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Xu N, Hu H, Wang Y, Zhang Z, Zhang Q, Ke M, Lu T, Penuelas J, Qian H. Geographic patterns of microbial traits of river basins in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162070. [PMID: 36764554 DOI: 10.1016/j.scitotenv.2023.162070] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
River microbiotas contribute to critical geochemical processes and ecological functions of rivers but are sensitive to variations of environmental drivers. Understanding the geographic pattern of river microbial traits in biogeochemical processes can provide important insights into river health. Many studies have characterized river microbial traits in specific situations, but the geographic patterns of these traits and environmental drivers at a large scale are unknown. We reanalyzed 4505 raw 16S rRNA sequences samples for microbiota from river basins in China. The results indicated differences in the diversity, composition, and structure of microbiotas across diverse river basins. Microbial diversity and functional potential in the river basins decreased over time in northern China and increased in southern China due to niche differentiation, e.g., the Yangtze River basin was the healthiest ecosystem. River microbiotas were mainly involved in the cycling of carbon and nitrogen in the river ecosystems and participated in potential organic metabolic functions. Anthropogenic pollutants discharge was the most critical environmental driver for the microbial traits, e.g., antibiotic discharge, followed by climate change. The prediction by machine-learning models indicated that the continuous discharge of antibiotics and climate change led to high ecological risks for the rivers. Our study provides guidelines for improving the health of river ecosystems and for the formulation of strategies to restore the rivers.
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Affiliation(s)
- Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China
| | - Hang Hu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF- CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain; CREAF, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, China.
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Li Y, Hou Y, Hou Q, Long M, Yang Y, Wang Z, Liao Y. Long-term plastic mulching decreases rhizoplane soil carbon sequestration by decreasing microbial anabolism. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161713. [PMID: 36682553 DOI: 10.1016/j.scitotenv.2023.161713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Ridge-furrow with plastic mulching (RFPM) is a widely used agricultural practice in rain-fed farmlands. However, the impact of microbial related metabolism on soil organic carbon (SOC) is not fully understood. Amino sugar analysis, high-throughput sequencing, and high-throughput qPCR approaches are combined to investigate this topic, based on a long-term experiment. Treatments include flat planting without mulching (FP), ridge-furrow without mulching (RF), and RFPM. RFPM significantly decreases rhizoplane SOC contents, while bulk SOC contents change insignificantly across treatments. In terms of microbial metabolic pathways, RFPM decreases indicators of the in vivo metabolic pathway, whereas those of the ex vivo pathway are increased. In terms of microbial community features, core taxa module #1 is dominated by Sphingomonadaceae. These are putative high yield (Y) strategists, according to the microbial life-history strategy framework. They are closely related to the in vivo pathway and are most predictive for SOC; their abundance is highest under FP and lowest under RFPM. Core taxa module #2 is dominated by Chitinophagaceae, putative resource acquisition (A) strategists, that are closely related to the ex vivo pathway. Their abundance in the rhizoplane is highest under RFPM and lowest under FP. The RFPM-induced decline in SOC occurs simultaneously with the abundance of A-strategists with in vivo pathway but not the Y-strategists with ex vivo pathway. Overall, the result of this study shows a trade-off. In RFPM practice, the ex vivo microbial pathway is enhanced along with the abundance of A-strategists. This is not the case for the in vivo pathway and associated abundance of Y-strategists, which are closely associated with SOC. Our findings underlined the impact of rhizoplane microbial metabolic pathways on SOC status is key to agricultural practices in drylands such as RFPM, and advanced our understanding of how microbes affect the carbon cycling in dryland farming.
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Affiliation(s)
- Yüze Li
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Yuting Hou
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Quanming Hou
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Mei Long
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Yali Yang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110164, Liaoning, PR China
| | - Ziting Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China; College of Agronomy, Guangxi University, Nanning, 530004, Guangxi, PR China; Guangxi Key Laboratory of Sugarcane Biology, Nanning, 530004, Guangxi, PR China.
| | - Yuncheng Liao
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, PR China.
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53
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Shu X, Hu Y, Liu W, Xia L, Zhang Y, Zhou W, Liu W, Zhang Y. Linking between soil properties, bacterial communities, enzyme activities, and soil organic carbon mineralization under ecological restoration in an alpine degraded grassland. Front Microbiol 2023; 14:1131836. [PMID: 37180269 PMCID: PMC10167489 DOI: 10.3389/fmicb.2023.1131836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/17/2023] [Indexed: 04/08/2023] Open
Abstract
Soil organic carbon (SOC) mineralization is affected by ecological restoration and plays an important role in the soil C cycle. However, the mechanism of ecological restoration on SOC mineralization remains unclear. Here, we collected soils from the degraded grassland that have undergone 14 years of ecological restoration by planting shrubs with Salix cupularis alone (SA) and, planting shrubs with Salix cupularis plus planting mixed grasses (SG), with the extremely degraded grassland underwent natural restoration as control (CK). We aimed to investigate the effect of ecological restoration on SOC mineralization at different soil depths, and to address the relative importance of biotic and abiotic drivers of SOC mineralization. Our results documented the statistically significant impacts of restoration mode and its interaction with soil depth on SOC mineralization. Compared with CK, the SA and SG increased the cumulative SOC mineralization but decreased C mineralization efficiency at the 0-20 and 20-40 cm soil depths. Random Forest analyses showed that soil depth, microbial biomass C (MBC), hot-water extractable organic C (HWEOC), and bacterial community composition were important indicators that predicted SOC mineralization. Structural equal modeling indicated that MBC, SOC, and C-cycling enzymes had positive effects on SOC mineralization. Bacterial community composition regulated SOC mineralization via controlling microbial biomass production and C-cycling enzyme activities. Overall, our study provides insights into soil biotic and abiotic factors in association with SOC mineralization, and contributes to understanding the effect and mechanism of ecological restoration on SOC mineralization in a degraded grassland in an alpine region.
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Affiliation(s)
- Xiangyang Shu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yufu Hu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Weijia Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Longlong Xia
- Institute for Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Karlsruhe, Baden-Wurttemberg, Germany
| | - Yanyan Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Wei Zhou
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Wanling Liu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yulin Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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Wei J, Lu J, Nie Y, Li C, Du H, Xu Y. Amino Acids Drive the Deterministic Assembly Process of Fungal Community and Affect the Flavor Metabolites in Baijiu Fermentation. Microbiol Spectr 2023; 11:e0264022. [PMID: 36943039 PMCID: PMC10100711 DOI: 10.1128/spectrum.02640-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 02/22/2023] [Indexed: 03/23/2023] Open
Abstract
Nutrient fluctuation is ubiquitous in fermentation ecosystems. However, the microbial community assembly mechanism and metabolic characteristics in response to nutrient variation are still unclear. Here, we used Baijiu fermentation as a case example to study the responses of microbial community assembly and metabolic characteristics to the variation of amino acids using high-throughput sequencing and metatranscriptomics analyses. We chose two fermentation groups (group A with low amino acid and group B with high amino acid contents). The two groups showed similar succession patterns in the bacterial community, whereas they showed different succession in the fungal community wherein Pichia was dominant in group A and Zygosaccharomyces was dominant in group B. The β-nearest taxon index (βNTI) revealed that bacterial community was randomly formed, whereas fungal community assembly was a deterministic process. Variance partitioning analysis and redundancy analysis revealed that amino acids showed the largest contribution to the fungal community (37.64%, P = 0.005) and were more tightly associated with it in group B. Further study revealed that serine was positively related to Zygosaccharomyces and promoted its growth and ethanol production. Metatranscriptomic analysis revealed that the differential metabolic pathways between the two groups mainly included carbohydrate metabolism and amino acid metabolism, which explained the differences of ethanol production and volatile metabolites (such as isoamylol, isobutanol, and 2-methyl-1-butanol). Then these metabolic pathways were constructed and related gene expression and active microorganisms were listed. Our study provides a systematical understanding of the roles of amino acids in both ecological maintenance and flavor metabolism in fermentation ecosystems. IMPORTANCE In spontaneous fermented foods production, nutrient fluctuation is a critical factor affecting microbial community assembly and metabolic function. Revealing the microbial community assembly mechanism and how it regulates its metabolic characteristics in response to nutrient variation is helpful to the management of the fermentation process. This study provides a systematical understanding of the effect of amino acids on the microbial community assembly and flavor metabolisms using Baijiu fermentation as a case example. The data of this study highlight the importance of the nutrient management in fermentation ecosystems.
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Affiliation(s)
- Junlin Wei
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jun Lu
- Guizhou Guotai Liquor Group Co. Ltd., Guizhou, China
| | - Yao Nie
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Changwen Li
- Guizhou Guotai Liquor Group Co. Ltd., Guizhou, China
| | - Hai Du
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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55
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Carbon Emission and Biodiversity of Arctic Soil Microbial Communities of the Novaya Zemlya and Franz Josef Land Archipelagos. Microorganisms 2023; 11:microorganisms11020482. [PMID: 36838447 PMCID: PMC9962458 DOI: 10.3390/microorganisms11020482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Cryogenic soils are the most important terrestrial carbon reservoir on the planet. However, the relationship between soil microbial diversity and CO2 emission by cryogenic soils is poorly studied. This is especially important in the context of rising temperatures in the high Arctic which can lead to the activation of microbial processes in soils and an increase in carbon input from cryogenic soils into the atmosphere. Here, using high-throughput sequencing of 16S rRNA gene amplicons, we analyzed microbial community composition and diversity metrics in relation to soil carbon dioxide emission, water-extractable organic carbon and microbial biomass carbon in the soils of the Barents Sea archipelagos, Novaya Zemlya and Franz Josef Land. It was found that the highest diversity and CO2 emission were observed on the Hooker and Heiss Islands of the Franz Josef Land archipelago, while the diversity and CO2 emission levels were lower on Novaya Zemlya. Soil moisture and temperature were the main parameters influencing the composition of soil microbial communities on both archipelagos. The data obtained show that CO2 emission levels and community diversity on the studied islands are influenced mostly by a number of local factors, such as soil moisture, microclimatic conditions, different patterns of vegetation and fecal input from animals such as reindeer.
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56
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Lee J, Yun J, Yang Y, Jung JY, Lee YK, Yuan J, Ding W, Freeman C, Kang H. Attenuation of Methane Oxidation by Nitrogen Availability in Arctic Tundra Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2647-2659. [PMID: 36719133 DOI: 10.1021/acs.est.2c05228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
CH4 emission in the Arctic has large uncertainty due to the lack of mechanistic understanding of the processes. CH4 oxidation in Arctic soil plays a critical role in the process, whereby removal of up to 90% of CH4 produced in soils by methanotrophs can occur before it reaches the atmosphere. Previous studies have reported on the importance of rising temperatures in CH4 oxidation, but because the Arctic is typically an N-limited system, fewer studies on the effects of inorganic nitrogen (N) have been reported. However, climate change and an increase of available N caused by anthropogenic activities have recently been reported, which may cause a drastic change in CH4 oxidation in Arctic soils. In this study, we demonstrate that excessive levels of available N in soil cause an increase in net CH4 emissions via the reduction of CH4 oxidation in surface soil in the Arctic tundra. In vitro experiments suggested that N in the form of NO3- is responsible for the decrease in CH4 oxidation via influencing soil bacterial and methanotrophic communities. The findings of our meta-analysis suggest that CH4 oxidation in the boreal biome is more susceptible to the addition of N than in other biomes. We provide evidence that CH4 emissions in Arctic tundra can be enhanced by an increase of available N, with profound implications for modeling CH4 dynamics in Arctic regions.
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Affiliation(s)
- Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Ji Young Jung
- Korea Polar Research Institute, Incheon21990, South Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon21990, South Korea
| | - Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
| | - Chris Freeman
- School of Natural Sciences, Bangor University, BangorLL57 2UW, U.K
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
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57
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Paquis P, Hengst MB, Florez JZ, Tapia J, Molina V, Pérez V, Pardo-Esté C. Short-term characterisation of climatic-environmental variables and microbial community diversity in a high-altitude Andean wetland (Salar de Huasco, Chile). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160291. [PMID: 36410480 DOI: 10.1016/j.scitotenv.2022.160291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Microbial community structures are shaped by geochemical factors and their interactions with the lithosphere, hydrosphere, and atmosphere through the processes of chemical mobilisation and mineralisation. High-altitude wetlands and salt flats in the central Andes are characterised by pronounced physicochemical gradients and extreme climatic conditions, representing hotspots of microbial diversity. We here hypothesise about the existence of direct relationships between the local microbiology and the climate cyclicity variables based on meteorological and biogeochemical patterns that develop over a short time scale (five years). We have here analysed the interactions between hydrometeorological and biogeochemical variables and the microbial communities of the Salar de Huasco. These results were obtained by correlating 16S cDNA and DNA gene Illumina sequences with meteorological/satellite data collected both at monitoring stations and by remote sensing between the years 2015 and 2020. The precipitation levels and flooded areas (i.e., areas covered and/or saturated with permanent water) detected in the Salar de Huasco revealed a marked hydric cyclicity that correlated seasonally with intra-annual wet and dry seasons. Overall, at this site, wet periods occurred from December to April, and dry periods from May to November. Meteorological variables such as solar radiation, air temperature, relative humidity, wind speed, atmospheric pressure, and wind direction were well-defined, showing a potential association with the hydrogeology of the area, which is directly related to the wetlands' flooded areas. Finally, the microbial presence and potentially active microbial communities were determined through the sequencing of the 16S gene (DNA and cDNA, respectively), this were associated with climatic seasonality and spatially distributed physical and chemical heterogeneity. Other non-local inter-annual scale processes, such as El Niño-Southern Oscillation (ENSO) events, modify the physical and chemical context of the wetland, thus forming unique ecological niches in the Andean Mountains.
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Affiliation(s)
- Pablo Paquis
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile; Departamento de Ciencias Geológicas, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile; Programa de Doctorado en Ciencias mención Geología, Universidad Católica del Norte, Antofagasta, Chile.
| | - Martha B Hengst
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile.
| | - July Z Florez
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile; Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas y HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile.
| | - Joseline Tapia
- Departamento de Ciencias Geológicas, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile.
| | - Verónica Molina
- Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas y HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile; Centro COPAS Coastal, Universidad de Concepción, Concepción, Chile.
| | - Vilma Pérez
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Australia.
| | - Coral Pardo-Esté
- Departamento de Ciencias Farmacéuticas, Facultad de Ciencias, Universidad Católica del Norte, Antofagasta, Chile.
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Qi JY, Yao XB, Lu J, He LX, Cao JL, Kan ZR, Wang X, Pan SG, Tang XR. A 40 % paddy surface soil organic carbon increase after 5-year no-tillage is linked with shifts in soil bacterial composition and functions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160206. [PMID: 36400297 DOI: 10.1016/j.scitotenv.2022.160206] [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: 08/14/2022] [Revised: 10/26/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Soil organic carbon (SOC) is related to soil fertility, crop yield, and climate change mitigation. Paddy soil is a significant carbon (C) sink, but its C sequestration potential has not been realized as the various driving factors are still not fully understood. We performed a 5-year paddy field experiment in southern China to estimate tillage effects on SOC accumulation and its relation with soil bacteria. The C input from rice residue, SOC content, CO2 flux, soil bacterial community composition, and predicted functions were analyzed. No-tillage (NT) increased (p < 0.05) rice residue C inputs (by 12.6 %-15.9 %), SOC (by 40 % at the surface soil layer compared with conventional tillage, CT), and CO2 fluxes compared with reduced tillage (RT) and CT. Also, NT significantly altered the soil bacterial community. The random forest model showed that the predicted bacterial functions of "Degradation/Utilization/Assimilation Other", "C1 Compound Assimilation", and "Amin and Polyamine Degradation" were the most important functions associated with SOC accumulation. Analysis of metabolic pathway differences indicated that NT significantly decreased the BENZCOA-PWY (anaerobic aromatic compound degradation) and the AST-PWY (L-arginine degradation II). Therefore, the rapid paddy SOC increase is associated with both residue C input (from higher rice yields) and the degradation functions regulated by soil bacteria.
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Affiliation(s)
- Jian-Ying Qi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Xiang-Bin Yao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Jian Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Long-Xin He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Jun-Li Cao
- Shanxi Center for Testing of Functional Agro⁃Products, Shanxi Agricultural University, Taiyuan 030031, China
| | - Zheng-Rong Kan
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xing Wang
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Sheng-Gang Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China
| | - Xiang-Ru Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; Scientific Observing and Experimental Station of Crop Cultivation in South China, Ministry of Agriculture and Rural Affairs, Guangzhou 510642, China; Guangzhou Key Laboratory for Science and Technology of Fragrant Rice, Guangzhou 510642, China.
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Soil organic carbon, aggregation and fungi community after 44 years of no-till and cropping systems in the Central Great Plains, USA. Arch Microbiol 2023; 205:84. [PMID: 36750497 DOI: 10.1007/s00203-023-03421-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/11/2023] [Accepted: 01/18/2023] [Indexed: 02/09/2023]
Abstract
Implementing sustainable agricultural land management practices such as no-till (NT) and diversified crops are important for maintaining soil health properties. This study focuses on the soil health of three long-term (44 years) tillage systems, NT, reduced tillage (RT), and conventional tillage (CT), in monoculture winter wheat-fallow (W-F) (Triticum aestivum L.) and wheat-soybean (W-S) (Glycine max (L.) Merrill) rotation. Soil organic carbon (C) was higher in NT than CT in the surface 0-5 cm, but not different in the 5-15 cm, demonstrating SOC stratification on the soil profile. The soil water content was higher in NT followed by RT and CT in the top 0-5 cm. We found an association between increased carbon, aggregation, and AMF biomass. Greater soil aggregation, carbon and AMF were observed in NT at 0-5 cm soil depth. The W-S cropping system had greater soil microbial community composition based on fungi biomass, AMF and fungal to bacteria ratio from phospholipid fatty acid analysis (PLFA). Large macroaggregates were positively correlated with total C and N, microbial biomass, Gram + , and AMF. Soil water content was positively correlated with macroaggregates, total C and N, and AC. No-till increased soil carbon content even after 44 years of cultivation. By implementing conservation tillage systems and diversified crop rotation, soil quality can be improved through greater soil organic C, water content, greater soil structure, and higher AMF biomass than CT practice in the Central Great Plains.
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Li X, Li D, Jiang Y, Xu J, Ren X, Zhang Y, Wang H, Lu Q, Yan J, Ahmed T, Li B, Guo K. The effects of microbial fertilizer based Aspergillus brunneoviolaceus HZ23 on pakchoi growth, soil properties, rhizosphere bacterial community structure, and metabolites in newly reclaimed land. Front Microbiol 2023; 14:1091380. [PMID: 36814570 PMCID: PMC9939755 DOI: 10.3389/fmicb.2023.1091380] [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: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 02/09/2023] Open
Abstract
Introduction Pakchoi is an important leafy vegetable in China. Due to industrialization and urbanization, pakchoi has been cultivated in newly reclaimed mountainous lands in Zhejiang Province, China in recent years. However, immature soil is not suitable for plant growth and needs to be modified by the application of different organic fertilizer or microbial fertilizer based plant-growth-promoting microbe. In 2021, a high efficient plant-growth-promoting fungi (PGPF; Aspergillus brunneoviolaceus HZ23) was obtained from newly reclaimed land of Zhejiang Province, China. In order to valuate microbial fertilizer based A. brunneoviolaceus HZ23 (MF-HZ23) on pakchoi growth in immature soil, we investigated the effect of MF-HZ23 on soil properties, rhizosphere bacterial community structure, and metabolites of pakchoi rhizosphere soil samples. Methods The field experiment (four treatments, MF-HZ23, MF-ZH23 + CCF, CCF and the control) was completely randomly designed and carried out on newly reclaimed land in Yangqingmiao Village of Fuyang district, Hangzhou City, Zhejiang Province, China. In order to evaluate the influence of microbial fertilizer based A. brunneoviolaceus HZ23 on pakchoi in the newly reclaimed land, the number of pakchoi leaves, total fresh and dry weight of the seedlings was counted. In addition, the soil properties, including the pH, OMC, total N, AHN, available P, the genome sequencing, and metabolomics assay were also detected. Results The results revealed a significant difference between MF-HZ23 and the control in soil properties, bacterial community structure, and metabolites. Indeed, compared with the control, MF-HZ23 caused 30.66, 71.43, 47.31, 135.84, and 2099.90% increase in the soil pH, organic matter contents (OMC), total nitrogen (N), alkaline hydrolysis nitrogen (AHN), and available phosphorus (P), respectively. Meanwhile, MF-HZ23 caused 50.78, 317.47, and 34.40% increase in the relative abundance of Proteobacteria, Bacteroidota, and Verrucomicrobiota and 75.55, 23.27, 69.25, 45.88, 53.42, and 72.44% reduction in the relative abundance of Acidobacteriota, Actinobacteriota, Chloroflexi, Planctomycetota, Patescibacteria, and WPS-2, respectively, compared with the control based on 16S amplicon sequencing of soil bacteria. Furthermore, redundancy discriminant analysis (RDA) of bacterial communities and soil properties indicated that the main variables of bacterial communities included available P, AHN, pH, OMC, and total N. In addition, non-targeted metabolomics techniques (UHPLC-MS analysis) revealed that MF-HZ23 resulted in a great change in the kinds of metabolites in the rhizosphere soil. Indeed, in MF-HZ23 and the control group, there were six differentially expressed metabolites (DEMs) belong to organoheterocyclic compounds, organic acids and derivatives, organic nitrogen compounds, and these six DEMs were significantly positively correlated with 23 genus of bacteria, which showed complicated interactions between bacteria and DEMs in pakchoi rhizosphere soil. Conclutions Overall, the results of this study revealed significant modification in physical, chemical, and biological properties of pakchoi soil. Microbial fertilizer based PGPF A. brunneoviolaceus HZ23 (MF-HZ23) can be used as a good amendment for newly reclaimed land.
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Affiliation(s)
- Xuqing Li
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Dingyi Li
- Department of Biological Environment, Material and Environmental CollegeShanxi Jinzhong Institute of Technology, Jinzhong, China
| | - Yugen Jiang
- Agricultural Technology Extension Center of Fuyang District, Hangzhou, China
| | - Jun Xu
- Agricultural Technology Extension Center of Fuyang District, Hangzhou, China
| | - Xiaoxu Ren
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Ya Zhang
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Hong Wang
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Qiujun Lu
- Hangzhou Agricultural and Rural Affairs Guarantee Center, Hangzhou, China,*Correspondence: Qiujun Lu, ✉
| | - Jianli Yan
- Institute of Vegetable, Hangzhou Academy of Agricultural Sciences, Hangzhou, China,Jianli Yan, ✉
| | - Temoor Ahmed
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Bin Li
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Kai Guo
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China,Kai Guo, ✉
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Li H, Luo QP, Zhao S, Zhou YY, Huang FY, Yang XR, Su JQ. Effect of phenol formaldehyde-associated microplastics on soil microbial community, assembly, and functioning. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130288. [PMID: 36335899 DOI: 10.1016/j.jhazmat.2022.130288] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Increasing investigations explore the effects of plastic pollutants on bacterial communities, diversity, and functioning in various ecosystems. However, the impact of microplastics (MPs) on the eukaryotic community, microbial assemblages, and interactions is still limited. Here, we investigated bacterial and micro-eukaryotic communities and functioning in soils with different concentrations of phenol formaldehyde-associated MPs (PF-MPs), and revealed the factors, such as soil properties, microbial community assembly, and interactions between microbes, influencing them. Our results showed that a high concentration (1%) of PF-MPs decreased the microbial interactions and the contribution of deterministic processes to the community assembly of microbes, and consequently changed the communities of bacteria, but not eukaryotes. A significant and negative relationship was determined between N2O emission rate and functional genes related to nitrification, indicating that the competitive interactions between functional microbes would affect the nitrogen cycling of soil ecosystem. We further found that vegetable biomass weakly decreased in treatments with a higher concentration of PF-MPs and positively related to the diversity of micro-eukaryotic communities and functional diversity of bacterial communities. These results suggest that a high concentration of the PF-MPs would influence crop growth by changing microbial communities, interactions, and eukaryotic and functional diversity. Our findings provide important evidence for agriculture management of phenol formaldehyde and suggest that we must consider their threats to microbial community compositions, diversity, and assemblage in soils due to the accumulation of PF-MPs widely used in the field.
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Affiliation(s)
- Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, PR China.
| | - Qiu-Ping Luo
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Sha Zhao
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Yan-Yan Zhou
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, PR China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, PR China.
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Garneau L, Beauregard PB, Roy S. Deciphering the role of non- Frankia nodular endophytes in alder through in vitro and genomic characterization. Can J Microbiol 2023; 69:72-87. [PMID: 36288604 DOI: 10.1139/cjm-2022-0073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Endophytic bacterial populations are well-positioned to provide benefits to their host plants such as nutrient acquisition and plant hormone level manipulation. Actinorhizal plants such as alders are well known for their microbial symbioses that allow them to colonize harsh environments whether natural or anthropized. Although the nitrogen-fixing actinobacterium Frankia sp. is the main endophyte found in alder root nodules, other bacterial genera, whose roles remain poorly defined, inhabit this niche. In this study, we isolated a diverse panel of non-Frankia nodular endophytes (NFNE). Some NFNE were isolated from alders grown from surface-sterilized seeds and maintained in sterile conditions, suggesting these may have been seed-borne. In vitro testing of 24 NFNE revealed some possessed putative plant growth promotion traits. Their genomes were also sequenced to identify genes related to plant growth promotion traits. This study highlights the complexity of the alder nodular microbial community. It paves the way for further understanding of the biology of nodules and could help improve land reclamation practices that involve alders.
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Affiliation(s)
- Louis Garneau
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, Canada, J1K 2R1
| | - Pascale B Beauregard
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, Canada, J1K 2R1
| | - Sébastien Roy
- Centre SÈVE, Département de biologie, Faculté des Sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, Canada, J1K 2R1
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Tondera K, Chazarenc F, Brisson J, Chagnon PL. Structure and impact of root-associated fungi in treatment wetland mesocosms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159958. [PMID: 36343819 DOI: 10.1016/j.scitotenv.2022.159958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 10/18/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Root fungal endophytes have been shown to play a positive role in soil phytoremediation by immobilizing or degrading contaminants. In comparison, little is known about their ecological functions and possible role in improving plant performance in treatment wetlands. In a greenhouse study, we compared the structure of fungal communities associated with Phragmites australis roots in treatment wetland mesocosms fed with pre-treated wastewater to mesocosms fed with drinking water. We evaluated the role of water source as an environmental filter structuring fungal communities, and correlated the relative abundances of fungal taxa with key services delivered by the wetlands (i.e., biomass production and nutrient removal). Mesocosms fed with wastewater had higher fungal alpha-diversity. Contrary to expectations, many fungi were unique to drinking water-fed mesocosms, suggesting that the oligotrophic conditions prevailing in these mesocosms benefited specific fungal taxa. On the other hand, wastewater-fed mesocosms had a slightly higher proportion of sequence reads belonging to fungal species recognized as potential endophytes and phytopathogens, highlighting the potential role of wastewater as a source of plant-associated fungi. Interestingly, we found contrasted association patterns between fungal species' relative abundances and different treatment wetland services (e.g., N vs P removal), such that some fungi were positively associated with N removal but negatively associated with P removal. This suggests that fungal endophytes may be functionally complementary in their contribution to distinct mesocosm services, thus supporting arguments in favor of microbial diversity in phytotechnologies. Because of the wide alpha-diversity of fungal communities, and the fact that with current databases, most species remained unassigned to a specific function (or even guild), further investigation is needed to link fungal community structure and service delivery in treatment wetlands.
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Affiliation(s)
- Katharina Tondera
- INRAE, REVERSAAL, F-69625 Villeurbanne, France; IMT Atlantique Bretagne-Pays de Loire, Department of Energy Systems and Environment, 44307 Nantes, France.
| | | | - Jacques Brisson
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, Montréal, Canada.
| | - Pierre-Luc Chagnon
- Institut de recherche en biologie végétale, Département de sciences biologiques, Université de Montréal, Montréal, Canada.
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Lee J, Zhou X, Seo YO, Lee ST, Yun J, Yang Y, Kim J, Kang H. Effects of vegetation shift from needleleaf to broadleaf species on forest soil CO 2 emission. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158907. [PMID: 36150592 DOI: 10.1016/j.scitotenv.2022.158907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Forest soil harbors diverse microbial communities with decisive roles in ecosystem processes. Vegetation shift from needleleaf to broadleaf species is occurring across the globe due to climate change and anthropogenic activities, potentially change forest soil microbial communities and C cycle. However, our knowledge on the impact of such vegetation shift on soil microbial community and activities, and its consequences on forest soil C dynamics are still not well established. Here, we examined the seasonal variation of soil CO2 emission, soil extracellular enzyme activities (EEAs), and soil bacterial, fungal communities in subtropical forest from broadleaf, needleleaf, and mixed stands. In addition, soil CO2 emission and soil EEAs were measured in temperate forest during the growing season. Soil organic matter (SOM) content significantly differs between broadleaf and needleleaf forests and primarily distinguish various soil chemical and microbial characteristics. Significantly higher EEAs and soil CO2 emission in broadleaf forest compared to needleleaf forest were observed both in subtropical and temperate forests. The relative abundance of Basidiomycota positively correlated with SOM and EEAs and indirectly increase soil CO2 emission whereas the relative abundance of Ascomycota exhibits opposite trend, suggesting that soil fungal communities play a key role in determining the different microbial activities between broadleaf and needleleaf stands. The temperature sensitivity of soil CO2 emission was significantly higher in broadleaf forest compared to needleleaf forest, further suggesting that the soil organic carbon in broadleaf forests is more vulnerable to warming.
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Affiliation(s)
- Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea; Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - Xue Zhou
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea; College of Agricultural Science and Engineering, Hohai University, China
| | - Yeon Ok Seo
- Warm Temperate and Subtropical Forest Research Center, National Institute of Forest Science, Republic of Korea
| | - Sang Tae Lee
- Lab of Silvicultural Practices and Management, National Institute of Forest Science, Republic of Korea
| | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea
| | - Jinhyun Kim
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Republic of Korea.
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Fan Q, Chen Y, Xu R, Guo Z. Characterization of keystone taxa and microbial metabolic potentials in copper tailing soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:1216-1230. [PMID: 35913696 DOI: 10.1007/s11356-022-22294-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Copper mining has caused serious soil contamination and threaten the balance of underground ecosystem. Effects of metal contamination on the soil microbial community assembly and their multifunctionality are still unclear. In this study, the keystone taxa and microbial metabolic potential of soil microorganisms surrounding a typical copper tailing were investigated. Results showed that pH and metal contents of adjacent soil in copper tailing increased, which largely reduced soil microbial communities' diversity. Metal contaminated soils enriched a group of keystone taxa with metal-tolerance such as Bacteroidota (20-54%) and Firmicutes (24-48%), which were distinct from the uncontaminated background soils that dominated by Proteobacteria (19-24%) and Actinobacteria (13-24%). In the contaminated soils, these keystone taxa were identified as Alistipes, Bacteroides, and Faecalibacterium, suggesting their adaptation to the metal-rich environment. Co-occurrence network analysis showed that the microbial community was loosely connected in the metal contaminated soils with a lower number of nodes and links. Co-occurrence networks further revealed that the dynamics of keystone taxa significantly correlated with copper content. Functional gene analysis of soil microorganisms indicated that metal contamination might inhibit important microbial metabolic potentials, such as secondary metabolites biosynthesis, carbon fixation, and nitrogen fixation. Results also found the flexible adaptation strategies of soil microbial communities to metal-rich environments with metal-resistance or bio-transformation, such as efflux (CusB/CusF/CzsB and pcoB/copB) and oxidation (aoxAB). These findings provide insight into the interaction between keystone taxa and soil environment, which is helpful to reveal the microbial metabolic potential and physiological characteristics in tailing contaminated soils.
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Affiliation(s)
- Qiao Fan
- Hunan Research Academy of Environmental Sciences, Changsha, 410014, People's Republic of China
| | - Yeqiang Chen
- Hunan Research Academy of Environmental Sciences, Changsha, 410014, People's Republic of China
| | - Rui Xu
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, People's Republic of China.
| | - Zhaohui Guo
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, People's Republic of China
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Liao H, Li C, Ai S, Li X, Ai X, Ai Y. A simulated ecological restoration of bare cut slope reveals the dosage and temporal effects of cement on ecosystem multifunctionality in a mountain ecosystem. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116672. [PMID: 36343402 DOI: 10.1016/j.jenvman.2022.116672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 09/23/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Cement is a critical building material used in the restorations of bare cut slopes. Yet, how cement affects ecosystem's functions and their undertakers remains elusive. Here, we revealed the dosage and temporal effects of cement on plant and soil traits, extracellular enzymes, greenhouse gas fluxes and microbiome using simulation experiments. The results showed that soil pH increased with the cement content at 1st day but relatively constant values around 7 to 7.5 were detected in the flowing days. The β-1,4-glucosidase, phenol oxidase, leucine aminopeptidase and acid phosphatase showed high activities under high cement content, and they generally increased with the cultivations except for acid phosphatase. CH4 fluxes at 16th day were less than zero, and they increased to peak around at 37th to 44th days followed by decreasing until reaching to relatively stable fluctuations around 0. Despite of decrease patterns, N2O fluxes stayed around zero across the temporal gradient except for the maximum around at 30th day in 2%, 5% and 8% cement treatment. Microbial diversity decreased with the cement content, in which there were a recovery trend for bacteria. By integrating above- and belowground ecosystem traits into a multifunctionality index, we identified a potential optimum cement content (11%). PLSPM showed that multifunctionality was affected by the shifts in soil bacterial community, enzyme activity and greenhouse gases while these components were effected by other environmental changes resulted from cement. Our results demonstrate that cement determines multifunctionality through mediating microbial community and activity, providing new insights for designing in situ experiments and ecological restoration strategies for bare cut slopes.
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Affiliation(s)
- Haijun Liao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China; CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Chaonan Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Shenghao Ai
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu, 610041, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China.
| | - Xiangzhen Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, PR China.
| | - Xiaoyan Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China.
| | - Yingwei Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, PR China.
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Castellano-Hinojosa A, Noling JW, Bui HX, Desaeger JA, Strauss SL. Effect of fumigants and non-fumigants on nematode and weed control, crop yield, and soil microbial diversity and predicted functionality in a strawberry production system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 852:158285. [PMID: 36030874 DOI: 10.1016/j.scitotenv.2022.158285] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/26/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Fumigants are commonly used to control soil-borne pathogens of high-value crops, but they may also impact non-target soil microorganisms. Increasing interest in the use of sustainable management practices to control plant- and root-parasitic nematodes has resulted in the formulation of non-fumigant nematicides (chemicals or bionematicides) which are considered environmentally friendly alternatives to fumigants. However, the impact of these new products compared to standard fumigants on soil-borne pathogens, plant production, and the diversity and composition of non-target microbial communities in all crops remains unclear. To begin to address this knowledge gap, we examined the effect of fumigants commonly used in Florida (United States) strawberry production and newly formulated non-fumigant nematicides on nematode and weed control, plant growth, crop yield, and bacterial and fungal community diversity and predicted functionality. We found the standard fumigants increased crop yields and reduced weed pressure more than non-fumigants. Both fumigants and non-fumigants were an efficient management strategy to control sting nematodes. Treatments also impacted the abundance of specific beneficial and antagonistic taxa. Both fumigants and non-fumigants reduced soil bacterial and fungal diversity, an effect that remained for six months, thus suggesting a potential residual impact of these products on soil microorganisms. However, only fumigants altered soil microbial community composition and reduced network complexity, inducing a decrease or even a loss of some predicted bacterial and fungal functions, particularly during the first weeks after fumigation. Nevertheless, soil collected at the end of the season showed significant levels of root-knot nematode suppression in a growth chamber experiment, irrespective of the previous treatment. By linking the effect of fumigants and non-fumigants on soil-borne pests, plant and production, and the soil microbiome, this study increases our knowledge regarding the environmental impact of these products.
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Southwest Florida Research and Education Center, Department of Soil and Water Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL 34142, USA
| | - Joseph W Noling
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 14625 Co Rd 672, Wimauma, FL 33598, USA
| | - Hung Xuan Bui
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 14625 Co Rd 672, Wimauma, FL 33598, USA
| | - Johan A Desaeger
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 14625 Co Rd 672, Wimauma, FL 33598, USA
| | - Sarah L Strauss
- Southwest Florida Research and Education Center, Department of Soil and Water Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29N, Immokalee, FL 34142, USA.
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Multiple anthropogenic pressures eliminate the effects of soil microbial diversity on ecosystem functions in experimental microcosms. Nat Commun 2022; 13:4260. [PMID: 35871070 PMCID: PMC9308766 DOI: 10.1038/s41467-022-31936-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 07/06/2022] [Indexed: 12/11/2022] Open
Abstract
Biodiversity is crucial for the provision of ecosystem functions. However, ecosystems are now exposed to a rapidly growing number of anthropogenic pressures, and it remains unknown whether biodiversity can still promote ecosystem functions under multifaceted pressures. Here we investigated the effects of soil microbial diversity on soil functions and properties when faced with an increasing number of simultaneous global change factors in experimental microcosms. Higher soil microbial diversity had a positive effect on soil functions and properties when no or few (i.e., 1–4) global change factors were applied, but this positive effect was eliminated by the co-occurrence of numerous global change factors. This was attributable to the reduction of soil fungal abundance and the relative abundance of an ecological cluster of coexisting soil bacterial and fungal taxa. Our study indicates that reducing the number of anthropogenic pressures should be a goal in ecosystem management, in addition to biodiversity conservation. It is unclear whether the positive effects of biodiversity on ecosystem functioning are maintained under multifaceted anthropogenic disturbance. In this experiment, the authors show that multiple simultaneous stressors can negate the positive effect of microbial diversity on soil functions.
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Dong Y, Zhang ZR, Mishra S, Wong ACN, Huang JF, Wang B, Peng YQ, Gao J. Diversity and metabolic potentials of microbial communities associated with pollinator and cheater fig wasps in fig-fig wasp mutualism system. Front Microbiol 2022; 13:1009919. [DOI: 10.3389/fmicb.2022.1009919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/14/2022] [Indexed: 11/21/2022] Open
Abstract
Microbial symbionts can influence a myriad of insect behavioral and physiological traits. However, how microbial communities may shape or be shaped by insect interactions with plants and neighboring species remains underexplored. The fig-fig wasp mutualism system offers a unique model to study the roles of microbiome in the interactions between the plants and co-habiting insects because a confined fig environment is shared by two fig wasp species, the pollinator wasp (Eupristina altissima and Eupristina verticillata) and the cheater wasp (Eupristina sp1 and Eupristina sp2). Here, we performed whole genome resequencing (WGS) on 48 individual fig wasps (Eupristina spp.) from Yunnan, China, to reveal the phylogenetic relationship and genetic divergence between pollinator and congeneric cheater wasps associated with the Ficus trees. We then extracted metagenomic sequences to explore the compositions, network structures, and functional capabilities of microbial communities associated with these wasps. We found that the cheaters and pollinators from the same fig species are sister species, which are highly genetically divergent. Fig wasps harbor diverse but stable microbial communities. Fig species dominate over the fig wasp genotype in shaping the bacterial and fungal communities. Variation in microbial communities may be partially explained by the filtering effect from fig and phylogeny of fig wasps. It is worth noting that cheaters have similar microbial communities to their sister pollinators, which may allow cheaters to coexist and gain resources from the same fig species. In terms of metabolic capabilities, some bacteria such as Desulfovibrio and Lachnospiraceae are candidates involved in the nutritional uptake of fig wasps. Our results provide novel insights into how microbiome community and metabolic functions may couple with the fig-wasp mutualistic systems.
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Soil microbiome disruption reveals specific and general plant-bacterial relationships in three agroecosystem soils. PLoS One 2022; 17:e0277529. [PMID: 36383522 PMCID: PMC9668122 DOI: 10.1371/journal.pone.0277529] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
Abstract
Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, often resulting in increased crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members of the soil microbiome. Here, we applied soil microbiome disruption in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on rhizosphere bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases in ways both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abundances of Pseudomonas and Sporocytophaga, regardless of the disrupted soil in which it was grown. Whereas the promotion of Bosea, Dyadobacter and Luteoliobacter was shared by all four crops when grown in disrupted soils. In summary, soil disruption followed by crop introduction amplified the plant colonization of potential beneficial bacterial genera in the rhizosphere.
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71
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Jiang W, Chen R, Zhao L, Qin L, Fan H, Chen X, Wang Y, Yin C, Mao Z. Chemical fumigants control apple replant disease: Microbial community structure-mediated inhibition of Fusarium and degradation of phenolic acids. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129786. [PMID: 36007363 DOI: 10.1016/j.jhazmat.2022.129786] [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: 06/17/2022] [Revised: 07/31/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Fusarium and phenolic acids in apple replant soil have deleterious effects on soil, which affects the growth of young replanted apple trees. Here, we studied the effects of different chemical fumigants (metham sodium, dazomet, calcium cyanamide, 1,3-dichloropropene, and methyl bromide) on Fusarium and phenolic acids in soil. The chemical fumigants disturbed the apple replant soil microbial community to different degrees in the order from highest to the lowest as methyl bromide > 1,3-dichloropropene > dazomet > metham sodium > calcium cyanamide. Compared with the control, the total numbers of Operational Taxonomic Unit (OTU) were 104.63 % and 9.38 % lower in the methyl bromide and calcium cyanamide treatments, respectively while the average contents of Fusarium were 88.04 % and 59.18% lower in these treatments, respectively. Higher disturbance degrees resulted in a slower recovery rate of the soil microbial community, which facilitated the transformation of the soil into a disease-suppressing state. During the recovery process, the roots recruited Streptomyces OTU2796 and Bacillus OTU2243, which alleviated Fusarium-induced stress via the synthesis of polyketones and macrolides. The roots also recruited Sphingomonas OTU3488, OTU5572, and OTU8147, which alleviated phenolic acid-induced stress through the degradation of benzoate and polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Weitao Jiang
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Ran Chen
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Lei Zhao
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Lei Qin
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Hai Fan
- College of Chemistry and Material Science Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Xuesen Chen
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Yanfang Wang
- College of Chemistry and Material Science Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Chengmiao Yin
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Zhiquan Mao
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China.
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The Effect of Microbial Diversity and Biomass on Microbial Respiration in Two Soils along the Soil Chronosequence. Microorganisms 2022; 10:microorganisms10101920. [PMID: 36296195 PMCID: PMC9609397 DOI: 10.3390/microorganisms10101920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Microbial diversity plays an important role in the decomposition of soil organic matter. However, the pattern and drivers of the relationship between microbial diversity and decomposition remain unclear. In this study, we followed the decomposition of organic matter in soils where microbial diversity was experimentally manipulated. To produce a gradient of microbial diversity, we used soil samples at two sites of the same chronosequence after brown coal mining in Sokolov, Czech Republic. Soils were X-ray sterilized and inoculated by two densities of inoculum from both soils and planted with seeds of six local plant species. This created two soils each with four levels of microbial diversity characterized by next-generation sequencing. These eight soils were supplied, or not, by litter of the bushgrass Calamagrostisepigejos, and microbial respiration was measured to assess the rate of decomposition. A strong positive correlation was found between microbial diversity and decomposition of organic matter per gram of carbon in soil, which suggests that microbial diversity supports decomposition if the microbial community is limited by available carbon. In contrast, microbial respiration per gram of soil negatively correlated with bacterial diversity and positively with fungal biomass, suggesting that in the absence of a carbon limitation, decomposition rate is controlled by the amount of fungal biomass. Soils with the addition of grass litter showed a priming effect in the initial stage of decomposition compared to the samples without the addition of litter. Thus, the relationship between microbial diversity and the rate of decomposition may be complex and context dependent.
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73
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Cowan DA, Lebre PH, Amon C, Becker RW, Boga HI, Boulangé A, Chiyaka TL, Coetzee T, de Jager PC, Dikinya O, Eckardt F, Greve M, Harris MA, Hopkins DW, Houngnandan HB, Houngnandan P, Jordaan K, Kaimoyo E, Kambura AK, Kamgan-Nkuekam G, Makhalanyane TP, Maggs-Kölling G, Marais E, Mondlane H, Nghalipo E, Olivier BW, Ortiz M, Pertierra LR, Ramond JB, Seely M, Sithole-Niang I, Valverde A, Varliero G, Vikram S, Wall DH, Zeze A. Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes. MICROBIOME 2022; 10:131. [PMID: 35996183 PMCID: PMC9396824 DOI: 10.1186/s40168-022-01297-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/15/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents. RESULTS The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation. CONCLUSION This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.
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Affiliation(s)
- D A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - P H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Cer Amon
- Institut National Polytechnique Houphouet-Boigny, Cote d'Ivoire, Yamoussoukro, South Africa
| | - R W Becker
- Biodiversity Research Centre, Department of Agriculture and Natural Resources Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - H I Boga
- Taita Taveta University, Voi, Kenya
| | - A Boulangé
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
- UMR InterTryp, CIRAD-IRD, 34398, Montpellier, France
| | - T L Chiyaka
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - T Coetzee
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - P C de Jager
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - O Dikinya
- Department of Environmental Science, University of Botswana, Gaborone, Botswana
| | - F Eckardt
- Department of Geography, University of Cape Town, Cape Town, South Africa
| | - M Greve
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - M A Harris
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - D W Hopkins
- Scotland's Rural College, Edinburgh, EH9 3JG, UK
| | - H B Houngnandan
- Université Nationale d'Agriculture, Porto-Novo, Benin (Laboratoire de Microbiologie Des Sols Et d'Ecologie Microbienne), Porto-Novo, Benin
| | - P Houngnandan
- Université Nationale d'Agriculture, Porto-Novo, Benin (Laboratoire de Microbiologie Des Sols Et d'Ecologie Microbienne), Porto-Novo, Benin
| | - K Jordaan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Departamento de Genética Molecular Y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - E Kaimoyo
- University of Zambia, Lusaka, Zambia
| | | | - G Kamgan-Nkuekam
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - T P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - E Marais
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | - H Mondlane
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - E Nghalipo
- Biodiversity Research Centre, Department of Agriculture and Natural Resources Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - B W Olivier
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - M Ortiz
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - L R Pertierra
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - J-B Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Departamento de Genética Molecular Y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - M Seely
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | - I Sithole-Niang
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - A Valverde
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - G Varliero
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - S Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - D H Wall
- Department of Biology, Colorado State University, Fort Collins, USA
| | - A Zeze
- Institut National Polytechnique Houphouet-Boigny, Cote d'Ivoire, Yamoussoukro, South Africa
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74
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Bhaduri D, Sihi D, Bhowmik A, Verma BC, Munda S, Dari B. A review on effective soil health bio-indicators for ecosystem restoration and sustainability. Front Microbiol 2022; 13:938481. [PMID: 36060788 PMCID: PMC9428492 DOI: 10.3389/fmicb.2022.938481] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/29/2022] [Indexed: 11/30/2022] Open
Abstract
Preventing degradation, facilitating restoration, and maintaining soil health is fundamental for achieving ecosystem stability and resilience. A healthy soil ecosystem is supported by favorable components in the soil that promote biological productivity and provide ecosystem services. Bio-indicators of soil health are measurable properties that define the biotic components in soil and could potentially be used as a metric in determining soil functionality over a wide range of ecological conditions. However, it has been a challenge to determine effective bio-indicators of soil health due to its temporal and spatial resolutions at ecosystem levels. The objective of this review is to compile a set of effective bio-indicators for developing a better understanding of ecosystem restoration capabilities. It addresses a set of potential bio-indicators including microbial biomass, respiration, enzymatic activity, molecular gene markers, microbial metabolic substances, and microbial community analysis that have been responsive to a wide range of ecosystem functions in agricultural soils, mine deposited soil, heavy metal contaminated soil, desert soil, radioactive polluted soil, pesticide polluted soil, and wetland soils. The importance of ecosystem restoration in the United Nations Sustainable Development Goals was also discussed. This review identifies key management strategies that can help in ecosystem restoration and maintain ecosystem stability.
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Affiliation(s)
- Debarati Bhaduri
- ICAR-National Rice Research Institute, Cuttack, India
- *Correspondence: Debarati Bhaduri
| | - Debjani Sihi
- Department of Environmental Sciences, Emory University, Atlanta, GA, United States
| | - Arnab Bhowmik
- Department of Natural Resources and Environmental Design, North Carolina Agricultural and Technical State University, Greensboro, NC, United States
- Arnab Bhowmik
| | - Bibhash C. Verma
- Central Rainfed Upland Rice Research Station (ICAR-NRRI), Hazaribagh, India
| | | | - Biswanath Dari
- Agriculture and Natural Resources, Cooperative Extension at North Carolina Agricultural and Technical State University, Greensboro, NC, United States
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75
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Sadet-Bourgeteau S, Djemiel C, Chemidlin Prévost-Bouré N, Feder F. Dynamic of bacterial and archaeal diversity in a tropical soil over 6 years of repeated organic and inorganic fertilization. Front Microbiol 2022; 13:943314. [PMID: 36051761 PMCID: PMC9425033 DOI: 10.3389/fmicb.2022.943314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
The soil microbial community plays important roles in nutrient cycling, plant pathogen suppression, decomposition of residues and degradation of pollutants; as such, it is often regarded as a good indicator of soil quality. Repeated applications of mixed organic and inorganic materials in agriculture improve the soil microbial quality and in turn crop productivity. The soil microbial quality following several years of repeated fertilizer inputs has received considerable attention, but the dynamic of this community over time has never been assessed. We used high-throughput sequencing targeting 16S ribosomal RNA genes to investigate the evolution of the bacterial and archaeal community throughout 6 years of repeated organic and inorganic fertilizer applications. Soils were sampled from a field experiment in La Mare (Reunion Island, France), where different mixed organic-inorganic fertilizer inputs characterized by more or less stable organic matter were applied regularly for 6 years. Soil samples were taken each year, more than 6 months after the latest fertilizer application. The soil molecular biomass significantly increased in some organically fertilized plots (by 35–45% on average), 3–5 years after the first fertilizers application. The significant variations in soil molecular microbial biomass were explained by the fertilization practices (cumulated organic carbon inputs) and sometimes by the soil parameters (sand and soil carbon contents). The structure of the bacterial and archaeal community was more influenced by time than by the fertilization type. However, repeated fertilizer applications over time tended to modify the abundance of the bacterial phyla Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. To conclude, the present study highlights that the soil bacterial and archaeal community is lastingly modified after 6 years of repeated fertilizer inputs. These changes depend on the nature of the organic input and on the fertilization practice (frequency and applied quantity).
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Affiliation(s)
- Sophie Sadet-Bourgeteau
- Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- *Correspondence: Sophie Sadet-Bourgeteau,
| | - Christophe Djemiel
- Agroécologie, INRAE, Institut Agro Dijon, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Frederic Feder
- CIRAD, UPR Recyclage et Risque, Montpellier, France
- Recyclage et risque, Univ Montpellier, CIRAD, Montpellier, France
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76
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Shu X, He J, Zhou Z, Xia L, Hu Y, Zhang Y, Zhang Y, Luo Y, Chu H, Liu W, Yuan S, Gao X, Wang C. Organic amendments enhance soil microbial diversity, microbial functionality and crop yields: A meta-analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154627. [PMID: 35306065 DOI: 10.1016/j.scitotenv.2022.154627] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/22/2022] [Accepted: 03/13/2022] [Indexed: 06/14/2023]
Abstract
Fertilization plays an important role in changing soil microbial diversity, which is essential for determining crop yields. Yet, the influence of organic amendments on microbial diversity remains uncertain, and few studies have addressed the relative importance of microbial diversity versus other drivers of crop yields. Here, we synthesize 219 studies worldwide and found that organic amendments significantly increased microbial diversity components (i.e., Shannon, richness, and phylogenetic diversity) and shifted microbial community structure compared to mineral-only fertilization. The performance of microbial alpha diversity varied substantially with organic amendment types, microbial groups and changes in soil pH. Both microbial diversity and community structure exhibited significantly positive relationships with microbial functionality and crop yields. In addition, soil abiotic properties and microbial functionality had a much stronger impact on crop yields than microbial diversity and climate factors. Partial least squares path modeling showed that soil microbial diversity was an important underlying factor driving crop yields via boosting soil microbial functionality. Overall, our findings provide robust evidence for the positive diversity-functions relationships, emphasizing that substituting mineral fertilizers with organic amendments is a promising way to conserve microbial diversity and promote soil microbial functions and crop yields.
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Affiliation(s)
- Xiangyang Shu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Jia He
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhenghu Zhou
- Center for Ecological Research, Northeast Forestry University, Harbin 150040, China
| | - Longlong Xia
- Institute for Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Garmisch-Partenkirchen 82467, Germany
| | - Yufu Hu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yulin Zhang
- Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong 999077, China
| | - Yanyan Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiqi Luo
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 21008, China
| | - Weijia Liu
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuesong Gao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Changquan Wang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
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Hernández-Guzmán M, Pérez-Hernández V, Gómez-Acata S, Jiménez-Bueno N, Verhulst N, Muñoz-Arenas LC, Navarro-Noya YE, Luna-Guido ML, Dendooven L. Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study. Arch Microbiol 2022; 204:458. [PMID: 35788780 DOI: 10.1007/s00203-022-03060-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 05/01/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022]
Abstract
To increase our knowledge on how application of organic material alters soil microbial populations and functionality, shotgun metagenomic sequencing was used to determine the microbial communities and their potential functionality in an arable soil amended with young maize plants (Zea mays L.) in a laboratory experiment after 3 days. The relative abundance of bacterial and viral groups was strongly affected by organic material application, whereas that of the archaeal, protist and fungal groups was less affected. Cellulose degraders with copiotrophic lifestyle (e.g., Betaproteobacteria) were enriched in the amended soil, whereas the groups with slow growing oligotrophic and chemolithoautotrophic metabolism within Bacteria and Archaea were greater in the unamended than in the amended soil. The soil viral structure and richness were also affected. Caudovirales was the dominant viral family, with members of Siphoviridae enriched in the amended soil and members of Myoviridae in the unamended soil. More specialized metabolic traits related to both the degradation of complex C compounds and denitrification related genes were enriched in the young maize plant amended soil than in the unamended soil, whereas nitrification related genes were enriched in the latter. Copiotrophic life-style bacterial groups were enriched in the amended soil, whereas oligotrophic life-style bacterial groups in the unamended soil. Many bacterial and viral phylotypes were affected by the application of young maize plants, but the number of soil fungi, archaea and protists affected was smaller. Metabolic functionality was affected by the application of organic material as the relative abundance of genes involved in the denitrification process was higher in the maize plant amended soil than in the unamended soil and those involved in the nitrification process was higher in the unamended soil.
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Affiliation(s)
| | | | - Selene Gómez-Acata
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico
| | | | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, Mexico
| | | | | | - Marco L Luna-Guido
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico.
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78
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Djemiel C, Dequiedt S, Karimi B, Cottin A, Horrigue W, Bailly A, Boutaleb A, Sadet-Bourgeteau S, Maron PA, Chemidlin Prévost-Bouré N, Ranjard L, Terrat S. Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production. Front Microbiol 2022; 13:889788. [PMID: 35847063 PMCID: PMC9280627 DOI: 10.3389/fmicb.2022.889788] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/06/2022] [Indexed: 01/02/2023] Open
Abstract
Soils are fundamental resources for agricultural production and play an essential role in food security. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity-the backbone of the regulation of ecosystem services and "soil health" maintenance. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. Microbial communities are also sensitive to various environmental drivers and to management practices; as a result, they are ideal candidates for monitoring soil quality assessment. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. As regards prospects, we outline the importance of building up repositories of soil quality indicators. These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Battle Karimi
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
- Novasol Experts, Dijon, France
| | - Aurélien Cottin
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Walid Horrigue
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Arthur Bailly
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Ali Boutaleb
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Sophie Sadet-Bourgeteau
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Alain Maron
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Lionel Ranjard
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Sébastien Terrat
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
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79
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Zhou X, Sun H, Heinonsalo J, Pumpanen J, Berninger F. Microbial biodiversity contributes to soil carbon release: A case study on fire disturbed boreal forests. FEMS Microbiol Ecol 2022; 98:6617588. [PMID: 35749564 PMCID: PMC9303362 DOI: 10.1093/femsec/fiac074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/10/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial communities often possess enormous diversity, raising questions about whether this diversity drives ecosystem functioning, especially the influence of diversity on soil decomposition and respiration. Although functional redundancy is widely observed in soil microorganisms, evidence that species occupy distinct metabolic niches has also emerged. In this paper, we found that apart from the environmental variables, increases in microbial diversity, notably bacterial diversity, lead to an increase in soil C emissions. This was demonstrated using structural equation modelling (SEM), linking soil respiration with naturally differing levels of soil physio-chemical properties, vegetation coverage, and microbial diversity after fire disturbance. Our SEMs also revealed that models including bacterial diversity explained more variation of soil CO2 emissions (about 45%) than fungal diversity (about 38%). A possible explanation of this discrepancy is that fungi are more multifunctional than bacteria and, therefore, an increase in fungal diversity does not necessarily change soil respiration. Further analysis on functional genes suggested that bacterial and fungal diversities mainly explain the potential decomposition of recalcitrant C than of labile C. Overall, by incorporating microbial diversity and the environmental variables, the predictive power of models on soil C emission was significantly improved, indicating microbial diversity is crucial for predicting ecosystem functions.
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Affiliation(s)
- Xuan Zhou
- Department of Environmental and Biological Sciences, Joensuu campus, University of Eastern Finland, 80101, Joensuu, Finland
| | - Hui Sun
- Collaborative Innovation Center of Sustainable Forestry in China, College of Forestry, Nanjing Forestry University, 210037 Nanjing, China
| | - Jussi Heinonsalo
- Department of Forest Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Jukka Pumpanen
- Department of Environmental and Biological Sciences, Joensuu campus, University of Eastern Finland, 80101, Joensuu, Finland
| | - Frank Berninger
- Department of Environmental and Biological Sciences, Joensuu campus, University of Eastern Finland, 80101, Joensuu, Finland
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80
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Forsythe A, Fontaine N, Bissonnette J, Hayashi B, Insuk C, Ghosh S, Kam G, Wong A, Lausen C, Xu J, Cheeptham N. Microbial isolates with Anti-Pseudogymnoascus destructans activities from Western Canadian bat wings. Sci Rep 2022; 12:9895. [PMID: 35701553 PMCID: PMC9198084 DOI: 10.1038/s41598-022-14223-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/02/2022] [Indexed: 11/29/2022] Open
Abstract
Pseudogymnoascus destructans (Pd) is the causative agent of white-nose syndrome, which has resulted in the death of millions of bats in North America (NA) since 2006. Based on mortalities in eastern NA, the westward spread of infections likely poses a significant threat to western NA bats. To help prevent/reduce Pd infections in bats in western NA, we isolated bacteria from the wings of wild bats and screened for inhibitory activity against Pd. In total, we obtained 1,362 bacterial isolates from 265 wild bats of 13 species in western Canada. Among the 1,362 isolates, 96 showed inhibitory activity against Pd based on a coculture assay. The inhibitory activities varied widely among these isolates, ranging from slowing fungal growth to complete inhibition. Interestingly, host bats containing isolates with anti-Pd activities were widely distributed, with no apparent geographic or species-specific pattern. However, characteristics of roosting sites and host demography showed significant associations with the isolation of anti-Pd bacteria. Specifically, anthropogenic roosts and swabs from young males had higher frequencies of anti-Pd bacteria than those from natural roosts and those from other sex and age-groups, respectively. These anti-Pd bacteria could be potentially used to help mitigate the impact of WNS. Field trials using these as well as additional microbes from future screenings are needed in order to determine their effectiveness for the prevention and treatment against WNS.
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Affiliation(s)
- Adrian Forsythe
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Nick Fontaine
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Julianna Bissonnette
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Brandon Hayashi
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Chadabhorn Insuk
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada.,Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Soumya Ghosh
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada.,Department of Genetics, Natural and Agricultural Sciences, University of the Free State, Bloemfontein, South Africa
| | - Gabrielle Kam
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Aaron Wong
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada
| | - Cori Lausen
- Wildlife Conservation Society Canada, P.O. Box 606, Kaslo, BC, V0G 1M0, Canada.
| | - Jianping Xu
- Department of Biology, Faculty of Science, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - Naowarat Cheeptham
- Department of Biological Sciences, Faculty of Science, Thompson Rivers University, Kamloops, BC, V2C 08C, Canada.
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81
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Li L, Jiang X, Zhou Q, Chen J, Zang Y, Zhang Z, Gao C, Tang X, Shang S. Responses of Soil Microbiota to Different Control Methods of the Spartina alterniflora in the Yellow River Delta. Microorganisms 2022; 10:microorganisms10061122. [PMID: 35744640 PMCID: PMC9230759 DOI: 10.3390/microorganisms10061122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/20/2022] [Accepted: 05/27/2022] [Indexed: 02/01/2023] Open
Abstract
Spartina alterniflora invasion has negative effects on the structure and functioning of coastal wetland ecosystems. Therefore, many methods for controlling S. alterniflora invasion have been developed. S. alterniflora control methods can affect plant community, which results in changes in microbial communities and subsequent changes in soil ecological processes. However, the effects of controlling S. alterniflora on soil microbial communities remain poorly understood. We aimed to examine the responses of bacterial and fungal communities to invasion control methods (cutting plus tilling treatment: CT; mechanical rolling treatment: MR). Soil bacterial and fungal community diversity and composition structure were assessed using high-throughput sequencing technology. The findings of the study showed that bacterial diversity and richness in the CT treatment reduced substantially, but fungal diversity and richness did not show any remarkable change. Bacterial and fungal diversity and richness in the MR treatment were not affected considerably. In addition, the two control methods significantly changed the soil microbial community structure. The relative abundance of bacteria negatively associated with nutrient cycling increased considerably in the CT treatment. The considerable increases in the relative abundance of certain bacterial taxa in the MR treatment may promote soil nutrient cycling. Compared with mechanical rolling, soil bacterial community diversity and structure were more sensitive to cutting plus tilling.
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Affiliation(s)
- Liangyu Li
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China; (L.L.); (J.C.); (Y.Z.)
| | - Xiangyang Jiang
- Shandong Provincial Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 250299, China; (X.J.); (Q.Z.); (C.G.)
| | - Quanli Zhou
- Shandong Provincial Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 250299, China; (X.J.); (Q.Z.); (C.G.)
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China; (L.L.); (J.C.); (Y.Z.)
| | - Yu Zang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China; (L.L.); (J.C.); (Y.Z.)
| | - Zaiwang Zhang
- College of Biological and Environmental Engineering, Binzhou University, Binzhou 256601, China;
| | - Chen Gao
- Shandong Provincial Key Laboratory of Marine Ecological Restoration, Shandong Marine Resource and Environment Research Institute, Yantai 250299, China; (X.J.); (Q.Z.); (C.G.)
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China; (L.L.); (J.C.); (Y.Z.)
- Correspondence: (X.T.); (S.S.)
| | - Shuai Shang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266005, China; (L.L.); (J.C.); (Y.Z.)
- College of Biological and Environmental Engineering, Binzhou University, Binzhou 256601, China;
- Correspondence: (X.T.); (S.S.)
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82
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Totubaeva NE, Shalpykov KT. Dynamics of Microbiological Diversity of Soils in the Chu Valley during Land Use Change in Pastures. ARID ECOSYSTEMS 2022. [DOI: 10.1134/s2079096122020135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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83
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Lankau RA, George I, Miao M. Crop performance is predicted by soil microbial diversity across phylogenetic scales. Ecosphere 2022. [DOI: 10.1002/ecs2.4029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Richard A. Lankau
- Department of Plant Pathology University of Wisconsin‐Madison Madison Wisconsin USA
| | - Isabelle George
- Department of Plant Pathology University of Wisconsin‐Madison Madison Wisconsin USA
| | - Max Miao
- Department of Plant Pathology University of Wisconsin‐Madison Madison Wisconsin USA
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84
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Long-Term Compost Amendment Spurs Cellulose Decomposition by Driving Shifts in Fungal Community Composition and Promoting Fungal Diversity and Phylogenetic Relatedness. mBio 2022; 13:e0032322. [PMID: 35491853 PMCID: PMC9239258 DOI: 10.1128/mbio.00323-22] [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] [Indexed: 11/25/2022] Open
Abstract
Cellulose is the most abundant polysaccharide in plant biomass and an important precursor of soil organic matter formation. Fungi play a key role in carbon cycling dynamics because they tend to decompose recalcitrant materials. Here, we applied [12C]cellulose and [13C]cellulose to distinguish the effects of application of compost, nitrogen-phosphorus-potassium (NPK) fertilizer, and no fertilizer (control) for 27 years upon cellulose decomposition via RNA-based stable isotope probing (RNA-SIP). The loss ratio of added cellulose C in compost soil was 67.6 to 106.7% higher than in NPK and control soils during their 20-day incubation. Dothideomycetes (mainly members of the genus Cryptococcus) dominated cellulose utilization in compost soil, whereas the copiotrophic Sordariomycetes were more abundant in NPK and unfertilized soils. Compared with NPK and control soils, compost application increased the diversity of 13C-assimilating fungi. The 13C-labeled fungal communities in compost soil were more phylogenetically clustered and exhibited greater species relatedness than those in NPK and control soils, perhaps because of stringent filtering of narrow-spectrum organic resources and biological invasion originating from added compost. These changes led to an augmented decomposition capacity of fungal species for cellulose-rich substrates and reduced cellulose C sequestration efficiency. The RNA-SIP technique is more sensitive to responses of fungi to altered soil resource availability than DNA-SIP. Overall, long-term compost application modified fungal community composition and promoted fungal diversity and phylogenetic relatedness, accelerating the decomposition of substrate cellulose in soil. This work also highlights the RNA-SIP technique’s value for comprehensively assessing the contributions of active fungi to the substrate decomposition process.
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85
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Xu R, Tao W, Lin H, Huang D, Su P, Gao P, Sun X, Yang Z, Sun W. Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonic Acid (PFOS) on Soil Microbial Community. MICROBIAL ECOLOGY 2022; 83:929-941. [PMID: 34283261 DOI: 10.1007/s00248-021-01808-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
The extensive application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) causes their frequent detection in various environments. In this work, two typical PFASs, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), are selected to investigate their effects on soil microorganisms. Microbial community structure and microbe-microbe relationships were investigated by high-throughput sequencing and co-occurrence network analysis. Under 90 days of exposure, the alpha-diversity of soil microbial communities was increased with the PFOS treatment, followed by the PFOA treatment. The exposure of PFASs substantially changed the compositions of soil microbial communities, leading to the enrichment of more PFASs-tolerant bacteria, such as Proteobacteria, Burkholderiales, and Rhodocyclales. Comparative co-occurrence networks were constructed to investigate the microbe-microbe interactions under different PFASs treatments. The majority of nodes in the PFOA and PFOS networks were associated with the genus Azospirillum and Hydrogenophaga, respectively. The LEfSe analysis further identified a set of biomarkers in the soil microbial communities, such as Azospirillum, Methyloversatilis, Hydrogenophaga, Pseudoxanthomonas, and Fusibacter. The relative abundances of these biomarkers were also changed by different PFASs treatments. Functional gene prediction suggested that the microbial metabolism processes, such as nucleotide transport and metabolism, cell motility, carbohydrate transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis transport and catabolism, might be inhibited under PFAS exposure, which may further affect soil ecological services.
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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
| | - Wan Tao
- 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
| | - 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
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China
| | - Duanyi Huang
- 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
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Pingzhou Su
- 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
| | - 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
| | - 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
| | - Zhaohui Yang
- College of Environmental Science and Engineering, Hunan University, Changsha, 410082, People's Republic of 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, Xinxiang, China.
- Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, 808 Tianyuan Road, Guangzhou, Guangdong, China.
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86
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Rodriguez V, Moskwa LM, Oses R, Kühn P, Riveras-Muñoz N, Seguel O, Scholten T, Wagner D. Impact of Climate and Slope Aspects on the Composition of Soil Bacterial Communities Involved in Pedogenetic Processes along the Chilean Coastal Cordillera. Microorganisms 2022; 10:847. [PMID: 35630293 PMCID: PMC9143490 DOI: 10.3390/microorganisms10050847] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/13/2022] [Accepted: 04/16/2022] [Indexed: 02/04/2023] Open
Abstract
Soil bacteria play a fundamental role in pedogenesis. However, knowledge about both the impact of climate and slope aspects on microbial communities and the consequences of these items in pedogenesis is lacking. Therefore, soil-bacterial communities from four sites and two different aspects along the climate gradient of the Chilean Coastal Cordillera were investigated. Using a combination of microbiological and physicochemical methods, soils that developed in arid, semi-arid, mediterranean, and humid climates were analyzed. Proteobacteria, Acidobacteria, Chloroflexi, Verrucomicrobia, and Planctomycetes were found to increase in abundance from arid to humid climates, while Actinobacteria and Gemmatimonadetes decreased along the transect. Bacterial-community structure varied with climate and aspect and was influenced by pH, bulk density, plant-available phosphorus, clay, and total organic-matter content. Higher bacterial specialization was found in arid and humid climates and on the south-facing slope and was likely promoted by stable microclimatic conditions. The presence of specialists was associated with ecosystem-functional traits, which shifted from pioneers that accumulated organic matter in arid climates to organic decomposers in humid climates. These findings provide new perspectives on how climate and slope aspects influence the composition and functional capabilities of bacteria, with most of these capabilities being involved in pedogenetic processes.
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Affiliation(s)
- Victoria Rodriguez
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
| | - Lisa-Marie Moskwa
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
| | - Rómulo Oses
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama, Universidad de Atacama (CRIDESAT UDA), Copayapu 484, Copiapó 1530000, Chile;
| | - Peter Kühn
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Nicolás Riveras-Muñoz
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Oscar Seguel
- Facultad de Ciencias Agronómicas, Universidad de Chile, Av. Santa Rosa #11315, La Pintana, Santiago 8820808, Chile;
| | - Thomas Scholten
- Department of Geosciences, Soil Science and Geomorphology, University of Tübingen, 72070 Tübingen, Germany; (P.K.); (N.R.-M.); (T.S.)
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany; (V.R.); (L.-M.M.)
- Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany
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87
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Castellano-Hinojosa A, Boyd NS, Strauss SL. Impact of fumigants on non-target soil microorganisms: a review. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:128149. [PMID: 34999405 DOI: 10.1016/j.jhazmat.2021.128149] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Fumigants have been used for decades to control soil-borne pathogens of high-value crops, and increasing evidence indicates they can affect non-target soil microbial communities. Understanding the impacts of these products on soil microorganisms is of critical importance not only for evaluating their environmental safety, but also because soil microbial communities have a central role in soil quality and nutrient cycling, plant growth, and crop production. Thus, we conducted a systematic review and metanalysis study of fumigant impacts on non-target soil microorganisms. In general, we found that fumigation decreases the bacterial diversity and abundance of total bacteria and nitrogen-cycling genes by approximately 10-50% during the first four weeks after application compared to non-treated soils. These decreases appear transient and tend to diminish or disappear after four weeks. Increases in bacterial diversity and abundance can occur after fumigation but are less common. Fumigant application can also alter bacterial community composition during the first six weeks after treatment by significantly increasing and/or decreasing the relative abundance of bacterial taxa involved in key soil functions such as N-cycling and plant-growth promotion. Knowledge gaps and areas where future research efforts should be prioritized to improve our understanding of the impact of organic fumigants on non-target soil microorganisms are discussed.
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Affiliation(s)
- Antonio Castellano-Hinojosa
- Southwest Florida Research and Education Center, Department of Soil and Water Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29 N, Immokalee, FL 34142, USA
| | - Nathan S Boyd
- Gulf Coast Research and Education Center, Department of Horticulture, Institute of Food and Agricultural Sciences, University of Florida, 14625 C.R. 672, Wimauma, FL 33598, USA
| | - Sarah L Strauss
- Southwest Florida Research and Education Center, Department of Soil and Water Sciences, Institute of Food and Agricultural Sciences, University of Florida, 2685 State Rd 29 N, Immokalee, FL 34142, USA.
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88
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Gallego S, Brienza M, Béguet J, Chiron S, Martin-Laurent F. Impact of repeated irrigation of lettuce cultures with municipal wastewater on soil bacterial community diversity and composition. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:29236-29243. [PMID: 34117546 DOI: 10.1007/s11356-021-14734-4] [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: 01/06/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
The effect of wastewater irrigation on the diversity and composition of bacterial communities of soil mesocosms planted with lettuces was studied over an experiment made of five cultivation campaigns. A limited effect of irrigation with either raw or treated wastewater was observed in both α-diversity and β-diversity of soil bacterial communities. However, the irrigation with wastewater fortified with a complex mixture of fourteen relevant chemicals at 10 μg/L each, including pharmaceutical, biocide, and pesticide active substances, led to a drift in the composition of soil bacterial community. One hundred operational taxonomic units (OTUs) were identified as responsible for changes between treated and fortified wastewater irrigation treatments. Our findings indicate that under a realistic agronomical scenario, the irrigation of vegetables with domestic (treated or raw) wastewater has no effect on soil bacterial communities. Nevertheless, under the worst-case scenario tested here (i.e., wastewater fortified with a mixture of chemicals), non-resilient changes were observed suggesting that continuous/repeated irrigation with wastewater could lead to the accumulation of contaminants in soil and induce changes in bacterial communities with unknown functional consequences.
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Affiliation(s)
- Sara Gallego
- AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, UMR Agroécologie, INRAE, 17 rue Sully, BP86510, 21065, Dijon Cedex, France
| | - Monica Brienza
- UMR HydroSciences Montpellier, Montpellier University, IRD, 15 Avenue Charles Flahault, 34093, Montpellier Cedex 5, France
- Department of Science, University of Basilicata, Vial dell'Ateneo Lucano, 10 85100, Potenza, Italy
| | - Jérémie Béguet
- AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, UMR Agroécologie, INRAE, 17 rue Sully, BP86510, 21065, Dijon Cedex, France
| | - Serge Chiron
- UMR HydroSciences Montpellier, Montpellier University, IRD, 15 Avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Fabrice Martin-Laurent
- AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, UMR Agroécologie, INRAE, 17 rue Sully, BP86510, 21065, Dijon Cedex, France.
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89
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Yao Y, Zhao Y, Yao X, Bai Y, An L, Li X, Wu K. Impacts of Continuous Cropping on Fungal Communities in the Rhizosphere Soil of Tibetan Barley. Front Microbiol 2022; 13:755720. [PMID: 35185842 PMCID: PMC8854972 DOI: 10.3389/fmicb.2022.755720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/13/2022] [Indexed: 11/20/2022] Open
Abstract
Microbial community structures and keystone species play critical roles in soil ecological processes; however, their responses to the continuous cropping of plants are virtually unknown. Here, we investigated the community dynamics and keystone species of fungal communities in the rhizosphere soils of continuously cropped Tibetan barley (a principal cereal cultivated on the Qinghai–Tibetan Plateau). We found that the Chao1 and Phylogenetic Diversity (PD) indices decreased with increased cropping years. The relative abundance of the genera Cystofilobasidium, Mucor, and Ustilago increased with the extension of continuous cropping years, whereas Fusarium showed the opposite pattern. Furthermore, long-term monocropped Tibetan barley simplified the complexity of the co-occurrence networks. Keystone operational taxonomic units (OTUs) changed with continuous cropping, and most of the keystone OTUs belonged to the phylum Ascomycota, suggesting their important roles in rhizosphere soil. Overall, this study revealed that the continuous cropping of Tibetan barley impacted both on the richness, phylogenetic diversity, and co-occurrence network of fungal community in the rhizosphere. These findings enhance our understanding of how rhizosphere fungal communities respond to monocropped Tibetan barley.
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Affiliation(s)
- Youhua Yao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, China
| | - Yuan Zhao
- College of Eco-Environmental Engineering, Qinghai University, Xining, China
| | - Xiaohua Yao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, China
| | - Yixiong Bai
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, China
| | - Likun An
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, China
| | - Xin Li
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, China
| | - Kunlun Wu
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, China
- Qinghai Subcenter of National Hulless Barley Improvement, Xining, China
- *Correspondence: Kunlun Wu,
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90
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Microbial Nitrogen Transformation Potential in Sediments of Two Contrasting Lakes Is Spatially Structured but Seasonally Stable. mSphere 2022; 7:e0101321. [PMID: 35107340 PMCID: PMC8809388 DOI: 10.1128/msphere.01013-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The nitrogen (N) cycle is of global importance, as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbially mediated processes, few studies have investigated the microbial communities involved. In an integrated biogeochemical and microbiological study on a eutrophic and oligotrophic lake, we estimated N removal rates from pore water concentration gradients in sediments. Simultaneously, the abundance of different microbial N transformation genes was investigated using metagenomics on a seasonal and spatial scale. We observed that contrasting nutrient concentrations in sediments were associated with distinct microbial community compositions and significant differences in abundances of various N transformation genes. For both characteristics, we observed a more pronounced spatial than seasonal variability within each lake. The eutrophic Lake Baldegg showed a higher denitrification potential with higher nosZ gene (N2O reductase) abundances and higher nirS:nirK (nitrite reductase) ratios, indicating a greater capacity for complete denitrification. Correspondingly, this lake had a higher N removal efficiency. The oligotrophic Lake Sarnen, in contrast, had a higher potential for nitrification. Specifically, it harbored a high abundance of Nitrospira, including some with the potential for comammox. Our results demonstrate that knowledge of the genomic N transformation potential is important for interpreting N process rates and understanding how the lacustrine sedimentary N cycle responds to variations in trophic conditions. IMPORTANCE Anthropogenic nitrogen (N) inputs can lead to eutrophication in surface waters, especially in N-limited coastal ecosystems. Lakes effectively remove reactive N by transforming it to N2 through microbial denitrification or anammox. The rates and distributions of these microbial processes are affected by factors such as the amount and quality of settling organic material and nitrate concentrations. However, the microbial communities mediating these N transformation processes in freshwater lake sediments remain largely unknown. We provide the first seasonally and spatially resolved metagenomic analysis of the N cycle in sediments of two lakes with different trophic states. We show that lakes with different trophic states select for distinct communities of N-cycling microorganisms with contrasting functional potentials for N transformation.
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91
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Jamil FN, Hashim AM, Yusof MT, Saidi NB. Analysis of soil bacterial communities and physicochemical properties associated with Fusarium wilt disease of banana in Malaysia. Sci Rep 2022; 12:999. [PMID: 35046475 PMCID: PMC8770495 DOI: 10.1038/s41598-022-04886-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/03/2022] [Indexed: 12/19/2022] Open
Abstract
Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (TR4) is a soil-borne disease that infects bananas, causing severe economic losses worldwide. To reveal the relationship between bacterial populations and FW, the bacterial communities of healthy and TR4-infected rhizosphere and bulk soils were compared using 16S rRNA gene sequencing. Soil physicochemical properties associated with FW were also analyzed. We found the community structure of bacteria in the healthy and TR4 infected rhizosphere was significantly different compared to bulk soil within the same farm. The rhizosphere soils of infected plants exhibited higher richness and diversity than healthy plant with significant abundance of Proteobacteria. In the healthy rhizosphere soil, beneficial bacteria such as Burkholderia and Streptomyces spp. were more abundant. Compared to the infected rhizosphere soil, healthy rhizosphere soil was associated with RNA metabolism and transporters pathways and a high level of magnesium and cation exchange capacity. Overall, we reported changes in the key taxa of rhizospheric bacterial communities and soil physicochemical properties of healthy and FW-infected plants, suggesting their potential role as indicators for plant health.
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Affiliation(s)
- Fatin Nadiah Jamil
- Institute of Biosciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Amalia Mohd Hashim
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Mohd Termizi Yusof
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Noor Baity Saidi
- Institute of Biosciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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92
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Vieira CK, Dos Anjos Borges LG, Bortolini JG, Soares CRFS, Giongo A, Stürmer SL. Does a decrease in microbial biomass alter mycorrhizal attributes and soil quality indicators in coal mining areas under revegetation process? THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 802:149843. [PMID: 34455279 DOI: 10.1016/j.scitotenv.2021.149843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Losses of microbial diversity in degraded ecosystems still have obscure consequences, especially when considering the interaction between arbuscular mycorrhizal fungi (AMF) and soil bacteria. This study investigates the effect of decreasing microbial biomass on mycorrhizal attributes and soil quality indicators. The dilution-to-extinction approach was applied in microcosms to search for associations among bacterial diversity, mycorrhizal attributes, and soil quality indicators. The experiment was conducted with four soil treatments (undiluted control 100 = D0, 10-3 = D3, 10-6 = D6, and 10-9 = D9) from a short-term (two years = 2Y) and a long-term (15 years = 15Y) coal mine revegetation area. Microcosms were inoculated with 300 spores of Acaulospora colombiana, Gigaspora albida, and Claroideoglomus etunicatum with millet as the host plant. Results included the total number of AMF spores, mycorrhizal colonization, soil aggregation, glomalin, fluorescein diacetate hydrolysis (FDA), basal soil respiration, microbial biomass, and soil bacterial microbiome. Larger differences were observed between areas than between dilution treatments within the sampling area. Attributes that presented differences in the dilutions compared to D0 2Y samples were mycorrhizal colonization (D0 = 85% and D9 = 43.3%), FDA (D0 = 77.2% and D9 = 55.5%), extractable glomalin-related soil protein (D0 = 0.09 and D9 = 0.11) and bacterial diversity (D0 = 7.3 and D6 = 5.3). D0 15Y samples presented differences in microbial biomass nitrogen (D0: 232.0) and bacterial diversity (D0: 7.9, D9: 5.6) compared to the dilutions. Bacterial microbiome present in the D0 samples formed distinct clusters as to other samples and correlated with soil aggregation and basal respiration attributes. Results suggest that AMF inoculation and dilution-to-extinction did not affect soil quality indicators preeminently, but the bacterial community is affected and can influence the process of environmental revegetation. A long-term revegetation period is substantial to improve quality indicators and establish the diversity of microorganisms and consequently revegetation in areas impacted by coal mining.
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Affiliation(s)
- Caroline Krug Vieira
- Universidade Regional de Blumenau (FURB), Programa de Pós-Graduação em Engenharia Ambiental, 89030-903 Blumenau, SC, Brazil
| | - Luiz Gustavo Dos Anjos Borges
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Instituto do Petróleo e dos Recursos Naturais (IPR), 90619-900 Porto Alegre, RS, Brazil
| | | | | | - Adriana Giongo
- Universidade Regional de Blumenau (FURB), Programa de Pós-Graduação em Engenharia Ambiental, 89030-903 Blumenau, SC, Brazil; Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Sidney Luiz Stürmer
- Universidade Regional de Blumenau (FURB), Departamento de Ciências Naturais (DCN), 89030-903 Blumenau, SC, Brazil.
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93
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Jayaramaiah RH, Egidi E, Macdonald CA, Wang J, Jeffries TC, Megharaj M, Singh BK. Soil initial bacterial diversity and nutrient availability determine the rate of xenobiotic biodegradation. Microb Biotechnol 2022; 15:318-336. [PMID: 34689422 PMCID: PMC8719800 DOI: 10.1111/1751-7915.13946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 01/23/2023] Open
Abstract
Understanding the relative importance of soil microbial diversity, plants and nutrient management is crucial to implement an effective bioremediation approach to xenobiotics-contaminated soils. To date, knowledge on the interactive effects of soil microbiome, plant and nutrient supply on influencing biodegradation potential of soils remains limited. In this study, we evaluated the individual and interactive effects of soil initial bacterial diversity, nutrient amendments (organic and inorganic) and plant presence on the biodegradation rate of pyrene, a polycyclic aromatic hydrocarbon. Initial bacterial diversity had a strong positive impact on soil biodegradation potential, with soil harbouring higher bacterial diversity showing ~ 2 times higher degradation rates than soils with lower bacterial diversity. Both organic and inorganic nutrient amendments consistently improved the degradation rate in lower diversity soils and had negative (inorganic) to neutral (organic) effect in higher diversity soils. Interestingly, plant presence/type did not show any significant effect on the degradation rate in most of the treatments. Structural equation modelling demonstrated that initial bacterial diversity had a prominent role in driving pyrene biodegradation rates. We provide novel evidence that suggests that soil initial microbial diversity, and nutrient amendments should be explicitly considered in the design and employment of bioremediation management strategies for restoring natural habitats disturbed by organic pollutants.
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Affiliation(s)
- Ramesha H. Jayaramaiah
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
| | - Eleonora Egidi
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
- Global Centre for Land‐based InnovationWestern Sydney UniversityPenrithNSW2751Australia
| | - Catriona A. Macdonald
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
| | - Jun‐Tao Wang
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
- Global Centre for Land‐based InnovationWestern Sydney UniversityPenrithNSW2751Australia
| | - Thomas C. Jeffries
- Global Centre for Land‐based InnovationWestern Sydney UniversityPenrithNSW2751Australia
- School of ScienceWestern Sydney UniversityPenrithNSW2751Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental RemediationThe University of NewcastleCallaghanNSW2308Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2751Australia
- Global Centre for Land‐based InnovationWestern Sydney UniversityPenrithNSW2751Australia
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94
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Singh AK, Liu W, Zakari S, Wu J, Yang B, Jiang XJ, Zhu X, Zou X, Zhang W, Chen C, Singh R, Nath AJ. A global review of rubber plantations: Impacts on ecosystem functions, mitigations, future directions, and policies for sustainable cultivation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 796:148948. [PMID: 34273842 DOI: 10.1016/j.scitotenv.2021.148948] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/06/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The growing global need for latex is driving rubber plantation (RP) expansion since the last century, with >2 Mha of cultivation area being established in the last decade. Southeast Asia is the hotspot for rubber cultivation at other land-use costs. Although rubber cultivation has improved the economic status of farmers, it has altered the habitat's ecology and ecosystem functions (EF). However, studies on the impacts of RP on EF are limited, and a clear overview is not available. To bridge this gap, we conducted an inclusive review of the EF of RP, including soil carbon storage, aboveground biomass (AGB) and belowground biomass (BGB), litter production and decomposition, respiration, and biodiversity (plants, animals, soil fauna, and microbes). We compared the EF in RP (monoculture) with those in forests because the conversion of forests to RP is prevalent in the tropics and because most RP studies used forests as reference ecosystems. We found RP generally have lower EF than forests. The impacts of RP on some EF are more severe (e.g., AGB, BGB, and plant diversity), causing decreases of >55%, and the effects are consistently negative irrespective of plantation age. However, including agroforestry or polyculture, integrated pest management, cover cropping, mulching, and composting can improve the EF in RP to some extent. We highlighted research gaps, particularly substantial research gaps concerning the influence of plant diversity treatments (i.e., agroforestry) performed in RP on EF. Additionally, more empirical data on the significance of spatial and temporal levels are required, such as how the impact on EF could vary with climate and RP age, as we showed some examples where EF differs spatially and temporally. More importantly, further research on plantation management to offset EF losses is needed. Finally, we emphasized knowledge gaps and suggested future directions and policies for improving EF in RP.
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Affiliation(s)
- Ashutosh Kumar Singh
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Wenjie Liu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Sissou Zakari
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Laboratory of Hydraulics and Environmental Modeling (HydroModE-Lab), Faculté d'Agronomie, Université de Parakou, 03 BP 351 Parakou, Benin
| | - Junen Wu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Bin Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Xiao Jin Jiang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Xiai Zhu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Xin Zou
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Wanjun Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Chunfeng Chen
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - Rishikesh Singh
- Integrative Ecology Laboratory (IEL), Institute of Environment & Sustainable Development (IESD), Banaras Hindu University, Varanasi 221005, India
| | - Arun Jyoti Nath
- Department of Ecology and Environmental Science, Assam University, Silchar 788011, India
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95
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Ding Y, Song X, Cao X, He L, Liu S, Yu Z. Healthier Communities of Phytoplankton and Bacteria Achieved via the Application of Modified Clay in Shrimp Aquaculture Ponds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111569. [PMID: 34770083 PMCID: PMC8583407 DOI: 10.3390/ijerph182111569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 11/25/2022]
Abstract
The composition and stability of microbial communities in aquaculture water are crucial for the healthy growth of shrimp and present considerable risk to aquatic ecosystems. The modified clay (MC) method has been proposed as an efficient and safe solution for the mitigation of harmful algal blooms (HABs). Currently, the effects of MC on microbial communities in aquaculture water remain unknown. Here, we adopted the MC method to regulate shrimp-culture water quality and evaluated the effects of MC on the composition and stability of phytoplankton together with bacteria communities through high-throughput sequencing. On the one hand, a prominent change in the composition of microbial community was observed, with green algae becoming the most abundant genera and pathogens being infrequent in the MC-treated pond, which was more conducive to the growth of shrimp than that in the control pond. Moreover, MC could increase the diversity and stability of the microbial community structure in the water column, which had a higher anti-interference ability, as demonstrated by the analysis of the diversity and molecular ecological network. Taken together, MC could reduce the possibility for the occurrence of HABs and maintain a stable microbial community, which is beneficial for the health and high yield of shrimp.
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Affiliation(s)
- Yu Ding
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xiuxian Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
- Correspondence: ; Tel.: +86-532-82898587
| | - Xihua Cao
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Liyan He
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shanshan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhiming Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.D.); (X.C.); (L.H.); (S.L.); (Z.Y.)
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Chinese Academy of Sciences, Beijing 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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96
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Kroeger ME, Rae DeVan M, Thompson J, Johansen R, Gallegos‐Graves LV, Lopez D, Runde A, Yoshida T, Munsky B, Sevanto S, Albright MBN, Dunbar J. Microbial community composition controls carbon flux across litter types in early phase of litter decomposition. Environ Microbiol 2021; 23:6676-6693. [PMID: 34390621 PMCID: PMC9291330 DOI: 10.1111/1462-2920.15705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/02/2021] [Indexed: 11/30/2022]
Abstract
Leaf litter decomposition is a major carbon input to soil, making it a target for increasing soil carbon storage through microbiome engineering. We expand upon previous findings to show with multiple leaf litter types that microbial composition can drive variation in carbon flow from litter decomposition and specific microbial community features are associated with synonymous patterns of carbon flow among litter types. Although plant litter type selects for different decomposer communities, within a litter type, microbial composition drives variation in the quantity of dissolved organic carbon (DOC) measured at the end of the decomposition period. Bacterial richness was negatively correlated with DOC quantity, supporting our hypothesis that across multiple litter types there are common microbial traits linked to carbon flow patterns. Variation in DOC abundance (i.e. high versus low DOC) driven by microbial composition is tentatively due to differences in bacterial metabolism of labile compounds, rather than catabolism of non-labile substrates such as lignin. The temporal asynchrony of metabolic processes across litter types may be a substantial impediment to discovering more microbial features common to synonymous patterns of carbon flow among litters. Overall, our findings support the concept that carbon flow may be programmed by manipulating microbial community composition.
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Affiliation(s)
- Marie E. Kroeger
- Bioscience DivisionLos Alamos National Laboratory, Mailstop M888Los AlamosNM87545USA
| | - M. Rae DeVan
- Bioscience DivisionLos Alamos National Laboratory, Mailstop M888Los AlamosNM87545USA
| | - Jaron Thompson
- Department of Chemical and Biological EngineeringColorado State UniversityFort CollinsCO80523USA
| | - Renee Johansen
- Bioscience DivisionLos Alamos National Laboratory, Mailstop M888Los AlamosNM87545USA
- Manaaki Whenua – Landcare Research, Private Bag 92170Auckland Mail CentreAucklandNew Zealand
| | | | - Deanna Lopez
- Bioscience DivisionLos Alamos National Laboratory, Mailstop M888Los AlamosNM87545USA
| | - Andreas Runde
- Bioscience DivisionLos Alamos National Laboratory, Mailstop M888Los AlamosNM87545USA
| | - Thomas Yoshida
- Chemical Diagnostics and EngineeringLos Alamos National Laboratory, Mailstop K484Los AlamosNM87544USA
| | - Brian Munsky
- Department of Chemical and Biological EngineeringColorado State UniversityFort CollinsCO80523USA
- School of Biomedical EngineeringColorado State UniversityFort CollinsCO80523USA
| | - Sanna Sevanto
- Earth and Environmental Sciences DivisionLos Alamos National Laboratory, Mailstop J495Los AlamosNM87545USA
| | | | - John Dunbar
- Bioscience DivisionLos Alamos National Laboratory, Mailstop M888Los AlamosNM87545USA
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97
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Blagodatskaya E, Tarkka M, Knief C, Koller R, Peth S, Schmidt V, Spielvogel S, Uteau D, Weber M, Razavi BS. Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces. Front Microbiol 2021; 12:625697. [PMID: 34777265 PMCID: PMC8581545 DOI: 10.3389/fmicb.2021.625697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 09/01/2021] [Indexed: 12/30/2022] Open
Abstract
In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.
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Affiliation(s)
- Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- Agro-Technological Institute, RUDN University, Moscow, Russia
| | - Mika Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research Halle–Jena–Leipzig, Leipzig, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Stephan Peth
- Institute of Soil Science, University of Hannover, Hanover, Germany
| | | | - Sandra Spielvogel
- Department Soil Science, Institute for Plant Nutrition and Soil Science, Christian-Albrechts University Kiel, Kiel, Germany
| | - Daniel Uteau
- Department of Soil Science, Faculty of Organic Agricultural Sciences, University of Kassel, Kassel, Germany
| | | | - Bahar S. Razavi
- Department of Soil and Plant Microbiome, Institute of Phytopathology, Christian-Albrechts-University of Kiel, Kiel, Germany
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98
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Bowd EJ, Banks SC, Bissett A, May TW, Lindenmayer DB. Disturbance alters the forest soil microbiome. Mol Ecol 2021; 31:419-447. [PMID: 34687569 DOI: 10.1111/mec.16242] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/24/2021] [Accepted: 10/11/2021] [Indexed: 12/21/2022]
Abstract
Billions of microorganisms perform critical below-ground functions in all terrestrial ecosystems. While largely invisible to the naked eye, they support all higher lifeforms, form symbiotic relationships with ~90% of terrestrial plant species, stabilize soils, and facilitate biogeochemical cycles. Global increases in the frequency of disturbances are driving major changes in the structure and function of forests. However, despite their functional significance, the disturbance responses of forest microbial communities are poorly understood. Here, we explore the influence of disturbance on the soil microbiome (archaea, fungi and bacteria) of some of the world's tallest and most carbon-dense forests, the Mountain Ash forests of south-eastern Australia. From 80 sites, we identified 23,277 and 19,056 microbial operational taxonomic units from the 0-10 cm and 20-30 cm depths of soil respectively. From this extensive data set, we found the diversity and composition of these often cryptic communities has been altered by human and natural disturbance events. For instance, the diversity of ectomycorrhizal fungi declined with clearcut logging, the diversity of archaea declined with salvage logging, and bacterial diversity and overall microbial diversity declined with the number of fires. Moreover, we identified key associations between edaphic (soil properties), environmental (slope, elevation) and spatial variables and the composition of all microbial communities. Specifically, we found that soil pH, manganese, magnesium, phosphorus, iron and nitrate were associated with the composition of all microbial communities. In a period of widespread degradation of global forest ecosystems, our findings provide an important and timely insight into the disturbance responses of soil microbial communities, which may influence key ecological functions.
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Affiliation(s)
- Elle J Bowd
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
| | - Sam C Banks
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia.,College of Engineering, IT and the Environment, Research Institute for Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Andrew Bissett
- The Commonwealth Scientific and Industrial Research Organization, CSIRO Oceans and Atmosphere, Hobart, TAS, Australia
| | - Tom W May
- Royal Botanic Gardens Victoria, Melbourne, VIC, Australia
| | - David B Lindenmayer
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
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99
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Wang S, Bao X, Feng K, Deng Y, Zhou W, Shao P, Zheng T, Yao F, Yang S, Liu S, Shi R, Bai Z, Xie H, Yu J, Zhang Y, Zhang Y, Sha L, Song Q, Liu Y, Zhou J, Zhang Y, Li H, Wang Q, Han X, Zhu Y, Liang C. Warming-driven migration of core microbiota indicates soil property changes at continental scale. Sci Bull (Beijing) 2021; 66:2025-2035. [PMID: 36654172 DOI: 10.1016/j.scib.2021.01.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/15/2020] [Accepted: 12/21/2020] [Indexed: 02/03/2023]
Abstract
Terrestrial species are predicted to migrate northward under global warming conditions, yet little is known about the direction and magnitude of change in microbial distribution patterns. In this continental-scale study with more than 1600 forest soil samples, we verify the existence of core microbiota and lump them into a manageable number of eco-clusters based on microbial habitat preferences. By projecting the abundance differences of eco-clusters between future and current climatic conditions, we observed the potential warming-driven migration of the core microbiota under warming, partially verified by a field warming experiment at Southwest China. Specifically, the species that favor low pH are potentially expanding and moving northward to medium-latitudes (25°-45°N), potentially implying that warm temperate forest would be under threat of soil acidification with warming. The eco-cluster of high-pH with high-annual mean temperature (AMT) experienced significant abundance increases at middle- (35°-45°N) to high-latitudes (> 45°N), especially under Representative Concentration Pathway (RCP) 8.5, likely resulting in northward expansion. Furthermore, the eco-cluster that favors low-soil organic carbon (SOC) was projected to increase under warming scenarios at low-latitudes (< 25°N), potentially an indicator of SOC storage accumulation in warmer areas. Meanwhile, at high-latitudes (> 45°N) the changes in relative abundance of this eco-cluster is inversely related with the temperature variation trends, suggesting microbes-mediated soil organic carbon changes are more responsive to temperature variation in colder areas. These results have vital implications for the migration direction of microbial communities and its potential ecological consequences in future warming scenarios.
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Affiliation(s)
- Shang Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China
| | - Xuelian Bao
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Kai Feng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Science, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Wenjun Zhou
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna 666303, China
| | - Pengshuai Shao
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Tiantian Zheng
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Fei Yao
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Shan Yang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Shengen Liu
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Rongjiu Shi
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Zhen Bai
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Hongtu Xie
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Jinghua Yu
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Ying Zhang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Yiping Zhang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna 666303, China
| | - Liqing Sha
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna 666303, China
| | - Qinghai Song
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna 666303, China
| | - Yuntong Liu
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Xishuangbanna 666303, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman 73019 OK, USA
| | - Yuguang Zhang
- Institute of Forest Ecology, Environment and Protection, and the Key Laboratory of Forest Ecology and Environment of State Forestry Administration, Chinese Academy of Forestry, Beijing 100091, China
| | - Hui Li
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Qingkui Wang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Xingguo Han
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yongguan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Chao Liang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China.
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100
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Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil. Sci Rep 2021; 11:19320. [PMID: 34588474 PMCID: PMC8481224 DOI: 10.1038/s41598-021-97942-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/30/2021] [Indexed: 11/11/2022] Open
Abstract
Microbial decomposition drives the transformation of plant-derived substrates into microbial products that form stable soil organic matter (SOM). Recent theories have posited that decomposition depends on an interaction between SOM chemistry with microbial diversity and resulting function (e.g., enzymatic capabilities, growth rates). Here, we explicitly test these theories by coupling quantitative stable isotope probing and metabolomics to track the fate of 13C enriched substrates that vary in chemical composition as they are assimilated by microbes and transformed into new metabolic products in soil. We found that differences in forest nutrient economies (e.g., nutrient cycling, microbial competition) led to arbuscular mycorrhizal (AM) soils harboring greater diversity of fungi and bacteria than ectomycorrhizal (ECM) soils. When incubated with 13C enriched substrates, substrate type drove shifts in which species were active decomposers and the abundance of metabolic products that were reduced or saturated in the highly diverse AM soils. The decomposition pathways were more static in the less diverse, ECM soil. Importantly, the majority of these shifts were driven by taxa only present in the AM soil suggesting a strong link between microbial identity and their ability to decompose and assimilate substrates. Collectively, these results highlight an important interaction between ecosystem-level processes and microbial diversity; whereby the identity and function of active decomposers impacts the composition of decomposition products that can form stable SOM.
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