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Wu C, Wu Y, Li F, Ding X, Yi S, Hang S, Ge F, Zhang M. Reducing the accumulation of cadmium and phenanthrene in rice by optimizing planting spacing: Role of low-abundance but core rhizobacterial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171856. [PMID: 38522531 DOI: 10.1016/j.scitotenv.2024.171856] [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: 01/05/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
Optimizing planting spacing is a common agricultural practice for enhancing rice growth. However, its effect on the accumulation of cadmium (Cd) and phenanthrene (Phen) in soil-rice systems and the response mechanisms of rhizobacteria to co-contaminants remain unclear. This study found that reducing rice planting spacing to 5 cm and 10 cm significantly decreased the bioavailability of Cd (by 7.9 %-29.5 %) and Phen (by 12.9 %-47.6 %) in the rhizosphere soil by converting them into insoluble forms. The increased accumulation of Cd and Phen in roots and iron plaques (IPs) ultimately led to decreased Cd (by 32.2 %-39.9 %) and Phen (by 4.2 %-17.3 %) levels in brown rice, and also significantly affected the composition of rhizobacteria. Specifically, reducing rice planting spacing increased the abundance of low-abundance but core rhizobacteria in the rhizosphere soil and IPs, including Bacillus, Clostridium, Sphingomonas, Paenibacillus, and Leifsonia. These low-abundance but core rhizobacteria exhibited enhanced metabolic capacities for Cd and Phen, accompanied by increased abundances of Cd-resistance genes (e.g., czcC and czcB) and Phen-degradation genes (e.g., pahE4 and pahE1) within the rhizosphere soil and IPs. Reduced planting spacing had no noticeable impact on rice biomass. These findings provide new insights into the role of low-abundance but core rhizobacterial communities in Cd and Phen uptake by rice, highlighting the potential of reduced planting spacing as an eco-friendly strategy for ensuring the safety of rice production on contaminated paddy soils.
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Affiliation(s)
- Chen Wu
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan 411105, China; Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan 411105, China; The Experimental Teaching Center in College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Yujun Wu
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan 411105, China; Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan 411105, China; The Experimental Teaching Center in College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Feng Li
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan 411105, China; Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan 411105, China; The Experimental Teaching Center in College of Environment and Resources, Xiangtan University, Xiangtan 411105, China.
| | - Xiangxi Ding
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan 411105, China; Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan 411105, China; The Experimental Teaching Center in College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Shengwei Yi
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan 411105, China; Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan 411105, China; The Experimental Teaching Center in College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Sicheng Hang
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan 411105, China; Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan 411105, China; The Experimental Teaching Center in College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Fei Ge
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Hunan Provincial University Key Laboratory for Environmental and Ecological Health, Xiangtan 411105, China; Hunan Provincial University Key Laboratory for Environmental Behavior and Control Principle of New Pollutants, Xiangtan 411105, China; The Experimental Teaching Center in College of Environment and Resources, Xiangtan University, Xiangtan 411105, China
| | - Ming Zhang
- Department of Environmental Engineering, China Jiliang University, Hangzhou 310018, China
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Banerjee S, Zhao C, Garland G, Edlinger A, García-Palacios P, Romdhane S, Degrune F, Pescador DS, Herzog C, Camuy-Velez LA, Bascompte J, Hallin S, Philippot L, Maestre FT, Rillig MC, van der Heijden MGA. Biotic homogenization, lower soil fungal diversity and fewer rare taxa in arable soils across Europe. Nat Commun 2024; 15:327. [PMID: 38184663 PMCID: PMC10771452 DOI: 10.1038/s41467-023-44073-6] [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: 03/01/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024] Open
Abstract
Soil fungi are a key constituent of global biodiversity and play a pivotal role in agroecosystems. How arable farming affects soil fungal biogeography and whether it has a disproportional impact on rare taxa is poorly understood. Here, we used the high-resolution PacBio Sequel targeting the entire ITS region to investigate the distribution of soil fungi in 217 sites across a 3000 km gradient in Europe. We found a consistently lower diversity of fungi in arable lands than grasslands, with geographic locations significantly impacting fungal community structures. Prevalent fungal groups became even more abundant, whereas rare groups became fewer or absent in arable lands, suggesting a biotic homogenization due to arable farming. The rare fungal groups were narrowly distributed and more common in grasslands. Our findings suggest that rare soil fungi are disproportionally affected by arable farming, and sustainable farming practices should protect rare taxa and the ecosystem services they support.
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Affiliation(s)
- Samiran Banerjee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA.
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
| | - Cheng Zhao
- ETH Zurich, Institute for Environmental Decisions, 8092, Zurich, Switzerland
| | - Gina Garland
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Anna Edlinger
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
- Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3, 6708 PB, Wageningen, The Netherlands
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland
| | - Sana Romdhane
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Florine Degrune
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
| | - David S Pescador
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28940, Madrid, Spain
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, 28933, Móstoles, Spain
| | - Chantal Herzog
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland
| | - Lennel A Camuy-Velez
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, 58102, USA
| | - Jordi Bascompte
- University of Zurich, Department of Evolutionary Biology and Environmental Studies, 8057, Zurich, Switzerland
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 750 07, Uppsala, Sweden
| | - Laurent Philippot
- University Bourgogne Franche Comte, INRAE, Institut Agro Dijon, Agroecologie, Dijon, France
| | - Fernando T Maestre
- Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente del Raspeig, Alicante, Spain
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente, del Raspeig, Alicante, Spain
| | - Matthias C Rillig
- Freie Universität Berlin, Institute of Biology, Altensteinstr. 6, 14195, Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195, Berlin, Germany
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil Interactions Group, 8046, Zurich, Switzerland.
- University of Zurich, Department of Plant and Microbial Biology, 8057, Zurich, Switzerland.
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Kajan K, Osterholz H, Stegen J, Gligora Udovič M, Orlić S. Mechanisms shaping dissolved organic matter and microbial community in lake ecosystems. WATER RESEARCH 2023; 245:120653. [PMID: 37742402 DOI: 10.1016/j.watres.2023.120653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 07/17/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
Lakes are active components of the global carbon cycle and host a range of processes that degrade and modify dissolved organic matter (DOM). Through the degradation of DOM molecules and the synthesis of new compounds, microbes in aquatic environments strongly and continuously influence chemodiversity, which can feedback to influence microbial diversity. Developing a better understanding of the biodiversity patterns that emerge along spatial and environmental gradients is one of the key objectives of community ecology. A changing climate may affect ecological feedback, including those that affect microbial communities. To maintain the function of a lake ecosystem and predict carbon cycling in the environment, it is increasingly important to understand the coupling between microbial and DOM diversity. To unravel the biotic and abiotic mechanisms that control the structure and patterns of DOM and microbial communities in lakes, we combined high-throughput sequencing and ultra-high resolution mass spectrometry together with a null modeling approach. The advantage of null models is their ability to evaluate the relative influences of stochastic and deterministic assembly processes in both DOM and microbial community assemblages. The present study includes spatiotemporal signatures of DOM and the microbial community in six temperate lakes contrasting continental and Mediterranean climates during the productive season. Different environmental conditions and nutrient sources characterized the studied lakes. Our results have shown high covariance between molecular-level DOM diversity and the diversity of individual microbial communities especially with diversity of microeukaryotes and free-living bacteria indicating their dynamic feedback. We found that the differences between lakes and climatic regions were mainly reflected in the diversity of DOM at the molecular formula-level and the microeukaryota community. Furthermore, using null models the DOM assembly was governed by deterministic variable selection operating consistently and strongly within and among lakes. In contrast, microbial community assembly processes were highly variable across lakes with different trophic status and climatic regions. Difference in the processes governing DOM and microbial composition does not indicate weak coupling between these components, rather it suggests that distinct factors may be influencing microbial communities and DOM assemblages separately. Further understanding of the DOM-microbe coupling (or lack thereof) is key to formulating predictive models of future lake ecology and function.
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Affiliation(s)
- Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | - Helena Osterholz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany; Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - James Stegen
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, P. O. Box 999, Richland, WA 99352, USA
| | - Marija Gligora Udovič
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia.
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Ramond P, Siano R, Sourisseau M, Logares R. Assembly processes and functional diversity of marine protists and their rare biosphere. ENVIRONMENTAL MICROBIOME 2023; 18:59. [PMID: 37443126 PMCID: PMC10347826 DOI: 10.1186/s40793-023-00513-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023]
Abstract
BACKGROUND The mechanisms shaping the rare microbial biosphere and its role in ecosystems remain unclear. We developed an approach to study ecological patterns in the rare biosphere and use it on a vast collection of marine microbiomes, sampled in coastal ecosystems at a regional scale. We study the assembly processes, and the ecological strategies constituting the rare protistan biosphere. Using the phylogeny and morpho-trophic traits of these protists, we also explore their functional potential. RESULTS Taxonomic community composition remained stable along rank abundance curves. Conditionally rare taxa, driven by selection processes, and transiently rare taxa, with stochastic distributions, were evidenced along the rank abundance curves of all size-fractions. Specific taxa within the divisions Sagenista, Picozoa, Telonemia, and Choanoflagellida were rare across time and space. The distribution of traits along rank abundance curves outlined a high functional redundancy between rare and abundant protists. Nevertheless, trophic traits illustrated an interplay between the trophic groups of different size-fractions. CONCLUSIONS Our results suggest that rare and abundant protists are evolutionary closely related, most notably due to the high microdiversity found in the rare biosphere. We evidenced a succession of assembly processes and strategies of rarity along rank abundance curves that we hypothesize to be common to most microbiomes at the regional scale. Despite high functional redundancy in the rare protistan biosphere, permanently rare protists were evidenced, and they could play critical functions as bacterivores and decomposers from within the rare biosphere. Finally, changes in the composition of the rare protistan biosphere could be influenced by the trophic regime of aquatic ecosystems. Our work contributes to understanding the role of rare protists in microbiomes.
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Affiliation(s)
- Pierre Ramond
- Institute of Marine Sciences (ICM), Department of Marine Biology and Oceanography, CSIC, Barcelona, Catalunya, 08003, Spain.
| | - Raffaele Siano
- DYNECO/Pelagos, Ifremer-Centre de Brest, Technopôle Brest Iroise, Plouzané, 29280, France
| | - Marc Sourisseau
- DYNECO/Pelagos, Ifremer-Centre de Brest, Technopôle Brest Iroise, Plouzané, 29280, France
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), Department of Marine Biology and Oceanography, CSIC, Barcelona, Catalunya, 08003, Spain
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Araujo ASF, Jia X, Miranda ARL, Pereira APDA, Melo VMM, Rocha SMB, Costa RM, Saraiva TCDS, Mendes LW, Salles JF. Changes in the bacterial rare biosphere after permanent application of composted tannery sludge in a tropical soil. CHEMOSPHERE 2023; 313:137487. [PMID: 36521745 DOI: 10.1016/j.chemosphere.2022.137487] [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: 10/06/2022] [Revised: 11/21/2022] [Accepted: 12/03/2022] [Indexed: 06/17/2023]
Abstract
Composted tannery sludge (CTS) promotes shifts in soil chemical properties, affecting microbial communities. Although the effect of CTS application on the bacterial community has been studied, it is unclear whether this impact discriminates between the dominant and rare species. This present study investigated how the dominant and rare bacterial communities respond over time to different concentrations of CTS application (0, 2.5, 5, 10, and 20 tons/ha) for 180 days. The richness of operational taxonomic units (OTU) was 30-fold higher in the rare than in the dominant biosphere. While some phyla shifted their relative abundance differently in the dominant and rare biosphere, some genera increased their relative abundance under higher CTS concentrations, such as Nocardioides (∼100%), Rubrobacter (∼300%), and Nordella (∼400%). Undominated processes largely governed the dominant biosphere (76.97%), followed by homogeneous (12.51%) and variable (8.03%) selection, and to a lesser extent, the dispersal limitation (2.48%). The rare biosphere was driven by the CTS application as evidenced by the exclusively homogeneous selection (100%). This study showed that the rare biosphere was more sensitive to changes in soil chemical parameters due to CTS application, which evidences the importance explore this portion of the bacterial community for its biotechnological use in contaminated soils.
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Affiliation(s)
| | - Xiu Jia
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747AG, the Netherlands
| | | | | | | | | | | | | | - Lucas William Mendes
- Centro de Energia Nuclear na Agricultura, Universidade de Sao Paulo, Piracicaba, SP Brazil
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen 9747AG, the Netherlands
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Ye F, Sun Z, Moore SS, Wu J, Hong Y, Wang Y. Discrepant Effects of Flooding on Assembly Processes of Abundant and Rare Communities in Riparian Soils. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02152-z. [PMID: 36502425 DOI: 10.1007/s00248-022-02152-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Numerous rare species coexist with a few abundant species in microbial communities and together play an essential role in riparian ecosystems. Relatively little is understood, however, about the nature of assembly processes of these communities and how they respond to a fluctuating environment. In this study, drivers controlling the assembly of abundant and rare subcommunities for bacteria and archaea in a riparian zone were determined, and their resulting patterns on these processes were analyzed. Abundant and rare bacteria and archaea showed a consistent variation in the community structure along the riparian elevation gradient, which was closely associated with flooding frequency. The community assembly of abundant bacteria was not affected by any measured environmental variables, while soil moisture and ratio of submerged time to exposed time were the two most decisive factors determining rare bacterial community. Assembly of abundant archaeal community was also determined by these two factors, whereas rare archaea was significantly associated with soil carbon-nitrogen ratio and total carbon content. The assembly process of abundant and rare bacterial subcommunities was driven respectively by dispersal limitation and variable selection. Undominated processes and dispersal limitation dominated the assembly of abundant archaea, whereas homogeneous selection primarily driven rare archaea. Flooding may therefore play a crucial role in determining the community assembly processes by imposing disturbances and shaping soil niches. Overall, this study reveals the assembly patterns of abundant and rare communities in the riparian zone and provides further insight into the importance of their respective roles in maintaining a stable ecosystem during times of environmental perturbations.
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Affiliation(s)
- Fei Ye
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Zhaohong Sun
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Selina Sterup Moore
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Padua, Italy
| | - Jiapeng Wu
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China
| | - Yiguo Hong
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
| | - Yu Wang
- Institute of Environmental Research at Greater Bay, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, 510006, China.
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