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Ogola HJO, Ijoma GN, Edokpayi JN. Exploring the dichotomy: Shotgun metagenomics reveals diversity of beneficial and pathogenic protist community in arid wetlands of northeastern South Africa. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174306. [PMID: 38942318 DOI: 10.1016/j.scitotenv.2024.174306] [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: 04/09/2024] [Revised: 06/09/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
Arid regions harbor seasonal and permanent wetlands, as biodiversity hotspots crucial for ecosystem services despite harsh conditions. These wetlands, typically dependent on episodic intense rainfall, are understudied compared to their humid counterparts. While the diversity of plants and animals in these wetlands is well-known, the microbial communities remain largely unexplored. To address this knowledge gap, we employed metagenome sequencing technologies to profile protist communities, including pathogenic protozoa, and their associated functional pathways, in sediment of permanent and seasonal arid freshwater wetlands across northern South Africa. Results revealed a core community of protists dominated by phylum Apicomplexa (66.73 %), Euglenazoa (19.03 %), Bacillariophyta (5.44 %), Metamonada (4.65 %), Cryptophyta (1.90 %), and Amoebazoa (1.21 %). Seasonal wetlands showed significantly higher protist diversity compared to permanent wetlands (Shannon index, p = 0.019; Chao1, p = 0.0095). A high abundance and diversity of human and zoonotic pathogenic protists (87.67 %) was observed, with lower levels of photoautotrophs (6.69 %) and limited diversity of phagotrophs (5.64 %). Key photoautotrophs identified included diatoms (Thalassiosiraceae and Phaeodactylaceae) and cryptophytes (genus Hemiselmis and Cryptophyta), with consumers/phagotrophs exhibited a correlation with the bacterial community abundance (r2 = 0.218, p < 0.001). Pathogenic protozoans identified, include malaria-causing Plasmodium, kinetoplastids (genus Besnoita, Theilleria, Neospora, Toxoplasma, Encephalitozoon, and Babesia) and waterborne protozoans of public health importance (such as Cryptosporidium parvum and Giardia lamblia). Furthermore, the enrichment of pathogenesis-associated pathways (amino acid biosynthesis, peptidoglycan maturation, heme biosynthesis and degradation, and the Calvin-Benson-Bassham cycle), along with virulence gene families identified, highlighted these wetlands as potential reservoirs for infectious diseases. Our results unveil a baseline protist taxonomic and functional composition within arid wetlands, including beneficial and pathogenic protozoa. The close proximity of these wetlands to human activity raises concern for local and transboundary spread of these pathogens. Thus, continued monitoring is vital for disease control and preserving these unique ecosystems.
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Affiliation(s)
- Henry Joseph Oduor Ogola
- Department of Environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa (UNISA), Florida Campus, Roodepoort 1709, South Africa.
| | - Grace Nkechinyere Ijoma
- Department of Environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa (UNISA), Florida Campus, Roodepoort 1709, South Africa
| | - Joshua Nosa Edokpayi
- Water and Environmental Management Research Group, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou, 0950, South Africa
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Mau RL, Hayer M, Purcell AM, Geisen S, Hungate BA, Schwartz E. Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices. Appl Environ Microbiol 2024; 90:e0080024. [PMID: 38920364 PMCID: PMC11267882 DOI: 10.1128/aem.00800-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding.IMPORTANCEEcosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.
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Affiliation(s)
- Rebecca L. Mau
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, Arizona, USA
| | - Alicia M. Purcell
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, the Netherlands
| | - Bruce A. Hungate
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
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Karlicki M, Bednarska A, Hałakuc P, Maciszewski K, Karnkowska A. Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning. FEMS Microbiol Ecol 2024; 100:fiae104. [PMID: 39039016 DOI: 10.1093/femsec/fiae104] [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: 03/04/2024] [Revised: 06/21/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024] Open
Abstract
Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.
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Affiliation(s)
- Michał Karlicki
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Anna Bednarska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Department of Hydrobiology, Institute of Functional Biology and Ecology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
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Hu Y, Zhang H, Sun X, Zhang B, Wang Y, Rafiq A, Jia H, Liang C, An S. Impact of grassland degradation on soil multifunctionality: Linking to protozoan network complexity and stability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172724. [PMID: 38663601 DOI: 10.1016/j.scitotenv.2024.172724] [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: 02/08/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024]
Abstract
Soil protozoa, as predators of microbial communities, profoundly influence multifunctionality of soils. Understanding the relationship between soil protozoa and soil multifunctionality (SMF) is crucial to unraveling the driving mechanisms of SMF. However, this relationship remains unclear, particularly in grassland ecosystems that are experiencing degradation. By employing 18S rRNA gene sequencing and network analysis, we examined the diversity, composition, and network patterns of the soil protozoan community along a well-characterized gradient of grassland degradation at four alpine sites, including two alpine meadows (Cuona and Jiuzhi) and two alpine steppes (Shuanghu and Gonghe) on the Qinghai-Tibetan Plateau. Our findings showed that grassland degradation decreased SMF for 1-2 times in all four sites but increased soil protozoan diversity (Shannon index) for 13.82-298.01 % in alpine steppes. Grassland degradation-induced changes in soil protozoan composition, particularly to the Intramacronucleata with a large body size, were consistently observed across all four sites. The enhancing network complexity (average degree), stability (robustness), and cooperative relationships (positive correlation) are the responses of protozoa to grassland degradation. Further analyses revealed that the increased network complexity and stability led to a decrease in SMF by affecting microbial biomass. Overall, protozoa increase their diversity and strengthen their cooperative relationships to resist grassland degradation, and emphasize the critical role of protozoan network complexity and stability in regulating SMF. Therefore, not only protozoan diversity and composition but also their interactions should be considered in evaluating SMF responses to grassland degradation, which has important implications for predicting changes in soil function under future scenarios of anthropogenic change.
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Affiliation(s)
- Yang Hu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China; College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Haolin Zhang
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Xinya Sun
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Bicheng Zhang
- Institute of Soil and Water Conservation, CAS & MWR, Yangling, Shannxi 712100, China; University of Chinese Academy of Science, Beijing 100049, China
| | - Yubin Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Anum Rafiq
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, China
| | - Hongtao Jia
- College of Resources and Environment, Xinjiang Agricultural University, Urumqi 830052, China
| | - Chao Liang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dry Land Farming on Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, 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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Guo S, Jiao Z, Yan Z, Yan X, Deng X, Xiong W, Tao C, Liu H, Li R, Shen Q, Kowalchuk GA, Geisen S. Predatory protists reduce bacteria wilt disease incidence in tomato plants. Nat Commun 2024; 15:829. [PMID: 38280866 PMCID: PMC10821857 DOI: 10.1038/s41467-024-45150-0] [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: 06/13/2023] [Accepted: 01/16/2024] [Indexed: 01/29/2024] Open
Abstract
Soil organisms are affected by the presence of predatory protists. However, it remains poorly understood how predatory protists can affect plant disease incidence and how fertilization regimes can affect these interactions. Here, we characterise the rhizosphere bacteria, fungi and protists over eleven growing seasons of tomato planting under three fertilization regimes, i.e conventional, organic and bioorganic, and with different bacterial wilt disease incidence levels. We find that predatory protists are negatively associated with disease incidence, especially two ciliophoran Colpoda OTUs, and that bioorganic fertilization enhances the abundance of predatory protists. In glasshouse experiments we find that the predatory protist Colpoda influences disease incidence by directly consuming pathogens and indirectly increasing the presence of pathogen-suppressive microorganisms in the soil. Together, we demonstrate that predatory protists reduce bacterial wilt disease incidence in tomato plants via direct and indirect reductions of pathogens. Our study provides insights on the role that predatory protists play in plant disease, which could be used to design more sustainable agricultural practices.
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Affiliation(s)
- Sai Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Zixuan Jiao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Zhiguang Yan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Xinyue Yan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Xuhui Deng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, PR China.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, 6700 AA, Wageningen, The Netherlands
- Netherlands Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands
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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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Guo P, Li C, Liu J, Chai B. Predation has a significant impact on the complexity and stability of microbial food webs in subalpine lakes. Microbiol Spectr 2023; 11:e0241123. [PMID: 37787559 PMCID: PMC10714739 DOI: 10.1128/spectrum.02411-23] [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: 06/08/2023] [Accepted: 08/18/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE As an important part of microbial food webs, protists transfer organic carbon and nutrients to higher trophic levels in aquatic ecosystems. Protist predation often influences the abundance and composition of bacterial communities. However, we still do not understand whether and how predation affects the complexity and stability of microbial food webs. This study assessed the seasonal dynamic characteristics and driving factors of microbial food webs in terms of complexity and stability. Our findings have implications for future surveys to reveal the effects of climate and environmental changes.
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Affiliation(s)
- Ping Guo
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
- Central Laboratory, Changzhi Medical College, Changzhi, China
| | - Cui Li
- Faculty of Environment Economics, Shanxi University of Finance and Economics, Taiyuan, China
| | - Jinxain Liu
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Baofeng Chai
- Shanxi Key Laboratory of Ecological Restoration on Loess Plateau, Institute of Loess Plateau, Shanxi University, Taiyuan, China
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Rozo-Montoya N, Bedoya-Urrego K, Alzate JF. Monitoring potentially pathogenic protists in sewage sludge using Metataxonomics. Food Waterborne Parasitol 2023; 33:e00210. [PMID: 37808003 PMCID: PMC10558727 DOI: 10.1016/j.fawpar.2023.e00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023] Open
Abstract
Intestinal parasites continue to pose a significant threat to human health worldwide, particularly among children. Contaminated water and soil serve as major transmission vehicles for these parasites and intestinal protists are among the most prevalent parasites in both developed and developing nations. Traditionally, parasites have been studied using human or animal fecal samples, while studying them in environmental samples has been challenging due to technical limitations. However, advancements in Next-Generation Sequencing (NGS) and bioinformatic approaches now enable the detection of parasite DNA in environmental samples. In this study, we applied a metataxonomic and phylogenetic strategy to detect and classify DNA of protists present in sewage sludge from two major cities in Colombia: Medellin and Cali. We successfully detected several human pathogenic parasites including Giardia intestinalis, Entamoeba histolytica, and Blastocystis sp., among other protists, in all sludge samples examined. We also investigated the entry and exit of parasite DNA from the San Fernando wastewater treatment plant (WWTP). We observed a higher number of parasite DNA sequences in the plant's influent wastewater, but we also detected the discharge of DNA from pathogenic parasites in both effluent waters and biosolids.
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Affiliation(s)
- Nicolas Rozo-Montoya
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Katherine Bedoya-Urrego
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Centro Nacional de Secuenciación Genómica CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellín, Colombia
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
- Grupo Pediaciencias, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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10
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Yue Y, Liu C, Xu B, Wang Y, Lv Q, Zhou Z, Li R, Kowalchuk GA, Jousset A, Shen Q, Xiong W. Rhizosphere shapes the associations between protistan predators and bacteria within microbiomes through the deterministic selection on bacterial communities. Environ Microbiol 2023; 25:3623-3629. [PMID: 37849426 DOI: 10.1111/1462-2920.16528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
The assembly of bacterial communities in the rhizosphere is well-documented and plays a crucial role in supporting plant performance. However, we have limited knowledge of how plant rhizosphere determines the assembly of protistan predators and whether the potential associations between protistan predators and bacterial communities shift due to rhizosphere selection. To address this, we examined bacterial and protistan taxa from 443 agricultural soil samples including bulk and rhizosphere soils. Our results presented distinct patterns of bacteria and protistan predators in rhizosphere microbiome assembly. Community assembly of protistan predators was determined by a stochastic process in the rhizosphere and the diversity of protistan predators was reduced in the rhizosphere compared to bulk soils, these may be attributed to the indirect impacts from the altered bacterial communities that showed deterministic process assembly in the rhizosphere. Interestingly, we observed that the plant rhizosphere facilitates more close interrelationships between protistan predators and bacterial communities, which might promote a healthy rhizosphere microbial community for plant growth. Overall, our findings indicate that the potential predator-prey relationships within the microbiome, mediated by plant rhizosphere, might contribute to plant performance in agricultural ecosystems.
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Affiliation(s)
- Yang Yue
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Chen Liu
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Boting Xu
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yijin Wang
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qihui Lv
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zeyuan Zhou
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Rong Li
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Alexandre Jousset
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Utrecht, The Netherlands
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - Wu Xiong
- Key Lab of Organic-Based Fertilizers of China, Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, China
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11
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Simister RL, Iulianella Phillips BP, Wickham AP, Cayer EM, Hart CJR, Winterburn PA, Crowe SA. DNA sequencing, microbial indicators, and the discovery of buried kimberlites. COMMUNICATIONS EARTH & ENVIRONMENT 2023; 4:387. [PMID: 38665197 PMCID: PMC11041713 DOI: 10.1038/s43247-023-01020-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 09/19/2023] [Indexed: 04/28/2024]
Abstract
Population growth and technological advancements are placing growing demand on mineral resources. New and innovative exploration technologies that improve detection of deeply buried mineralization and host rocks are required to meet these demands. Here we used diamondiferous kimberlite ore bodies as a test case and show that DNA amplicon sequencing of soil microbial communities resolves anomalies in microbial community composition and structure that reflect the surface expression of kimberlites buried under 10 s of meters of overburden. Indicator species derived from laboratory amendment experiments were employed in an exploration survey in which the species distributions effectively delineated the surface expression of buried kimberlites. Additional indicator species derived directly from field observations improved the blind discovery of kimberlites buried beneath similar overburden types. Application of DNA sequence-based analyses of soil microbial communities to mineral deposit exploration provides a powerful illustration of how genomics technologies can be leveraged in the discovery of critical new resources.
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Affiliation(s)
- Rachel L. Simister
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Bianca P. Iulianella Phillips
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Andrew P. Wickham
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Erika M. Cayer
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Craig J. R. Hart
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Peter A. Winterburn
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- MDRU-Mineral Deposit Research Unit, Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Sean A. Crowe
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
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12
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Köninger J, Ballabio C, Panagos P, Jones A, Schmid MW, Orgiazzi A, Briones MJI. Ecosystem type drives soil eukaryotic diversity and composition in Europe. GLOBAL CHANGE BIOLOGY 2023; 29:5706-5719. [PMID: 37449367 DOI: 10.1111/gcb.16871] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023]
Abstract
Soil eukaryotes play a crucial role in maintaining ecosystem functions and services, yet the factors driving their diversity and distribution remain poorly understood. While many studies focus on some eukaryotic groups (mostly fungi), they are limited in their spatial scale. Here, we analyzed an unprecedented amount of observational data of soil eukaryomes at continental scale (787 sites across Europe) to gain further insights into the impact of a wide range of environmental conditions (climatic and edaphic) on their community composition and structure. We found that the diversity of fungi, protists, rotifers, tardigrades, nematodes, arthropods, and annelids was predominantly shaped by ecosystem type (annual and permanent croplands, managed and unmanaged grasslands, coniferous and broadleaved woodlands), and higher diversity of fungi, protists, nematodes, arthropods, and annelids was observed in croplands than in less intensively managed systems, such as coniferous and broadleaved woodlands. Also in croplands, we found more specialized eukaryotes, while the composition between croplands was more homogeneous compared to the composition of other ecosystems. The observed high proportion of overlapping taxa between ecosystems also indicates that DNA has accumulated from previous land uses, hence mimicking the land transformations occurring in Europe in the last decades. This strong ecosystem-type influence was linked to soil properties, and particularly, soil pH was driving the richness of fungi, rotifers, and annelids, while plant-available phosphorus drove the richness of protists, tardigrades, and nematodes. Furthermore, the soil organic carbon to total nitrogen ratio crucially explained the richness of fungi, protists, nematodes, and arthropods, possibly linked to decades of agricultural inputs. Our results highlighted the importance of long-term environmental variables rather than variables measured at the time of the sampling in shaping soil eukaryotic communities, which reinforces the need to include those variables in addition to ecosystem type in future monitoring programs and conservation efforts.
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Affiliation(s)
- Julia Köninger
- Departamento de Ecología y Biología Animal, Universidade de Vigo, Vigo, Spain
- European Commission, Joint Research Centre, Ispra, Italy
| | | | - Panos Panagos
- European Commission, Joint Research Centre, Ispra, Italy
| | - Arwyn Jones
- European Commission, Joint Research Centre, Ispra, Italy
| | | | | | - Maria J I Briones
- Departamento de Ecología y Biología Animal, Universidade de Vigo, Vigo, Spain
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13
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Garrido-Sanz D, Čaušević S, Vacheron J, Heiman CM, Sentchilo V, van der Meer JR, Keel C. Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere. MICROBIOME 2023; 11:214. [PMID: 37770950 PMCID: PMC10540321 DOI: 10.1186/s40168-023-01660-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/31/2023] [Indexed: 09/30/2023]
Abstract
BACKGROUND Plant-beneficial bacterial inoculants are of great interest in agriculture as they have the potential to promote plant growth and health. However, the inoculation of the rhizosphere microbiome often results in a suboptimal or transient colonization, which is due to a variety of factors that influence the fate of the inoculant. To better understand the fate of plant-beneficial inoculants in complex rhizosphere microbiomes, composed by hundreds of genotypes and multifactorial selection mechanisms, controlled studies with high-complexity soil microbiomes are needed. RESULTS We analysed early compositional changes in a taxa-rich natural soil bacterial community under both exponential nutrient-rich and stationary nutrient-limited growth conditions (i.e. growing and stable communities, respectively) following inoculation with the plant-beneficial bacterium Pseudomonas protegens in a bulk soil or a wheat rhizosphere environment. P. protegens successfully established under all conditions tested and was more abundant in the rhizosphere of the stable community. Nutrient availability was a major factor driving microbiome composition and structure as well as the underlying assembly processes. While access to nutrients resulted in communities assembled mainly by homogeneous selection, stochastic processes dominated under the nutrient-deprived conditions. We also observed an increased rhizosphere selection effect under nutrient-limited conditions, resulting in a higher number of amplicon sequence variants (ASVs) whose relative abundance was enriched. The inoculation with P. protegens produced discrete changes, some of which involved other Pseudomonas. Direct competition between Pseudomonas strains partially failed to replicate the observed differences in the microbiome and pointed to a more complex interaction network. CONCLUSIONS The results of this study show that nutrient availability is a major driving force of microbiome composition, structure and diversity in both the bulk soil and the wheat rhizosphere and determines the assembly processes that govern early microbiome development. The successful establishment of the inoculant was facilitated by the wheat rhizosphere and produced discrete changes among other members of the microbiome. Direct competition between Pseudomonas strains only partially explained the microbiome changes, indicating that indirect interactions or spatial distribution in the rhizosphere or soil interface may be crucial for the survival of certain bacteria. Video Abstract.
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Affiliation(s)
- Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
| | - Senka Čaušević
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Clara M Heiman
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
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14
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Lin C, Li LJ, Ren K, Zhou SYD, Isabwe A, Yang LY, Neilson R, Yang XR, Cytryn E, Zhu YG. Phagotrophic protists preserve antibiotic-resistant opportunistic human pathogens in the vegetable phyllosphere. ISME COMMUNICATIONS 2023; 3:94. [PMID: 37660098 PMCID: PMC10475086 DOI: 10.1038/s43705-023-00302-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/04/2023]
Abstract
Food safety of leafy greens is an emerging public health issue as they can harbor opportunistic human pathogens (OHPs) and expose OHPs to consumers. Protists are an integral part of phyllosphere microbial ecosystems. However, our understanding of protist-pathogen associations in the phyllosphere and their consequences on public health remains poor. Here, we examined phyllosphere protists, human pathogen marker genes (HPMGs), and protist endosymbionts from four species of leafy greens from major supermarkets in Xiamen, China. Our results showed that Staphylococcus aureus and Klebsiella pneumoniae were the dominant human pathogens in the vegetable phyllosphere. The distribution of HPMGs and protistan communities differed between vegetable species, of which Chinese chive possessed the most diverse protists and highest abundance of HPMGs. HPMGs abundance positively correlated with the diversity and relative abundance of phagotrophic protists. Whole genome sequencing further uncovered that most isolated phyllosphere protists harbored multiple OHPs which carried antibiotic resistance genes, virulence factors, and metal resistance genes and had the potential to HGT. Colpoda were identified as key phagotrophic protists which positively linked to OHPs and carried diverse resistance and virulence potential endosymbiont OHPs including Pseudomonas nitroreducens, Achromobacter xylosoxidans, and Stenotrophomonas maltophilia. We highlight that phyllosphere protists contribute to the transmission of resistant OHPs through internalization and thus pose risks to the food safety of leafy greens and human health. Our study provides insights into the protist-OHP interactions in the phyllosphere, which will help in food safety surveillance and human health.
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Affiliation(s)
- Chenshuo Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Li-Juan Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Kexin Ren
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Shu-Yi-Dan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Xingke Road 723, Tianhe District, Guangzhou, 510650, China
| | - Alain Isabwe
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Le-Yang Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
- University of Chinese Academy of Sciences, 19A Yuquan Road, 100049, Beijing, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Eddie Cytryn
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, 7528809, Rishon Lezion, Israel
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China.
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15
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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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16
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Wang Z, Huang W, Liu Z, Zeng J, He Z, Shu L. The neonicotinoid insecticide imidacloprid has unexpected effects on the growth and development of soil amoebae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161884. [PMID: 36716868 DOI: 10.1016/j.scitotenv.2023.161884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/15/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Neonicotinoid pesticides are the most widely used insecticides worldwide and have become a global environmental issue. Previous studies have shown that imidacloprid, the most used neonicotinoid, can negatively affect a wide range of organisms, including non-target insects, fish, invertebrates, and mammals. Imidacloprid can also accumulate and persist in soils, posing threats to the terrestrial ecosystem. However, we know little about one ecologically important group of organisms, the single-celled soil protists. In this study, we used a soil amoeba, Dictyostelium discoideum, to test whether and how imidacloprid affects the growth and development of soil amoebae. We provide the first empirical evidence that environmental concentrations of imidacloprid negatively impact the fitness and development of soil amoebae. In addition, the adverse effects did not show a dose-response relationship with increased imidacloprid concentrations, where no significant difference was observed among the treatment groups. Further transcriptome analyses showed that imidacloprid affected amoeba's key DEGs related to phagocytosis, cell division, morphogenesis, and cytochrome P450. Moreover, soil amoebae show both conserved and novel transcriptional responses to imidacloprid. In conclusion, this study has expanded the non-target list of imidacloprid from animals and plants to single-celled protists, and we believe the impact of neonicotinoid pesticides on the microbiome is significantly underestimated and deserves more studies.
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Affiliation(s)
- Zihe Wang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Wei Huang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhiwei Liu
- School of Life Sciences, Jiaying University, Meizhou 514015, China
| | - Jiaxiong Zeng
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China.
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17
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Nguyen TBA, Chen QL, Yan ZZ, Li C, He JZ, Hu HW. Trophic interrelationships of bacteria are important for shaping soil protist communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36992636 DOI: 10.1111/1758-2229.13143] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/16/2023] [Indexed: 06/19/2023]
Abstract
Protists occupy multiple trophic positions in soil food webs and significantly contribute to organic matter decomposition and biogeochemical cycling. Protists can ingest bacteria and fungi as main food sources while being subjected to predation of invertebrates, but our understanding of how bottom-up and top-down regulations structure protists in natural soil habitats is limited. Here, we disentangle the effects of trophic regulations to the diversity and structure of soil protists in natural settings across northern and eastern Australia. Bacterial and invertebrate diversity were identified as important drivers of the diversity of functional groups of protists. Moreover, the compositions of protistan taxonomic and functional groups were better predicted by bacteria and fungi, than by soil invertebrates. There were strong trophic interconnections between protists and bacteria in multiple organismic network analysis. Altogether, the study provided new evidence that, bottom-up control of bacteria played an important role in shaping the soil protist community structure, which can be derived from feeding preferences of protists on microbial prey, and their intimate relationships in soil functioning or environmental adaptation. Our findings advance our knowledge about the impacts of different trophic groups on key soil organismic communities, with implications for ecosystem functions and services.
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Affiliation(s)
- Thi Bao Anh Nguyen
- School of Agriculture and Food, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Qing-Lin Chen
- School of Agriculture and Food, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Zhen-Zhen Yan
- School of Agriculture and Food, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Chaoyu Li
- School of Agriculture and Food, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Ji-Zheng He
- School of Agriculture and Food, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia
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18
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Li LJ, Lin C, Huang XR, An XL, Li WJ, Su JQ, Zhu YG. Characterizing potential pathogens from intracellular bacterial community of protists in wastewater treatment plants. ENVIRONMENT INTERNATIONAL 2023; 171:107723. [PMID: 36584423 DOI: 10.1016/j.envint.2022.107723] [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] [Received: 10/19/2022] [Revised: 12/25/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Protists are a trophically diverse and biogeochemically significant component of water environments and are widely reported as hosts of bacteria. However, the potential role of protists in wastewater treatment plants (WWTPs) as reservoirs for human pathogens does not appear to have received adequate attention. Here, a combination of fluorescence-activated cell sorting and Illumina sequencing was applied to characterize the dynamics of the internalized bacterial community of the enriched protists from the influents and effluents of five WWTPs. The results showed that Proteobacteria (mainly Betaproteobacteria) dominate the intracellular bacterial communities of protists in both influents and effluents of WWTPs, accounting for 72.6% of the total intracellular bacterial communities. The most frequently detected genus was Sulfuricurvum in the influent samples, Chryseobacterium and Pseudomonas were most prevalent in the effluent samples. Compared with the influents, a more diverse and abundant intracellular bacterial community was observed in the effluents. Moreover, the potential intracellular bacterial pathogens were 26 times higher in effluents than in influents, with Pseudomonas fluorescens and Pseudomonas putida significantly enriched in effluents. This work provides insights into the dynamics of bacterial communities and potential pathogens harbored by protists in the influents and effluents from WWTPs, contributing to the improved evaluation of biosafety in WWTPs.
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Affiliation(s)
- Li-Juan Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Chenshuo Lin
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Rong Huang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Wen-Jing Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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19
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Metabarcoding Approaches for Soil Eukaryotes, Protists, and Microfauna. Methods Mol Biol 2022; 2605:1-16. [PMID: 36520386 DOI: 10.1007/978-1-0716-2871-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There have been major developments in the molecular characterization of soil protist and micrometazoan diversity, leading to a better understanding of these minute soil eukaryotes. Like in all newly developing research fields, several approaches are currently used in parallel to study these organisms. Here, we synthesize these various approaches and propose a best practice manual that should help researchers to efficiently target soil eukaryotic diversity as a whole. We cover the whole working pipeline, ranging from sampling to nucleic acids extraction to bioinformatic processing and sequence identification. Synchronous approaches to molecularly survey microbial-sized eukaryotes and other soil biodiversity groups are needed in order to provide a cumulative knowledge of soil biodiversity, as here shown for the soil eukaryome. This will be crucial in understanding the important ecosystem functions provided by soil biodiversity.
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20
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Guerra CA, Berdugo M, Eldridge DJ, Eisenhauer N, Singh BK, Cui H, Abades S, Alfaro FD, Bamigboye AR, Bastida F, Blanco-Pastor JL, de Los Ríos A, Durán J, Grebenc T, Illán JG, Liu YR, Makhalanyane TP, Mamet S, Molina-Montenegro MA, Moreno JL, Mukherjee A, Nahberger TU, Peñaloza-Bojacá GF, Plaza C, Picó S, Verma JP, Rey A, Rodríguez A, Tedersoo L, Teixido AL, Torres-Díaz C, Trivedi P, Wang J, Wang L, Wang J, Zaady E, Zhou X, Zhou XQ, Delgado-Baquerizo M. Global hotspots for soil nature conservation. Nature 2022; 610:693-698. [PMID: 36224389 DOI: 10.1038/s41586-022-05292-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/30/2022] [Indexed: 11/09/2022]
Abstract
Soils are the foundation of all terrestrial ecosystems1. However, unlike for plants and animals, a global assessment of hotspots for soil nature conservation is still lacking2. This hampers our ability to establish nature conservation priorities for the multiple dimensions that support the soil system: from soil biodiversity to ecosystem services. Here, to identify global hotspots for soil nature conservation, we performed a global field survey that includes observations of biodiversity (archaea, bacteria, fungi, protists and invertebrates) and functions (critical for six ecosystem services) in 615 composite samples of topsoil from a standardized survey in all continents. We found that each of the different ecological dimensions of soils-that is, species richness (alpha diversity, measured as amplicon sequence variants), community dissimilarity and ecosystem services-peaked in contrasting regions of the planet, and were associated with different environmental factors. Temperate ecosystems showed the highest species richness, whereas community dissimilarity peaked in the tropics, and colder high-latitudinal ecosystems were identified as hotspots of ecosystem services. These findings highlight the complexities that are involved in simultaneously protecting multiple ecological dimensions of soil. We further show that most of these hotspots are not adequately covered by protected areas (more than 70%), and are vulnerable in the context of several scenarios of global change. Our global estimation of priorities for soil nature conservation highlights the importance of accounting for the multidimensionality of soil biodiversity and ecosystem services to conserve soils for future generations.
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Affiliation(s)
- Carlos A Guerra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany. .,Institute of Biology, Martin Luther University Halle Wittenberg, Halle(Saale), Germany. .,Institute of Biology, Leipzig University, Leipzig, Germany.
| | - Miguel Berdugo
- Institute of Integrative Biology, Department of Environment Systems Science, ETH Zürich, Zürich, Switzerland
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Biology, Leipzig University, Leipzig, Germany
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Haiying Cui
- Institute of Grassland Science, School of Life Science, Northeast Normal University, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, China.,Departamento de Sistemas Físicos, Químicos y Naturales, Universidad Pablo de Olavide, Seville, Spain
| | - Sebastian Abades
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, Huechuraba, Chile
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, Huechuraba, Chile.,Instituto de Ecología & Biodiversidad (IEB), Santiago, Chile
| | | | - Felipe Bastida
- CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | | | - Asunción de Los Ríos
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jorge Durán
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,Misión Biolóxica de Galicia, Consejo Superior de Investigaciones Científicas, Pontevedra, Spain
| | - Tine Grebenc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Javier G Illán
- Department of Entomology, College of Agricultural, Human, and Natural Resource Sciences, Washington State University, Pullman, WA, USA
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Thulani P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Steven Mamet
- Department of Soil Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Marco A Molina-Montenegro
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.,CEAZA, Universidad Católica del Norte, Coquimbo, Chile
| | - José L Moreno
- CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Arpan Mukherjee
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | | | | | - César Plaza
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Sergio Picó
- Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - Jay Prakash Verma
- Institute of Environment and Sustainable Development, Banaras Hindu University, Varanasi, India
| | - Ana Rey
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Alexandra Rodríguez
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Alberto L Teixido
- Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Brazil
| | - Cristian Torres-Díaz
- Grupo de Investigación en Biodiversidad y Cambio Global (GI BCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Juntao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Ling Wang
- Institute of Grassland Science, School of Life Science, Northeast Normal University, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, China
| | - Jianyong Wang
- Institute of Grassland Science, School of Life Science, Northeast Normal University, Key Laboratory of Vegetation Ecology of the Ministry of Education, Jilin Songnen Grassland Ecosystem National Observation and Research Station, Changchun, China
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Institute of Plant Sciences, Gilat Research Center, Negev, Israel
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xin-Quan Zhou
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Seville, Spain. .,Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Seville, Spain.
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21
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N.H. Sarjuni M, A.M. Dolit S, K. Khamis A, Abd-Aziz N, R. Azman N, A. Asli U. Regenerating Soil Microbiome: Balancing Microbial CO 2 Sequestration and Emission. CARBON SEQUESTRATION 2022. [DOI: 10.5772/intechopen.104740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Soil microbiome plays a significant role in soil’s ecosystem for soils to be physically and biologically healthy. Soil health is fundamental for plant growth and crops productivity. In the introduction part, the roles and dynamics of the microbial community in soils, primarily in the cycle of soil organic carbon and CO2 release and absorption, are deliberated. Next, the impact of crop management practices and climate change on the soil carbon balance are described, as well as other issues related to soil degradation, such as unbalanced nutrient recycling and mineral weathering. In response to these issues, various approaches to soil regeneration have been developed in order to foster an efficient and active soil microbiome, thereby balancing the CO2 cycle and carbon sequestration in the soil ecosystem.
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22
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Lara E, Singer D, Geisen S. Discrepancies between prokaryotes and eukaryotes need to be considered in soil DNA-based studies. Environ Microbiol 2022; 24:3829-3839. [PMID: 35437903 PMCID: PMC9790305 DOI: 10.1111/1462-2920.16019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/30/2022]
Abstract
Metabarcoding approaches are exponentially increasing our understanding of soil biodiversity, with a major focus on the bacterial part of the microbiome. Part of the soil diversity are also eukaryotes that include fungi, algae, protists and Metazoa. Nowadays, soil eukaryotes are targeted with the same approaches developed for bacteria and archaea (prokaryotes). However, fundamental differences exist between domains. After providing a short historical overview of the developments of metabarcoding applied to environmental microbiology, we compile the most important differences between domains that prevent direct method transfers between prokaryotic and eukaryotic soil metabarcoding approaches, currently dominated by short-read sequencing. These include the existence of divergent diversity concepts and the variations in eukaryotic morphology that affect sampling and DNA extraction. Furthermore, eukaryotes experienced much more variable evolutionary rates than prokaryotes, which prevent capturing the entire eukaryotic diversity in a soil with a single amplification protocol fit for short-read sequencing. In the final part we focus on future potentials for optimization of eukaryotic metabarcoding that include superior possibility of functionally characterizing eukaryotes and to extend the current information obtained, such as by adding a real quantitative component. This review should optimize future metabarcoding approaches targeting soil eukaryotes and kickstart this promising research direction.
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Affiliation(s)
- Enrique Lara
- Real Jardín Botánico‐CSIC, Plaza de Murillo 2Madrid28014Spain
| | - David Singer
- UMR CNRS 6112 LPG‐BIAFAngers University, 2 Boulevard LavoisierAngers49045France
| | - Stefan Geisen
- Laboratory of NematologyWageningen UniversityWageningen6700 AAThe Netherlands
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23
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Guo S, Tao C, Jousset A, Xiong W, Wang Z, Shen Z, Wang B, Xu Z, Gao Z, Liu S, Li R, Ruan Y, Shen Q, Kowalchuk GA, Geisen S. Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health. THE ISME JOURNAL 2022; 16:1932-1943. [PMID: 35461357 PMCID: PMC9296445 DOI: 10.1038/s41396-022-01244-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/18/2022]
Abstract
Plant health is strongly impacted by beneficial and pathogenic plant microbes, which are themselves structured by resource inputs. Organic fertilizer inputs may thus offer a means of steering soil-borne microbes, thereby affecting plant health. Concurrently, soil microbes are subject to top-down control by predators, particularly protists. However, little is known regarding the impact of microbiome predators on plant health-influencing microbes and the interactive links to plant health. Here, we aimed to decipher the importance of predator-prey interactions in influencing plant health. To achieve this goal, we investigated soil and root-associated microbiomes (bacteria, fungi and protists) over nine years of banana planting under conventional and organic fertilization regimes differing in Fusarium wilt disease incidence. We found that the reduced disease incidence and improved yield associated with organic fertilization could be best explained by higher abundances of protists and pathogen-suppressive bacteria (e.g. Bacillus spp.). The pathogen-suppressive actions of predatory protists and Bacillus spp. were mainly determined by their interactions that increased the relative abundance of secondary metabolite Q genes (e.g. nonribosomal peptide synthetase gene) within the microbiome. In a subsequent microcosm assay, we tested the interactions between predatory protists and pathogen-suppressive Bacillus spp. that showed strong improvements in plant defense. Our study shows how protistan predators stimulate disease-suppressive bacteria in the plant microbiome, ultimately enhancing plant health and yield. Thus, we suggest a new biological model useful for improving sustainable agricultural practices that is based on complex interactions between different domains of life.
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Affiliation(s)
- Sai Guo
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.,Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.,Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Alexandre Jousset
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.,Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.,Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Zhe Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.,Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.,Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Beibei Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou, 570228, PR China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.,Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Zhilei Gao
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Shanshan Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.,Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China. .,Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - Yunze Ruan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bio-resources, College of Tropical Crops, Hainan University, Haikou, 570228, PR China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China. .,Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, PR China.
| | - George A Kowalchuk
- Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, 6700 AA, Wageningen, The Netherlands.,Netherlands Department of Terrestrial Ecology, Netherlands Institute for Ecology, (NIOO-KNAW), 6708 PB, Wageningen, The Netherlands
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24
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Jassey VEJ, Hamard S, Lepère C, Céréghino R, Corbara B, Küttim M, Leflaive J, Leroy C, Carrias JF. Photosynthetic microorganisms effectively contribute to bryophyte CO 2 fixation in boreal and tropical regions. ISME COMMUNICATIONS 2022; 2:64. [PMID: 37938283 PMCID: PMC9723567 DOI: 10.1038/s43705-022-00149-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 04/26/2023]
Abstract
Photosynthetic microbes are omnipresent in land and water. While they critically influence primary productivity in aquatic systems, their importance in terrestrial ecosystems remains largely overlooked. In terrestrial systems, photoautotrophs occur in a variety of habitats, such as sub-surface soils, exposed rocks, and bryophytes. Here, we study photosynthetic microbial communities associated with bryophytes from a boreal peatland and a tropical rainforest. We interrogate their contribution to bryophyte C uptake and identify the main drivers of that contribution. We found that photosynthetic microbes take up twice more C in the boreal peatland (~4.4 mg CO2.h-1.m-2) than in the tropical rainforest (~2.4 mg CO2.h-1.m-2), which corresponded to an average contribution of 4% and 2% of the bryophyte C uptake, respectively. Our findings revealed that such patterns were driven by the proportion of photosynthetic protists in the moss microbiomes. Low moss water content and light conditions were not favourable to the development of photosynthetic protists in the tropical rainforest, which indirectly reduced the overall photosynthetic microbial C uptake. Our investigations clearly show that photosynthetic microbes associated with bryophyte effectively contribute to moss C uptake despite species turnover. Terrestrial photosynthetic microbes clearly have the capacity to take up atmospheric C in bryophytes living under various environmental conditions, and therefore potentially support rates of ecosystem-level net C exchanges with the atmosphere.
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Affiliation(s)
- Vincent E J Jassey
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Université Toulouse 3-Paul Sabatier (UT3), CNRS, 31062, Toulouse, France.
| | - Samuel Hamard
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Université Toulouse 3-Paul Sabatier (UT3), CNRS, 31062, Toulouse, France
| | - Cécile Lepère
- Laboratoire Microorganismes, Génome Et Environnement (LMGE), Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
| | - Régis Céréghino
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Université Toulouse 3-Paul Sabatier (UT3), CNRS, 31062, Toulouse, France
| | - Bruno Corbara
- Laboratoire Microorganismes, Génome Et Environnement (LMGE), Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
| | - Martin Küttim
- Institute of Ecology, School of Natural Sciences and Health, Tallinn University, Uus-Sadama 5, 10120, Tallinn, Estonia
| | - Joséphine Leflaive
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Université Toulouse 3-Paul Sabatier (UT3), CNRS, 31062, Toulouse, France
| | - Céline Leroy
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
- ECOFOG, AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles, Campus Agronomique, Kourou, France
| | - Jean-François Carrias
- Laboratoire Microorganismes, Génome Et Environnement (LMGE), Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
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25
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Xiong W, Delgado-Baquerizo M, Shen Q, Geisen S. Pedogenesis shapes predator-prey relationships within soil microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 828:154405. [PMID: 35276178 DOI: 10.1016/j.scitotenv.2022.154405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/22/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Pedogenesis determines soil physicochemical properties and many biodiversity facets, including belowground microbial bacteria and fungi. At the local scale, top-down predation by microbial protists regulates the soil microbiome, while the microbiome also affects protistan communities. However, it remains unknown how pedogenesis affects protistan communities and the potential protist-microbiome predator-prey relationships. With 435 soil samples representing different stages of pedogenesis ranging in soil age from centuries to millennia, we examined the influence of pedogenesis on the main protistan groups, and the interrelationships between protistan predators and microbial prey biomass. We revealed an enrichment in the diversity of total protists across pedogenesis and increasing richness of phototrophic protists in the medium compared with the early stages of pedogenesis. The richness of predatory protists accumulated throughout pedogenesis, which was more strongly determined by microbial biomass than environmental factors. Predator-prey associations were stronger in the young and the medium soils than in the older soils, likely because prey biomass accumulated in the latter and might be no longer limit predators. Together, our work provides evidence that pedogenesis shapes predatory protists differently than their prey, leading to shifts in predator-prey relationships. This knowledge is critical to better understand how soil food webs develop across soil development which might lead to changes in ecosystem functions.
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Affiliation(s)
- Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico, 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.
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving Fertilizers, Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing 210095, Jiangsu, People's Republic of China.
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, 6700 ES Wageningen, the Netherlands.
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26
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Yu H, He Z, He Z, Yan Q, Shu L. Soil Amoebae Affect Iron and Chromium Reduction through Preferential Predation between Two Metal-Reducing Bacteria. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:9052-9062. [PMID: 35544746 DOI: 10.1021/acs.est.1c08069] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Soil protists are essential but often overlooked in soil and could impact microbially driven element cycling in natural ecosystems. However, how protists influence heavy metal cycling in soil remains poorly understood. In this study, we used a model protist, Dictyostelium discoideum, to explore the effect of interactions between soil amoeba and metal-reducing bacteria on the reduction of soil Fe(III) and Cr(VI). We found that D. discoideum could preferentially prey on the Fe(III)-reducing bacterium Shewanella decolorationis S12 and significantly decrease its biomass. Surprisingly, this predation pressure also stimulated the activity of a single S. decolorationis S12 bacterium to reduce Fe(III) by enhancing the content of electron-transfer protein cyt c, intracellular ATP synthesis, and reactive oxygen species (e.g., H2O2). We also found that D. discoideum could not prey on the Cr(VI)-reducing bacterium Brevibacillus laterosporus. In contrast, B. laterosporus became edible to amoebae in the presence of S. decolorationis S12, and their Cr(VI) reduction ability decreased under amoeba predation pressure. This study provides direct evidence that protists can affect the Cr and Fe cycling via the elective predation pressure on the metal-reducing bacteria, broadening our horizons of predation of protists on soil metal cycling.
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Affiliation(s)
- Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhenzhen He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
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27
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Amacker N, Gao Z, Hu J, Jousset ALC, Kowalchuk GA, Geisen S. Protist feeding patterns and growth rate are related to their predatory impacts on soil bacterial communities. FEMS Microbiol Ecol 2022; 98:6582216. [PMID: 35524686 PMCID: PMC9126823 DOI: 10.1093/femsec/fiac057] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/22/2022] [Accepted: 05/05/2022] [Indexed: 11/15/2022] Open
Abstract
Predatory protists are major consumers of soil micro-organisms. By selectively feeding on their prey, they can shape soil microbiome composition and functions. While different protists are known to show diverging impacts, it remains impossible to predict a priori the effect of a given species. Various protist traits including phylogenetic distance, growth rate and volume have been previously linked to the predatory impact of protists. Closely-related protists,however, also showed distinct prey choices which could mirror specificity in their dietary niche. We, therefore, aimed to estimate the dietary niche breadth and overlap of eight protist isolates on 20 bacterial species in plate assays. To assess the informative value of previously suggested and newly proposed (feeding-related) protist traits, we related them to the impacts of predation of each protist on a protist-free soil bacterial community in a soil microcosm via 16S rRNA gene amplicon sequencing. We could demonstrate that each protist showed a distinct feeding pattern in vitro. Further, the assayed protist feeding patterns and growth rates correlated well with the observed predatory impacts on the structure of soil bacterial communities. We thus conclude that in vitro screening has the potential to inform on the specific predatory impact of selected protists.
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Affiliation(s)
- Nathalie Amacker
- Ecology and Biodiversity group, Institute of Environmental Biology, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Zhilei Gao
- Ecology and Biodiversity group, Institute of Environmental Biology, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jie Hu
- Ecology and Biodiversity group, Institute of Environmental Biology, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,UMR 6553 Ecobio, CNRS, University of Rennes, Avenue du Général Leclerc, 35042, Rennes Cedex, France
| | - Alexandre L C Jousset
- Ecology and Biodiversity group, Institute of Environmental Biology, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - George A Kowalchuk
- Ecology and Biodiversity group, Institute of Environmental Biology, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, 6700 ES Wageningen, The Netherlands
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Calderón‐Sanou I, Zinger L, Hedde M, Martinez‐Almoyna C, Saillard A, Renaud J, Gielly L, Khedim N, Lionnet C, Ohlmann M, Consortium O, Münkemüller T, Thuiller W. Energy and physiological tolerance explain multi‐trophic soil diversity in temperate mountains. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Irene Calderón‐Sanou
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Lucie Zinger
- Département de biologie Institut de Biologie de l’ENS (IBENS) École normale supérieure CNRS INSERM Université PSL Paris France
| | - Mickael Hedde
- Eco&Sols Univ Montpellier CIRAD INRA IRD Montpellier SupAgro Montpellier France
| | - Camille Martinez‐Almoyna
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Amelie Saillard
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Julien Renaud
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Ludovic Gielly
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Norine Khedim
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
- Univ. Savoie Mont‐Blanc Univ. Grenoble Alpes CNRS EDYTEM Chambéry France
| | - Clement Lionnet
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Marc Ohlmann
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | | | - Tamara Münkemüller
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
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29
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Geisen S, Thakur MP. Special Issue–Causes and consequences of microbiome changes. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2021.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Aslani F, Geisen S, Ning D, Tedersoo L, Bahram M. Towards revealing the global diversity and community assembly of soil eukaryotes. Ecol Lett 2021; 25:65-76. [PMID: 34697894 DOI: 10.1111/ele.13904] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 01/01/2023]
Abstract
Soil fungi, protists, and animals (i.e., the eukaryome) play a critical role in key ecosystem functions in terrestrial ecosystems. Yet, we lack a holistic understanding of the processes shaping the global distribution of the eukaryome. We conducted a molecular analysis of 193 composite soil samples spanning the world's major biomes. Our analysis showed that the importance of selection processes was higher in the community assemblage of smaller-bodied and wider niche breadth organisms. Soil pH and mean annual precipitation were the primary determinants of the community structure of eukaryotic microbes and animals, respectively. We further found contrasting latitudinal diversity patterns and strengths for soil eukaryotic microbes and animals. Our results point to a potential link between body size and niche breadth of soil eukaryotes and the relative effect of ecological processes and environmental factors in driving their biogeographic patterns.
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Affiliation(s)
- Farzad Aslani
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Daliang Ning
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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31
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Cross-Sectional Analysis of the Microbiota of Human Gut and Its Direct Environment in a Household Cohort with High Background of Antibiotic Use. Microorganisms 2021; 9:microorganisms9102115. [PMID: 34683436 PMCID: PMC8539590 DOI: 10.3390/microorganisms9102115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/31/2021] [Accepted: 09/29/2021] [Indexed: 01/01/2023] Open
Abstract
Comprehensive insight into the microbiota of the gut of humans and animals, as well as their living environment, in communities with a high background of antibiotic use and antibiotic resistance genes is scarce. Here, we used 16S rRNA gene sequencing to describe the (dis)similarities in the microbiota of feces from humans (n = 107), domestic animals (n = 36), water (n = 89), and processed food (n = 74) in a cohort with individual history of antibiotic use in northern Vietnam. A significantly lower microbial diversity was observed among individuals who used antibiotics in the past 4 months (n = 44) compared to those who did not (n = 63). Fecal microbiota of humans was more diverse than nonhuman samples and shared a small part of its amplicon sequence variants (ASVs) with feces from animals (7.4% (3.2–9.9)), water (2.2% (1.2–2.8)), and food (3.1% (1.5–3.1)). Sharing of ASVs between humans and companion animals was not associated with the household. However, we did observe a correlation between an Enterobacteriaceae ASV and the presence of extended-spectrum beta-lactamase CTX-M-group-2 encoding genes in feces from humans and animals (p = 1.6 × 10−3 and p = 2.6 × 10−2, respectively), hinting toward an exchange of antimicrobial-resistant strains between reservoirs.
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Abstract
Microbes dominate the planet's biodiversity in terms of species number and by driving essential Earth system functions such as the carbon cycle. Soils contain most of this microbial biodiversity. Only recently, we have started to better understand the diversity of bacteria and fungi at the global scale. Here, I list my views on some shortcomings of contemporary soil microbiome studies and potential solutions to overcome them. In particular, I highlight that (soil) microbiome studies should become more holistic in terms of (i) taxa and resolution targeted, (ii) by adding functional to taxonomic information, and (iii) by integrating temporal analysis into spatial analyses. Considering those elements with the methodology that is now available will advance our understanding on (soil) microbiomes to reliably address major ecological hypotheses and to advance insights into the importance for life on Earth.
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Affiliation(s)
- Stefan Geisen
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
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Fermani P, Metz S, Balagué V, Descy JP, Morana C, Logares R, Massana R, Sarmento H. Microbial eukaryotes assemblages and potential novel diversity in four tropical East-African Great Lakes. FEMS Microbiol Ecol 2021; 97:6335480. [PMID: 34338764 DOI: 10.1093/femsec/fiab114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/30/2021] [Indexed: 01/21/2023] Open
Abstract
East-African Great Lakes are old and unique natural resources heavily utilized by their bordering countries. In those lakes, ecosystem functioning is dominated by pelagic processes, where microorganisms are key components, however protistan diversity is barely known. We investigated the community composition of small eukaryotes (< 10 µm) in surface waters of four African Lakes (Kivu, Edward, Albert and Victoria) by sequencing the 18S rRNA gene. Moreover, in the meromictic Lake Kivu, two stations were vertically studied. We found high protistan diversity distributed in 779 operational taxonomic units (OTUs), spanning in eleven high-rank lineages, being Alveolata (31%), Opisthokonta (20%) and Stramenopiles (17%) the most represented supergroups. Surface protistan assemblage were associated to conductivity and productivity gradients; whereas depth, had a strong effect on protistan community in Kivu, with higher contribution of heterotrophic organisms. Approximately 40% of OTUs had low similarity (< 90%) with reported sequences in public databases, these were mostly coming from deep anoxic waters of Kivu, suggesting a high extent of novel diversity. We also detected several taxa so far considered exclusive of marine ecosystems. Our results unveiled a complex and largely undescribed protistan community, in which several lineages have adapted to different niches after crossing the salinity boundary.
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Affiliation(s)
- Paulina Fermani
- Laboratorio de Ecología Acuática. Instituto Tecnológico de Chascomús (UNSAM-CONICET) Chascomús, Buenos Aires, Argentina
| | - Sebastián Metz
- University of Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | - Vanessa Balagué
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | | | - Cédric Morana
- Unit of Chemical Oceanography, University of Liège, Liège, Belgium
| | - Ramiro Logares
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Ramon Massana
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Hugo Sarmento
- Departamento de Hidrobiologia (DHb), Universidade Federal de São Carlos, São Carlos - SP, Brazil
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34
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Wilden B, Traunspurger W, Geisen S. Inventory of the benthic eukaryotic diversity in the oldest European lake. Ecol Evol 2021; 11:11207-11215. [PMID: 34429912 PMCID: PMC8366835 DOI: 10.1002/ece3.7907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 11/22/2022] Open
Abstract
We have profound knowledge on biodiversity on Earth including plants and animals. In the recent decade, we have also increased our understanding on microorganisms in different hosts and the environment. However, biodiversity is not equally well studied among different biodiversity groups and Earth's systems with eukaryotes in freshwater sediments being among the least known. In this study, we used high-throughput sequencing of the 18S rRNA gene to investigate the entire diversity of benthic eukaryotes in three distinct habitats (littoral sediment and hard substrate, profundal sediment) of Lake Ohrid, the oldest European lake. Eukaryotic sequences were dominated by annelid and arthropod animals (54% of all eukaryotic reads) and protists (Ochrophyta and Ciliophora; together 40% of all reads). Eukaryotic diversity was 15% higher in the deep profundal than on either near-surface hard substrates or littoral sediments. The three habitats differed in their taxonomic and functional community composition. Specifically, heterotrophic organisms accounted for 92% of the reads in the profundal, whereas phototrophs accounted for 43% on the littoral hard substrate. The profundal community was the most homogeneous, and its network was the most complex, suggesting its highest stability among the sampled habitats.
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Affiliation(s)
- Benjamin Wilden
- Department of Animal EcologyBielefeld UniversityBielefeldGermany
| | | | - Stefan Geisen
- Laboratory of NematologyWageningen UniversityWageningenThe Netherlands
- Netherlands Department of Terrestrial EcologyNetherlands Institute for Ecology (NIOO‐KNAW)WageningenThe Netherlands
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