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Zhang R, Rong L, Zhang L. Soil nutrient variability mediates the effects of erosion on soil microbial communities: results from a modified topsoil removal method in an agricultural field in Yunnan plateau, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3659-3671. [PMID: 34392483 DOI: 10.1007/s11356-021-15894-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Soil erosion can affect the nature and distribution of soil carbon and nutrients, directly and indirectly influencing microbially facilitated processes of mineralization, ammoniation, and nitrification, thus affecting soil nutrients cycling. However, little is known about how soil erosion affects soil microorganisms. Since 2012, we conducted a modified soil erosion simulation experiment of topsoil removal method in an agricultural field to simulate erosion depths of 5, 10, 20, 30, and 40 cm versus a control (0 cm). The results showed that Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, Actinobacteria, and Firmicutes were the dominant soil microbial (here: Bacteria and Archaea) phyla, and Acidothermus, Candidatus Solibacter, Acidibacter, Bryobacter, and Actinospica were the dominant genera in all samples. The relative abundance of Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, Thaumarchaeota, Acidothermus, Candidatus Solibacter, Acidibacter, Bryobacter, Actinospica, and Rhodanobacter decreased with the increase of erosion depths, while Chloroflexi and Firmicutes increased with the increase of erosion depths. Soil microbial community structure was altered significantly at 30- and 40-cm soil erosion depth in comparison to control. Soil nutrient variability caused by soil erosion had a greater impact on soil microbial community composition than that of soil mechanical composition. Soil erosion indirectly affected microbial community composition through negative effects on soil available potassium, total phosphorus, total nitrogen, and sand content. We thus highlight the importance of soil nutrients monitoring in different soil erosion levels to make the proper ecological restoration strategies to improve soil environment which soil microorganisms depend on.
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Affiliation(s)
- Ruihuan Zhang
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, People's Republic of China
| | - Li Rong
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, People's Republic of China.
- Yunnan Key Laboratory of International Rivers and Trans-boundary Eco-security, Yunnan University, Kunming, People's Republic of China.
| | - Lanlan Zhang
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, People's Republic of China
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102
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Jiao S, Lu Y, Wei G. Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems. GLOBAL CHANGE BIOLOGY 2022; 28:140-153. [PMID: 34610173 DOI: 10.1111/gcb.15917] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/30/2021] [Indexed: 05/14/2023]
Abstract
Belowground biodiversity supports multiple ecosystem functions and services that humans rely on. However, there is a dearth of studies exploring the determinants of the biodiversity-ecosystem function (BEF) relationships, particularly in intensely managed agricultural ecosystems. Here, we reported significant and positive relationships between soil biodiversity of multiple organism groups and multiple ecosystem functions in 228 agricultural fields, relating to crop yield, nutrient provisioning, element cycling, and pathogen control. The relationships were influenced by the types of organisms that soil phylotypes with larger sizes or at higher trophic levels, for example, invertebrates or protist predators, appeared to exhibit weaker or no BEF relationships when compared to those with smaller sizes or at lower trophic levels, for example, archaea, bacteria, fungi, and protist phototrophs. Particularly, we highlighted the role of soil network complexity, reflected by co-occurrence patterns among multitrophic-level organisms, in enhancing the link between soil biodiversity and ecosystem functions. Our results represent a significant advance in forecasting the impacts of belowground multitrophic organisms on ecosystem functions in agricultural systems, and suggest that soil multitrophic network complexity should be considered a key factor in enhancing ecosystem productivity and sustainability under land-use intensification.
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Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, China
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103
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Yu Y, Liu L, Wang J, Zhang Y, Xiao C. Effects of warming on the bacterial community and its function in a temperate steppe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148409. [PMID: 34146803 DOI: 10.1016/j.scitotenv.2021.148409] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
As a significant environmental issue, global warming will have a significant impact on soil microorganisms, especially soil bacteria. However, the effects of warming on the network structure of bacterial communities and the function of ecosystems remain unclear. Therefore, we examined the effects of three-year simulated field warming on the complexity of soil bacterial communities and predicted functions in a temperate steppe of Inner Mongolia. Warming significantly increased the α-diversity of bacteria in 2018 but did not affect it in 2019 and 2020. Warming increased network complexity and stability and keystone taxa, and these bacterial taxa also associated more closely with each other, indicating that the protection of interactions between bacterial taxa is very important for the conservation of biodiversity. Warming significantly increased aerobic chemoheterotrophy, ureolysis, and chemoheterotrophy, suggesting that warming increased the ability of bacteria to decompose organic matter and the emission of greenhouse gases, such as CO2 and CH4. Collectively, warming will alter soil bacterial community structure and its potential functions, further affecting key functions in grassland belowground ecosystems.
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Affiliation(s)
- Yang Yu
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Lu Liu
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Jing Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Yushu Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Chunwang Xiao
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China.
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104
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Lahlali R, Ibrahim DS, Belabess Z, Kadir Roni MZ, Radouane N, Vicente CS, Menéndez E, Mokrini F, Barka EA, Galvão de Melo e Mota M, Peng G. High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects. Heliyon 2021; 7:e08142. [PMID: 34693062 PMCID: PMC8515249 DOI: 10.1016/j.heliyon.2021.e08142] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 08/08/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022] Open
Abstract
Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.
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Affiliation(s)
- Rachid Lahlali
- Plant Pathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknes, BP S/40, 50001, Meknes, Morocco
| | - Dina S.S. Ibrahim
- Department of Nematodes Diseases and Central Lab of Biotechnology, Plant Pathology Research Institute, Agricultural Research Center (ARC), 12619, Egypt
| | - Zineb Belabess
- Plant Protection Laboratory. Regional Center of Agricultural Research of Oujda, National Institute of Agricultural Research, Avenue Mohamed VI, BP428 60000 Oujda, Morocco
| | - Md Zohurul Kadir Roni
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences (JIRCAS), 1091-1 Maezato-Kawarabaru, Ishigaki, Okinawa, 907-0002, Japan
| | - Nabil Radouane
- Plant Pathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknes, BP S/40, 50001, Meknes, Morocco
- Department of Biology, Laboratory of Functional Ecology and Environmental Engineering, FST-Fez, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Cláudia S.L. Vicente
- MED – Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research (IIFA), Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
- INIAV, I.P. - Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Esther Menéndez
- INIAV, I.P. - Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, 2780-159 Oeiras, Portugal
- Department of Microbiology and Genetics / Spanish-Portuguese Institute for Agricultural Research (CIALE). University of Salamanca, 37007, Salamanca, Spain
| | - Fouad Mokrini
- Plant Protection Laboratory, INRA, Centre Régional de la Recherche Agronomique (CRRA), Rabat, Morocco
| | - Essaid Ait Barka
- Unité de Recherche Résistance Induite et Bio-protection des Plantes, EA 4707, USC, INRAe1488, Université de Reims Champagne-Ardenne, France
| | - Manuel Galvão de Melo e Mota
- NemaLab, MED – Mediterranean Institute for Agriculture, Environment and Development & Department of Biology, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Gary Peng
- Saskatoon Research Development Centre, Agriculture and Agri-Food, Saskatchewan, Canada
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105
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Zhang W, Shen J, Wang J. Linking pollution to biodiversity and ecosystem multifunctionality across benthic-pelagic habitats of a large eutrophic lake: A whole-ecosystem perspective. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117501. [PMID: 34380215 DOI: 10.1016/j.envpol.2021.117501] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 05/24/2021] [Accepted: 05/29/2021] [Indexed: 05/27/2023]
Abstract
Biodiversity loss is often an important driver of the deterioration of ecosystem functioning in freshwater ecosystems. However, it is far from clear how multiple ecosystem functions (i.e., ecosystem multifunctionality, EMF) relate to biodiversity across the benthic-pelagic habitats of entire ecosystems or how environmental stress such as eutrophication and heavy metals enrichment might regulate the biodiversity-EMF relationships. Here, we explored the biodiversity and EMF across benthic-pelagic habitats of the large eutrophic Lake Taihu in China, and further examined abiotic factors underlying the spatial variations in EMF and its relationships with biodiversity. In our results, EMF consistently showed positive relationships to the biodiversity of multiple taxonomic groups, such as benthic bacteria, bacterioplankton and phytoplankton. Both sediment heavy metals and total phosphorus significantly explained the spatial variations in the EMF, whereas the former were more important than the latter. Further, sediment heavy metals mediated EMF through the diversity of benthic bacteria and bacterioplankton, while nutrients such as phosphorus in both the sediments and overlaying water altered EMF via phytoplankton diversity. This indicates the importance of pollution in regulating the relationships between biodiversity and EMF in freshwater environments. Our findings provide evidence that freshwater biodiversity loss among phytoplankton and bacteria will likely weaken ecosystem functioning. Our results further suggest that abiotic factors such as heavy metals, beyond nutrient enrichment, may provide relatively earlier signals of impaired ecosystem functioning during eutrophication process.
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Affiliation(s)
- Weizhen Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Ji Shen
- School of Geography and Ocean Science, Nanjing University, Nanjing, 210023, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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106
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Li X, Chen J, Zhang Q, Li X, Zhou X, Tao Y. Microbial community responses to multiple soil disinfestation change drivers. Appl Microbiol Biotechnol 2021; 105:6993-7007. [PMID: 34453565 DOI: 10.1007/s00253-021-11528-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 08/11/2021] [Accepted: 08/15/2021] [Indexed: 11/28/2022]
Abstract
Soil continuous cropping obstacles lead to yield and economic losses in agriculture. Reductive soil disinfestation (RSD) is an effective technology for alleviating it. However, the key factors influencing microbial community composition and how do they promote functional transformation of core microbes under RSD practice remain poorly understood. Hence, a short-term field experiment was performed integrating real-time polymerase chain reaction, average well color development (AWCD), and MiSeq pyrosequencing to investigate relationships between environmental factors and microorganisms in five different disinfestation treatments, i.e., untreated monoculture soil (CK), soil with high temperature heating (HT), soil with dazomet (DZ), RSD with sugarcane bagasse (SB), or with bean dregs (BD). The results showed that compared to non-RSD treatments, both RSD treatments significantly increased soil microbial abundance and soil available K and organic matter (OM). Further analysis found that available K and OM were the key factors inducing microbial community change. Additionally, relative to non-RSD treatments, the relative abundances of phyla Proteobacteria, Acidobacteria, Rokubacteria, and Ascomycota were higher, whereas those of Actinobacteria, Gemmatimonadetes, and Basidiomycota were lower in RSD treatments. Changes in microbial diversity and abundance led to variation of soil microbial community functions. AWCD and community function prediction showed that, in contrast with non-RSD treatments, soil metabolism activity significantly increased, bacterial community functions including terpenoids and polyketides metabolism, signal transduction and cell motility increased, and the number of saprotroph fungi increased under RSD treatments. Overall, RSD incorporated with sugarcane bagasse or bean dregs efficiently improved soil fertility, and considerably increased soil microbial activity and function, which may benefit future sustainable agriculture production. Key points • Reductive soil disinfestation can alleviate continuous cropping obstacles by improving soil fertility. • Organic matter and available potassium as the key factors affected microbial community reconstruction and function. • Reductive soil disinfestation can improve soil metabolic activity and functional diversity by altering microorganism community.
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Affiliation(s)
- Xin Li
- Hunan Vegetable Research Institute, Changsha, 410125, Hunan, China
| | - Jie Chen
- Hunan Academy of Agricultural Sciences, Changsha, 410125, Hunan, China
| | - Qingzhuang Zhang
- Hunan Vegetable Research Institute, Changsha, 410125, Hunan, China
| | - Xuefeng Li
- Hunan Vegetable Research Institute, Changsha, 410125, Hunan, China
| | - Xiangyu Zhou
- Hunan Vegetable Research Institute, Changsha, 410125, Hunan, China
| | - Yu Tao
- Hunan Vegetable Research Institute, Changsha, 410125, Hunan, China.
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107
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Retention of Matured Trees to Conserve Fungal Diversity and Edible Sporocarps from Short-Rotation Pinus radiata Plantations in Ethiopia. J Fungi (Basel) 2021; 7:jof7090702. [PMID: 34575740 PMCID: PMC8471983 DOI: 10.3390/jof7090702] [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: 07/23/2021] [Revised: 08/08/2021] [Accepted: 08/21/2021] [Indexed: 11/19/2022] Open
Abstract
This study is conducted in the short-rotation plantations from the Afromontane Region of Ethiopia. Sporocarps were sampled weekly in a set of permanent plots (100 m2) in young, medium-aged, and mature Pinus radiata (Don) plantations. Fungal richness, diversity, and sporocarp yields were estimated. Composite soil samples were also collected from each plot to determine explanatory edaphic variables for taxa composition. We collected 92 fungal taxa, of which 8% were ectomycorrhizal (ECM). Taxa richness, the Shannon diversity index, and ECM species richness were higher in mature stands. Interestingly, 26% of taxa were classified as edible. Sporocarp yield showed increasing trends towards matured stands. OM and C/N ratio significantly affected fungal composition and sporocarp production. The deliberate retention of mature trees in a patch form rather than clear felling of the plantations could be useful to conserve and promote fungal diversity and production, including valuable taxa such as Morchella, Suillus, and Tylopilus in older stands. This approach has important implications for forest floor microhabitats, which are important for macrofungal occurrence and production. Thus, this strategy could improve the economic outputs of these plantations in the Afromontane Region, while the mature trees could serve as a bridge for providing fungal inocula to the new plantations.
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108
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Metagenomic Study of the Community Structure and Functional Potentials in Maize Rhizosphere Microbiome: Elucidation of Mechanisms behind the Improvement in Plants under Normal and Stress Conditions. SUSTAINABILITY 2021. [DOI: 10.3390/su13148079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The community of microbes in the rhizosphere region is diverse and contributes significantly to plant growth and crop production. Being an important staple and economic crop, the maize rhizosphere microbiota has been studied in the past using culture-dependent techniques. However, these limited culturing methods often do not help in understanding the complex community of microbes in the rhizosphere. Moreover, the vital biogeochemical processes carried out by these organisms are yet to be fully characterized. Herein, shotgun metagenomics, which enables the holistic study of several microbial environments, was employed to examine the community structure and functional potentials of microbes in the maize rhizosphere and to assess the influence of environmental variables on these. The dominant microbial phyla found in the soil environments include Actinobacteria, Microsporidia, Bacteroidetes, Thaumarchaeota, Proteobacteria and Firmicutes. Carbohydrate metabolism, protein metabolism and stress metabolism constitute the major functional categories in the environments. The beta diversity analysis indicated significant differences (p = 0.01) in the community structure and functional categories across the samples. A correlation was seen between the physical and chemical properties of the soil, and the structural and functional diversities. The canonical correspondence analysis carried out showed that phosphorus, N-NO3, potassium and organic matter were the soil properties that best influenced the structural and functional diversities of the soil microbes. It can be inferred from this study that the maize rhizosphere is a hotspot for microorganisms of agricultural and biotechnological importance which can be used as bioinoculants for sustainable agriculture.
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109
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Hugoni M, Galland W, Lecomte S, Bruto M, Barakat M, Piola F, Achouak W, Haichar FEZ. Effects of the Denitrification Inhibitor "Procyanidins" on the Diversity, Interactions, and Potential Functions of Rhizosphere-Associated Microbiome. Microorganisms 2021; 9:1406. [PMID: 34209897 PMCID: PMC8306639 DOI: 10.3390/microorganisms9071406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 12/04/2022] Open
Abstract
Some plant secondary metabolites, such as procyanidins, have been demonstrated to cause biological denitrification inhibition (BDI) of denitrifiers in soils concomitantly with a gain in plant biomass. The present work evaluated whether procyanidins had an impact on the diversity of nontarget microbial communities that are probably involved in soil fertility and ecosystem services. Lettuce plants were grown in two contrasting soils, namely Manziat (a loamy sand soil) and Serail (a sandy clay loam soil) with and without procyanidin amendment. Microbial diversity was assessed using Illumina sequencing of prokaryotic 16S rRNA gene and fungal ITS regions. We used a functional inference to evaluate the putative microbial functions present in both soils and reconstructed the microbial interaction network. The results showed a segregation of soil microbiomes present in Serail and Manziat that were dependent on specific soil edaphic variables. For example, Deltaproteobacteria was related to total nitrogen content in Manziat, while Leotiomycetes and Firmicutes were linked to Ca2+ in Serail. Procyanidin amendment did not affect the diversity and putative activity of microbial communities. In contrast, microbial interactions differed according to procyanidin amendment, with the results showing an enrichment of Entotheonellaeota and Mucoromycota in Serail soil and of Dependentiae and Rozellomycetes in Manziat soil.
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Affiliation(s)
- Mylène Hugoni
- VetAgro Sup, UMR Ecologie Microbienne, Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69622 Villeurbanne, France; (M.H.); (W.G.); (S.L.)
- Institut Universitaire de France (IUF), CEDEX 05, F-75231 Paris, France
| | - William Galland
- VetAgro Sup, UMR Ecologie Microbienne, Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69622 Villeurbanne, France; (M.H.); (W.G.); (S.L.)
| | - Solène Lecomte
- VetAgro Sup, UMR Ecologie Microbienne, Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, F-69622 Villeurbanne, France; (M.H.); (W.G.); (S.L.)
| | - Maxime Bruto
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon, Université Lyon 1, CNRS, UMR5558, 43 bd du 11 Novembre 1918, F-69622 Villeurbanne, France;
| | - Mohamed Barakat
- Laboratory of Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille University, CEA, CNRS, BIAM, F-13108 Saint-Paul-Lez-Durance, France; (M.B.); (W.A.)
| | - Florence Piola
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France;
| | - Wafa Achouak
- Laboratory of Microbial Ecology of the Rhizosphere (LEMiRE), Aix Marseille University, CEA, CNRS, BIAM, F-13108 Saint-Paul-Lez-Durance, France; (M.B.); (W.A.)
| | - Feth el Zahar Haichar
- Microbiologie, Adaptation, Pathogénie, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, 10 rue Raphaël Dubois, F-69622 Villeurbanne, France
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Oszust K, Pylak M, Frąc M. Trichoderma-Based Biopreparation with Prebiotics Supplementation for the Naturalization of Raspberry Plant Rhizosphere. Int J Mol Sci 2021; 22:ijms22126356. [PMID: 34198606 PMCID: PMC8232080 DOI: 10.3390/ijms22126356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 11/16/2022] Open
Abstract
The number of raspberry plants dying from a sudden outbreak of gray mold, verticillium wilt, anthracnosis, and phytophthora infection has increased in recent times, leading to crop failure. The plants suffer tissue collapse and black roots, symptoms similar to a Botrytis-Verticillium-Colletotrichum-Phytophthora disease complex. A sizeable number of fungal isolates were acquired from the root and rhizosphere samples of wild raspberries from different locations. Subsequent in vitro tests revealed that a core consortium of 11 isolates of selected Trichoderma spp. was the most essential element for reducing in phytopathogen expansion. For this purpose, isolates were characterized by the efficiency of their antagonistic properties against Botrytis, Verticillium, Colletotrichum and Phytophthora isolates and with hydrolytic properties accelerating the decomposition of organic matter in the soil and thus making nutrients available to plants. Prebiotic additive supplementation with a mixture of adonitol, arabitol, erythritol, mannitol, sorbitol, and adenosine was proven in a laboratory experiment to be efficient in stimulating the growth of Trichoderma isolates. Through an in vivo pathosystem experiment, different raspberry naturalization-protection strategies (root inoculations and watering with native Trichoderma isolates, applied separately or simultaneously) were tested under controlled phytotron conditions. The experimental application of phytopathogens attenuated raspberry plant and soil properties, while Trichoderma consortium incorporation exhibited a certain trend of improving these features in terms of a short-term response, depending on the pathosystem and naturalization strategy. What is more, a laboratory-scale development of a biopreparation for the naturalization of the raspberry rhizosphere based on the Trichoderma consortium was proposed in the context of two application scenarios. The first was a ready-to-use formulation to be introduced while planting (pellets, gel). The second was a variant to be applied with naturalizing watering (soluble powder).
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111
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Song X, Wang Q, Jin P, Chen X, Tang S, Wei C, Li K, Ding X, Tang Z, Fu H. Enhanced biostimulation coupled with a dynamic groundwater recirculation system for Cr(VI) removal from groundwater: A field-scale study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145495. [PMID: 33770851 DOI: 10.1016/j.scitotenv.2021.145495] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
A large gap exists between laboratory findings and successful implementation of bioremediation technologies for the treatment of chromium (Cr)-contaminated sites. This work conducted the enhanced bioremediation of Cr(VI) in situ via the addition of organic carbon (ethanol) coupled with a dynamic groundwater recirculation (DGR)-based system in a field-scale study. The DGR system was applied to successfully (1) remove Cr(VI) from groundwater via enhanced flushing by the recirculation system and (2) deliver the biostimulant to the heterogeneous subsurface environment, including a sand/cobble aquifer and a fractured bedrock aquifer. The results showed that the combined extraction and bioreduction of Cr(VI) were able to reduce Cr(VI) concentrations from 1000 to 2000 mg/L to below the clean-up goal of 0.1 mg/L within the operation period of 52 days. The effectiveness of Cr(VI) bioremediation and the relationship between microbial communities and geochemical parameters were evaluated. Multiple-line of evidence demonstrated that the introduction of ethanol significantly stimulated a variety of bacteria, including those responsible for denitrification, sulfate reduction and reduction of Cr(VI), which contributed to the establishment of reducing conditions in both aquifers. Cr(VI) was removed from groundwater via combined mechanisms of physical removal through the DGR system and the bioreduction of Cr(VI) followed by precipitation. In particular, it was found competitive growth among Cr(VI)-reducing bacteria (such as the enrichment of Geobacter, along with the reduced relative abundance of Acinetobacter and Pseudomonas) was induced by ethanol injection. Furthermore, Cr(VI), total organic carbon, NO2-, and SO42- played important roles in shaping the composition of the microbial community and its functions.
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Affiliation(s)
- Xin Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Peng Jin
- EPCR Innovation and Technology LLC, PA 19406, USA
| | - Xing Chen
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shiyue Tang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changlong Wei
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Kang Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiaoyan Ding
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiwen Tang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Fu
- Nanjing Kangdi Environmental Protection Technology Co., LTD, Nanjing 21000, China
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Drivers controlling spatial and temporal variation of microbial properties and dissolved organic forms (DOC and DON) in fen soils with persistently low water tables. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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113
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Liu C, Wang S, Yan J, Huang Q, Li R, Shen B, Shen Q. Soil fungal community affected by regional climate played an important role in the decomposition of organic compost. ENVIRONMENTAL RESEARCH 2021; 197:111076. [PMID: 33794176 DOI: 10.1016/j.envres.2021.111076] [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: 01/12/2021] [Revised: 03/20/2021] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
A large amount of organic compost, produced with agricultural and breeding industry wastes by composting, is widely used in agriculture in China. The microbial decomposition of organic compost is a major flux in the nutrition cycle in sustainable agricultural soils. To explore the mechanism of organic compost mineralization in soil, in situ decomposition experiments of organic compost buried in soils were arranged in three different latitude regions located in Jilin, Jiangsu, and Yunnan in China. The results showed that organic compost had different decomposition rates at the three different sites, with the highest decomposition rate in Yunnan, followed by Jiangsu and Jilin. The decomposition rates of unsterilized organic compost were significantly greater than those of sterilized organic compost, indicating that the microorganisms in organic compost also made important contributions to the decomposition process. The soil microbial diversity and community structure among the three sites were significantly different. The fungal community, especially fungal richness, rather than the bacterial community in the soil, plays a major role in the decomposition of organic compost. The annual average temperature is an important environmental factor affecting fungal richness. This study will provide a reference for formulating agricultural fertilization models in different regions.
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Affiliation(s)
- Chao 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, China; The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Sainan 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, China; The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jiao 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, China; The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qian Huang
- 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, China; The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, 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, China; The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Biao 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, China; The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, 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, China; The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
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114
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Effects of Different Land Use Types on Active Autotrophic Ammonia and Nitrite Oxidizers in Cinnamon Soils. Appl Environ Microbiol 2021; 87:e0009221. [PMID: 33837020 DOI: 10.1128/aem.00092-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Land use types with different disturbance gradients show many variations in soil properties, but the effects of different land use types on soil nitrifying communities and their ecological implications remain poorly understood. Using 13CO2-DNA-based stable isotope probing (DNA-SIP), we examined the relative importance and active community composition of ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in soils under three land use types, forest, cropland, and greenhouse vegetable soil, representing three interference gradients. Soil net nitrification rate was in the order forest soil > cropland soil > greenhouse vegetable soil. DNA-SIP showed that active AOA outcompeted AOB in the forest soil, whereas AOB outperformed AOA in the cropland and greenhouse vegetable soils. Cropland soil was richer in NOB than in AOA and AOB. Phylogenetic analysis revealed that ammonia oxidation in the forest soil was predominantly catalyzed by the AOA Nitrosocosmicus franklandus cluster within the group 1.1b lineage. The 13C-labeled AOB were overwhelmingly dominated by Nitrosospira cluster 3 in the cropland soil. The active AOB Nitrosococcus watsonii lineage was observed in the greenhouse vegetable soil, and it played an important role in nitrification. Active NOB communities were closely affiliated with Nitrospira in the forest and cropland soils, and with Nitrolancea and Nitrococcus in the greenhouse vegetable soil. Canonical correlation analysis showed that soil pH and organic matter content significantly affected the active nitrifier community composition. These results suggest that land use types with different disturbance gradients alter the distribution of active nitrifier communities by affecting soil physicochemical properties. IMPORTANCE Nitrification plays an important role in the soil N cycle, and land use management has a profound effect on soil nitrifiers. It is unclear how different gradients of land use affect active ammonia-oxidizing archaea and bacteria and nitrite-oxidizing bacteria. Our research is significant because we determined the response of nitrifiers to human disturbance, which will greatly improve our understanding of the niche of nitrifiers and the differences in their physiology.
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115
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Ding L, Wang P. Afforestation suppresses soil nitrogen availability and soil multifunctionality on a subtropical grassland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143663. [PMID: 33360134 DOI: 10.1016/j.scitotenv.2020.143663] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/04/2020] [Accepted: 11/07/2020] [Indexed: 06/12/2023]
Abstract
Microbes simultaneously drive multiple functions (multifunctionality) that support human well-being. However, the structure and function of microbial communities and their impact on soil multifunctionality following grassland afforestation remains unknown, thus hindering our ability to formulate conservation policies. We compared soil bacterial and fungal communities, soil abiotic properties, and soil nitrogen (N) function and multifunctionality in the afforested sites that were previously grassland, on a subtropical plateau in China. We also explored the degree to which the niche complementarity effect and the selection effect of microbes are linked to soil N function and multifunctionality. We found that afforestation of grassland significantly decreased pH, available N concentration and density, and soil multifunctionality. However, afforestation significantly increased C (carbon) limitation and shifted soil microbes from being limited by N to, instead, being co-limited by N and P (phosphorus). The significant decrease in available N was primarily driven by soil microbes. In shaping soil N availability, the effect of bacterial diversities was stronger than that of fungal diversities, and the effect of fungal functional diversities was stronger than that of bacterial functional diversities. The effect of functional diversities was greater than that of all the significant changes in the functions and, also, the significant changes in the N-related functions. These results further emphasized that functional niche complementarity dominated soil N availability. In addition, bacterial taxonomic diversities showed positive effects of niche complementarity on soil multifunctionality; ultimately, the losses in bacterial taxonomic diversities derived from the increases in C limitation and the shifts in NP limitation combined to impaired soil multifunctionality. Our results suggested that the optimization of soil microbial functional diversities might increase soil N availability, and that minimizing losses of soil microbial taxonomic diversities by optimizing soil abiotic environments might improve soil multifunctionality.
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Affiliation(s)
- Leilei Ding
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
| | - Puchang Wang
- Guizhou Institution of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China.
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116
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Feng Y, Yang J, Liu W, Yan Y, Wang Y. Hydroxyapatite as a passivator for safe wheat production and its impacts on soil microbial communities in a Cd-contaminated alkaline soil. JOURNAL OF HAZARDOUS MATERIALS 2021; 404:124005. [PMID: 33069995 DOI: 10.1016/j.jhazmat.2020.124005] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/28/2020] [Accepted: 09/14/2020] [Indexed: 05/21/2023]
Abstract
The remediation of Cd-contaminated alkaline soil plays a critical role in safe wheat production. In this study, hydroxyapatite (HAP), a functional environmental remediation material, was selected to investigate the effects of HAP on cadmium accumulation in winter wheat (Triticum aestivum L.), Cd bioavailability in alkaline soil moderately polluted with Cd (2.46 mg kg-1) and the soil bacterial community via pot experiments. The results showed HAP effectively inhibited Cd accumulation in the grains of two investigated wheat cultivars by hindering root uptake. The Cd concentrations decreased by 49.9-81.9%, and 35.7-92.4% in the grains of Zhoumai-30 and Zhengmai-7698, respectively. HAP increased the soil pH and reduced the bioavailability of Cd. 16S rRNA sequencing analysis indicated that the changes of soil physicochemical properties changed the diversity and composition of the bacterial community by increasing the relative abundance of beneficial soil bacteria. These results demonstrated the application of 2.5% HAP combined with planting Zhengmai-7698 treatment was a potential remediation method for safe wheat production, and also benefited soil P and N cycling by increasing the relative abundance of beneficial bacteria. The good performance of HAP in inhabiting Cd accumulation in wheat grains indicated it is a promising material for safe wheat production.
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Affiliation(s)
- Ya Feng
- College of Chemistry & Environmental Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianjun Yang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Wei Liu
- College of Chemistry & Environmental Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
| | - Yubo Yan
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China; School of Chemistry and Chemical Engineering, Huaiyin Normal University, Huai'an 223300, China
| | - Yihao Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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117
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Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil. Sci Rep 2021; 11:831. [PMID: 33437021 PMCID: PMC7804402 DOI: 10.1038/s41598-020-80840-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/29/2020] [Indexed: 01/04/2023] Open
Abstract
Soil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.
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118
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Taskin E, Boselli R, Fiorini A, Misci C, Ardenti F, Bandini F, Guzzetti L, Panzeri D, Tommasi N, Galimberti A, Labra M, Tabaglio V, Puglisi E. Combined Impact of No-Till and Cover Crops with or without Short-Term Water Stress as Revealed by Physicochemical and Microbiological Indicators. BIOLOGY 2021; 10:biology10010023. [PMID: 33401423 PMCID: PMC7824270 DOI: 10.3390/biology10010023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 01/05/2023]
Abstract
Simple Summary Farming systems in which no-till (NT) and cover crops (CC) are preferred as alternatives to conventional practices have the promise of being more resilient and climate smart. Our field study aimed to assess the long-term impact of NT plus CC, with vs. without short-term water stress, on soil microbial biodiversity, enzymatic activities, and the distribution of C and N pools within soil aggregates. We found that the diversity of bacteria and fungi in the soil was positively affected by NT + CC, especially under water stress conditions. Under NT + CC, the presence of important plant growth-promoting rhizobacteria was revealed. Soil enzymatic activity confirmed the depleting impact of conventional tillage. Soil C and N were increased under NT + CC due to their inclusion into large soil aggregates that are beneficial for long-term C and N stabilization in soils. Water stress was found to have detrimental effects on aggregates formation and limited C and N inclusion within aggregates. The microbiological and physicochemical parameters correlation supported the hypothesis that long-term NT + CC is a valuable strategy for sustainable agroecosystems, due to its contribution to soil C and N stabilization while enhancing the biodiversity and enzymes. Abstract Combining no-till and cover crops (NT + CC) as an alternative to conventional tillage (CT) is generating interest to build-up farming systems’ resilience while promoting climate change adaptation in agriculture. Our field study aimed to assess the impact of long-term NT + CC management and short-term water stress on soil microbial communities, enzymatic activities, and the distribution of C and N within soil aggregates. High-throughput sequencing (HTS) revealed the positive impact of NT + CC on microbial biodiversity, especially under water stress conditions, with the presence of important rhizobacteria (e.g., Bradyrhizobium spp.). An alteration index based on soil enzymes confirmed soil depletion under CT. C and N pools within aggregates showed an enrichment under NT + CC mostly due to C and N-rich large macroaggregates (LM), accounting for 44% and 33% of the total soil C and N. Within LM, C and N pools were associated to microaggregates within macroaggregates (mM), which are beneficial for long-term C and N stabilization in soils. Water stress had detrimental effects on aggregate formation and limited C and N inclusion within aggregates. The microbiological and physicochemical parameters correlation supported the hypothesis that long-term NT + CC is a promising alternative to CT, due to the contribution to soil C and N stabilization while enhancing the biodiversity and enzymes.
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Affiliation(s)
- Eren Taskin
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Roberta Boselli
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
| | - Andrea Fiorini
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
| | - Chiara Misci
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Federico Ardenti
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
| | - Francesca Bandini
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
| | - Lorenzo Guzzetti
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Davide Panzeri
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Nicola Tommasi
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Andrea Galimberti
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Massimo Labra
- Dipartimento di Biotecnologie e Bioscienze (BtBs), Università degli Studi di Milano-Bicocca, 20126 Milano, Italy; (L.G.); (D.P.); (N.T.); (A.G.); (M.L.)
| | - Vincenzo Tabaglio
- Dipartimento di Scienze delle Produzioni Vegetali Sostenibili (DI.PRO.VE.S.), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (R.B.); (A.F.); (F.A.)
- Correspondence: ; Tel.: +39-05-2359-9222
| | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per la sostenibilità della filiera agro-alimentare (DISTAS), Facoltà di Scienze Agrarie Alimentari ed Ambientali, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy; (E.T.); (C.M.); (F.B.); (E.P.)
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119
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Yu Z, Ling L, Singh BP, Luo Y, Xu J. Gain in carbon: Deciphering the abiotic and biotic mechanisms of biochar-induced negative priming effects in contrasting soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141057. [PMID: 32795757 DOI: 10.1016/j.scitotenv.2020.141057] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/04/2020] [Accepted: 07/17/2020] [Indexed: 06/11/2023]
Abstract
The biochar-induced priming effects (PEs) were investigated by applying maize straw (C4) derived biochar to eight C3 soils, with a gradient of pH and a sub-gradient of soil organic carbon (SOC). To decipher the physicochemical and microbial mechanisms, we adopted C-isotopic analysis, high-throughput sequencing and multivariate statistical analyses such as random forest (RF) and structure equation modeling (SEM). Negative and neutral PEs were observed up to -48.5% of relative PEs during 28 days of incubation. All the acidic soils exhibited negative PEs, so as the neutral Alfisol and alkaline Aridisol, which had a suppression effect on SOC mineralization accounted for -29.4 and -32.0% of relative PEs. Among all abiotic factors, soil silt-clay fraction and the initial pH values play the most important roles in PEs determination through directly inhibiting PEs by protection SOC and indirectly shaping bacterial communities respectively. On the whole community level, biochar treatments defined much less microbiome (0.6% and 1.2% for variance of bacterial and fungal community) than soil types (93.5% and 83.3% respectively) across soils. Thus, the initial community (i.e., bacteria alpha-diversity and copiotrophic bacteria as revealed by SEM) of different soils might be more critical for PE prediction. Furthermore, co-occurrence network analysis indicated out-competition of fungi by bacteria with increase of mutual exclusion and decrease of fungal occupancy. This could exacerbate negative PEs in soils with lower bacterial alpha-diversity and dominance by copiotrophys due to less functional complementary for recalcitrant SOC decomposition.
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Affiliation(s)
- Zhuyun Yu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Hebei Key Laboratory of Wetland Ecology and Conservation, Hengshui University, Hengshui 053000, China
| | - Lu Ling
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Bhupinder Pal Singh
- Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW 2568, Australia
| | - Yu Luo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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120
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Craig H, Kennedy JP, Devlin DJ, Bardgett RD, Rowntree JK. Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: A field-based experiment. Ecol Evol 2020; 10:13957-13967. [PMID: 33391694 PMCID: PMC7771162 DOI: 10.1002/ece3.6989] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/03/2020] [Accepted: 10/14/2020] [Indexed: 11/25/2022] Open
Abstract
Loss of plant biodiversity can result in reduced abundance and diversity of associated species with implications for ecosystem functioning. In ecosystems low in plant species diversity, such as Neotropical mangrove forests, it is thought that genetic diversity within the dominant plant species could play an important role in shaping associated communities. Here, we used a manipulative field experiment to study the effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on the composition and richness of associated soil bacterial communities. Using terminal restriction fragment length polymorphism (T-RFLP) community fingerprinting, we found that bacterial community composition differed among R. mangle maternal genotypes but not with genetic diversity. Bacterial taxa richness, total soil nitrogen, and total soil carbon were not significantly affected by maternal genotypic identity or genetic diversity of R. mangle. Our findings show that genotype selection in reforestation projects could influence soil bacterial community composition. Further research is needed to determine what impact these bacterial community differences might have on ecosystem processes, such as carbon and nitrogen cycling.
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Affiliation(s)
- Hayley Craig
- Department of Earth and Environmental SciencesThe University of ManchesterManchesterUK
| | - John Paul Kennedy
- Department of Natural Sciences, Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
- Smithsonian Marine StationFort PierceFLUSA
| | - Donna J. Devlin
- Department of Life SciencesTexas A&M University Corpus ChristiCorpus ChristiTXUSA
| | - Richard D. Bardgett
- Department of Earth and Environmental SciencesThe University of ManchesterManchesterUK
| | - Jennifer K. Rowntree
- Department of Natural Sciences, Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
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Montes de Oca-Vásquez G, Solano-Campos F, Vega-Baudrit JR, López-Mondéjar R, Vera A, Moreno JL, Bastida F. Organic amendments exacerbate the effects of silver nanoparticles on microbial biomass and community composition of a semiarid soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140919. [PMID: 32711321 DOI: 10.1016/j.scitotenv.2020.140919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/24/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Increased utilization of silver nanoparticles (AgNPs) can result in an accumulation of these particles in the environment. The potential detrimental effects of AgNPs in soil may be associated with the low fertility of soils in semiarid regions that are usually subjected to restoration through the application of organic amendments. Microbial communities are responsible for fundamental processes related to soil fertility, yet the potential impacts of low and realistic AgNPs concentrations on soil microorganisms are still unknown. We studied the effects of realistic citrate-stabilized AgNPs concentrations (0.015 and 1.5 μg kg-1) at two exposure times (7 and 30 days) on a sandy clay loam Mediterranean soil unamended (SU) and amended with compost (SA). We assessed soil microbial biomass (microbial fatty acids), soil enzyme activities (urease, β-glucosidase, and alkaline phosphatase), and composition of the microbial community (bacterial 16S rRNA gene and fungal ITS2 sequencing) in a microcosm experiment. In the SA, the two concentrations of AgNPs significantly decreased the bacterial biomass after 7 days of incubation. At 30 days of incubation, only a significant decrease in the Gram+ was observed at the highest AgNPs concentration. In contrast, in the SU, there was a significant increase in bacterial biomass after 30 days of incubation at the lowest AgNPs concentration. Overall, we found that fungal biomass was more resistant to AgNPs than bacterial biomass, in both SA and SU. Further, the AgNPs changed the composition of the soil bacterial community in SA, the relative abundance of some bacterial taxa in SA and SU, and fungal richness in SU at 30 days of incubation. However, AgNPs did not affect the activity of extracellular enzymes. This study demonstrates that the exposure time and organic amendments modulate the effects of realistic concentrations of AgNPs in the biomass and composition of the microbial community of a Mediterranean soil.
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Affiliation(s)
- Gabriela Montes de Oca-Vásquez
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica; Doctorado en Ciencias Naturales para el Desarrollo (DOCINADE), Instituto Tecnológico de Costa Rica, Universidad Nacional, Universidad Estatal a Distancia, Costa Rica.
| | - Frank Solano-Campos
- School of Biological Sciences, Universidad Nacional, Campus Omar Dengo, 86-3000 Heredia, Costa Rica
| | - José R Vega-Baudrit
- National Nanotechnology Laboratory, National Center for High Technology, 10109 Pavas, San José, Costa Rica; Laboratory of Polymer Science and Technology, School of Chemistry, Universidad Nacional, Campus Omar Dengo, 86-3000 Heredia, Costa Rica
| | - Rubén López-Mondéjar
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, Praha 4 14220, Czech Republic
| | - Alfonso Vera
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - José L Moreno
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100 Murcia, Spain
| | - Felipe Bastida
- CEBAS-CSIC. Department of Soil and Water Conservation. Campus Universitario de Espinardo, 30100 Murcia, Spain
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Land-use intensity indirectly affects soil multifunctionality via a cascade effect of plant diversity on soil bacterial diversity. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Manasa MRK, Katukuri NR, Darveekaran Nair SS, Haojie Y, Yang Z, Guo RB. Role of biochar and organic substrates in enhancing the functional characteristics and microbial community in a saline soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 269:110737. [PMID: 32425164 DOI: 10.1016/j.jenvman.2020.110737] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
In sustaining the soil quality, soil salinization has become a major challenge due to the increasing salinity rate of 10% annually. Despite, the serious concerns, the influence of soil amendments on microbial communities and its related attributes have limited findings. Therefore, the present study aims to investigate the potential of three various biochars, digestate (DI), and its compost (COM) in reclamation of saline soil under closed ecosystem. The decrease in the pH was displayed by lignite char, and electrical conductivity by lignite char plus COM addition among all the treatments. The subside in Na +, with a significant rise in K +, was exhibited in soils amended with DI plus DI biochar as a combined ameliorate over control. The negative priming effects on native soil organic carbon (nSOC) due to the decreased substrate bioavailability, in corn straw and DI biochars ameliorates were noted. The urease and alkaline phosphatase activity were pronounced higher in COM. However, the catalase and fluorescein diacetate activity were greater in lignite char plus DI and COM respectively. The co-addition of biochar and organic substrates shifted microbial community, is in correspondence with the relative abundance of the phylum. Overall, the abundance of Firmicutes and Actinobacteria was higher in soils under a combination of lignite char with DI and COM respectively. Likely, the abundance of Euryarchaeota was dominant in the co-application of corn straw biochar and DI. Redundancy analysis revealed the intactness between bacterial genera and their metabolisms with K +, and Mg 2+. PICRUSt disclosed the enhanced metabolic functions in soil with amalgam of DI and its biochar. The findings showed that the application of DI and its biochar mixture, as an amendment could be a better approach in the long-term reclamation of saline soil.
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Affiliation(s)
- M R K Manasa
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Naveen Reddy Katukuri
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Sree Sankar Darveekaran Nair
- Single-Cell Center, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yang Haojie
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zhiman Yang
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China; Dalian National Laboratory for Clean Energy, Dalian, 116023, PR China.
| | - Rong Bo Guo
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, PR China; Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province, 266101, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China; Dalian National Laboratory for Clean Energy, Dalian, 116023, PR China.
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Wakung’oli M, Amoo AE, Enagbonma BJ, Babalola OO. Termite Societies Promote the Taxonomic and Functional Diversity of Archaeal Communities in Mound Soils. BIOLOGY 2020; 9:biology9060136. [PMID: 32630446 PMCID: PMC7345372 DOI: 10.3390/biology9060136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 12/04/2022]
Abstract
Recent studies involving microbial communities in termite mounds have been more focused on bacteria and fungi with little attention given to archaea, which play significant roles in nutrient cycling. Thus, we aimed at characterizing the archaeal taxonomic and functional diversity in two termite mound soils using the shotgun sequencing method with the assumption that termite activities could promote archaeal diversity. Our findings showed that termite mound soils have archaeal groups that are taxonomically different from their surrounding soils, with Euryarchaeota, Korarchaeota, and Nanoarchaeota being predominant while Thaumarchaeota and Crenarchaeota were predominant in the surrounding soils. Additionally, the observed nutrient pathways: phosphorus, nitrogen, and sulfur were all significantly more predominant in termite mound soils than in their comparative surrounding soils. Alpha diversity showed that archaea were not significantly different within termite mound soils and the surrounding soils. The beta diversity revealed significant differences in the archaeal taxonomic composition and their functional categories between the termite mounds and surrounding soils. Our canonical correspondence analysis revealed that the distribution of archaeal communities was likely dependent on the soil properties. Our results suggested that termite activities may promote the diversity of archaea; with some of our sequences grouped as unclassified archaea, there is a need for further research to unveil their identity.
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