpha diversity of microbial eukaryotes followed by sediment depth and heavy metal, including chromium (Cr), zinc (Zn), and plumbum (Pb). Geographic distance and water depth surpassed other environmental factors to be the primary factors shaping the microbial eukaryotic communities. Dispersal limitation was the primary driver of the microbial eukaryotic communities, followed by drift and homogeneous selection. Overall, our study shed new light on the spatial distribution patterns and controlling factors of benthic microbial eukaryotes in a subtropical bay which is subjected to increasing anthropogenic pressure.
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Affiliation(s)
- Rong Gu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Ping Sun
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen, China
| | - Ying Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Fengling Yu
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Dapeng Xu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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26
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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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27
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Lara E, Dumack K, García-Martín JM, Kudryavtsev A, Kosakyan A. Amoeboid protist systematics: A report on the "Systematics of amoeboid protists" symposium at the VIIIth ECOP/ISOP meeting in Rome, 2019. Eur J Protistol 2020; 76:125727. [PMID: 32755801 DOI: 10.1016/j.ejop.2020.125727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/22/2020] [Accepted: 06/25/2020] [Indexed: 01/21/2023]
Abstract
Amoeboid protists are extremely abundant and diverse in natural systems where they often play outstanding ecological roles. They can be found in almost all major eukaryotic divisions, and genomic approaches are bringing major changes in our perception of their deep evolutionary relationships. At fine taxonomic levels, the generalization of barcoding is revealing a considerable and unsuspected specific diversity that can be appreciated with careful morphometric analyses based on light and electron microscopic observations. We provide examples on the difficulties and advances in amoeboid protists systematics in a selection of groups that were presented at the VIIIth ECOP/ISOP meeting in Rome, 2019. We conclude that, in all studied groups, important taxonomical rearrangements will certainly take place in the next few years, and systematics must be adapted to incorporate these changes. Notably, nomenclature should be flexible enough to integrate many new high level taxa, and a unified policy must be adopted to species description and to the establishment of types.
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Affiliation(s)
- Enrique Lara
- Real Jardín Botánico de Madrid, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain.
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | | | - Alexander Kudryavtsev
- Laboratory of Cellular and Molecular Protistology, Zoological Institute of the Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint-Petersburg, Russia; Department of Invertebrate Zoology, Faculty of Biology, Saint-Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint-Petersburg, Russia
| | - Anush Kosakyan
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice, Czech Republic
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28
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Bugge Harder C, Nyrop Albers C, Rosendahl S, Aamand J, Ellegaard-Jensen L, Ekelund F. Successional trophic complexity and biogeographical structure of eukaryotic communities in waterworks' rapid sand filters. FEMS Microbiol Ecol 2020; 95:5569652. [PMID: 31518408 DOI: 10.1093/femsec/fiz148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/12/2019] [Indexed: 11/13/2022] Open
Abstract
As groundwater-fed waterworks clean their raw inlet water with sand filters, a variety of pro- and eukaryotic microbial communities develop on these filters. While several studies have targeted the prokaryotic sand filter communities, little is known about the eukaryotic communities, despite the obvious need for knowledge of microorganisms that get in contact with human drinking water. With a new general eukaryotic primer set (18S, V1-V3 region), we performed FLX-454 sequencing of material from 21 waterworks' sand filters varying in age (3-40 years) and geographical location on a 250 km east-west axis in Denmark, and put the data in context of their previously published prokaryotic communities. We find that filters vary highly in trophic complexity depending on age, from simple systems with bacteria and protozoa (3-6 years) to complex, mature systems with nematodes, rotifers and turbellarians as apex predators (40 years). Unlike the bacterial communities, the eukaryotic communities display a clear distance-decay relationship that predominates over environmental variations, indicating that the underlying aquifers feeding the filters harbor distinct eukaryotic communities with limited dispersal in between. Our findings have implications for waterworks' filter management, and offer a window down to the largely unexplored eukaryotic microbiology of groundwater aquifers.
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Affiliation(s)
- Christoffer Bugge Harder
- Department of Biology, Copenhagen University, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark.,Department of Biology, Microbial Ecology Group, Lund University, Ecology Building, Solvegatan 37, SE 223-62, Lund, Sweden.,Department of Plant and Soil Science, Texas Tech University, Bayer Plant Science Building, 2911 15th Street, Lubbock, TX 79409, USA
| | - Christian Nyrop Albers
- Department of Geochemistry, Geological Survey of Denmark & Greenland, Ø Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Søren Rosendahl
- Department of Biology, Copenhagen University, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Jens Aamand
- Department of Geochemistry, Geological Survey of Denmark & Greenland, Ø Voldgade 10, DK-1350, Copenhagen, Denmark
| | - Lea Ellegaard-Jensen
- Department of Geochemistry, Geological Survey of Denmark & Greenland, Ø Voldgade 10, DK-1350, Copenhagen, Denmark.,Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Flemming Ekelund
- Department of Biology, Copenhagen University, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
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29
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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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30
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Choi J, Park JS. Comparative analyses of the V4 and V9 regions of 18S rDNA for the extant eukaryotic community using the Illumina platform. Sci Rep 2020; 10:6519. [PMID: 32300168 PMCID: PMC7162856 DOI: 10.1038/s41598-020-63561-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Illumina sequencing is a representative tool for understanding the massive diversity of microbial eukaryotes in natural ecosystems. Here, we investigated the eukaryotic community in a pond (salinity of 2–4) on Dokdo (island) in the East Sea, Korea, using Illumina sequencing with primer sets for the V4 and V9 regions of 18S rDNA from 2016 to 2018 for the first time. Totally, 1,413 operational taxonomic units (OTUs) and 915 OTUs were detected using the V9 and V4 primer sets, respectively. Taxonomic analyses of these OTUs revealed that although the V4 primer set failed to describe the extant diversity for some major sub-division groups, the V9 primer set represented their diversity. Moreover, the rare taxa with <1% of total reads were exclusively detected using V9 primer set. Hence, the diversity of the eukaryotic community can vary depending on the choice of primers. The Illumina sequencing data of the V9 region of 18S rDNA may be advantageous for estimating the richness of the eukaryotic community including a rare biosphere, whereas the simultaneous application of two biomarkers may be suitable for understanding the molecular phylogenetic relationships. We strongly recommend both biomarkers be used to assess the diversity and phylogenetic relationship within the eukaryotic community in natural samples.
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Affiliation(s)
- Jaeho Choi
- Department of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jong Soo Park
- Department of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, 41566, Republic of Korea. .,Kyungpook Institute of Oceanography, Kyungpook National University, Daegu, 41566, Republic of Korea.
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Suleiman AKA, Harkes P, van den Elsen S, Holterman M, Korthals GW, Helder J, Kuramae EE. Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133885. [PMID: 31756853 DOI: 10.1016/j.scitotenv.2019.133885] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/25/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial-microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.
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Affiliation(s)
- Afnan K A Suleiman
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands.
| | - Paula Harkes
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Sven van den Elsen
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Martijn Holterman
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Gerard W Korthals
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands; Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Johannes Helder
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands.
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The disappearing periglacial ecosystem atop Mt. Kilimanjaro supports both cosmopolitan and endemic microbial communities. Sci Rep 2019; 9:10676. [PMID: 31337772 PMCID: PMC6650471 DOI: 10.1038/s41598-019-46521-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 06/18/2019] [Indexed: 11/08/2022] Open
Abstract
Microbial communities have not been studied using molecular approaches at high elevations on the African continent. Here we describe the diversity of microbial communities from ice and periglacial soils from near the summit of Mt. Kilimanjaro by using both Illumina and Sanger sequencing of 16S and 18S rRNA genes. Ice and periglacial soils contain unexpectedly diverse and rich assemblages of Bacteria and Eukarya indicating that there may be high rates of dispersal to the top of this tropical mountain and/or that the habitat is more conducive to microbial life than was previously thought. Most bacterial OTUs are cosmopolitan and an analysis of isolation by geographic distance patterns of the genus Polaromonas emphasized the importance of global Aeolian transport in the assembly of bacterial communities on Kilimanjaro. The eukaryotic communities were less diverse than the bacterial communities and showed more evidence of dispersal limitations and apparent endemism. Cercozoa dominated the 18S communities, including a high abundance of testate amoebae and a high diversity of endemic OTUs within the Vampyrellida. These results argue for more intense study of this unique high-elevation "island of the cryosphere" before the glaciers of Kilimanjaro disappear forever.
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Patterns of protist diversity associated with raw sewage in New York City. ISME JOURNAL 2019; 13:2750-2763. [PMID: 31289345 PMCID: PMC6794324 DOI: 10.1038/s41396-019-0467-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/28/2019] [Accepted: 06/07/2019] [Indexed: 12/31/2022]
Abstract
Protists are ubiquitous components of terrestrial and aquatic environments, as well as animal and human microbiomes. Despite this, little is known about protists in urban environments. The ~7400-mile sewer system of New York City (NYC) collects human waste from ~8 million human inhabitants as well as from animals, street runoff, and groundwater, providing an ideal system to study these microbes. We used 18S rRNA amplicon sequencing and shotgun metagenomic sequencing to profile raw sewage microbial communities. Raw sewage samples were collected over a 12-month period from 14 treatment plants of the five NYC boroughs, and compared with samples from other environments including soil, stormwater, and sediment. Sewage contained a diverse protist community dominated by free-living clades, and communities were highly differentiated across environments. Seasonal differences in protist composition were observed; however, network analysis and functional profiling demonstrated that sewage communities were robust and functionally consistent. Protists typically associated with human and animal guts or feces were frequently detected. Abundance of these parasites varied significantly both spatially and temporally, suggesting that spikes could reflect trends in the source population. This underscores sewage as a valuable model system for monitoring patterns in urban microbes and provides a baseline protist metagenome of NYC.
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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: 42] [Impact Index Per Article: 8.4] [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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Huang Y, Huang J. Coupled effects of land use pattern and hydrological regime on composition and diversity of riverine eukaryotic community in a coastal watershed of Southeast China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 660:787-798. [PMID: 30743964 DOI: 10.1016/j.scitotenv.2019.01.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/14/2018] [Accepted: 01/06/2019] [Indexed: 06/09/2023]
Abstract
The coupled effects of land use pattern and hydrological regime on composition and diversity of riverine eukaryotic community are needed for understanding riverine ecosystem health and algal blooming mechanism. In-situ monitoring and 18S rRNA gene sequencing were used to investigate spatiotemporal variations of eukaryotic community in three types of watershed with different dominant land use type (i.e. urban, forest, and natural) during three seasons (i.e. dry, transition, and wet seasons) in a coastal watershed of Southeast China. Results showed that agricultural and urban watersheds had significantly higher diversity in dry and transition seasons, and higher richness in transition and wet seasons than those in forest watershed. The non-metric multidimensional scaling analysis further verified great spatiotemporal variations of eukaryotic community. Stramenopiles, Alveolata, Animalia, and Eukaryota, dominated the sequences reads for all sampling sites in three seasons. Agricultural watershed had the highest relative abundant of Animalia, whereas Eukaryota was the most abundant in urban watershed and forest watershed had the highest relative abundance of Stramenopiles and Alveolata. The RDA ordination showed that Builtup and streamflow were two most important factors for moderate taxa and abundant taxa, respectively. Variation partitioning revealed that land use pattern and hydrological regime together explained 54.4%, 61% and 67.2% variances of the composition of eukaryotic community. Among three sampling seasons, the relative contribution of land use pattern was higher than that of hydrological regime. The results of this investigation demonstrated how land use pattern and hydrological regime affected the composition and diversity of riverine eukaryotic community. The findings can provide a useful insight into the riverine eukaryotic communities and their underlying ecological mechanisms in coastal China watersheds.
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Affiliation(s)
- Yaling Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Jinliang Huang
- Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China; Coastal and Ocean Management Institute, Xiamen University, Xiamen 361102, China.
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36
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Abraham JS, Sripoorna S, Maurya S, Makhija S, Gupta R, Toteja R. Techniques and tools for species identification in ciliates: a review. Int J Syst Evol Microbiol 2019; 69:877-894. [DOI: 10.1099/ijsem.0.003176] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ciliates are highly divergent unicellular eukaryotic organisms with nuclear dualism and a highly specialized ciliary pattern. They inhabit all biotopes and play crucial roles in regulating microbial food webs as they prey on bacteria, protists and even on microscopic animals. Nevertheless, subtle morphological differences and tiny sizes hinder proper species identification for many ciliates. In the present review, an attempt has been made to elaborate the various approaches used by modern day ciliate taxonomists for species identification. The different approaches involved in taxonomic characterization of ciliates such as classical (using live-cell observations, staining techniques, etc.), molecular (involving various marker genes) and statistical (delimitation of cryptic species) methods have been reviewed. Ecological and behavioural aspects in species identification have also been discussed. In present-day taxonomy, it is important to use a ‘total evidence’ approach in identifying ciliates, relying on both classical and molecular information whenever possible. This integrative approach will help in the mergence of classical methods with modern-day tools for comprehensive species description in future.
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Affiliation(s)
- Jeeva Susan Abraham
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - S. Sripoorna
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Swati Maurya
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Seema Makhija
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
| | - Renu Gupta
- Maitreyi College, University of Delhi, Bapu dham, Chanakyapuri, New Delhi 110021, India
| | - Ravi Toteja
- Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji, New Delhi 110019, India
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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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38
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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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39
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Schostag M, Priemé A, Jacquiod S, Russel J, Ekelund F, Jacobsen CS. Bacterial and protozoan dynamics upon thawing and freezing of an active layer permafrost soil. ISME JOURNAL 2019; 13:1345-1359. [PMID: 30692629 DOI: 10.1038/s41396-019-0351-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/17/2018] [Accepted: 12/23/2018] [Indexed: 11/09/2022]
Abstract
The active layer of soil overlaying permafrost in the Arctic is subjected to annual changes in temperature and soil chemistry, which we hypothesize to affect the overall soil microbial community. We investigated changes in soil microorganisms at different temperatures during warming and freezing of the active layer soil from Svalbard, Norway. Soil community data were obtained by direct shotgun sequencing of total extracted RNA. No changes in soil microbial communities were detected when warming from -10 to -2 °C or when freezing from -2 to -10 °C. In contrast, within a few days we observed changes when warming from -2 to +2 °C with a decrease in fungal rRNA and an increase in several OTUs belonging to Gemmatimonadetes, Bacteroidetes and Betaproteobacteria. Even more substantial changes occurred when incubating at 2 °C for 16 days, with declines in total fungal potential activity and decreases in oligotrophic members from Actinobacteria and Acidobacteria. Additionally, we detected an increase in transcriptome sequences of bacterial phyla Bacteriodetes, Firmicutes, Betaproteobacteria and Gammaproteobacteria-collectively presumed to be copiotrophic. Furthermore, we detected an increase in putative bacterivorous heterotrophic flagellates, likely due to predation upon the bacterial community via grazing. Although this grazing activity may explain relatively large changes in the bacterial community composition, no changes in total 16S rRNA gene copy number were observed and the total RNA level remained stable during the incubation. Together, these results are showing the first comprehensive ecological evaluation across prokaryotic and eukaryotic microbial communities on thawing and freezing of soil by application of the TotalRNA technique.
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Affiliation(s)
- Morten Schostag
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Anders Priemé
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Samuel Jacquiod
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.,INRA Dijon, UMR1347 Agroécologie, Dijon, France
| | - Jakob Russel
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Ekelund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Suhr Jacobsen
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark. .,Geological Survey of Denmark and Greenland, Copenhagen, Denmark. .,Department of Environmental Science, Aarhus University, Roskilde, Denmark.
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40
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Lupatini M, Korthals GW, Roesch LFW, Kuramae EE. Long-term farming systems modulate multi-trophic responses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 646:480-490. [PMID: 30056235 DOI: 10.1016/j.scitotenv.2018.07.323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/12/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Soil microbiome and multi-trophic relationships are essential for the stability and functioning of agroecosystems. However, little is known about how farming systems and alternative methods for controlling plant pathogens modulate microbial communities, soil mesofauna and plant productivity. In this study, we assessed the composition of eukaryotic microbial groups using a high-throughput sequencing approach (18S rRNA gene marker), the populations of parasitic and free-living nematodes, plant productivity and their inter-relationships in long-term conventional and organic farming systems. The diversity of the fungal community increased in the organic farming system compared to the conventional farming system, whereas the diversity of the protist community was similar between the two farming systems. Compared to conventional farming, organic farming increased the population of free-living nematodes and suppressed plant parasitic nematodes belonging to Meloidogynidae and Pratylenchidae. Fungal diversity and community structure appeared to be related to nematode suppression in the system receiving organic fertilizer, which was characterized by component microbial groups known to be involved in the suppression of soil pathogens. Unraveling the microbiome and multi-trophic interactions in different farming systems may permit the management of the soil environment toward more sustainable control of plant pathogens.
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Affiliation(s)
- Manoeli Lupatini
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Gerard W Korthals
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Luiz F W Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, 97300-000 São Gabriel, Brazil
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands.
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41
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Johansen JL, Rønn R, Ekelund F. Toxicity of cadmium and zinc to small soil protists. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 242:1510-1517. [PMID: 30144724 DOI: 10.1016/j.envpol.2018.08.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/10/2018] [Accepted: 08/12/2018] [Indexed: 06/08/2023]
Abstract
Small heterotrophic protists (flagellates and naked amoebae) are very abundant in soil and play a key role in maintaining soil services. Hence, knowledge on how xenobiotics affect these organisms is essential in ecosystem management. Cadmium (Cd) is an increasing environmental issue as both industrial deposition and recycling of heavy metal rich waste products have led to Cd enrichment of soils. Evaluation of toxicity of Cd to micro-organisms is often performed using a solution of pure Cd (e.g. CdCl) in liquid culture. This approach may be highly misleading as interactions between Cd and other substances, e.g. various ions or inherent soil components often strongly modify Cd toxicity. Hence, we compared the toxic effect of Cd to small heterotrophic protists in soil microcosms and liquid culture. We also evaluated how zinc (Zn) affects Cd toxicity, as Zn usually accompanies Cd in a ratio of c. 100:1, and is known to impede Cd toxicity. In the soil microcosms, we also monitored the primary food source of the protists, i.e. culturable bacteria, and used soil respiration as a proxy of soil functioning. Finally, we examined to what extent Cd actually sorbs to soil. We found 1) that c. 103 times more Cd was required to obtain the same effect in the soil microcosms compared to the liquid culture, 2) that soil sorption explains why Cd, even though highly toxic in aqueous solutions, has very limited effect when applied to soil, and 3) (very surprisingly) that in our experimental systems Zn was as toxic as Cd. Our study suggests that Cd toxicity to soil protists will be small because most Cd in soil will be sorbed to the soil matrix and because the Zn:Cd ratio of 100:1 in most substances, incl. pollutants, will mean that lethal Zn effects will occur before Cd reaches toxic levels.
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Affiliation(s)
- Jesper Liengaard Johansen
- Center for Bioenergy Recycling, ASHBACK, Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, DK2100, Copenhagen, Denmark.
| | - Regin Rønn
- Center for Bioenergy Recycling, ASHBACK, Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, DK2100, Copenhagen, Denmark
| | - Flemming Ekelund
- Center for Bioenergy Recycling, ASHBACK, Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, DK2100, Copenhagen, Denmark
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42
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Birrer SC, Dafforn KA, Simpson SL, Kelaher BP, Potts J, Scanes P, Johnston EL. Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:1383-1394. [PMID: 29801231 DOI: 10.1016/j.scitotenv.2018.05.065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/04/2018] [Accepted: 05/05/2018] [Indexed: 06/08/2023]
Abstract
Coastal waterways are increasingly exposed to multiple stressors, e.g. contaminants that can be delivered via pulse or press exposures. Therefore, it is crucial that ecological impacts can be differentiated among stressors to manage ecosystem threats. We investigated microbial community development in sediments exposed to press and pulse stressors. Press exposures were created with in situ mesocosm sediments containing a range of 'metal' concentrations (sediment contaminated with multiple metal(loid)s) and organic enrichment (fertiliser), while the pulse exposure was simulated by a single dose of organic fertiliser. All treatments and exposure concentrations were crossed in a fully factorial field experiment. We used amplicon sequencing to compare the sensitivity of the 1) total (DNA) and active (RNA) component of 2) bacterial (16S rRNA) and eukaryotic (18S rRNA) communities to contaminant exposures. Overall microbial community change was greater when exposed to press than pulse stressors, with the bacterial community responding more strongly than the eukaryotes. The total bacterial community represents a more time-integrated measure of change and proved to be more sensitive to multiple stressors than the active community. Metals and organic enrichment treatments interacted such that the effect of metals was weaker when the sediment was organically enriched. Taxa-level analyses revealed that press enrichment resulted in potential functional changes, mainly involving nitrogen cycling. Furthermore, enrichment generally reduced the abundance of active eukaryotes in the sediment. As well as demonstrating interactive impacts of metals and organic enrichment, this study highlights the sensitivity of next-generation sequencing for ecosystem biomonitoring of interacting stressors and identifies opportunities for more targeted application.
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Affiliation(s)
- Simone C Birrer
- Applied Marine and Estuarine Ecology Lab, School of BEES, University of New South Wales, Sydney 2052, NSW, Australia; The Sydney Institute of Marine Science, Mosman 2088, NSW, Australia.
| | - Katherine A Dafforn
- The Sydney Institute of Marine Science, Mosman 2088, NSW, Australia; Department of Environmental Sciences, Macquarie University, North Ryde NSW 2109, Australia
| | | | - Brendan P Kelaher
- National Marine Science Centre and Centre for Coastal Biogeochemistry Research, Southern Cross University, Coffs Harbour 2450, NSW, Australia
| | - Jaimie Potts
- NSW Office of Environment and Heritage, Lidcombe 2141, NSW, Australia
| | - Peter Scanes
- NSW Office of Environment and Heritage, Lidcombe 2141, NSW, Australia
| | - Emma L Johnston
- Applied Marine and Estuarine Ecology Lab, School of BEES, University of New South Wales, Sydney 2052, NSW, Australia; The Sydney Institute of Marine Science, Mosman 2088, NSW, Australia
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43
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Venter PC, Nitsche F, Arndt H. The Hidden Diversity of Flagellated Protists in Soil. Protist 2018; 169:432-449. [PMID: 29870898 DOI: 10.1016/j.protis.2018.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 11/18/2022]
Abstract
Protists are among the most diverse and abundant eukaryotes in soil. However, gaps between described and sequenced protist morphospecies still present a pending problem when surveying environmental samples for known species using molecular methods. The number of sequences in the molecular PR2 database (∼130,000) is limited compared to the species richness expected (>1 million protist species) - limiting the recovery rate. This is important, since high throughput sequencing (HTS) methods are used to find associative patterns between functional traits, taxa and environmental parameters. We performed HTS to survey soil flagellates in 150 grasslands of central Europe, and tested the recovery rate of ten previously isolated and cultivated cercomonad species, among locally found diversity. We recovered sequences for reference soil flagellate species, but also a great number of their phylogenetically evaluated genetic variants, among rare and dominant taxa with presumably own biogeography. This was recorded among dominant (cercozoans, Sandona), rare (apusozoans) and a large hidden diversity of predominantly aquatic protists in soil (choanoflagellates, bicosoecids) often forming novel clades associated with uncultured environmental sequences. Evaluating the reads, instead of the OTUs that individual reads are usually clustered into, we discovered that much of this hidden diversity may be lost due to clustering.
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Affiliation(s)
- Paul Christiaan Venter
- University of Cologne, Cologne Biocenter, Institute of Zoology, Department of General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany
| | - Frank Nitsche
- University of Cologne, Cologne Biocenter, Institute of Zoology, Department of General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany
| | - Hartmut Arndt
- University of Cologne, Cologne Biocenter, Institute of Zoology, Department of General Ecology, Zuelpicher Str. 47b, D-50674 Koeln (Cologne), Germany.
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44
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Heger TJ, Giesbrecht IJW, Gustavsen J, Del Campo J, Kellogg CTE, Hoffman KM, Lertzman K, Mohn WW, Keeling PJ. High-throughput environmental sequencing reveals high diversity of litter and moss associated protist communities along a gradient of drainage and tree productivity. Environ Microbiol 2018; 20:1185-1203. [PMID: 29417706 DOI: 10.1111/1462-2920.14061] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 11/29/2022]
Abstract
Although previous studies, mostly based on microscopy analyses of a few groups of protists, have suggested that protists are abundant and diverse in litter and moss habitats, the overall diversity of moss and litter associated protists remains elusive. Here, high-throughput environmental sequencing was used to characterize the diversity and community structure of litter- and moss-associated protists along a gradient of soil drainage and forest primary productivity in a temperate rainforest in British Columbia. We identified 3262 distinct protist OTUs from 36 sites. Protists were strongly structured along the landscape gradient, with a significant increase in alpha diversity from the blanket bog ecosystem to the zonal forest ecosystem. Among all investigated environmental variables, calcium content was the most strongly associated with the community composition of protists, but substrate composition, plant cover and other edaphic factors were also significantly correlated with these communities. Furthermore, a detailed phylogenetic analysis of unicellular opisthokonts identified OTUs covering most lineages, including novel OTUs branching with Discicristoidea, the sister group of Fungi, and with Filasterea, one of the closest unicellular relatives to animals. Altogether, this study provides unprecedented insight into the community composition of moss- and litter-associated protists.
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Affiliation(s)
- Thierry J Heger
- Soil Science Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Delémont, Switzerland.,Botany Department, University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada
| | - Ian J W Giesbrecht
- Hakai Institute, Heriot Bay, BC, Canada.,School of Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - Julia Gustavsen
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Javier Del Campo
- Botany Department, University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada
| | - Colleen T E Kellogg
- Hakai Institute, Heriot Bay, BC, Canada.,Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Kira M Hoffman
- Hakai Institute, Heriot Bay, BC, Canada.,School of Environmental Studies, University of Victoria, Victoria, BC, Canada
| | - Ken Lertzman
- Hakai Institute, Heriot Bay, BC, Canada.,School of Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - William W Mohn
- Hakai Institute, Heriot Bay, BC, Canada.,Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Patrick J Keeling
- Botany Department, University of British Columbia, Vancouver, BC, Canada.,Hakai Institute, Heriot Bay, BC, Canada
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45
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Grattepanche J, Walker LM, Ott BM, Paim Pinto DL, Delwiche CF, Lane CE, Katz LA. Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data. Bioessays 2018; 40:e1700198. [DOI: 10.1002/bies.201700198] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/16/2018] [Indexed: 01/09/2023]
Affiliation(s)
| | - Laura M. Walker
- Department of Biological Sciences, Smith CollegeNorthamptonMA 01063USA
| | - Brittany M. Ott
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege ParkMD 20742USA
| | | | - Charles F. Delwiche
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege ParkMD 20742USA
| | - Christopher E. Lane
- Department of Biological SciencesUniversity of Rhode IslandKingstonRI 02881USA
| | - Laura A. Katz
- Department of Biological Sciences, Smith CollegeNorthamptonMA 01063USA
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46
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Geisen S, Mitchell EAD, Adl S, Bonkowski M, Dunthorn M, Ekelund F, Fernández LD, Jousset A, Krashevska V, Singer D, Spiegel FW, Walochnik J, Lara E. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol Rev 2018; 42:293-323. [DOI: 10.1093/femsre/fuy006] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 02/12/2018] [Indexed: 12/27/2022] Open
Affiliation(s)
- Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel 2000, Switzerland
| | - Sina Adl
- Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, Canada
| | - Michael Bonkowski
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Institute of Zoology, Terrestrial Ecology, Zülpicher Straße 47b, 50674 Köln, Germany
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger Straße, 67663 Kaiserslautern, Germany
| | - Flemming Ekelund
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Leonardo D Fernández
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Avenida Viel 1497, Santiago, Chile
| | - Alexandre Jousset
- Department of Ecology and Biodiversity, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Valentyna Krashevska
- University of Göttingen, J.F. Blumenbach Institute of Zoology and Anthropology, Untere Karspüle 2, 37073 Göttingen, Germany
| | - David Singer
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
| | - Frederick W Spiegel
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, United States of America
| | - Julia Walochnik
- Molecular Parasitology, Institute of Tropical Medicine, Medical University, 1090 Vienna, Austria
| | - Enrique Lara
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel 2000, Switzerland
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
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47
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Zhang W, Pan Y, Yang J, Chen H, Holohan B, Vaudrey J, Lin S, McManus GB. The diversity and biogeography of abundant and rare intertidal marine microeukaryotes explained by environment and dispersal limitation. Environ Microbiol 2017; 20:462-476. [PMID: 28881067 DOI: 10.1111/1462-2920.13916] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/15/2017] [Accepted: 08/26/2017] [Indexed: 02/03/2023]
Abstract
Benthic microeukaryotes are key ecosystem drivers in marine sandy beaches, an important and dynamic environment; however, little is known about their diversity and biogeography on a large spatial scale. Here, we investigated the community composition and geographical distributions of benthic microeukaryotes using high-throughput sequencing of the 18S rRNA gene and quantified the contributions of environmental factors and spatial separation on the distribution patterns of both rare and abundant taxa. We collected 36 intertidal samples at 12 sandy beaches from four regions that spanned distances from 0.001 to 12,000 km. We found 12,890 operational taxonomic units (OTUs; 97% sequence identity level) including members of all eukaryotic super-groups and several phyla of uncertain position. Arthropoda and Diatomeae dominated the sequence reads in abundance, but Ciliophora and Discoba were the most diverse groups across all samples. About one-third of the OTUs could not be definitively classified at a similarity level of 80%, supporting the view that a large number of rare and minute marine species may have escaped previous characterization. We found generally similar geographical patterns for abundant and rare microeukaryotic sub-communities, and both showed a significant distance-decay similarity trend. Variation partitioning showed that both rare and abundant sub-communities exhibited a slightly stronger response to environmental factors than spatial (distance) factors. However, the abundant sub-community was strongly correlated with variations in spatial, environmental and sediment grain size factors (66% of variance explained), but the rare assemblage was not (16%). This suggests that different or more complex mechanisms generate and maintain diversity in the rare biosphere in this habitat.
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Affiliation(s)
- Wenjing Zhang
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361005, People's Republic of China.,Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Yongbo Pan
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361005, People's Republic of China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Huihuang Chen
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Bridget Holohan
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Jamie Vaudrey
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Marine Biodiversity and Global Change Research Center, Xiamen University, Xiamen 361005, People's Republic of China.,Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
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48
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Sapp M, Ploch S, Fiore-Donno AM, Bonkowski M, Rose LE. Protists are an integral part of the Arabidopsis thaliana
microbiome. Environ Microbiol 2017; 20:30-43. [DOI: 10.1111/1462-2920.13941] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/19/2017] [Accepted: 09/21/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Melanie Sapp
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Sebastian Ploch
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25; 60325 Frankfurt am Main Germany
| | - Anna M. Fiore-Donno
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Michael Bonkowski
- Institute of Zoology, Department of Terrestrial Ecology, Zülpicher Str 47b; Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne; Zülpicher Strasse 50674 Köln Germany
| | - Laura E. Rose
- Institute of Population Genetics, Universitätstrasse 1; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University; Universitätstrasse 40225 Düsseldorf Germany
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49
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Fiore-Donno AM, Rixen C, Rippin M, Glaser K, Samolov E, Karsten U, Becker B, Bonkowski M. New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts. Mol Ecol Resour 2017; 18:229-239. [PMID: 29058814 DOI: 10.1111/1755-0998.12729] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 08/31/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023]
Abstract
We describe the performance of a new metabarcoding approach to investigate the environmental diversity of a prominent group of widespread unicellular organisms, the Cercozoa. Cercozoa is an immensely large group of protists, and although it may dominate in soil and aquatic ecosystems, its environmental diversity remains undersampled. We designed PCR primers targeting the hypervariable region V4 of the small subunit ribosomal RNA (SSU or 18S) gene, which is the recommended barcode marker for Cercozoa. The length of the amplified fragment (c. 350 bp) is suitable for Illumina MiSeq, the most cost-effective platform for molecular environmental surveys. We provide barcoded primers, an economical alternative to multiple libraries for multiplex sequencing of over a hundred samples. In silico, our primers matched 68% of the cercozoan sequences of the reference database and performed better than previously proposed new-generation sequencing primers. In mountain grassland soils and in biological soil crusts from a variety of climatic regions, we were able to detect cercozoan sequences encompassing nearly the whole range of the phylum. We obtained 901 operational taxonomic units (OTUs) at 97% similarity threshold from 26 samples, with c. 50,000 sequences per site, and only 8% of noncercozoan sequences. We could report a further increase in the diversity of Cercozoa, as only 43% of the OTUs were 97%-100% similar to any known sequence. Our study thus provides an advanced tool for cercozoan metabarcoding and to investigate their diversity and distribution in the environment.
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Affiliation(s)
- Anna Maria Fiore-Donno
- Institute of Zoology, Terrestrial Ecology, Cluster of Excellence in Plant Sciences, University of Cologne, Cologne, Germany
| | - Christian Rixen
- Institute for Snow and Avalanche Research SLF, Davos Dorf, Switzerland
| | - Martin Rippin
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Karin Glaser
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Elena Samolov
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Ulf Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Burkhard Becker
- Institute of Botany, University of Cologne, Cologne, Germany
| | - Michael Bonkowski
- Institute of Zoology, Terrestrial Ecology, Cluster of Excellence in Plant Sciences, University of Cologne, Cologne, Germany
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50
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Borg Dahl M, Brejnrod AD, Unterseher M, Hoppe T, Feng Y, Novozhilov Y, Sørensen SJ, Schnittler M. Genetic barcoding of dark-spored myxomycetes (Amoebozoa)-Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies. Mol Ecol Resour 2017; 18:306-318. [PMID: 29024429 DOI: 10.1111/1755-0998.12725] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 09/26/2017] [Accepted: 10/01/2017] [Indexed: 12/18/2022]
Abstract
Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.
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Affiliation(s)
- Mathilde Borg Dahl
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Asker D Brejnrod
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Thomas Hoppe
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Yun Feng
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
| | - Yuri Novozhilov
- V.L. Komarov Botanical Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Schnittler
- Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany
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