1
|
Yang J, Ouyang L, Chen S, Zhang C, Zheng J, He S. Amendments affect the community assembly and co-occurrence network of microorganisms in Cd and Pb tailings of the Eucalyptus camaldulensis rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 930:172365. [PMID: 38641118 DOI: 10.1016/j.scitotenv.2024.172365] [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: 12/03/2023] [Revised: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024]
Abstract
Mining tailings containing large amounts of Pb and Cd cause severe regional ecosystem pollution. Soil microorganisms play a regulatory role in the restoration of degraded ecosystems. The remediation of heavy metal-contaminated tailings with amendments and economically valuable Eucalyptus camaldulensis is a research hotspot due to its cost-effectiveness and sustainability. However, the succession and co-occurrence patterns of these microbial communities in this context remain unclear. Tailing samples of five kinds of Cd and Pb were collected in E. camaldulensis restoration models. Physicochemical properties, the proportions of different Cd and Pb forms, microbial community structure, and the co-occurrence network of rhizosphere tailings during different restoration process (organic bacterial manure, organic manure, inorganic fertilizer, bacterial agent) were considered. Organic and organic bacterial manures significantly increased pH, cation exchange capacity, and the proportion of residual Pb. Still, there was a significant decrease in the proportion of reducible Pb. The changes in microbial communities were related to physicochemical properties and the types of amendments. Organic and organic bacterium manures decreased the relative abundance of oligotrophic groups and increased the relative abundance of syntrophic groups. Inorganic fertilizers and bacterial agents decreased the relative abundance of saprophytic fungi. B. subtilis would play a better role in the environment improved by organic manure, increasing the relative abundance of beneficial microorganism and reducing the relative abundance of pathogenic microorganism. pH, cation exchange capacity, and the proportion of different forms of Pb were the main factors affecting the bacterial and fungi variation. All four amendments transformed the main critical groups of the microbial network structure from acidophilus and pathogenic microorganisms to beneficial microorganisms. Heavy metal-resistant microorganisms, stress-resistant microorganisms, beneficial microorganisms that promote nutrient cycling, and copiotrophic groups have become critical to building stable rhizosphere microbial communities. The topological properties and stability of the rhizosphere co-occurrence network were also enhanced. Adding organic and organic bacterium manures combined with E. camaldulensis to repair Cd and Pb tailings improved (1) pH and cation exchange capacity, (2) reduced the biological toxicity of Pb, (3) enhanced the stability of microbial networks, and (4) improved ecological network relationships. These positive changes are conducive to the restoration of the ecological functions of tailings.
Collapse
Affiliation(s)
- Jiaqi Yang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Linnan Ouyang
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China.
| | - Shaoxiong Chen
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Cheng Zhang
- Experimental Forest Farm of Qingyuan County,Qingyuan 323800, China
| | - Jiaqi Zheng
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| | - Shae He
- Research Institute of Fast-growing Trees, Chinese Academy of Forestry, State Key Laboratory of Efficient Production of Forest Resources, Zhanjiang 524022, China
| |
Collapse
|
2
|
Fiard M, Militon C, Sylvi L, Migeot J, Michaud E, Jézéquel R, Gilbert F, Bihannic I, Devesa J, Dirberg G, Cuny P. Uncovering potential mangrove microbial bioindicators to assess urban and agricultural pressures on Martinique island in the eastern Caribbean Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172217. [PMID: 38583633 DOI: 10.1016/j.scitotenv.2024.172217] [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: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Martinique's mangroves, which cover 1.85 ha of the island (<0.1 % of the total area), are considerably vulnerable to local urban, agricultural, and industrial pollutants. Unlike for temperate ecosystems, there are limited indicators that can be used to assess the anthropogenic pressures on mangroves. This study investigated four stations on Martinique Island, with each being subject to varying anthropogenic pressures. An analysis of mangrove sediment cores approximately 18 cm in depth revealed two primary types of pressures on Martinique mangroves: (i) an enrichment in organic matter in the two stations within the highly urbanized bay of Fort-de-France and (ii) agricultural pressure observed in the four studied mangrove stations. This pressure was characterized by contamination, exceeding the regulatory thresholds, with dieldrin, total DDT, and metals (As, Cu and Ni) found in phytosanitary products. The mangroves of Martinique are subjected to varying degrees of anthropogenic pressure, but all are subjected to contamination by organochlorine pesticides. Mangroves within the bay of Fort-de-France experience notably higher pressures compared to those in the island's northern and southern regions. In these contexts, the microbial communities exhibited distinct responses. The microbial biomass and the abundance of bacteria and archaea were higher in the two less-impacted stations, while in the mangrove of Fort-de-France, various phyla typically associated with polluted environments were more prevalent. These differences in the microbiota composition led to the identification of 65 taxa, including Acanthopleuribacteraceae, Spirochaetaceae, and Pirellulaceae, that could potentially serve as indicators of an anthropogenic influence on the mangrove sediments of Martinique Island.
Collapse
Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Jonathan Migeot
- Impact Mer consulting, expertise, and R&D firm, 20 rue Karukéra, 97200 Fort de France, Martinique/FWI, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Ronan Jézéquel
- CEDRE, 715 rue Alain Colas, 29218 Brest CEDEX 2, France.
| | - Franck Gilbert
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier, Toulouse, France.
| | | | - Jeremy Devesa
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| |
Collapse
|
3
|
Yue J, Zhang D, Cao M, Li Y, Liang Q, Liu F, Dong Y. Response of microbial community composition and function to land use in mining soils of Xikuang Mountain in Hunan. PLoS One 2024; 19:e0299550. [PMID: 38743658 PMCID: PMC11093284 DOI: 10.1371/journal.pone.0299550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/12/2024] [Indexed: 05/16/2024] Open
Abstract
Nine land types in the northern mining area (BKQ) (mining land, smelting land, living area), the old mining area (LKQ) (whole-ore heap, wasteland, grassland), and southern mining area (NKQ) (grassland, shrubs, farmland) of Xikuang Mountain were chosen to explore the composition and functions of soil bacterial communities under different habitats around mining areas. The composition and functions of soil bacterial communities were compared among the sampling sites using 16S rRNA high-throughput sequencing and metagenomic sequencing. α diversity analysis showed the soil bacterial diversity and abundance in the old mining area were significantly higher than those in the northern mining area. β diversity analysis demonstrated that the soil bacterial community composition was highly similar among different vegetation coverages in the southern mining area. Microbial community function analysis showed the annotated KEGG function pathways and eggNOG function composition were consistent between the grassland of the old mining area and the grassland of the southern mining area. This study uncovers the soil bacterial community composition and functions among different habitats in the mining areas of Xikuang Mountain and will underlie soil ecosystem restoration in different habitats under heavy metal pollution around the mining areas there.
Collapse
Affiliation(s)
- Jiao Yue
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - Dongpeng Zhang
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - Miaomiao Cao
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - Yukui Li
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - Qianwen Liang
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - Fei Liu
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - YuQiang Dong
- School of life Sciences, Huaibei Normal University, Huaibei, China
| |
Collapse
|
4
|
Jiao F, Qian L, Wu J, Zhang D, Zhang J, Wang M, Sui X, Zhang X. Diversity and Composition of Soil Acidobacterial Communities in Different Temperate Forest Types of Northeast China. Microorganisms 2024; 12:963. [PMID: 38792792 PMCID: PMC11124458 DOI: 10.3390/microorganisms12050963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
To gain an in-depth understanding of the diversity and composition of soil Acidobacteria in five different forest types in typical temperate forest ecosystems and to explore their relationship with soil nutrients. The diversity of soil Acidobacteria was determined by high-throughput sequencing technology. Soil Acidobacteria's alpha-diversity index and soil nutrient content differed significantly among different forest types. β-diversity and the composition of soil Acidobacteria also varied across forest types. Acidobacterial genera, such as Acidobacteria_Gp1, Acidobacteria_Gp4, and Acidobacteria_Gp17, play key roles in different forests. The RDA analyses pointed out that the soil pH, available nitrogen (AN), carbon to nitrogen (C/N) ratio, available phosphorus (AP), total carbon (TC), and total phosphorus (TP) were significant factors affecting soil Acidobacteria in different forest types. In this study, the diversity and composition of soil Acidobacteria under different forest types in a temperate forest ecosystem were analyzed, revealing the complex relationship between them and soil physicochemical properties. These findings not only enhance our understanding of soil microbial ecology but also provide important guidance for ecological conservation and restoration strategies for temperate forest ecosystems.
Collapse
Affiliation(s)
- Feng Jiao
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Lili Qian
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Jinhua Wu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Dongdong Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Junying Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Mingyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education & Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region & Key Laboratory of Microbiology, College of Heilongjiang Province & School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Xianbang Zhang
- Heilongjiang Zhongyangzhan Black-Billed Capercaillie National Nature Reserve Service Center, Nenjiang 161400, China
| |
Collapse
|
5
|
Chen H, Cheng M, Wen Y, Xiang Y. Leaf carbon chemistry effectively manipulated soil microbial profiles and induced metabolic adjustments under different revegetation types in the loess Plateau, China. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 359:120880. [PMID: 38669879 DOI: 10.1016/j.jenvman.2024.120880] [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: 12/11/2023] [Revised: 02/22/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
Microorganisms are essential components of underground life systems and drive elemental cycling between plants and soil. Yet, in the ecologically fragile Loess Plateau, scant attention has been paid to the response of microbial communities to organic carbon (C) chemistry of both leaves and soils under different revegetation conditions, as well as subsequent alternation in their C metabolic functions. Here, Fourier transform infrared (FTIR) spectrum, amplicon sequencing of 16S rRNA and ITS, and temporal incubation with Biolog-Eco 96 plates were combined to explore the vegetative heterogeneity of microbial community properties and metabolic functions, as well as their regulatory mechanisms in three typical revegetation types including Robinia pseudoacacia L. (RF), Caragana korshinskii KOM. (SL), and abandoned grassland (AG). We observed higher bacterial-to-fungal ratios (B: F = 270.18) and richer copiotrophic bacteria (Proteobacteria = 33.08%) in RF soil than those in AG soil, suggesting that microbes were dominated by r-strategists in soil under RF treatment, which is mainly related to long-term priming of highly bioavailable leaf C (higher proportion of aromatic and hydrophilic functional groups and lower hydrophobicity). Conversely, microbial taxa in AG soil, which was characterized by higher leaf organic C hydrophobicity (1.39), were dominated by relatively more abundant fungi (lower B: F ratio = 149.49) and oligotrophic bacteria (Actinobacteria = 29.30%). The co-occurrence network analysis showed that microbial interactive associations in RF and AG soil were more complex and connective than in SL soil. Furthermore, Biolog-Eco plate experiments revealed that microorganisms tended to utilize labile C compounds (carbohydrates and amino acids) in RF soil and resistant C compounds (polymers) in AG soil, which were consistent with the substrate adaptation strategies of predominant microbial trophic groups in different revegetation environments. Meanwhile, we observed greater microbial metabolic activity and diversity advantages in RF vegetation. Collectively, we suggest that besides the nutrient variables in the leaf-soil system, the long-term regulation of the microbial community by the C chemistry of the leaf sequentially alters the microbial metabolic profiles in a domino-like manner. RF afforestation is more conducive to restoring soil microbial fertility (including microbial abundance, diversity, interactive association, and metabolic capacity). Our study potentially paves the way for achieving well-managed soil health and accurate prediction of C pool dynamics in areas undergoing ecological restoration of the Loess Plateau.
Collapse
Affiliation(s)
- Haoning Chen
- School of Environmental &Resource Sciences, Shanxi University, Taiyuan, 030006, China
| | - Man Cheng
- School of Environmental &Resource Sciences, Shanxi University, Taiyuan, 030006, China.
| | - Yongli Wen
- School of Environmental &Resource Sciences, Shanxi University, Taiyuan, 030006, China.
| | - Yun Xiang
- School of Environmental &Resource Sciences, Shanxi University, Taiyuan, 030006, China; College of Resources and Environment, Shanxi Agricultural University, Jinzhong, 030801, China
| |
Collapse
|
6
|
Wu H, Cui H, Fu C, Li R, Qi F, Liu Z, Yang G, Xiao K, Qiao M. Unveiling the crucial role of soil microorganisms in carbon cycling: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168627. [PMID: 37977383 DOI: 10.1016/j.scitotenv.2023.168627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.
Collapse
Affiliation(s)
- Haowei Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Huiling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Chenxi Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Ran Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Fengyuan Qi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Zhelun Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Keqing Xiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| | - Min Qiao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
| |
Collapse
|
7
|
Liu X, Yang H, Yang K. Optimizing the hydrolysis-acidification stage in municipal wastewater treatment: comparison of immobilized fillers and granular sludge. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:6288-6300. [PMID: 38147258 DOI: 10.1007/s11356-023-31649-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/17/2023] [Indexed: 12/27/2023]
Abstract
The decomposition of organic macromolecules in sewage currently benefits substantially from hydrolysis-acidification. The full use of its qualities can help domestic sewage to biodegrade more quickly, which promotes the subsequent aerobic reactions. This study evaluated the hydrolysis-acidification performance of granular sludge and filler in residential sewage. Both forms were highly effective at producing volatile fatty acids (VFAs) at the beginning of the reaction, but the granular sludge gradually disintegrated over time, particularly at low temperatures. The production of VFAs decreased (68.08 mg/L), and the effluent dissolved organic nitrogen (DON) increased (6.23 mg/L). However, the effluent of fillers remained at a lower level (1.3 mg/L) and produced more VFAs (74.13 mg/L). High-throughput sequencing revealed that the filler included a greater quantity of hydrolytic-acidifying bacteria than the granular sludge, which resulted in higher performance. In this study, the optimal form of utilizing hydrolytic acidifying bacteria was discussed to provide a theoretical basis to improve the full utilization of organic matter in domestic sewage and the removal of as much total nitrogen as possible.
Collapse
Affiliation(s)
- Xuyan Liu
- Hebei GEO University, Shijiazhuang, 050031, China
- Hebei Province Collaborative Innovation Center for Sustainable Utilization of Water Resources and Optimization of Industrial Structure, Shijiazhuang, 050031, China
| | - Hong Yang
- Key Laboratory of Beijing Water Quality Science and Water Environment Recovery Engineering, Beijing University of Technology, No. 100, Pingleyuan, Chaoyang District, Beijing, 100124, China
| | - Kai Yang
- Shijiazhuang University, Shijiazhuang, 050035, China.
| |
Collapse
|
8
|
Dai W, Liu Y, Yao D, Wang N, Shao J, Ye X, Cui Z, Zong H, Tian L, Chen X, Wang H. Biogeographic distribution, assembly processes and potential nutrient cycling functions of myxobacteria communities in typical agricultural soils in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167255. [PMID: 37741390 DOI: 10.1016/j.scitotenv.2023.167255] [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: 07/15/2023] [Revised: 08/26/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
Predatory myxobacteria are important soil micropredators with the potential to regulate soil microbial community structure and ecosystem function. However, the biogeographic distribution patterns, assembly processes, and potential nutrient cycling functions of myxobacteria communities in typical agricultural soils in China are still poorly understood. High-throughput sequencing, phylogenetic zero modeling, and the multi-nutrient cycling index were used to assess the biogeographic distribution, assembly processes, and soil ecosystem functions of predation myxobacteria communities in typical agricultural soils of six long-term fertilization ecological experimental stations. The results demonstrated a hump-shaped distribution of myxobacteria α-diversity along the latitudinal gradient and significant differences in myxobacteria β-diversity in typical agricultural soils (P < 0.05). Bacterial richness, soil organic carbon, and pH were the most important predictors of myxobacteria α-diversity, whereas geographic factors and soil pH were the most significant ecological predictors of myxobacteria β-diversity. Myxobacteria community assembly is dominated by deterministic processes, especially homogeneous selection, primarily driven by soil pH and bacterial richness. In addition, we revealed the ecological significance of myxobacteria communities in typical agricultural soil microbial networks and the potential link between myxobacteria communities and soil nutrient cycling. These findings enhance our understanding of the biogeographic distribution, community assembly, ecological predictors, and relationships with soil nutrient cycling of myxobacteria communities in typical agricultural soils, paving the way for a more predictive understanding of the effect of predatory myxobacteria communities on soil ecosystem function, which is essential for the development of sustainable agriculture.
Collapse
Affiliation(s)
- Wei Dai
- 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 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Yang Liu
- 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 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Dandan Yao
- 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 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Ning Wang
- 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 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Jinpeng Shao
- 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 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Zong
- Shandong Linyi Tobacco Co., Ltd., Linyi 276000, Shandong, China
| | - Lei Tian
- Shandong Linyi Tobacco Co., Ltd., Linyi 276000, Shandong, China
| | - XiuZhai Chen
- Shandong Linyi Tobacco Co., Ltd., Linyi 276000, Shandong, China.
| | - Hui Wang
- 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 100000, China; University of Chinese Academy of Sciences, Nanjing 211135, China.
| |
Collapse
|
9
|
Gogoleva N, Chervyatsova O, Balkin A, Kuzmina L, Shagimardanova E, Kiseleva D, Gogolev Y. Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms. ENVIRONMENTAL MICROBIOME 2023; 18:82. [PMID: 37990336 PMCID: PMC10662634 DOI: 10.1186/s40793-023-00538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave's Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave. RESULTS The cave's biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique "CaveCurd" community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO2 content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces. CONCLUSIONS The Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave's ancient rock paintings.
Collapse
Affiliation(s)
- Natalia Gogoleva
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondsee, 5310, Austria.
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia.
| | | | - Alexander Balkin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of the Russian Academy of Sciences, Orenburg, 460000, Russia
| | - Lyudmila Kuzmina
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054, Russia
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Loginov Moscow Clinical Scientific Center, Moscow, 111123, Russia
| | - Daria Kiseleva
- Institute of Geology and Geochemistry, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, 620016, Russia
- Institute of Fundamental Education, Ural Federal University named after the first President of Russia B.N. Yeltsin, Ekaterinburg, 620002, Russia
| | - Yuri Gogolev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Kazan, 420111, Russia
| |
Collapse
|
10
|
Chen Y, Du Z, Weng ZH, Sun K, Zhang Y, Liu Q, Yang Y, Li Y, Wang Z, Luo Y, Gao B, Chen B, Pan Z, Van Zwieten L. Formation of soil organic carbon pool is regulated by the structure of dissolved organic matter and microbial carbon pump efficacy: A decadal study comparing different carbon management strategies. GLOBAL CHANGE BIOLOGY 2023; 29:5445-5459. [PMID: 37424182 DOI: 10.1111/gcb.16865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
To achieve long-term increases in soil organic carbon (SOC) storage, it is essential to understand the effects of carbon management strategies on SOC formation pathways, particularly through changes in microbial necromass carbon (MNC) and dissolved organic carbon (DOC). Using a 14-year field study, we demonstrate that both biochar and maize straw lifted the SOC ceiling, but through different pathways. Biochar, while raising SOC and DOC content, decreased substrate degradability by increasing carbon aromaticity. This resulted in suppressed microbial abundance and enzyme activity, which lowered soil respiration, weakened in vivo turnover and ex vivo modification for MNC production (i.e., low microbial carbon pump "efficacy"), and led to lower efficiency in decomposing MNC, ultimately resulting in the net accumulation of SOC and MNC. In contrast, straw incorporation increased the content and decreased the aromaticity of SOC and DOC. The enhanced SOC degradability and soil nutrient content, such as total nitrogen and total phosphorous, stimulated the microbial population and activity, thereby boosting soil respiration and enhancing microbial carbon pump "efficacy" for MNC production. The total C added to biochar and straw plots were estimated as 27.3-54.5 and 41.4 Mg C ha-1 , respectively. Our results demonstrated that biochar was more efficient in lifting the SOC stock via exogenous stable carbon input and MNC stabilization, although the latter showed low "efficacy". Meanwhile, straw incorporation significantly promoted net MNC accumulation but also stimulated SOC mineralization, resulting in a smaller increase in SOC content (by 50%) compared to biochar (by 53%-102%). The results address the decadal-scale effects of biochar and straw application on the formation of the stable organic carbon pool in soil, and understanding the causal mechanisms can allow field practices to maximize SOC content.
Collapse
Affiliation(s)
- Yalan Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Zhangliu Du
- Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Zhe Han Weng
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Ke Sun
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yuqin Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Qin Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yan Yang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yang Li
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Zhibo Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Yu Luo
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, Zhejiang University, Hangzhou, China
| | - Bo Gao
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing, China
| | - Bin Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Zezhen Pan
- Department of Environmental Science and Engineering, Fudan University, Shanghai, China
| | - Lukas Van Zwieten
- NSW Department of Primary Industries, Wollongbar Primary Industries Institute, Wollongbar, New South Wales, Australia
| |
Collapse
|
11
|
Nnadi MO, Bingle L, Thomas K. Bacterial community dynamics and associated genes in hydrocarbon contaminated soil during bioremediation using brewery spent grain. Access Microbiol 2023; 5:acmi000519.v3. [PMID: 37424545 PMCID: PMC10323799 DOI: 10.1099/acmi.0.000519.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/05/2023] [Indexed: 07/11/2023] Open
Abstract
Brewery spent grain (BSG) has previously been exploited in bioremediation. However, detailed knowledge of the associated bacterial community dynamics and changes in relevant metabolites and genes over time is limited. This study investigated the bioremediation of diesel contaminated soil amended with BSG. We observed complete degradation of three total petroleum hydrocarbon (TPH C10-C28) fractions in amended treatments as compared to one fraction in the unamended, natural attenuation treatments. The biodegradation rate constant (k) was higher in amended treatments (0.1021k) than in unamended (0.059k), and bacterial colony forming units increased significantly in amended treatments. The degradation compounds observed fitted into the elucidated diesel degradation pathways and quantitative PCR results showed that the gene copy numbers of all three associated degradation genes, alkB, catA and xylE, were significantly higher in amended treatments. High-throughput sequencing of 16S rRNA gene amplicons showed that amendment with BSG enriched autochthonous hydrocarbon degraders. Also, community shifts of the genera Acinetobacter and Pseudomonas correlated with the abundance of catabolic genes and degradation compounds observed. This study showed that these two genera are present in BSG and thus may be associated with the enhanced biodegradation observed in amended treatments. The results suggest that the combined evaluation of TPH, microbiological, metabolite and genetic analysis provides a useful holistic approach to assessing bioremediation.
Collapse
Affiliation(s)
- Mabel Owupele Nnadi
- Faculty of Health Sciences & Wellbeing, University of Sunderland, Chester Road, Sunderland SR1 3SD, UK
| | - Lewis Bingle
- Faculty of Health Sciences & Wellbeing, University of Sunderland, Chester Road, Sunderland SR1 3SD, UK
| | - Keith Thomas
- Brewlab, Unit One, West Quay Court, Sunderland SR5 2TE, UK
| |
Collapse
|
12
|
Costa GMD, Costa SS, Baraúna RA, Castilho BP, Pinheiro IC, Silva A, Schaan AP, Ribeiro-Dos-Santos Â, Graças DAD. Effects of Degradation on Microbial Communities of an Amazonian Mangrove. Microorganisms 2023; 11:1389. [PMID: 37374891 DOI: 10.3390/microorganisms11061389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2023] Open
Abstract
Mangroves provide a unique ecological environment for complex microbial communities, which play important roles in biogeochemical cycles, such as those for carbon, sulfur, and nitrogen. Microbial diversity analyses of these ecosystems help us understand the changes caused by external influences. Amazonian mangroves occupy an area of 9000 km2, corresponding to 70% of the mangroves in Brazil, on which studies of microbial biodiversity are extremely scarce. The present study aimed to determine changes in microbial community structure along the PA-458 highway, which fragmented a mangrove zone. Mangrove samples were collected from three zones, (i) degraded, (ii) in the process of recovery, and (iii) preserved. Total DNA was extracted and submitted for 16S rDNA amplification and sequencing on an MiSeq platform. Subsequently, reads were processed for quality control and biodiversity analyses. The most abundant phyla were Proteobacteria, Firmicutes, and Bacteroidetes in all three mangrove locations, but in significantly different proportions. We observed a considerable reduction in diversity in the degraded zone. Important genera involved in sulfur, carbon, and nitrogen metabolism were absent or dramatically reduced in this zone. Our results show that human impact in the mangrove areas, caused by the construction of the PA-458 highway, has resulted in a loss of biodiversity.
Collapse
Affiliation(s)
- Gleyciane Machado da Costa
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Sávio Souza Costa
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Rafael Azevedo Baraúna
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Bruno Pureza Castilho
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
| | - Izabel Cruz Pinheiro
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
| | - Artur Silva
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Ana Paula Schaan
- Laboratory of Medical and Human Genetics, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratory of Medical and Human Genetics, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| | - Diego Assis das Graças
- Laboratory of Biological Engineering, Guamá Science and Technology Park, Belém 66075-750, Brazil
- Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075-110, Brazil
| |
Collapse
|
13
|
Azziz G, Frade C, Igual JM, Del Pino A, Lezama F, Valverde Á. Legume Overseeding and P Fertilization Increases Microbial Activity and Decreases the Relative Abundance of AM Fungi in Pampas Natural Pastures. Microorganisms 2023; 11:1383. [PMID: 37374885 DOI: 10.3390/microorganisms11061383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Natural grasslands provide a valuable resource for livestock grazing. In many parts of South America, legume overseeding and P fertilization are commonly used to enhance primary productivity. The effect of this practice on the plant community is well established. However, how this management regime affects the soil microbiome is less known. Here, to contribute to filling this knowledge gap, we analyzed the effect of Lotus subbiflorus overseeding, together with P fertilization, on soil microbial community diversity and activity in the Uruguayan Pampa region. The results showed that plant communities in the natural grassland paddocks significantly differed from those of the managed paddocks. In contrast, neither microbial biomass and respiration nor microbial diversity was significantly affected by management, although the structure of the bacterial and fungal communities were correlated with those of the plant communities. AM Fungi relative abundance, as well as several enzyme activities, were significantly affected by management. This could have consequences for the C, N, and P content of SOM in these soils, which in turn might affect SOM degradation.
Collapse
Affiliation(s)
- Gastón Azziz
- Laboratorio de Microbiología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo 12900, Uruguay
| | - Cristina Frade
- Grupo de Interacción Planta-Microorganismo, Instituto de Recursos Naturales y Agrobiología de Salamanca, CSIC, 37008 Salamanca, Spain
| | - José M Igual
- Grupo de Interacción Planta-Microorganismo, Instituto de Recursos Naturales y Agrobiología de Salamanca, CSIC, 37008 Salamanca, Spain
| | - Amabelia Del Pino
- Departamento de Suelos y Aguas, Facultad de Agronomía, Universidad de la República, Montevideo 12900, Uruguay
| | - Felipe Lezama
- Departamento de Sistemas Ambientales, Facultad de Agronomía, Universidad de la República, Montevideo 12900, Uruguay
| | - Ángel Valverde
- Grupo de Interacción Planta-Microorganismo, Instituto de Recursos Naturales y Agrobiología de Salamanca, CSIC, 37008 Salamanca, Spain
| |
Collapse
|
14
|
Oh S, Cho K, Park S, Kwon MJ, Chung J, Lee S. Denitrification dynamics in unsaturated soils with different porous structures and water saturation degrees: A focus on the shift in microbial community structures. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130413. [PMID: 36436452 DOI: 10.1016/j.jhazmat.2022.130413] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Despite its environmental significance, little is known about denitrification in vadose zones owing to the complexity of such environments. Here, we investigated denitrification in unsaturated soils with different pore distributions. To this end, we performed batch-type denitrification experiments and analyzed microbial community shifts before and after possible reactions with nitrates to clarify the relevant denitrifying mechanism in the microcosms. For quantitative comparison, pore distribution in the test soil samples was characterized based on the uniformity coefficient (Cu) and water saturation degree (SD). Micro-CT analysis of the soil pore distribution confirmed that the proportion of bigger-sized pores increased with decreasing Cu. However, oxygen diffusion into the system was controlled by SD rather than Cu. Within a certain SD range (51-67%), the pore condition changed abruptly from an oxic to an anoxic state. Consequently, denitrification occurred even under unsaturated soil conditions when the SD increased beyond 51-67%. High throughput sequencing revealed that the same microbial species were potentially responsible for denitrification under both partially (SD 67%), and fully saturated (SD of 100%) conditions, implying that the mechanism of denitrification in a vadose zone, if it exists, might be possibly similar under varying conditions.
Collapse
Affiliation(s)
- Sungjik Oh
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea
| | - Kyungjin Cho
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea
| | - Saerom Park
- Urban Water Circulation Research Center, Department of Land, Water and Environment Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Jaeshik Chung
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea.
| | - Seunghak Lee
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea; Graduate School of Energy and Environment (KU-KIST Green School), Korea University, Seoul 02841, South Korea.
| |
Collapse
|
15
|
Lei J, Wu H, Li X, Guo W, Duan A, Zhang J. Response of Rhizosphere Bacterial Communities to Near-Natural Forest Management and Tree Species within Chinese Fir Plantations. Microbiol Spectr 2023; 11:e0232822. [PMID: 36688690 PMCID: PMC9927156 DOI: 10.1128/spectrum.02328-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Near-natural forest management plays an important role in the maintenance of the long-term productivity and soil fertility of plantations. We conducted high-throughput absolute quantitative sequencing of 16S rRNA genes to compare the structures and diversity of rhizosphere soil bacterial communities among a pure Chinese fir (Cunninghamia lanceolata) plantation (S), a Cunninghamia lanceolata-Castanopsis hystrix-Michelia hedyosperma mixed plantation (SHX), and a Cunninghamia lanceolata-Castanopsis fissa mixed plantation (SD). The results revealed that near-natural forest management improved the rhizosphere soil properties of Chinese fir, especially the phosphorus content. Rhizosphere soil bacterial communities of Chinese fir in SHX and SD contained higher total absolute abundances and more unique operational taxonomic units (OTUs) than the pure plantation forest. Planctomycetes and Actinobacteria were abundant in SD, and Actinobacteria were enriched in SHX. The tree species also had an impact on the rhizosphere soil bacterial communities. For the rhizosphere soils of different tree species of SHX, the available phosphorus (AP) content of the rhizosphere of Chinese fir significantly surpassed those of Castanopsis hystrix and Michelia hedyosperma. Bacteria related to nitrogen fixing, such as Burkholderiales and Rhizobiales, were more abundant in Chinese fir in SD than in Castanopsis fissa. Acdiobacteria and Proteobacteria underpinned the differences found in the compositions of soil bacteria. The pH and soil organic matter were key variables influencing the rhizosphere soil bacterial communities. Our results demonstrated that in Chinese fir plantations, 12 years of near-natural management of introduced broad-leaved tree species can drive alterations of the physicochemical characteristics, bacterial community structure, and composition of rhizosphere soil, with tree species identity further influencing the rhizosphere soil bacterial community. IMPORTANCE Near-natural forest management is an important way to change the soil fertility decline and productivity reduction of pure Chinese fir plantations. At present, many detailed studies have been carried out on the impact of near-natural forest management on Chinese fir plantations at home and abroad. However, there are still few studies on the response of rhizosphere bacterial communities to near-natural forest management. Our study determined absolute quantities of Chinese fir rhizosphere bacterial communities in different mixed patterns. The results underscore the importance of near-natural forest management for Chinese fir plantation rhizosphere bacterial communities and provide new information on soil factors that affect rhizosphere bacterial communities in South China.
Collapse
Affiliation(s)
- Jie Lei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
| | - Hanbin Wu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
| | - Xiaoyan Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
| | - Wenfu Guo
- Experimental Center of Tropical Forestry, Chinese Academy of Forestry, Pingxiang, People's Republic of China
| | - Aiguo Duan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, People's Republic of China
| |
Collapse
|
16
|
Chen L, Chen S, Zhang Y, Long Y, Kong X, Wang S, Li L, Wang F, Sun Y, Xu A. Co-occurrence network of microbial communities affected by application of anaerobic fermentation residues during phytoremediation of ionic rare earth tailings area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:159223. [PMID: 36208748 DOI: 10.1016/j.scitotenv.2022.159223] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 04/14/2023]
Abstract
The long-term exploitation of ionic rare earth elements (REEs) in southern China has produced a large-scale of abandoned tailings area. While the application of anaerobic fermentation residues to cultivate economically valuable remediation plants (e.g. energy plant) has become a hotspot due to their merits in low-cost and sustainability in recent years, the succession and co-occurrence patterns of these microbial communities remain unclear. In this study, soil samples were collected from the sustainable restoration area, natural restoration area and tailings area. The composition and diversity of bacterial and fungal communities on five soil samples were evaluated using high-throughput sequencing technology. The results shown that the phytoremediation with anaerobic fermentation residues could significantly improve the physicochemical properties (especially for soil nutrients) and microbial diversity of soil within 3 years, while these parameters in natural restoration area were lower. The nonmetric multidimensional scaling (NMDS) ordinations revealed the shifts of microbial communities depending on soil physicochemical properties and plant species, and soil nutrients were the main factors affecting the microbial variation explained by the variation partition analysis (VPA). The soil nutrient accumulation obviously changed the proportion of oligotrophic and copiotrophic groups, among which the copiotrophic groups were significantly increased, such as Proteobacteria, Bacteroidetes, Gemmatimonadetes and Glomeromycota. The microbial co-occurrence network analysis indicated that application of anaerobic fermentation residues could significantly improve the topological properties and the stability of microbial network. The copiotrophic groups (e.g. Proteobacteria, Ascomycota) became the key to assemble stable network structure. Moreover, herbaceous plants could increase the proportion of fungi (e.g. Ascomycota) in microbial network, which improved the topological properties with bacteria synergistically. Therefore, the soil environment of REEs tailings area was effectively optimized by anaerobic fermentation residues and herbaceous plants, which furthered understanding of co-occurrence pattern and mutualistic relationships of microbial communities during sustainable restoration.
Collapse
Affiliation(s)
- Liumeng Chen
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China; Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Shasha Chen
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Yi Zhang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yun Long
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Xiaoying Kong
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China.
| | - Shujia Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Lianhua Li
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Fei Wang
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yongmin Sun
- Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China
| | - An Xu
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| |
Collapse
|
17
|
Sui X, Frey B, Yang L, Liu Y, Zhang R, Ni H, Li MH. Soil Acidobacterial community composition changes sensitively with wetland degradation in northeastern of China. Front Microbiol 2022; 13:1052161. [PMID: 36620014 PMCID: PMC9816132 DOI: 10.3389/fmicb.2022.1052161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Acidobacteria are a major component of the soil bacteria and are conducted for many soil functions, and the soil Acidobacterial structure and diversity are affected by climate changes and human activities. However, soil Acidobacterial structure and diversity in wetland ecosystems are still limited recognized. The current study aimed to study the Acidobacterial community and diversity in relation to soil environmental factors along a typical degradation series from primitive wetland to forest in a representative fresh wetland in northeastern China. In this research, we assessed the soil Acidobacterial community composition, using Illumina MiSeq sequencing along a typical degradation series from primitive wetland to forest in a representative fresh wetland in northeastern China. The soil physico chemical properties changed significantly among the eight degrade stages (p < 0.05). The α diversity index (Shannon and Chao1 index) of soil Acidobacteria changed significantly between different degradation stages (p < 0.05). Principal Coordinates Analysis (PCoA) revealed that the soil acidobacteiral communities obviously separated into wetland group and forest group. The most abundant subgroups of Acidobacteria accounted for 31% (Gp1), 5% (Gp2), 12% (Gp3), 2% (Gp4), 5% (Gp6), and 2% (Gp7) in soils within eight successional series. The compositions of soil Acidobacteria in wetland stages were significantly affected by soil moisture content, soil total nitrogen and available nitrogen contents, while those in forest stages were significantly driven by soil pH, soil organic carbon, total nitrogen, available phosphorus and soil moisture content. Our results indicated that the soil Acidobacterial community was mainly structured by soil physico chemical parameters, and wetland degradation towards forests will greatly influence the soil Acidobacterial structure and thus the wetland functions.
Collapse
Affiliation(s)
- Xin Sui
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Beat Frey
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
| | - Libin Yang
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Yingnan Liu
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Rongtao Zhang
- Institute of Nature and Ecology, Heilongjiang Academy of Sciences, Harbin, China
| | - Hongwei Ni
- Heilongjiang Academy of Forestry, Harbin, China
| | - Mai-He Li
- Snow and Landscape Research WSLSwiss Federal Institute for Forest, , Birmensdorf, Switzerland
- Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains, Ministry of Education, School of Geographical Sciences, Northeast Normal University, Changchun, China
- School of Life Science, Hebei University, Baoding, China
| |
Collapse
|
18
|
Pu T, Liu J, Dong J, Qian J, Zhou Z, Xia C, Wei G, Duan B. Microbial community diversity and function analysis of Aconitum carmichaelii Debeaux in rhizosphere soil of farmlands in Southwest China. Front Microbiol 2022; 13:1055638. [PMID: 36590406 PMCID: PMC9797738 DOI: 10.3389/fmicb.2022.1055638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Understanding how microbial communities affect plant growth is crucial for sustainable productivity and ecological health. However, in contrast with the crop system, there is limited information on the microbial community associated with the medicinal plant. We observed that altitude was the most influential factor on the soil microbial community structures of Aconitum carmichaelii Debeaux. For community composition, bacterial reads were assigned to 48 phyla, with Proteobacteria, Acidobacteriota, and Actinobacteriota being the dominant phyla. The fungal reads were assigned to seven phyla, and Ascomycota was the predominant phylum detected in most groups. The four dominant phyla were categorized as keystone taxa in the co-occurrence networks, suggesting that they may be involved in soil disease suppression and nutrient mobility. Bacterial co-occurrence networks had fewer edges, lower average degree, and lower density at YL1, HQ1, HQ2, BC, and DL than fungal networks, creating less intricate rhizosphere network patterns. Furthermore, the bacterial and fungal communities showed strong distance decay of similarity across the sampling range. Overall, this study improves our understanding of regulating rhizosphere microbial communities in soil systems and also provides potential production strategies for planting A. carmichaelii.
Collapse
Affiliation(s)
- Tingting Pu
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jie Liu
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jingjing Dong
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Jun Qian
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Zhongyu Zhou
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Conglong Xia
- College of Pharmaceutical Science, Dali University, Dali, China
| | - Guangfei Wei
- College of Pharmaceutical Science, Dali University, Dali, China,Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China,*Correspondence: Guangfei Wei, ; Baozhong Duan,
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, China,*Correspondence: Guangfei Wei, ; Baozhong Duan,
| |
Collapse
|
19
|
Building a Cell House from Cellulose: The Case of the Soil Acidobacterium Acidisarcina polymorpha SBC82T. Microorganisms 2022; 10:microorganisms10112253. [DOI: 10.3390/microorganisms10112253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Acidisarcina polymorpha SBC82T is a recently described representative of the phylum Acidobacteriota from lichen-covered tundra soil. Cells of this bacterium occur within unusual saccular chambers, with the chamber envelope formed by tightly packed fibrils. These extracellular structures were most pronounced in old cultures of strain SBC82T and were organized in cluster-like aggregates. The latter were efficiently destroyed by incubating cell suspensions with cellulase, thus suggesting that they were composed of cellulose. The diffraction pattern obtained for 45-day-old cultures of strain SBC82T by using small angle X-ray scattering was similar to those reported earlier for mature wood samples. The genome analysis revealed the presence of a cellulose biosynthesis locus bcs. Cellulose synthase key subunits A and B were encoded by the bcsAB gene whose close homologs are found in genomes of many members of the order Acidobacteriales. More distant homologs of the acidobacterial bcsAB occurred in representatives of the Proteobacteria. A unique feature of bcs locus in strain SBC82T was the non-orthologous displacement of the bcsZ gene, which encodes the GH8 family glycosidase with a GH5 family gene. Presumably, these cellulose-made extracellular structures produced by A. polymorpha have a protective function and ensure the survival of this acidobacterium in habitats with harsh environmental conditions.
Collapse
|
20
|
Kenya E, Kinyanjui G, Kipnyargis A, Kinyua F, Mwangi M, Khamis F, Mwirichia R. Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya. Heliyon 2022; 8:e11577. [PMID: 36411924 PMCID: PMC9674510 DOI: 10.1016/j.heliyon.2022.e11577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/14/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.
Collapse
Affiliation(s)
- Eucharia Kenya
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Grace Kinyanjui
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Alex Kipnyargis
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Franklin Kinyua
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
| | - Mary Mwangi
- Department of Biochemistry and Biotechnology, Kenyatta University, P. O. Box 43844-00100, Nairobi, Kenya
| | - Fathiya Khamis
- International Centre of Insect Physiology and Ecology (ICIPE), P. O. Box 30772-00100, Nairobi, Kenya
| | - Romano Mwirichia
- Department of Biological Sciences, University of Embu, P. O. Box 6-60100, Embu, Kenya
- Corresponding author.
| |
Collapse
|
21
|
Bai Z, Zheng L, Bai Z, Jia A, Wang M. Long-term cultivation alter soil bacterial community in a forest-grassland transition zone. Front Microbiol 2022; 13:1001781. [PMID: 36246280 PMCID: PMC9557053 DOI: 10.3389/fmicb.2022.1001781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Changes in land use types can significantly affect soil porperties and microbial community composition in many areas. However, the underlying mechanism of shift in bacterial communities link to soil properties is still unclear. In this study, Illumina high-throughput sequencing was used to analyze the changes of soil bacterial communities in different land use types in a forest-grassland transition zone, North China. There are two different land use types: grassland (G) and cultivated land (CL). Meanwhile, cultivated land includes cultivated of 10 years (CL10) or 20 years (CL20). Compared with G, CL decreased soil pH, SOC and TN, and significantly increased soil EC, P and K, and soil properties varied significantly with different cultivation years. Grassland reclamation increases the diversity of bacterial communities, the relative abundance of Proteobacteria, Gemmatimonadetes and Bacteroidetes increased, while that of Actinobacteria, Acidobacteria, Rokubacteria and Verrucomicrobia decreased. However, the relative abundance of Proteobacteria decreased and the relative abundance of Chloroflexi and Nitrospirae increased with the increase of cultivated land years. Mantel test and RDA analysis showed that TP, AP, SOC and EC were the main factors affecting the diversity of composition of bacterial communities. In conclusion, soil properties and bacterial communities were significantly altered after long-term cultivation. This study provides data support for land use and grassland ecological protection in this region.
Collapse
|
22
|
Yang Y, Sun K, Liu J, Chen Y, Han L. Changes in soil properties and CO 2 emissions after biochar addition: Role of pyrolysis temperature and aging. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156333. [PMID: 35640750 DOI: 10.1016/j.scitotenv.2022.156333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Biochar has been regarded as an effective amendment for soil carbon sequestration and soil quality improvement. However, it remains unclear how pyrolysis temperature and biochar aging impact the responses of soil properties and CO2 emissions to biochar addition. Here, we investigated the effect of biochar on soil properties and CO2 emissions in a laboratory incubation using soils amended with/without fresh biochar produced at 300 (BC300), 450 (BC450), and 600 °C (BC600) and their corresponding naturally aged samples (aged in soil for 360 days). The results showed that biochar significantly increased soil total nitrogen (by 8-36%), available phosphorus (by 19-69%) and available potassium (by 1.5-4.2-fold) throughout the incubation. Both fresh and aged biochar promoted the formation of soil macroaggregate at the end of the incubation. Moreover, fresh and aged BC300 increased the soil dissolved organic matter (DOM) content, whereas for BC450 and BC600, at the beginning, the content of soil DOM was reduced, but the effects finally became insignificant. Generally, fresh biochar had no significant effect on soil enzyme activities and soil bacterial richness and diversity, but an inhibitory effect occurred in the aged samples. Both fresh and aged BC300 increased soil CO2 emissions, which was due to the biochar-induced increase in soil DOM content and enrichment of copiotrophic bacteria (Proteobacteria) as well as the decline of oligotrophic bacteria (Acidobacteriota). A significant decrease in soil CO2 emissions was observed after fresh BC450 and BC600 addition, owing to the biochar-induced decline in soil DOM content, while an opposite trend was found in aged samples, which could be attributed to the shift of the dominant soil phylum from Acidobacteriota to Proteobacteria. These findings enhance our understanding of biochar's potential to improve soil quality and sequester soil carbon.
Collapse
Affiliation(s)
- Yan Yang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Ke Sun
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Jie Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Yalan Chen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Lanfang Han
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| |
Collapse
|
23
|
Cao J, Jiao Y, Che R, Holden NM, Zhang X, Biswas A, Feng Q. The effects of grazer exclosure duration on soil microbial communities on the Qinghai-Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156238. [PMID: 35623508 DOI: 10.1016/j.scitotenv.2022.156238] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 05/22/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
While determining the response of soil microbes to grazer exclosure duration is critical to understanding ecosystem restoration processes, few studies have focused on this issue. With seasonal grazing as a control, microbes of alpine grassland soils under 5, 13, 22, and 39 years of grazer exclosure situated in the eastern part of the Qinghai-Tibetan Plateau, were examined. Microbial diversity was determined through Illumina high-throughput sequencing of the 16S rRNA gene and an internal transcription spacer (ITS). We found that soil bacterial α-diversity showed insignificant differences between seasonal grazing and grazer exclosure and among the grazer exclosures of different durations, while fungal α-diversity under the 5-year grazer exclosure was significantly different from those under the other treatments. Soil microbial community profiles under the 13-, 22-, and 39-year grazer exclosures were significantly different compared to those under the seasonal grazing or 5-year grazer exclosure. Briefly, longer exclosure durations led to a higher relative abundance of multiple copiotrophic microbial lineages (e.g., β-Proteobacteria, Rhizobiales, and Frankiales), whereas several oligotrophic microbial lineages (e.g., Chloroflexi, Leotiomycetes, and Xylariales) gradually and significantly decreased. Functional predictions suggest that as grazer exclosure duration was extended, the relative abundance of nitrogen fixers increased, while the proportions of plant pathogenic fungi decreased. This indicates that long-term grazer exclosure duration may contribute to enhanced soil nitrogen fixation and grassland health by maintaining plant growth and decreasing the risk of plant disease. However, this may have a resource cost as plant productivity and soil organic carbon both decreased with the extension of grazer exclosure duration. Therefore, the agroecology effect of grazer exclosure duration on the diversity and abundance of soil nitrogen fixing bacteria and plant pathogen fungi, should be given more attention in the cold and humid portion of the Qinghai-Tibetan Plateau.
Collapse
Affiliation(s)
- Jianjun Cao
- College of Geography and Environmental Science, Northwest Normal University, Lanzhou 730070, China; Key Laboratory of Eco-functional Polymer Materials of the Ministry of Education, Northwest Normal University, Lanzhou 730070, China; Key Laboratory of Resource Environment and Sustainable Development of Oasis, College of Geography and Environmental Science, Northwest Normal University, Lanzhou 730070, China
| | - Yumeng Jiao
- College of Geography and Environmental Science, Northwest Normal University, Lanzhou 730070, China
| | - Rongxiao Che
- Institute of International Rivers and Eco-security, Yunnan University, Kunming 650091, China.
| | - Nicholas M Holden
- UCD School of Biosystems and Food Engineering, Agriculture and Food Science Centre, University College Dublin, Belfield, Dublin 4, Ireland
| | - Xiaofang Zhang
- Key Laboratory of Ecohydrology of Inland River Basin, Alashan Desert Eco-Hydrology Experimental Research Station, Northwest Institute of Ecology and Environmental Resources, Chinese Academy of Sciences, Lanzhou 730000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Asim Biswas
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada
| | - Qi Feng
- Key Laboratory of Ecohydrology of Inland River Basin, Alashan Desert Eco-Hydrology Experimental Research Station, Northwest Institute of Ecology and Environmental Resources, Chinese Academy of Sciences, Lanzhou 730000, China.
| |
Collapse
|
24
|
Zhang Y, Bo G, Shen M, Shen G, Yang J, Dong S, Shu Z, Wang Z. Differences in microbial diversity and environmental factors in ploughing-treated tobacco soil. Front Microbiol 2022; 13:924137. [PMID: 36171748 PMCID: PMC9511222 DOI: 10.3389/fmicb.2022.924137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
During agricultural production, plowing affects the existing traits of the planted soil, including environmental factors (physicochemical properties and soil enzymatic activity) and microbial community, but whether deep tillage and conventional tillage cause differences in soil microecology are unknown. In this study, the 16S rRNA high-throughput sequencing technology was combined with soil environmental factor detection to analyze the differences in microbial diversity of smokey soils at different depths. As a result, the composition and structure of microbial community varied in different soil depth after plowing. Two dominant phyla, Actinobacteria and Acidobacteria, have varied a lot between the deep-plowing treatment HS3 (the sample in 10–20 cm depth after deep-plowing treatment) sample and the conventional tillage HC3 (treatment the sample in 10–20 cm depth after conventional tillage) sample. The abundance of Actinobacteria has increased significantly, while the abundance of Acidobacteria has decreased significantly. Moreover, deep tillage increased the activity of sucrase (S-SC) and nitrate reductase (NR) in samples with soil depth below 20 cm. In summary, deep tillage disturbed spatial microbial diversity and environmental factors significantly. This would provide new guidance for improving farmland management strategies, optimizing the activation methods of soil layers, further improving crop planting soil, and increasing crop yield.
Collapse
Affiliation(s)
- Yuzhen Zhang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Guodong Bo
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Guodong Bo,
| | - Minchong Shen
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Guoming Shen
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Jianming Yang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Shanyu Dong
- Yichang Tobacco Company of Hubei Province, Yichang, China
| | - Zhaohe Shu
- Enshi Tobacco Company of Hubei Province, Enshi, China
- Zhaohe Shu,
| | - Zhaobao Wang
- Energy-Rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Zhaobao Wang,
| |
Collapse
|
25
|
Characterization of Microbial Communities and Naturally Occurring Radionuclides in Soilless Growth Media Amended with Different Concentrations of Biochar. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2030051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Biochar, derived from the pyrolysis of plant materials has the potential to enhance plant growth in soilless media. Howevetar, little is known about the impact of biochar amendments to soilless growth media, microbial community composition, and fate of chemical constituents in the media. In this study, different concentrations of biochar were added to soilless media and microbial composition, and chemical constituents were analyzed using metagenomics and gamma spectroscopy techniques, respectively. Across treatments, carboxyl-C, phenolic-C, and aromatic-C were the main carbon sources that influenced microbial community composition. Flavobacterium (39.7%), was the predominantly bacteria genus, followed by Acidibacter (12.2%), Terrimonas (10.1%), Cytophaga (7.5%), Ferruginibacter (6.0%), Lacunisphaera (5.9%), Cellvibrio (5.8%), Opitutus (4.8%), Mucilaginibacter (4.0%) and Bryobacter (4.0%). Negative relationships were found between Cytophaga and 226Ra (r = −0.84, p = 0.0047), 40K (r = −0.82, p = 0.0069) and 137Cs (r = −0.93, p = 0.0002). Similarly, Mucilaginibacter was negatively correlated with 226Ra (r = −0.83, p = 0.0054) and 137Cs (r = −0.87, p = 0.0021). Overall, the data suggest that high % biochar amended samples have high radioactivity concentration levels. Some microorganisms have less presence in high radioactivity concentration levels.
Collapse
|
26
|
Huber KJ, Pester M, Eichorst SA, Navarrete AA, Foesel BU. Editorial: Acidobacteria – Towards Unraveling the Secrets of a Widespread, Though Enigmatic, Phylum. Front Microbiol 2022; 13:960602. [PMID: 35814658 PMCID: PMC9267355 DOI: 10.3389/fmicb.2022.960602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Katharina J. Huber
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael Pester
- Department Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute for Microbiology, Technical University of Braunschweig, Braunschweig, Germany
| | - Stephanie A. Eichorst
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Acacio A. Navarrete
- Graduate Program in Environmental Sciences, University Brazil, São Paulo, Brazil
| | - Bärbel U. Foesel
- Working Group Biobank, Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
- *Correspondence: Bärbel U. Foesel
| |
Collapse
|
27
|
Meena M, Yadav G, Sonigra P, Nagda A, Mehta T, Swapnil P, Marwal A, Kumar S. Multifarious Responses of Forest Soil Microbial Community Toward Climate Change. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02051-3. [PMID: 35657425 DOI: 10.1007/s00248-022-02051-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.
Collapse
Affiliation(s)
- Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India.
| | - Garima Yadav
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Priyankaraj Sonigra
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Adhishree Nagda
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Tushar Mehta
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Prashant Swapnil
- Department of Botany, School of Biological Science, Central University of Punjab, Bhatinda, Punjab, 151401, India
| | - Avinash Marwal
- Department of Biotechnology, Vigyan Bhawan - Block B, New Campus, Mohanlal Sukhadia University, Udaipur, 313001, Rajasthan, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India
| |
Collapse
|
28
|
Responses of CO2 emissions and soil microbial community structures to organic amendment in two contrasting soils in Zambia. Sci Rep 2022; 12:6368. [PMID: 35430624 PMCID: PMC9013351 DOI: 10.1038/s41598-022-10368-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 04/06/2022] [Indexed: 12/05/2022] Open
Abstract
In sub-Saharan Africa, efforts have been made to increase soil carbon (C) content in agricultural ecosystems due to severe soil degradation. The use of organic materials is a feasible method for recovering soil organic C; however, the effects of organic amendments on soil microbial communities and C cycles under C-limited soil conditions are still unknown. In this study, we conducted field experiments in Zambia using organic amendments at two sites with contrasting C content. At both sites, temporal changes in soil carbon dioxide (CO2) emissions and prokaryotic community structures were monitored during the crop growing season (126 days). The organic amendments increased CO2 emissions and prokaryotic abundance at the Kabwe site, whereas no direct impacts were observed at the Lusaka site. We also observed a larger temporal variability in the soil microbial community structure at Kabwe than that at Lusaka. These contrasting results between the two soils may be due to the microbial community stability differences between each site. However, as organic amendments have considerable potential to enhance microbial abundance and consequently sequester C at the Kabwe site, site-specific strategies are required to address the issues of soil C depletion in drylands.
Collapse
|
29
|
Qian Z, Zhuang S, Gao J, Tang L, Harindintwali JD, Wang F. Aeration increases soil bacterial diversity and nutrient transformation under mulching-induced hypoxic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 817:153017. [PMID: 35026241 DOI: 10.1016/j.scitotenv.2022.153017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 05/22/2023]
Abstract
Soil oxygen (O2) deficiency induced by organic mulching is easy to overlook. Aeration has been shown to potentially alleviate soil hypoxia stress. However, the responses of soil bacterial communities to such mulching-induced hypoxic conditions and aeration remain elusive. Therefore, a three-year field experiment, consisting of mulching (T1), mulching with aeration (TA1, poor aeration; TA2, strong aeration), and no-mulching (CK) treatments, was conducted in bamboo (Phyllostachys praecox) plantations. According to our results, the strong aeration treatment (TA2) alleviated soil acidification, increased soil nutrient availability, and significantly increased soil O2 content by 18.44% (P < 0.05) when compared with T1. In addition, TA2 significantly increased soil β-glucosidase, invertase, urease, and acid phosphatase activities compared with CK and T1 (P < 0.05). The alpha diversity indices with TA2 treatment were the highest, indicating that aeration increased the species richness and diversity of bacteria. The changes in bacterial community composition associated with TA2 treatment (i.e., an increase in Firmicutes, Verrucomicrobia, and Faecalibacterium abundance and a decrease in Chloroflexi and Bradyrhizobium abundance) were mainly related to nutrient and O2 content. Mantel Test results suggested that soil O2 content and temperature were the key factors shaping bacterial community composition. Structural equation modeling revealed that soil O2 content had a positive and direct influence on bacterial community diversity. Functional annotation of prokaryotic taxa predicted that TA2 significantly increased the relative abundance of bacterial communities associated with nitrification, nitrogen fixation, and ureolysis. Our results demonstrated that optimal soil aeration conditions (17.60% of O2 content) could enhance the diversity and function of soil bacterial communities. Overall, the findings of this study could serve as a benchmark for alleviating soil hypoxia caused by organic mulches, which is important for increasing the functionality of nutrient cycling bacterial communities in the soil.
Collapse
Affiliation(s)
- Zhuangzhuang Qian
- State Key Lab of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, PR China
| | - Shunyao Zhuang
- State Key Lab of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Jianshuang Gao
- State Key Lab of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Luozhong Tang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, PR China
| | - Jean Damascene Harindintwali
- University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Fang Wang
- University of Chinese Academy of Sciences, Beijing 100049, PR China; CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| |
Collapse
|
30
|
Jones CM, Putz M, Tiemann M, Hallin S. Reactive nitrogen restructures and weakens microbial controls of soil N2O emissions. Commun Biol 2022; 5:273. [PMID: 35347224 PMCID: PMC8960841 DOI: 10.1038/s42003-022-03211-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/02/2022] [Indexed: 12/20/2022] Open
Abstract
AbstractThe global surplus of reactive nitrogen (Nr) in agricultural soils is accelerating nitrous oxide (N2O) emission rates, and may also strongly influence the microbial controls of this greenhouse gas resulting in positive feedbacks that further exacerbate N2O emissions. Yet, the link between legacy effects of Nr on microbial communities and altered regulation of N2O emissions is unclear. By examining soils with legacies of Nr-addition from 14 field experiments with different edaphic backgrounds, we show that increased potential N2O production is associated with specific phylogenetic shifts in communities of frequently occurring soil microbes. Inputs of Nr increased the complexity of microbial co-association networks, and altered the relative importance of biotic and abiotic predictors of potential N2O emissions. Our results provide a link between the microbial legacy of Nr addition and increased N2O emissions by demonstrating that biological controls of N2O emissions were more important in unfertilized soils and that these controls are weakened by increasing resource levels in soil.
Collapse
|
31
|
Padda KP, Puri A, Nguyen NK, Philpott TJ, Chanway CP. Evaluating the rhizospheric and endophytic bacterial microbiome of pioneering pines in an aggregate mining ecosystem post-disturbance. PLANT AND SOIL 2022; 474:213-232. [PMID: 35698622 PMCID: PMC9184430 DOI: 10.1007/s11104-022-05327-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/02/2022] [Indexed: 06/15/2023]
Abstract
AIMS Despite little soil development and organic matter accumulation, lodgepole pine (Pinus contorta var. latifolia) consistently shows vigorous growth on bare gravel substrate of aggregate mining pits in parts of Canadian sub-boreal forests. This study aimed to investigate the bacterial microbiome of lodgepole pine trees growing at an unreclaimed gravel pit in central British Columbia and suggest their potential role in tree growth and survival following mining activity. METHODS We characterized the diversity, taxonomic composition, and relative abundance of bacterial communities in rhizosphere and endosphere niches of pine trees regenerating at the gravel pit along with comparing them with a nearby undisturbed forested site using 16S rRNA high-throughput sequencing. Additionally, the soil and plant nutrient contents at both sites were also analyzed. RESULTS Although soil N-content at the gravel pit was drastically lower than the forest site, pine tissue N-levels at both sites were identical. Beta-diversity was affected by site and niche-type, signifying that the diversity of bacterial communities harboured by pine trees was different between both sites and among various plant-niches. Bacterial alpha-diversity was comparable at both sites but differed significantly between belowground and aboveground plant-niches. In terms of composition, pine trees predominantly associated with taxa that appear plant-beneficial including phylotypes of Rhizobiaceae, Acetobacteraceae, and Beijerinckiaceae at the gravel pit and Xanthobacteraceae, Acetobacteraceae, Beijerinckiaceae and Acidobacteriaceae at the forest site. CONCLUSIONS Our results suggest that, following mining activity, regenerating pine trees recruit bacterial communities that could be plant-beneficial and support pine growth in an otherwise severely N-limited disturbed environment. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11104-022-05327-2.
Collapse
Affiliation(s)
- Kiran Preet Padda
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC Canada
| | - Akshit Puri
- Present Address: School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
- UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Timothy J. Philpott
- British Columbia Ministry of Forests, Lands and Natural Resource Operations, Williams Lake, BC Canada
| | - Chris P. Chanway
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC Canada
| |
Collapse
|
32
|
Huber KJ, Vieira S, Sikorski J, Wüst PK, Fösel BU, Gröngröft A, Overmann J. Differential Response of Acidobacteria to Water Content, Soil Type, and Land Use During an Extended Drought in African Savannah Soils. Front Microbiol 2022; 13:750456. [PMID: 35222321 PMCID: PMC8874233 DOI: 10.3389/fmicb.2022.750456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Although climate change is expected to increase the extent of drylands worldwide, the effect of drought on the soil microbiome is still insufficiently understood as for dominant but little characterized phyla like the Acidobacteria. In the present study the active acidobacterial communities of Namibian soils differing in type, physicochemical parameters, and land use were characterized by high-throughput sequencing. Water content, pH, major ions and nutrients were distinct for sandy soils, woodlands or dry agriculture on loamy sands. Soils were repeatedly sampled over a 2-year time period and covered consecutively a strong rainy, a dry, a normal rainy and a weak rainy season. The increasing drought had differential effects on different soils. Linear modeling of the soil water content across all sampling locations and sampling dates revealed that the accumulated precipitation of the preceding season had only a weak, but statistically significant effect, whereas woodland and irrigation exerted a strong positive effect on water content. The decrease in soil water content was accompanied by a pronounced decrease in the fraction of active Acidobacteria (7.9-0.7%) while overall bacterial community size/cell counts remained constant. Notably, the strongest decline in the relative fraction of Acidobacteria was observed after the first cycle of rainy and dry season, rather than after the weakest rainy season at the end of the observation period. Over the 2-year period, also the β-diversity of soil Acidobacteria changed. During the first year this change in composition was related to soil type (loamy sand) and land use (woodland) as explanatory variables. A total of 188 different acidobacterial sequence variants affiliated with the "Acidobacteriia," Blastocatellia, and Vicinamibacteria changed significantly in abundance, suggesting either drought sensitivity or formation of dormant cell forms. Comparative physiological testing of 15 Namibian isolates revealed species-specific and differential responses in viability during long-term continuous desiccation or drying-rewetting cycles. These different responses were not determined by phylogenetic affiliation and provide a first explanation for the effect of drought on soil Acidobacteria. In conclusion, the response of acidobacterial communities to water availability is non-linear, most likely caused by the different physiological adaptations of the different taxa present.
Collapse
Affiliation(s)
- Katharina J. Huber
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Selma Vieira
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Pia K. Wüst
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Bärbel U. Fösel
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alexander Gröngröft
- Department of Geosciences, Institute of Soil Science, University of Hamburg, Hamburg, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| |
Collapse
|
33
|
Sikorski J, Baumgartner V, Birkhofer K, Boeddinghaus RS, Bunk B, Fischer M, Fösel BU, Friedrich MW, Göker M, Hölzel N, Huang S, Huber KJ, Kandeler E, Klaus VH, Kleinebecker T, Marhan S, von Mering C, Oelmann Y, Prati D, Regan KM, Richter-Heitmann T, Rodrigues JFM, Schmitt B, Schöning I, Schrumpf M, Schurig E, Solly EF, Wolters V, Overmann J. The Evolution of Ecological Diversity in Acidobacteria. Front Microbiol 2022; 13:715637. [PMID: 35185839 PMCID: PMC8847707 DOI: 10.3389/fmicb.2022.715637] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria. This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success.
Collapse
Affiliation(s)
- Johannes Sikorski
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vanessa Baumgartner
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Klaus Birkhofer
- Department of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Cottbus, Germany
| | - Runa S. Boeddinghaus
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Boyke Bunk
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Fischer
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Bärbel U. Fösel
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Markus Göker
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Norbert Hölzel
- Biodiversity and Ecosystem Research Group, Institute of Landscape Ecology, University Münster, Münster, Germany
| | - Sixing Huang
- Bioinformatics Group, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Katharina J. Huber
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ellen Kandeler
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | | | - Till Kleinebecker
- Institute of Landscape Ecology and Resources Management, University of GieBen, GieBen, Germany
| | - Sven Marhan
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Daniel Prati
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Kathleen M. Regan
- Soil Biology Department, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - João F. Matias Rodrigues
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Barbara Schmitt
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Ingo Schöning
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | - Marion Schrumpf
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | | | - Emily F. Solly
- Department for Biogeochemical Processes and Biogeochemical Integration, Max-Planck Institute for Biogeochemistry, Jena, Germany
| | | | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Microbiology, Faculty of Life Sciences, Technische Universität Braunschweig, Braunschweig, Germany
| |
Collapse
|
34
|
Bonomo MG, Calabrone L, Scrano L, Bufo SA, Di Tomaso K, Buongarzone E, Salzano G. Metagenomic monitoring of soil bacterial community after the construction of a crude oil flowline. ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:48. [PMID: 34978609 PMCID: PMC8724107 DOI: 10.1007/s10661-021-09637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 11/20/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to assess the metagenomic changes of soil bacterial community after constructing a crude oil flowline in Basilicata region, Italy. Soils identified a total of 56 taxa at the phylum level and 485 at the family level, with a different taxa distribution, especially in samples collected on 2014. Since microbiological diversity occurred in the soils collected after 2013 (the reference year), we performed a differential abundance analysis using DESeq2 by GAIA pipeline. In the forest area, 14 phyla and 126 families were differentially abundant (- 6.06 < logFC > 7.88) in 2014 compared to 2013. Nine families were differentially abundant in 2015, with logFC between - 3.16 and 4.66, while 20 families were significantly more abundant and 16 less abundant in 2016, with logFC between - 6.48 and 6.45. In the cultivated area, 33 phyla and 260 families showed differential abundance in 2014. In the next year (2015), 14 phyla were significantly more abundant and 19 less abundant, while 29 families were substantially more abundant and 139 less abundant, with fold changes ranging between - 5.67 and 4.01. In 2016, 33 phyla showed a significantly different abundance, as 14 were more abundant and 19 decreased, and 81 families showed a significantly increased amount with logFC between - 5.31 and 5.38. These results hypothesise that the analysed site is an altered soil where the development of particular bacterial groups attends to bioremediation processes, naturally occurring to restore optimal conditions.
Collapse
Affiliation(s)
| | - Luana Calabrone
- Department of Sciences, University of Basilicata, Potenza, Italy
| | - Laura Scrano
- Department of European Cultures, University of Basilicata, Potenza, Italy
| | - Sabino Aurelio Bufo
- Department of Sciences, University of Basilicata, Potenza, Italy
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, Johannesburg, South Africa
| | - Katia Di Tomaso
- Department of Sciences, University of Basilicata, Potenza, Italy
| | | | - Giovanni Salzano
- Department of Sciences, University of Basilicata, Potenza, Italy
| |
Collapse
|
35
|
Chang Y, Chen F, Zhu Y, You Y, Cheng Y, Ma J. Influence of revegetation on soil microbial community and its assembly process in the open-pit mining area of the Loess Plateau, China. Front Microbiol 2022; 13:992816. [PMID: 36090080 PMCID: PMC9453671 DOI: 10.3389/fmicb.2022.992816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 11/15/2022] Open
Abstract
Vegetation recovery is an important marker of ecosystem health in the mining area. Clarifying the influence of vegetation recovery on the characteristics of soil microbial community and its assembly process can improve our understanding of the ecological resilience and self-maintaining mechanism in the open-pit mining area. For this purpose, we employed MiSeq high-throughput sequencing coupled with null model analysis to determine the composition, molecular ecological network characteristics, key bacterial and fungal clusters, and the assembly mechanism of the soil microbial communities in shrubs (BL), coniferous forest (CF), broad-leaved forests (BF), mixed forest (MF), and the control plot (CK, the poplar plantation nearby that had been continuously grown for over 30 a without disturbance). The results showed that the vegetation restoration model had a significant influence on the α-diversity of the microbial community (p < 0.05). Compared with CK, Sobs and Shannon index of MF and CF have increased by 35.29, 3.50, and 25.18%, 1.05%, respectively, whereas there was no significant difference in the α-diversity of fungal community among different vegetation restoration types, Actinobacteria, Chloroflexi, Proteobacteria, and Acidobacteria were the dominant phyla. The diversity of the first two phyla was significantly higher than those of CK. However, the diversity of the last two phyla was dramatically lower than those of CK (p < 0.05). Ascomycota and Basidiomycota were dominant phyla in the fungal community. The abundance and diversity of Ascomycota were significantly higher than those of CK, while the abundance and diversity of the latter were considerably lower than those of CK (p < 0.05). The stochastic process governed the assembly of the soil microbial community, and the contribution rate to the bacterial community construction of CK, CF, BF, and MF was 100.0%. Except for MF, where the soil fungal community assembly was governed by the deterministic process, all other fungal communities were governed by the stochastic process. Proteobacteria and Acidobacteria are key taxa of the bacterial network, while Mortierellales, Thelebolales, Chaetothyriales, and Hypocreales are the key taxa of the fungal network. All these results might provide the theoretical foundation for restoring the fragile ecosystem in the global mining region.
Collapse
Affiliation(s)
- Yuanyuan Chang
- School of Public Policy and Management, China University of Mining and Technology, Xuzhou, China
| | - Fu Chen
- School of Public Policy and Management, China University of Mining and Technology, Xuzhou, China
- School of Public Administration, Hohai University, Nanjing, China
- *Correspondence: Fu Chen,
| | - Yanfeng Zhu
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou, China
- Engineering Research Center of Ministry of Education for Mine Ecological Restoration, Xuzhou, China
| | - Yunnan You
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou, China
| | - Yanjun Cheng
- School of Environment and Spatial Informatics, China University of Mining and Technology, Xuzhou, China
| | - Jing Ma
- School of Public Administration, Hohai University, Nanjing, China
| |
Collapse
|
36
|
Soil Bacterial and Fungal Community Responses to Throughfall Reduction in a Eucalyptus Plantation in Southern China. FORESTS 2021. [DOI: 10.3390/f13010037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In subtropical plantations in southern China, how soil microbial communities respond to climate change-induced drought is poorly understood. A field experiment was conducted in a subtropical Eucalyptus plantation to determine the impacts of 50% of throughfall reduction (TR) on soil microbial community composition, function, and soil physicochemical properties. Results showed that TR reduced soil water content (SWC) and soil available phosphorus (AP) content. TR significantly altered 196 bacterial operational taxonomic units (OTUs), most of them belonging to Acidobacteria, Actinobacteria, and Proteobacteria, while there were fewer changes in fungal OTUs. At the phylum level, TR increased the relative abundance of Acidobacteria at 0–20 cm soil depth by 37.18%, but failed to influence the relative abundance of the fungal phylum. Notably, TR did not alter the alpha diversity of the bacterial and fungal communities. The redundancy analysis showed that the bacterial communities were significantly correlated with SWC, and fungal communities were significantly correlated with AP content. According to predictions of bacterial and fungal community functions using PICRUSt2 and FUNGuild platforms, TR had different effects on both bacterial and fungal communities. Overall, SWC and AP decreased during TR, resulting in greater changes in soil bacterial community structure, but did not dramatically change soil fungal community structure.
Collapse
|
37
|
Lin Y, Grembi JA, Goots SS, Sebastian A, Albert I, Brennan RA. Advantageous microbial community development and improved performance of pilot-scale field systems treating high-risk acid mine drainage with crab shell. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126665. [PMID: 34351284 DOI: 10.1016/j.jhazmat.2021.126665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/25/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities are crucial to the effectiveness and stability of bioremediation systems treating acid mine drainage (AMD); however, little research has addressed how they correlate to system performance under changing environmental conditions. In this study, 16S rRNA gene sequencing and quantitative PCR (qPCR) were used to characterize microbial communities within different substrate combinations of crab shell (CS) and spent mushroom compost (SMC) and their association with chemical performance in pilot-scale vertical flow ponds (VFPs) treating high risk AMD in central Pennsylvania over 643 days of operation. As compared to a control containing SMC, VFPs containing CS sustained higher alkalinity, higher sulfate-reducing rates, and more thorough metals removal (>90% for Fe and Al, >50% for Mn and Zn). Correspondingly, CS VFPs supported the growth of microorganisms in key functional groups at increasing abundance and diversity over time, especially more diverse sulfate-reducing bacteria. Through changing seasonal and operational conditions over almost two years, the relative abundance of the core phyla shifted in all reactors, but the smallest changes in functional gene copies were observed in VFPs containing CS. These results suggest that the high diversity and stability of microbial communities associated with CS are consistent with effective AMD treatment.
Collapse
Affiliation(s)
- Yishan Lin
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA; State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Jessica A Grembi
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA; School of Medicine, Stanford University, Stanford, CA, USA
| | - Sara S Goots
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA; Calfee, Halter & Griswold, Cleveland, OH, USA
| | - Aswathy Sebastian
- Bioinformatics, Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - István Albert
- Bioinformatics, Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Rachel A Brennan
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA, USA.
| |
Collapse
|
38
|
Soil microbiota and microarthropod communities in oil contaminated sites in the European Subarctic. Sci Rep 2021; 11:19620. [PMID: 34608182 PMCID: PMC8490368 DOI: 10.1038/s41598-021-98680-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/01/2021] [Indexed: 02/08/2023] Open
Abstract
The present comprehensive study aimed to estimate the aftermath of oil contamination and the efficacy of removing the upper level of polluted soil under the conditions of the extreme northern taiga of northeastern European Russia. Soil samples from three sites were studied. Two sites were contaminated with the contents of a nearby sludge collector five years prior to sampling. The highly contaminated upper soil level was removed from one of them. The other was left for self-restoration. A chemical analysis of the soils was conducted, and changes in the composition of the soil zoocoenosis and bacterial and fungal microbiota were investigated. At both contaminated sites, a decrease in the abundance and taxonomic diversity of indicator groups of soil fauna, oribatid mites and collembolans compared to the background site were found. The pioneer eurytopic species Oppiella nova, Proisotoma minima and Xenyllodes armatus formed the basis of the microarthropod populations in the contaminated soil. A complete change in the composition of dominant taxonomic units was observed in the microbiota, both the bacterial and fungal communities. There was an increase in the proportion of representatives of Proteobacteria and Actinobacteria in polluted soils compared to the background community. Hydrocarbon-degrading bacteria-Alcanivorax, Rhodanobacter ginsengisoli, Acidobacterium capsulatum, and Acidocella-and fungi-Amorphotheca resinae abundances greatly increased in oil-contaminated soil. Moreover, among both bacteria and fungi, a sharp increase in the abundance of uncultivated organisms that deserve additional attention as potential oil degraders or organisms with a high resistance to oil contamination were observed. The removal of the upper soil level was partly effective in terms of decreasing the oil product concentration (from approximately 21 to 2.6 g/kg of soil) and preventing a decrease in taxonomic richness but did not prevent alterations in the composition of the microbiota or zoocoenosis.
Collapse
|
39
|
Zhang Y, Chen M, Zhao YY, Zhang AY, Peng DH, Lu F, Dai CC. Destruction of the soil microbial ecological environment caused by the over-utilization of the rice-crayfish co-cropping pattern. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147794. [PMID: 34029817 DOI: 10.1016/j.scitotenv.2021.147794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
The rice-crayfish co-cropping pattern is a traditional method for the intensive utilization of rice fields. In recent years, this pattern has been over-developed in many countries and regions, especially in China, because of its simple agronomic technology and high economic benefits. However, little is known about the potential ecological problems regarding soil microorganisms caused by the over-utilization of this pattern. The results show that rice-crayfish co-cropping, when over-utilized for a long time, reduced soil microbial richness and diversity compared with rice monocropping. A decrease in bacterial abundance in the nitrogen cycle and an increase in bacterial abundance in the carbon cycle led to a decrease in the nitrogen cycle function and an increase in the carbon cycle function. In an analysis of bacteria that are sensitive to cropping patterns, it was found that in the rice-crayfish co-cropping, the relative abundances of sensitive OTUs from Firmicutes (Bacillus and Clostridium) and Chloroflexi (Anaerolineaceae) were significantly higher during the entire growth period than those observed in the rice monocropping pattern, while the relative abundances of sensitive OTUs from Nitrospirae (Nitrospira), Gemmatimonadetes (Gemmatimonas), and Actinobacteria (Nocardioides) were significantly lower than those observed in the rice monocropping pattern. A network analysis shows that growth-period-sensitive OTUs drive the co-occurrence network modules, although the OTUs also have positive and negative correlations among modules but a positive synergistic effect on the regulation of soil nutrients. In addition, OTUs that were sensitive at the booting stage and filling stage were the key microbial groups in the rice-crayfish co-cropping and rice monocropping networks, respectively. Understanding the classifications and functions of sensitive microbes present during the rice growth period is the basis for formulating a microbial flora management strategy for the rice-crayfish co-cropping pattern, which is of great significance for adjusting agricultural management measures and controlling current soil microbial ecological problems.
Collapse
Affiliation(s)
- Yang Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Man Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Yuan-Yuan Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ai-Yue Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Da-Hong Peng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Fan Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Centre for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| |
Collapse
|
40
|
Soil Bacteria to Regulate Phoebe bournei Seedling Growth and Sustainable Soil Utilization under NPK Fertilization. PLANTS 2021; 10:plants10091868. [PMID: 34579400 PMCID: PMC8471390 DOI: 10.3390/plants10091868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 11/17/2022]
Abstract
Soil bacteria play a key role in the plant–soil system and can regulate the growth of Phoebe bournei seedlings under fertilization. However, there are few reports on how soil bacteria respond to fertilization and regulate seedling growth. This study adopted the “3414” field fertilization experiment, combined with soil microbial sequencing, nutrient contents, and biomass measurement, to explore the changes of soil chemical properties and bacterial structure under different NPK fertilization conditions and to establish the coupling relationship between soil bacteria, soil nutrients, and plant growth. The results showed that NPK fertilization decreased soil pH; increased soil N, P, and K content; reduced bacterial diversity and abundance; promoted the growth of dominant bacterial species; and enhanced Phoebe bournei seedlings’ soil N, P, and K elements. NPK fertilization promoted Proteobacteria growth, especially of three genera (Methylobacterium, Sphingobium, and Acinetobacter) and Actinobacteria, while it decreased Acidobacteria and Chloroflexi. By reducing the ratio of N to K and increasing P, NPK fertilization can slow soil acidification, promote bacterial reproduction, maintain P. bournei seedlings’ soil ecological stability, and balance the seedlings’ growth and sustainable soil utilization. AD3, Pseudomonas, and Rhodanobacter can be used as the marker species for N, P, and K fertilization, respectively, while Methylobacterium, Brevundimonas, Acinetobacter, and Sphingobium can be used as indicator species for soil pH and soil N, P, and K content changes, respectively. These results provided a theoretical basis and technical guidance for the effective fertilization and cultivation of robust P. bournei seedlings.
Collapse
|
41
|
Li Q, Zhang D, Cheng H, Song Z, Ren L, Hao B, Zhu J, Fang W, Yan D, Li Y, Wang Q, Cao A. Chloropicrin alternated with dazomet improved the soil's physicochemical properties, changed microbial communities and increased strawberry yield. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 220:112362. [PMID: 34087650 DOI: 10.1016/j.ecoenv.2021.112362] [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: 03/02/2021] [Revised: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
Chloropicrin (Pic) and dazomet (DZ) are effective soil fumigants that are often used to reduce soil-borne pathogens that would otherwise reduce crop yield. As Pic is scheduled to be banned, we investigated whether its consumption could be halved by alternating it with DZ. We observed that Pic alternated with DZ increased the soil NH4+-N content by 28.74-47.07 times, increased available potassium content by 40.80%-46.81% and increased electrical conductivity by 39.23%-85.81%. It generally improved the soil's physicochemical properties. High-throughput DNA sequencing showed that Pic alternated with DZ changed the taxonomic diversity of bacteria and fungi by increasing the relative abundance of Bacillus and Firmicutes, and by decreasing Proteobacteria, Acidobacteria and Sphingomonas. Moreover, Pic alternated with DZ can inhibit key soil pathogens by more than 90% and significantly increased strawberry yield by 78.22%-116.12%. In terms of strawberry production, we recommend using DZ in the first year and Pic in the second year. Our results showed significant ecological benefit and yield benefit when Pic consumption was halved by alternating it with DZ.
Collapse
Affiliation(s)
- Qingjie Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongyan Cheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhaoxin Song
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lirui Ren
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Baoqiang Hao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiahong Zhu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; State Key Laboratory for Biology of Plant Disease and Insect Pests, Beijing 100193, China.
| |
Collapse
|
42
|
Xu R, Sun X, Häggblom MM, Dong Y, Zhang M, Yang Z, Xiao E, Xiao T, Gao P, Li B, Sun W. Metabolic potentials of members of the class Acidobacteriia in metal-contaminated soils revealed by metagenomic analysis. Environ Microbiol 2021; 24:803-818. [PMID: 34081382 DOI: 10.1111/1462-2920.15612] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/18/2021] [Accepted: 05/23/2021] [Indexed: 01/09/2023]
Abstract
The relative abundance of Acidobacteriia correlated positively with the concentrations of arsenic (As), mercury (Hg), chromium (Cr), copper (Cu) and other metals, suggesting their adaptation of the metal-rich environments. Metagenomic binning reconstructed 29 high-quality metagenome-assembled genomes (MAGs) associated with Acidobacteriia, providing an opportunity to study their metabolic potentials. These MAGs contained genes to transform As, Hg and Cr through oxidation, reduction, efflux and demethylation, suggesting the potential of Acidobacteriia to transform such metal(loid)s. Additionally, genes associated with alleviation of acidic and metal stress were also detected in these MAGs. Acidobacteriia may have the capabilities to resist or transform metal(loid)s in acidic metal-contaminated sites. Moreover, these genes encoding metal transformation could be also identified in the Acidobacteriia-associated MAGs from five additional metal-contaminated sites across Southwest China, as well as Acidobacteriia-associated reference genomes from the NCBI database, suggesting that the capability of metal transformation may be widespread among Acidobacteriia members. This discovery provides an understanding of metabolic potentials of the Acidobacteriia in acidic metal-rich sites.
Collapse
Affiliation(s)
- Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA
| | - Yiran Dong
- School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, 430074, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, China
| | - Enzong Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Tangfu Xiao
- Key Laboratory of Water Quality and Conservation in the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China.,Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.,School of Environment, Henan Normal University, China.,Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, China
| |
Collapse
|
43
|
Sun X, Song B, Xu R, Zhang M, Gao P, Lin H, Sun W. Root-associated (rhizosphere and endosphere) microbiomes of the Miscanthus sinensis and their response to the heavy metal contamination. J Environ Sci (China) 2021; 104:387-398. [PMID: 33985741 DOI: 10.1016/j.jes.2020.12.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 06/12/2023]
Abstract
The plant root-associated microbiomes, including both the rhizosphere and the root endosphere microbial community, are considered as a critical extension of the plant genome. Comparing to the well-studied rhizosphere microbiome, the understanding of the root endophytic microbiome is still in its infancy. Miscanthus sinensis is a pioneering plant that could thrive on metal contaminated lands and holds the potential for phytoremediation applications. Characterizing its root-associated microbiome, especially the root endophytic microbiome, could provide pivotal knowledge for phytoremediation of mine tailings. In the current study, M. sinensis residing in two Pb/Zn tailings and one uncontaminated site were collected. The results demonstrated that the metal contaminant fractions exposed strong impacts on the microbial community structures. Their influences on the microbial community, however, gradually decreases from the bulk soil through the rhizosphere soil and finally to the endosphere, which resulting in distinct root endophytic microbial community structures compared to both the bulk and rhizosphere soil. Diverse members affiliated with the order Rhizobiales was identified as the core microbiome residing in the root of M. sinensis. In addition, enrichment of plant-growth promoting functions within the root endosphere were predicted, suggesting the root endophytes may provide critical services to the host plant. The current study provides new insights into taxonomy and potential functions of the root-associated microbiomes of the pioneer plant, M. sinensis, which may facilitate future phytoremediation practices.
Collapse
Affiliation(s)
- Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Benru Song
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
| |
Collapse
|
44
|
Isoprene-Degrading Bacteria from Soils Associated with Tropical Economic Crops and Framework Forest Trees. Microorganisms 2021; 9:microorganisms9051024. [PMID: 34068745 PMCID: PMC8150984 DOI: 10.3390/microorganisms9051024] [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: 04/21/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 11/17/2022] Open
Abstract
Isoprene, a volatile hydrocarbon emitted largely by plants, plays an important role in regulating the climate in diverse ways, such as reacting with free radicals in the atmosphere to produce greenhouse gases and pollutants. Isoprene is both deposited and formed in soil, where it can be consumed by some soil microbes, although much remains to be understood about isoprene consumption in tropical soils. In this study, isoprene-degrading bacteria from soils associated with tropical plants were investigated by cultivation and cultivation-independent approaches. Soil samples were taken from beneath selected framework forest trees and economic crops at different seasons, and isoprene degradation in soil microcosms was measured after 96 h of incubation. Isoprene losses were 4-31% and 15-52% in soils subjected to a lower (7.2 × 105 ppbv) and a higher (7.2 × 106 ppbv) concentration of isoprene, respectively. Sequencing of 16S rRNA genes revealed that bacterial communities in soil varied significantly across plant categories (framework trees versus economic crops) and the presence of isoprene, but not with isoprene concentration or season. Eight isoprene-degrading bacterial strains were isolated from the soils and, among these, four belong to the genera Ochrobactrum, Friedmanniella, Isoptericola and Cellulosimicrobium, which have not been previously shown to degrade isoprene.
Collapse
|
45
|
Cerecetto V, Smalla K, Nesme J, Garaycochea S, Fresia P, Sørensen SJ, Babin D, Leoni C. Reduced tillage, cover crops and organic amendments affect soil microbiota and improve soil health in Uruguayan vegetable farming systems. FEMS Microbiol Ecol 2021; 97:6129805. [PMID: 33547893 DOI: 10.1093/femsec/fiab023] [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] [Received: 08/05/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Conventional tillage and mineral fertilization (CTMF) jeopardize soil health in conventional vegetable production systems. Using a field experiment established in Uruguay in 2012, we aimed to compare the soil restoration potential of organic fertilization (compost and poultry manure) combined with conventional tillage and cover crop incorporated into the soil (CTOF) or with reduced tillage and the use of cover crop as mulch (RTOF). In 2017, table beet was cultivated under CTMF, CTOF and RTOF, and yields, soil aggregate composition and nutrients, as well as soil and table beet rhizosphere microbiota (here: bacteria and archaea) were evaluated. Microbiota was studied by high-throughput sequencing of 16S rRNA gene fragments amplified from total community DNA. RTOF exhibited higher soil aggregation, soil organic C, nutrient availability and microbial alpha-diversity than CTMF, and became more similar to an adjacent natural undisturbed site. The soil microbiota was strongly shaped by the fertilization source which was conveyed to the rhizosphere and resulted in differentially abundant taxa. However, 229 amplicon sequencing variants were found to form the core table beet rhizosphere microbiota shared among managements. In conclusion, our study shows that after only 5 years of implementation, RTOF improves soil health under intensive vegetable farming systems.
Collapse
Affiliation(s)
- Victoria Cerecetto
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany.,Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay
| | - Kornelia Smalla
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Joseph Nesme
- University of Copenhagen, Department of Biology, Section of Microbiology, Nørregade 10, 1165 Copenhagen, Denmark
| | - Silvia Garaycochea
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay
| | - Pablo Fresia
- Unidad Mixta Institut Pasteur de Montevideo + Instituto Nacional de Investigación Agropecuaria INIA (UMPI), Mataojo 2020, 11400 Montevideo, Uruguay
| | - Søren Johannes Sørensen
- University of Copenhagen, Department of Biology, Section of Microbiology, Nørregade 10, 1165 Copenhagen, Denmark
| | - Doreen Babin
- Julius Kühn Institute (JKI)-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Carolina Leoni
- Instituto Nacional de Investigación Agropecuaria (INIA), Programa de Producción y Sustentabilidad Ambiental, Estación Experimental INIA Las Brujas, Ruta 48 Km 10, 90200 Rincón del Colorado, Canelones, Uruguay
| |
Collapse
|
46
|
Silveira R, Silva MRSS, de Roure Bandeira de Mello T, Alvim EACC, Marques NCS, Kruger RH, da Cunha Bustamante MM. Bacteria and Archaea Communities in Cerrado Natural Pond Sediments. MICROBIAL ECOLOGY 2021; 81:563-578. [PMID: 32829441 DOI: 10.1007/s00248-020-01574-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Natural ponds in the Brazilian Cerrado harbor high biodiversity but are still poorly studied, especially their microbial assemblage. The characterization of the microbial community in aquatic environments is fundamental for understanding its functioning, particularly under the increasing pressure posed by land conversion and climate change. Here, we aim to characterize the structure (abundance, richness, and diversity) and composition of the Bacteria and Archaea in the sediment of two natural ponds belonging to different basins that primarily differ in size and depth in the Cerrado. Sediment samples were collected in the dry and rainy seasons and the transition periods between both. The structure and composition of Bacteria and Archaea were assessed by 16S rRNA gene pyrosequencing. We identified 45 bacterial and four archaeal groups. Proteobacteria and Acidobacteria dominated the bacterial community, while Euryarchaeota and Thaumarchaeota dominated the archaeal community. Seasonal fluctuations in the relative abundance of microbial taxa were observed, but pond characteristics were more determinant to community composition differences. Microbial communities are highly diverse, and local variability could partially explain the microbial structure's main differences. Functional predictions based in 16S rRNA gene accessed with Tax4Fun indicated an enriched abundance of predicted methane metabolism in the deeper pond, where higher abundance of methanogenic archaea Methanocella, Methanosaeta, and Methanomicrobiaceae was detected. Our dataset encompasses the more comprehensive survey of prokaryotic microbes in Cerrado's aquatic environments. Here, we present basic and essential information about composition and diversity, for initial insights into the ecology of Bacteria and Archaea in these environments.
Collapse
Affiliation(s)
- Rafaella Silveira
- Microbial Biology, Cellular Biology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil.
- Enzymology Laboratory, Cellular Biology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil.
- Ecosystems Laboratory, Ecology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil.
| | | | | | | | - Nubia Carla Santos Marques
- Ecosystems Laboratory, Ecology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil
| | - Ricardo Henrique Kruger
- Microbial Biology, Cellular Biology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil
- Enzymology Laboratory, Cellular Biology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil
| | - Mercedes Maria da Cunha Bustamante
- Microbial Biology, Cellular Biology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil.
- Ecosystems Laboratory, Ecology Department, Biology Institute, University of Brasília, Brasilia, DF, 70919-970, Brazil.
| |
Collapse
|
47
|
Distribution patterns of Acidobacteriota in different fynbos soils. PLoS One 2021; 16:e0248913. [PMID: 33750980 PMCID: PMC7984625 DOI: 10.1371/journal.pone.0248913] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/09/2021] [Indexed: 11/28/2022] Open
Abstract
The Acidobacteriota is ubiquitous and is considered as one of the major bacterial phyla in soils. The current taxonomic classifications of this phylum are divided into 15 class-level subdivisions (SDs), with only 5 of these SDs containing cultured and fully described species. Within the fynbos biome, the Acidobacteriota has been reported as one of the dominant bacterial phyla, with relative abundances ranging between 4–26%. However, none of these studies reported on the specific distribution and diversity of the Acidobacteriota within these soils. Therefore, in this study we aimed to first determine the relative abundance and diversity of the Acidobacteriota in three pristine fynbos nature reserve soils, and secondly, whether differences in the acidobacterial composition can be attributed to environmental factors, such as soil abiotic properties. A total of 27 soil samples were collected at three nature reserves, namely Jonkershoek, Hottentots Holland, and Kogelberg. The variable V4-V5 region of the 16S rRNA gene was sequenced using the Ion Torrent S5 platform. The mean relative abundance of the Acidobacteriota were 9.02% for Jonkershoek, 14.91% for Kogelberg, and most significantly (p<0.05), 18.42% for Hottentots Holland. A total of 33 acidobacterial operational taxonomic units (OTUs) were identified. The dominant subdivisions identified in all samples included SDs 1, 2, and 3. Significant differences were observed in the distribution and composition of these OTUs between nature reserves. The SD1 were negatively correlated to soil pH, hydrogen (H+), potassium (K+) and carbon (C). In contrast, SD2, was positively correlated to soil pH, phosphorus (P), and K+, and unclassified members of SD3 was positively correlated to H+, K, and C. This study is the first to report on the specific acidobacterial distribution in pristine fynbos soils in South Africa.
Collapse
|
48
|
Mayerhofer J, Wächter D, Calanca P, Kohli L, Roth T, Meuli RG, Widmer F. Environmental and Anthropogenic Factors Shape Major Bacterial Community Types Across the Complex Mountain Landscape of Switzerland. Front Microbiol 2021; 12:581430. [PMID: 33776948 PMCID: PMC7990788 DOI: 10.3389/fmicb.2021.581430] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
Mountain areas harbor large climatic and geographic gradients and form numerous habitats that promote high overall biodiversity. Compared to macroorganisms, knowledge about drivers of biodiversity and distribution of soil bacteria in mountain regions is still scarce but a prerequisite for conservation of bacterial functions in soils. An important question is, whether soil bacterial communities with similar structures share environmental preferences. Using metabarcoding of the 16S rRNA gene marker, we assessed soil bacterial communities at 255 sites of a regular grid covering the mountainous landscape of Switzerland, which is characterized by close location of biogeographic regions that harbor different land-use types. Distribution of bacterial communities was mainly shaped by environmental selection, as revealed by 47.9% variance explained by environmental factors, with pH (29%) being most important. Little additional variance was explained by biogeographic regions (2.8%) and land-use types (3.3%). Cluster analysis of bacterial community structures revealed six bacterial community types (BCTs), which were associated to several biogeographic regions and land-use types but overall differed mainly in their preference for soil pH. BCT I and II occurred at neutral pH, showed distinct preferences for biogeographic regions mainly differing in elevation and nutrient availability. BCT III and IV differed only in their preferred soil pH. BCT VI occurred in most acidic soils (pH 3.6) and almost exclusively at forest sites. BCT V occurred in soils with a mean pH of 4 and differed from BCT VI in preference for lower values of organic C, total nitrogen and their ratio. Indicator species and bipartite network analyses revealed 3,998 OTUs associating to different levels of environmental factors and BCTs. Taxonomic classification revealed opposing associations of taxa deriving from the same phyla. The results revealed that pH, land-use type, biogeographic region, and nutrient availability were the main factors shaping bacterial communities across Switzerland. Indicator species and bipartite network analyses revealed environmental preferences of bacterial taxa. Combining information of environmental factors and BCTs yielded increased resolution of the factors shaping soil bacterial communities and provided an improved biodiversity framework. OTUs exclusively associated to BCTs provide a novel resource to identify unassessed environmental drivers.
Collapse
Affiliation(s)
| | - Daniel Wächter
- Swiss Soil Monitoring Network, Agroscope, Zurich, Switzerland
| | | | | | | | | | | |
Collapse
|
49
|
Chuvochina M, Adame MF, Guyot A, Lovelock C, Lockington D, Gamboa-Cutz JN, Dennis PG. Drivers of bacterial diversity along a natural transect from freshwater to saline subtropical wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143455. [PMID: 33243518 DOI: 10.1016/j.scitotenv.2020.143455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
Tropical coastal wetlands provide a range of ecosystem services that are closely associated with microbially-driven biogeochemical processes. Knowledge of the main players and their drivers in those processes can have huge implications on the carbon and nutrient fluxes in wetland soils, and thus on the ecosystems services we derive from them. Here, we collected surface (0-5 cm) and subsurface (20-25 cm) soil samples along a transect from forested freshwater wetlands, to saltmarsh, and mangroves. For each sample, we measured a range of abiotic properties and characterised the diversity of bacterial communities using 16S rRNA gene amplicon sequencing. The alpha diversity of bacterial communities in mangroves exceeded that of freshwater wetlands, which were dominated by members of the Acidobacteria, Alphaproteobacteria and Verrucomicrobia, and associated with high soil pore-water concentrations of soluble reactive phosphorous, and nitrogen as nitrate and nitrite (N-NOX-). Bacterial communities in the saltmarsh were strongly stratified by depth and included members of the Actinobacteria, Chloroflexi, and Deltaproteobacteria. Finally, the mangroves were dominated by representatives of Deltaproteobacteria, mainly Desulfobacteraceae and Synthrophobacteraceae, and were associated with high salinity and soil pore-water concentrations of ammonium (N-NH4+). These communities suggest methane consumption in freshwater wetlands, and sulfate reduction in deep soils of marshes and in mangroves. Our work contributes to the important goal of describing reference conditions for specific wetlands in terms of both bacterial communities and their drivers. This information may be used to monitor change and assess wetland health and function.
Collapse
Affiliation(s)
- Maria Chuvochina
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia; National Centre for Groundwater Research and Training, Flinders University, Bedford Park 5042, Australia
| | | | - Adrien Guyot
- National Centre for Groundwater Research and Training, Flinders University, Bedford Park 5042, Australia; School of Civil Engineering, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Catherine Lovelock
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David Lockington
- National Centre for Groundwater Research and Training, Flinders University, Bedford Park 5042, Australia; School of Civil Engineering, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| |
Collapse
|
50
|
Undisturbed Soil Pedon under Birch Forest: Characterization of Microbiome in Genetic Horizons. SOIL SYSTEMS 2021. [DOI: 10.3390/soilsystems5010014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Vast areas of land in the forest-steppe of West Siberia are occupied by birch forests, the most common ecosystems there. However, currently, little is known about the microbiome composition in the underlying soil, especially along a sequence of soil genetic horizons. The study aimed at inventorying microbiome in genetic horizons of a typical Phaeozem under undisturbed birch forest in West Siberia. Bacteria and fungi were studied using 16S rRNA genes’ and ITS2 amplicon sequencing with Illumina MiSeq. Proteobacteria and Acidobacteria together accounted for two-thirds of the operational taxonomic units (OTUs) numbers and half of the sequences in each genetic horizon. Acidobacteria predominated in eluvial environments, whereas Proteobacteria, preferred topsoil. The fungal sequences were dominated by Ascomycota and Basidiomycota phyla. Basidiomycota was the most abundant in the topsoil, whereas Ascomycota increased down the soil profile. Thelephoraceae family was the most abundant in the A horizon, whereas the Pyronemataceae family dominants in the AEl horizon, ultimately prevailing in the subsoil. We conclude that soil genetic horizons shape distinct microbiomes, therefore soil horizontation should be accounted for while studying undisturbed soils. This study, representing the first description of bacterio- and mycobiomes in genetic horizons of the Phaeozem profile, provides a reference for future research.
Collapse
|