101
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Cao Y, Gao Y, Tian Y, Li J. Compost Addition Attenuates the Negative Impacts of High Soil Mineral Nitrogen Levels on Rhizosphere Microbial Characteristics and Enhances Cucumber Growth in Monoculture Systems. PLANTS (BASEL, SWITZERLAND) 2022; 11:1621. [PMID: 35807574 PMCID: PMC9269332 DOI: 10.3390/plants11131621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Due to the increase in the human population, it is necessary to seek efficient methods of increasing crop productivity and, simultaneously, sustaining the soil. One way is to grow high demand crops continuously without rotating with other crops. This practice is often accompanied by increased rates of fertilizer application that can affect efficient nitrogen (N) cycling in the plant rhizosphere soil which, in turn, affects both plant growth and environmental pollution. In the present study, twelve various cucumber soils were selected from monoculture systems presenting different cropping years and divided into two groups including soils with relatively high mineral N (HMN) content (N > 100 mg kg−1 soil) and those with a lower mineral N (LMN) content (N < 100 mg kg−1 soil). All soils were amended with the addition of compost alone or in combination with bacterial inoculation to evaluate their effects on plant growth, microbial numbers, N mineralization, and N cycling genes. In general, the HMN soils increased (p < 0.05) net N mineralization (NNM) but did not statistically (p > 0.05) affect plant biomass compared to the LMN soils; however, compost addition increased both NNM and plant biomass in the HMN soils. In addition, the HMN soils had higher fungal pathogen numbers (FPNs) but lower total microbial biomass (TMB) and bacterial numbers (BNs) compared to the LMN soils; however, compost addition decreased FPNs but increased TMB and BNs in the HMN soils (all p < 0.05). Plant biomass was positively related to TMB, BN and NNM but was negatively related to FPN (all p < 0.05). In summary, compost addition reduced the high mineral N levels’ adverse effects on the rhizosphere soil and plant growth.
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Affiliation(s)
- Yune Cao
- College of Agriculture, Ningxia University, Helanshan Xilu No. 489, Yinchuan 750021, China; (Y.C.); (Y.G.)
| | - Yanming Gao
- College of Agriculture, Ningxia University, Helanshan Xilu No. 489, Yinchuan 750021, China; (Y.C.); (Y.G.)
| | - Yongqiang Tian
- College of Agriculture, Ningxia University, Helanshan Xilu No. 489, Yinchuan 750021, China; (Y.C.); (Y.G.)
- College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Jianshe Li
- College of Agriculture, Ningxia University, Helanshan Xilu No. 489, Yinchuan 750021, China; (Y.C.); (Y.G.)
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102
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Hu W, Hou Q, Delgado-Baquerizo M, Stegen JC, Du Q, Dong L, Ji M, Sun Y, Yao S, Gong H, Xiong J, Xia R, Liu J, Aqeel M, Akram MA, Ran J, Deng J. Continental-scale niche differentiation of dominant topsoil archaea in drylands. Environ Microbiol 2022; 24:5483-5497. [PMID: 35706137 DOI: 10.1111/1462-2920.16099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/07/2022] [Indexed: 11/26/2022]
Abstract
Archaea represent a diverse group of microorganisms often associated with extreme environments. However, an integrated understanding of biogeographical patterns of the specialist Haloarchaea and the potential generalist ammonia-oxidizing archaea (AOA) across large-scale environmental gradients remains limited. We hypothesize that niche differentiation determines their distinct distributions along environmental gradients. To test the hypothesis, we use a continental-scale research network including 173 dryland sites across northern China. Our results demonstrate that Haloarchaea and AOA dominate topsoil archaeal communities. As hypothesized, Haloarchaea and AOA show strong niche differentiation associated with two ecosystem types mainly found in China's drylands (i.e., deserts vs. grasslands), and they differ in the degree of habitat specialization. The relative abundance and richness of Haloarchaea are higher in deserts due to specialization to relatively high soil salinity and extreme climates, while those of AOA are greater in grassland soils. Our results further indicate a divergence in ecological processes underlying the segregated distributions of Haloarchaea and AOA. Haloarchaea are governed primarily by environmental-based processes while the more generalist AOA are assembled mostly via spatial-based processes. Our findings add to existing knowledge of large-scale biogeography of topsoil archaea, advancing our predictive understanding on changes in topsoil archaeal communities in a drier world. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Weigang Hu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qingqing Hou
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistemico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, Sevilla, Spain.,Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | - James C Stegen
- Ecosystem Science Team, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Qiajun Du
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Longwei Dong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Mingfei Ji
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yuan Sun
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Shuran Yao
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Haiyang Gong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Junlan Xiong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Rui Xia
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jiayuan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Muhammad Adnan Akram
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.,School of Economics, Lanzhou University, Lanzhou, China
| | - Jinzhi Ran
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianming Deng
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
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103
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Zhao C, Hu J, Li Q, Fang Y, Liu D, Liu Z, Zhong R. Transfer of Nitrogen and Phosphorus From Cattle Manure to Soil and Oats Under Simulative Cattle Manure Deposition. Front Microbiol 2022; 13:916610. [PMID: 35774448 PMCID: PMC9238326 DOI: 10.3389/fmicb.2022.916610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022] Open
Abstract
Simulated cattle manure deposition was used to estimate nutrient transfer to soil and oats and to investigate changes in microbial community composition and functional groups in oat rhizospheres. Nutrient absorption and return efficiency were calculated as a series of standard calculation formulas, and total nutrient transfer efficiency was nutrient absorption efficiency plus nutrient return efficiency. In total, 74.83% of nitrogen (N) and 59.30% of phosphorus (P) in cattle manure were transferred to soil and oats, with 11.79% of N and 7.89% of P in cattle manure absorbed by oats, and the remainder sequestered in the soil for 80 days after sowing. Cattle manure increased oat root length, surface, and volume under 0.2 mm diameter, and improved relative abundance of the microbiome known to be beneficial. In response to cattle manure, several bacteria known to be beneficial, such as Proteobacteria, Bacteroidota, and Firmicutes at phyla the level and Pseudoxanthomonas, Pseudomonas, and Sphingomonas at the genus level, were positively related to oat biomass and nutrient accumulation. For fungal communities, the relative abundance of Ascomycota is the predominant phylum, which varied in a larger range in the control treatment (81.0–63.3%) than the cattle manure deposition treatment (37.0–42.9%) as plant growing days extend. The relevant abundance of Basidiomycota known as decomposer was higher in cattle manure deposition treatment compared to that in control treatment at 15 days after sowing. More importantly, cattle manure deposition inhibited trophic mode within pathotroph like Alternaria and Fusarium fungal genus and promoted saprotroph and symbiotroph.
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Affiliation(s)
- Chengzhen Zhao
- Jilin Provincial Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- School of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Juan Hu
- Jilin Provincial Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Qiang Li
- Jilin Provincial Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yi Fang
- Jilin Provincial Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Di Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ziguang Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Rongzhen Zhong
- Jilin Provincial Laboratory of Grassland Farming, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- *Correspondence: Rongzhen Zhong,
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104
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Zhong L, Qing J, Liu M, Cai X, Li G, Li FY, Chen G, Xu X, Xue K, Wang Y. Fungi and Archaea Control Soil N 2O Production Potential in Chinese Grasslands Rather Than Bacteria. Front Microbiol 2022; 13:844663. [PMID: 35651488 PMCID: PMC9149426 DOI: 10.3389/fmicb.2022.844663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas and the predominant stratospheric ozone-depleting substance. Soil is a major source of N2O but remains largely uncertain due to the complicated processes of nitrification and denitrification performed by various groups of microbes such as bacteria, fungi, and archaea. We used incubation experiments to measure the total fungal, archaeal, and bacterial N2O production potential and the microbial functional genes in soils along 3,000 km Chinese grassland transect, including meadow steppe, typical steppe, desert steppe, alpine meadow, and alpine steppe. The results indicated that fungi, archaea, and bacteria contributed 25, 34, and 19% to nitrification and 46, 29, and 15% to denitrification, respectively. The AOA and AOB genes were notably correlated with the total nitrification enzyme activity (TNEA), whereas both narG and nirK genes were significantly correlated with total denitrification enzyme activity (TDEA) at p < 0.01. The correlations between AOA and ANEA (archaeal nitrification enzyme activity), AOB and BNEA (bacterial nitrification enzyme activity), and narG, nirK, and BDEA (bacterial denitrification enzyme activity) showed higher coefficients than those between the functional genes and TNEA/TDEA. The structural equation modeling (SEM) results showed that fungi are dominant in N2O production processes, followed by archaea in the northern Chinese grasslands. Our findings indicate that the microbial functional genes are powerful predictors of the N2O production potential, after distinguishing bacterial, fungal, and archaeal processes. The key variables of N2O production and the nitrogen (N) cycle depend on the dominant microbial functional groups in the N-cycle in soils.
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Affiliation(s)
- Lei Zhong
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Jinwu Qing
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Min Liu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources, Chinese Academy of Sciences, Beijing, China
| | - Xiaoxian Cai
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Gaoyuan Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Frank Yonghong Li
- School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Guanyi Chen
- School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Xingliang Xu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources, Chinese Academy of Sciences, Beijing, China.,Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China
| | - Kai Xue
- Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanfen Wang
- Chinese Academy of Sciences (CAS) Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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105
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Abela AG, Fava S. Prenatal and early life factors and type 1 diabetes. Endocrine 2022; 77:48-56. [PMID: 35484448 PMCID: PMC9049652 DOI: 10.1007/s12020-022-03057-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND The prevalence of type 1 diabetes is increasing worldwide, suggesting that unknown environmental factors are becoming increasingly important in its pathogenesis. AIM The aim of the study was to investigate the possible role of a number of prenatal and perinatal factors in the aetiology of type 1 diabetes. METHODS Mothers of patients diagnosed with type 1 diabetes (cases) and mothers of children born on the same day and of the same sex as type 1 diabetes patients (controls) were interviewed on a number of prenatal and perinatal factors of interest. RESULTS Hand washing prior to eating, frequency of bathing and total stress score were found to be positively associated with the development of type 1 diabetes on univariate analyses. Hand-washing prior to eating and frequency of house cleaning were independently associated with an increased risk of type 1 diabetes, whilst getting dirty was associated with a reduced risk in multivariate analyses. There was no association of type 1 diabetes to removing of outdoor shoes indoors or to the age of first attendance to school or pre-school. There were also no significant associations to parental smoking, parental age, birth order, infant feeding, antibiotic use, mode of delivery or birth weight. CONCLUSION Our data suggest that factors that affect the skin or gut microbiome might be more important than infections or factors affecting the microbiome at other sites.
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Affiliation(s)
| | - Stephen Fava
- University of Malta Medical School & Mater Dei Hospital, Msida, Malta.
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106
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Yu S, Sayer EJ, Li Z, Mo Q, Wang M, Li Y, Li Y, Xu G, Hu Z, Wang F. Delayed wet season increases soil net N mineralization in a seasonally dry tropical forest. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153314. [PMID: 35124037 DOI: 10.1016/j.scitotenv.2022.153314] [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: 09/09/2021] [Revised: 01/02/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Seasonal precipitation regime plays a vital role in regulating nutrient dynamics in seasonally dry tropical forests. Present evidence suggests that not only wet season precipitation is increasing in the tropics of South China, but also that the wet season is occurring later. However, it is unclear how nutrient dynamics will respond to the projected precipitation regime changes. We assessed the impacts of altered seasonal precipitation on soil net N mineralization in a secondary tropical forest. Since 2013, by reducing throughfall and/or irrigating experimental plots, we delayed the wet season by two months from April-September to June-November (DW treatment) or increased annual precipitation by 25% in July and August (WW treatment). We measured soil net N mineralization rates and assessed soil microbial communities in January, April, August and November in 2015 and 2017. We found that a wetter wet season did not significantly affect soil microbes or net N mineralization rates, even in the mid-wet season (August) when soil water content in the WW treatment increased significantly. By contrast, a delayed wet season enhanced soil microbial biomass and altered microbial community structure, resulting in a two-fold increase in net N mineralization rates relative to controls in the early dry season (November). Structural equation modeling showed that the changes in net N mineralization during the early dry season were associated with altered soil microbial communities, dissolved organic N, and litterfall, which were all affected by enhanced soil water content. Our findings suggest that a delayed wet season could have a greater impact on N dynamics than increased precipitation during the wet season. Changes in the seasonal timing of rainfall might therefore influence the functioning of seasonally dry tropical forests.
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Affiliation(s)
- Shiqin Yu
- School of Geography and Remote Sensing, Guangzhou University, Guangzhou 510006, PR China; Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Emma J Sayer
- Lancaster Environment Center, Lancaster University, Lancaster LA1 4YQ, UK; Smithsonian Tropical Research Institute, Balboa, Ancon, Panama City, Panama
| | - Zhian Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China
| | - Qifeng Mo
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, PR China
| | - Mei Wang
- School of Geographic Sciences, South China Normal University, Guangzhou 510631, China
| | - Yingwen Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Yongxing Li
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China
| | - Guoliang Xu
- School of Geography and Remote Sensing, Guangzhou University, Guangzhou 510006, PR China
| | - Zhongmin Hu
- College of Ecology and Environment, Hainan University, Haikou 570228, China
| | - Faming Wang
- Xiaoliang Research Station of Tropical Coastal Ecosystems, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, and the CAS engineering Laboratory for Ecological Restoration of Island and Coastal Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, PR China.
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107
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Selim S, Akhtar N, Hagagy N, Alanazi A, Warrad M, El Azab E, Elamir MYM, Al-Sanea MM, Jaouni SKA, Abdel-Mawgoud M, Shah AA, Abdelgawad H. Selection of Newly Identified Growth-Promoting Archaea Haloferax Species With a Potential Action on Cobalt Resistance in Maize Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:872654. [PMID: 35665142 PMCID: PMC9161300 DOI: 10.3389/fpls.2022.872654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Soil contamination with cobalt (Co) negatively impacts plant growth and production. To combat Co toxicity, plant growth-promoting microorganisms for improving plant growth are effectively applied. To this end, unclassified haloarchaeal species strain NRS_31 (OL912833), belonging to Haloferax genus, was isolated, identified for the first time, and applied to mitigate the Co phytotoxic effects on maize plants. This study found that high Co levels in soil lead to Co accumulation in maize leaves. Co accumulation in the leaves inhibited maize growth and photosynthetic efficiency, inducing oxidative damage in the tissue. Interestingly, pre-inoculation with haloarchaeal species significantly reduced Co uptake and mitigated the Co toxicity. Induced photosynthesis improved sugar metabolism, allocating more carbon to defend against Co stress. Concomitantly, the biosynthetic key enzymes involved in sucrose (sucrose-P-synthase and invertases) and proline (pyrroline-5- carboxylate synthetase (P5CS), pyrroline-5-carboxylate reductase (P5CR)) biosynthesis significantly increased to maintain plant osmotic potential. In addition to their osmoregulation potential, soluble sugars and proline can contribute to maintaining ROS hemostasis. Maize leaves managed their oxidative homeostasis by increasing the production of antioxidant metabolites (such as phenolics and tocopherols) and increasing the activity of ROS-scavenging enzymes (such as POX, CAT, SOD, and enzymes involved in the AsA/GSH cycle). Inside the plant tissue, to overcome heavy Co toxicity, maize plants increased the synthesis of heavy metal-binding ligands (metallothionein, phytochelatins) and the metal detoxifying enzymes (glutathione S transferase). Overall, the improved ROS homeostasis, osmoregulation, and Co detoxification systems were the basis underlying Co oxidative stress, mitigating haloarchaeal treatment's impact.
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Affiliation(s)
- Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Nosheen Akhtar
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Nashwa Hagagy
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Awadh Alanazi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Mona Warrad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Quriat, Jouf University, Al-Quriat, Saudi Arabia
| | - Eman El Azab
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at Al-Quriat, Jouf University, Al-Quriat, Saudi Arabia
| | | | - Mohammad M. Al-Sanea
- Pharmaceutical Chemistry Department, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Soad K. Al Jaouni
- Hematology/Pediatric Oncology, Yousef Abdulatif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Anis Ali Shah
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Hamada Abdelgawad
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerpen, Belgium
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
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108
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Zheng J, Tao L, Dini-Andreote F, Luan L, Kong P, Xue J, Zhu G, Xu Q, Jiang Y. Dynamic Responses of Ammonia-Oxidizing Archaea and Bacteria Populations to Organic Material Amendments Affect Soil Nitrification and Nitrogen Use Efficiency. Front Microbiol 2022; 13:911799. [PMID: 35633707 PMCID: PMC9135446 DOI: 10.3389/fmicb.2022.911799] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 04/22/2022] [Indexed: 11/25/2022] Open
Abstract
Organic material amendments have been proposed as an effective strategy to promote soil health by enhancing soil fertility and promoting nitrogen (N) cycling and N use efficiency (NUE). Thus, it is important to investigate the extent to which the structure and function of ammonia-oxidizing archaea (AOA) and bacteria (AOB) differentially respond to the organic material amendments in field settings. Here, we conducted a 9-year field experiment to track the responses of AOA and AOB populations to the organic material amendments and measured the potential nitrification activity (PNA), plant productivity, and NUE in the plant rhizosphere interface. Our results revealed that the organic material amendments significantly enhanced the abundance and diversity of AOA and AOB populations. Further, significant differences were observed in the composition and co-occurrence network of AOA and AOB. A higher occurrence of potential competitive interactions between taxa and enumerated potential keystone taxa was observed in the AOA-AOB network. Moreover, we found that AOA was more important than AOB for PNA under the organic material amendments. Structural equation modeling suggested that the diversity of AOA and AOB populations induced by the potential competitive interactions with keystone taxa dynamically accelerated the rate of PNA, and positively affected plant productivity and NUE under the organic material amendments. Collectively, our study offers new insights into the ecology and functioning of ammonia oxidizers and highlights the positive effects of organic material amendments on nitrogen cycling dynamics.
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Affiliation(s)
- Jie Zheng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liang Tao
- Guangdong Key Laboratory of Integrated Agroenvironmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China
| | - Francisco Dini-Andreote
- Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Lu Luan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Peijun Kong
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingrong Xue
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Guofan Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Qinsong Xu
- College of Life Science, Nanjing Normal University, Nanjing, China
| | - Yuji Jiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- *Correspondence: Yuji Jiang,
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109
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Jiao K, Yang B, Wang H, Xu W, Zhang C, Gao Y, Sun W, Li F, Ji D. The individual and combined effects of polystyrene and silver nanoparticles on nitrogen transformation and bacterial communities in an agricultural soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153358. [PMID: 35077800 DOI: 10.1016/j.scitotenv.2022.153358] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
The effects of emerging contaminants micro/nanoplastics (MPs/NPs) and silver nanoparticles (Ag NPs) on health have attracted universal concern throughout the world. However, it is unclear on the combined effects of MPs/NPs and Ag NPs on the biogeochemistry cycle such as nitrogen transformation and functional microorganism in the soil. In the present study, we conducted a 45-day soil microcosm experiment with polystyrene (PS) MPs/NPs and Ag NPs to investigate their combined impact on nitrogen cycling and the bacterial community. The results showed that MPs or NPs exerted limited effects on nitrogen transformation in the soil. The combined effects of PS MPs/NPs and Ag NPs were mainly caused by the presence of Ag NPs. However, PS NPs alleviated the inhibition of anammox and denitrification induced by Ag NPs via upregulating anammox-related genes and elevating nitrate and nitrite reductase activities. PS MPs + Ag NPs treatment significantly reduced bacterial diversity. PS MPs/NPs + Ag NPs increased the relative abundances of denitrifying Cupriavidus by 0.32% and 0.06% but decreased nitrogen-fixing functional microorganisms of Microvirga (by 2.05% and 2.24%), Bacillus (by 0.16% and 0.22%), and Herbaspirillum (by 0.14% and 0.07%) at the genus level compared with Ag NPs alone. The significant downregulation of nitrogen-fixing genes (K02586, K02588, and K02591) was observed in PS MPs/NPs + Ag NPs treatment compared to Ag NPs in the nitrogen metabolism pathway. Moreover, g-Lysobacter and g-Aquimonas were identified as biomarkers in PS MPs + Ag NPs and PS NPs + Ag NPs by LEfSe analysis. Our study sheds the light that changes of functional microorganism abundances contributed to the alteration of nitrogen transformation. Taking the particle size of plastics into account will be helpful to accurately assess the combined ecological risks of plastics and nanomaterial contaminants.
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Affiliation(s)
- Keqin Jiao
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China; Shaanxi Key Laboratory of Land Consolidation, Xi'an 710054, China
| | - Baoshan Yang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China; Shaanxi Key Laboratory of Land Consolidation, Xi'an 710054, China
| | - Hui Wang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China; Shaanxi Key Laboratory of Land Consolidation, Xi'an 710054, China.
| | - Wenxue Xu
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China; Shaanxi Key Laboratory of Land Consolidation, Xi'an 710054, China
| | - Chuanfeng Zhang
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China; Shaanxi Key Laboratory of Land Consolidation, Xi'an 710054, China
| | - Yongchao Gao
- Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Shandong Provincial Key Laboratory of Applied Microbiology, 28789 East Jingshi Road, Jinan 250103, China
| | - Wen Sun
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China; Shaanxi Key Laboratory of Land Consolidation, Xi'an 710054, China
| | - Feng Li
- School of Water Conservancy and Environment, University of Jinan, Jinan 250022, China; Shaanxi Key Laboratory of Land Consolidation, Xi'an 710054, China
| | - Dandan Ji
- College of Environmental Science and Engineering, Qilu University of Technology (Shandong Academy of Science), Jinan 250353, China
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110
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Soils and sediments host Thermoplasmata archaea encoding novel copper membrane monooxygenases (CuMMOs). THE ISME JOURNAL 2022; 16:1348-1362. [PMID: 34987183 PMCID: PMC9038741 DOI: 10.1038/s41396-021-01177-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/02/2021] [Accepted: 12/10/2021] [Indexed: 01/22/2023]
Abstract
Copper membrane monooxygenases (CuMMOs) play critical roles in the global carbon and nitrogen cycles. Organisms harboring these enzymes perform the first, and rate limiting, step in aerobic oxidation of ammonia, methane, or other simple hydrocarbons. Within archaea, only organisms in the order Nitrososphaerales (Thaumarchaeota) encode CuMMOs, which function exclusively as ammonia monooxygenases. From grassland and hillslope soils and aquifer sediments, we identified 20 genomes from distinct archaeal species encoding divergent CuMMO sequences. These archaea are phylogenetically clustered in a previously unnamed Thermoplasmatota order, herein named the Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are more similar in structure to those in Nitrososphaerales than those of bacteria, and contain all functional residues required for general monooxygenase activity. Ca. Angelarchaeales genomes are significantly enriched in blue copper proteins (BCPs) relative to sibling lineages, including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins co-located with electron transport machinery. Ca. Angelarchaeales also encode significant capacity for peptide/amino acid uptake and degradation and share numerous electron transport mechanisms with the Nitrososphaerales. Ca. Angelarchaeales are detected at high relative abundance in some of the environments where their genomes originated from. While the exact substrate specificities of the novel CuMMOs identified here have yet to be determined, activity on ammonia is possible given their metabolic and ecological context. The identification of an archaeal CuMMO outside of the Nitrososphaerales significantly expands the known diversity of CuMMO enzymes in archaea and suggests previously unaccounted organisms contribute to critical global nitrogen and/or carbon cycling functions.
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Abstract
Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N2O), a potent greenhouse gas.
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112
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Reji L, Cardarelli EL, Boye K, Bargar JR, Francis CA. Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics. THE ISME JOURNAL 2022; 16:1140-1152. [PMID: 34873295 PMCID: PMC8940955 DOI: 10.1038/s41396-021-01167-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 11/17/2021] [Accepted: 11/26/2021] [Indexed: 02/03/2023]
Abstract
The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.
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Affiliation(s)
- Linta Reji
- grid.168010.e0000000419368956Department of Earth System Science, Stanford University, Stanford, CA USA ,grid.16750.350000 0001 2097 5006Present Address: Department of Geosciences, Princeton University, Princeton, NJ USA
| | - Emily L. Cardarelli
- grid.168010.e0000000419368956Department of Earth System Science, Stanford University, Stanford, CA USA ,grid.20861.3d0000000107068890Present Address: Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Kristin Boye
- grid.445003.60000 0001 0725 7771Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - John R. Bargar
- grid.445003.60000 0001 0725 7771Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA USA
| | - Christopher A. Francis
- grid.168010.e0000000419368956Department of Earth System Science, Stanford University, Stanford, CA USA
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113
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Water-driven microbial nitrogen transformations in biological soil crusts causing atmospheric nitrous acid and nitric oxide emissions. THE ISME JOURNAL 2022; 16:1012-1024. [PMID: 34764454 PMCID: PMC8941053 DOI: 10.1038/s41396-021-01127-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 01/12/2023]
Abstract
Biological soil crusts (biocrusts) release the reactive nitrogen gases (Nr) nitrous acid (HONO) and nitric oxide (NO) into the atmosphere, but the underlying microbial process controls have not yet been resolved. In this study, we analyzed the activity of microbial consortia relevant in Nr emissions during desiccation using transcriptome and proteome profiling and fluorescence in situ hybridization. We observed that < 30 min after wetting, genes encoding for all relevant nitrogen (N) cycling processes were expressed. The most abundant transcriptionally active N-transforming microorganisms in the investigated biocrusts were affiliated with Rhodobacteraceae, Enterobacteriaceae, and Pseudomonadaceae within the Alpha- and Gammaproteobacteria. Upon desiccation, the nitrite (NO2-) content of the biocrusts increased significantly, which was not the case when microbial activity was inhibited. Our results confirm that NO2- is the key precursor for biocrust emissions of HONO and NO. This NO2- accumulation likely involves two processes related to the transition from oxygen-limited to oxic conditions in the course of desiccation: (i) a differential regulation of the expression of denitrification genes; and (ii) a physiological response of ammonia-oxidizing organisms to changing oxygen conditions. Thus, our findings suggest that the activity of N-cycling microorganisms determines the process rates and overall quantity of Nr emissions.
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114
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Saud S, Wang D, Fahad S. Improved Nitrogen Use Efficiency and Greenhouse Gas Emissions in Agricultural Soils as Producers of Biological Nitrification Inhibitors. FRONTIERS IN PLANT SCIENCE 2022; 13:854195. [PMID: 35432390 PMCID: PMC9011059 DOI: 10.3389/fpls.2022.854195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/14/2022] [Indexed: 05/13/2023]
Abstract
Based on an analysis of the current situation of nitrogen fertiliser application, it is suggested that improving the nitrogen utilisation efficiency of crops is an important means of promoting the sustainable development of agriculture and realises the zero increase in chemical fertiliser application. Nitrate loss and nitrous oxide (N2O) emissions caused by nitrification and denitrification are the main reasons for the low utilisation rate of nitrogen fertilisers. N2O is a greenhouse gas that has caused a sharp increase in global temperature. Biological nitrification inhibition refers to releasing natural compounds that inhibit nitrification from plant roots. The natural compounds released are called biological nitrification inhibitors (BNIs), which specifically inhibit the activity of microorganisms in soil nitrification. Biological nitrification inhibitors can significantly improve rice (Oryza sativa), corn (Zea mays) and other crops by 5-10%, which can increase the nitrogen utilisation rate of corn by 3.1%, and reduce greenhouse gas N2O emissions. Compared with plants that do not produce BNI, the amount of N2O released can be reduced by up to 90%. The BNI released by Brachialactone (Brachiaria humidicola) accounted for 60-90% of the total inhibition of nitrification. In summary, biological nitrification inhibitors that inhibit nitrification, improve nitrogen utilisation and crop yield, and reduce greenhouse gas emissions play an important role. This paper reviews the plants known to release BNIs, reviews the plants known to inhibit soil nitrification but with unknown BNIs and further discusses the important role of bio nitrification inhibition in agricultural systems.
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Affiliation(s)
- Shah Saud
- College of Life Sciences, Linyi University, Linyi, China
| | - Depeng Wang
- College of Life Sciences, Linyi University, Linyi, China
| | - Shah Fahad
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, China
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115
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Bahram M, Espenberg M, Pärn J, Lehtovirta-Morley L, Anslan S, Kasak K, Kõljalg U, Liira J, Maddison M, Moora M, Niinemets Ü, Öpik M, Pärtel M, Soosaar K, Zobel M, Hildebrand F, Tedersoo L, Mander Ü. Structure and function of the soil microbiome underlying N 2O emissions from global wetlands. Nat Commun 2022; 13:1430. [PMID: 35301304 PMCID: PMC8931052 DOI: 10.1038/s41467-022-29161-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 02/23/2022] [Indexed: 01/16/2023] Open
Abstract
Wetland soils are the greatest source of nitrous oxide (N2O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N2O emissions from wetland soils are poorly understood. Using in situ N2O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N2O emissions. We show that N2O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N2O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N2O.
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Affiliation(s)
- Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia. .,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Mikk Espenberg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jaan Pärn
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | | | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kuno Kasak
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jaan Liira
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Maddison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ülo Niinemets
- Institute of Agricultural & Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kaido Soosaar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Falk Hildebrand
- Quadram Institute Bioscience, Norwich, Norfolk, UK.,Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Leho Tedersoo
- College of Science, King Saud University, Riyadh, Saudi Arabia.,Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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116
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Longepierre M, Feola Conz R, Barthel M, Bru D, Philippot L, Six J, Hartmann M. Mixed Effects of Soil Compaction on the Nitrogen Cycle Under Pea and Wheat. Front Microbiol 2022; 12:822487. [PMID: 35330614 PMCID: PMC8940171 DOI: 10.3389/fmicb.2021.822487] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Soil compaction caused by highly mechanized agriculture can constrain soil microbial diversity and functioning. Physical pressure on the soil decreases macropores and thereby limits oxygen diffusion. The associated shift from aerobic to anaerobic conditions can reduce nitrification and promote denitrification processes, leading to nitrogen (N) losses and N depletion that affect plant productivity. High soil moisture content during trafficking can exacerbate the negative effects of soil compaction. However, the extent to which soil moisture amplifies the effects of compaction on the soil microbiome and its control over N cycling is not well understood. Using a controlled greenhouse experiment with two different crops (pea and wheat), we compared the effects of compaction at three different soil moisture levels on soil physicochemical properties, microbial diversity, and the abundance of specific N species and quantification of associated microbial functional groups in the N cycle. Soil compaction increased bulk density from 15% (light compaction) to 25% (severe compaction). Compaction delayed germination in both crops and reduced yield by up to 60% for pea and 40% for wheat. Compaction further induced crop-specific shifts in microbial community structures. After compaction, the relative abundance of denitrifiers increased along with increased nitrate (NO3 -) consumption and elevated nitrous oxide (N2O) concentrations in the soil pores. Conversely, the relative abundance of nitrifiers remained stable under compaction, but potentially decelerated nitrification rates, resulting in ammonium (NH4 +) accumulation in the soil. This study showed that soil compaction effects are proportional to the initial soil moisture content, which could serve as a good indicator of compaction severity on agricultural fields. However, the impact of soil compaction on crop performance and on microbial communities and functions associated with the N cycle were not necessarily aligned. These findings demonstrate that not only the soil physical properties but also various biological indicators need to be considered in order to provide more precise recommendations for developing sustainable farming systems.
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Affiliation(s)
- Manon Longepierre
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Rafaela Feola Conz
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Matti Barthel
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - David Bru
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Laurent Philippot
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Johan Six
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland
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117
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Chamkhi I, El Omari N, Balahbib A, El Menyiy N, Benali T, Ghoulam C. Is the rhizosphere a source of applicable multi-beneficial microorganisms for plant enhancement? Saudi J Biol Sci 2022; 29:1246-1259. [PMID: 35241967 PMCID: PMC8864493 DOI: 10.1016/j.sjbs.2021.09.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 01/08/2023] Open
Abstract
The plant faces different pedological and climatic challenges that influence its growth and enhancement. While, plant-microbes interactions throught the rhizosphere offer several privileges to this hotspot in the service of plant, by attracting multi-beneficial mutualistic and symbiotic microorganisms as plant growth-promoting bacteria (PGPB), archaea, mycorrhizal fungi, endophytic fungi, and others…). Currently, numerous investigations showed the beneficial effects of these microbes on growth and plant health. Indeed, rhizospheric microorganisms offer to host plants the essential assimilable nutrients, stimulate the growth and development of host plants, and induce antibiotics production. They also attributed to host plants numerous phenotypes involved in the increase the resistance to abiotic and biotic stresses. The investigations and the studies on the rhizosphere can offer a way to find a biological and sustainable solution to confront these environmental problems. Therefore, the interactions between microbes and plants may lead to interesting biotechnological applications on plant improvement and the adaptation in different climates to obtain a biological sustainable agricultures without the use of chemical fertilizers.
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Key Words
- AMF, Arbuscular Mycorrhizal Fungi
- AOA, Ammonia-Oxidizing Archaea
- BMV, Brome Mosaic Virus
- C, Carbon
- CMV, Cucumber mosaic virus
- LDH, Layered double hydroxides
- MF, Mycorrhizal fungi
- Microorganisms
- P, Phosphorus
- PAL, L-Phenylalanine Ammonia Lyase
- PCA, Phenazine-1-Carboxylic Acid
- PGPR, Plant Growth-Promoting Rhizobacteria
- POX, Peroxidase
- PPO, Polyphenol Oxidase
- Plant growth promoting microbes
- Plant-microbes interactions
- Rhizosphere
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Affiliation(s)
- Imane Chamkhi
- Geo-Biodiversity and Natural Patrimony Laboratory (GeoBio), Geophysics, Natural Patrimony Research Center (GEOPAC), Scientific Institute, Mohammed V University in Rabat, Morocco.,University Mohammed VI Polytechnic, Agrobiosciences Program, Lot 660, Hay Moulay Rachid, Benguerir, Morocco
| | - Nasreddine El Omari
- Laboratory of Histology, Embryology, and Cytogenetic, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Abdelaali Balahbib
- Laboratory of Zoology and General Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Naoual El Menyiy
- Faculty of Science, University Sidi Mohamed Ben Abdellah, Fez, Morocco
| | - Taoufiq Benali
- Environment and Health Team, Polydisciplinary Faculty of Safi, Cadi Ayyad University, Safi, Morocco
| | - Cherki Ghoulam
- University Mohammed VI Polytechnic, Agrobiosciences Program, Lot 660, Hay Moulay Rachid, Benguerir, Morocco.,Cadi Ayyad University, Faculty of Sciences and Techniques, PO Box 549, Gueliz, Marrakech,Morocco
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118
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Zhang X, Zhang X, Li L, Fu G, Liu X, Xing S, Feng H, Chen B. The toxicity of hexavalent chromium to soil microbial processes concerning soil properties and aging time. ENVIRONMENTAL RESEARCH 2022; 204:111941. [PMID: 34474034 DOI: 10.1016/j.envres.2021.111941] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 07/23/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
Chromium (Cr) pollution has attracted much attention due to its biological toxicity. However, little is known regarding Cr toxicity to soil microorganisms. The present study assesses the toxicity of Cr(VI) on two microbial processes, potential nitrification rate (PNR) and substrate-induced respiration (SIR), in a wide range of agricultural soils and detected the abundance of soil bacteria, fungi, ammonia-oxidizing bacteria and archaea. The toxicity thresholds of 10% and 50% effective concentrations (EC10 and EC50) for PNR varied by 32.18- and 38.66-fold among different soils, while for SIR they varied by 391.21- and 16.31-fold, respectively. Regression model analysis indicated that for PNR, CEC as a single factor explained 27% of the variation in EC10, with soil clay being the key factor explaining 47.3% of the variation in EC50. For SIR, organic matter and pH were found to be the most vital predictors for EC10 and EC50, explaining 34% and 61.1% of variation, respectively. In addition, extended aging time was found to significantly attenuate the toxicity of Cr on PNR. SIR was mainly driven by total bacteria rather than fungi, while PNR was driven by both AOA and AOB. These results were helpful in deriving soil Cr toxicity threshold based on microbial processes, and provided a theoretical foundation for ecological risk assessments and establishing a soil environmental quality criteria for Cr.
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Affiliation(s)
- Xuemeng Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Linfeng Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Earth Sciences and Resources, China University of Geosciences, Beijing, 100083, China
| | - Gengxue Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Earth Sciences and Resources, China University of Geosciences, Beijing, 100083, China
| | - Xiaoying Liu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Earth Sciences and Resources, China University of Geosciences, Beijing, 100083, China
| | - Shuping Xing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyan Feng
- School of Earth Sciences and Resources, China University of Geosciences, Beijing, 100083, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Changes in Ammonia-Oxidizing Archaea and Bacterial Communities and Soil Nitrogen Dynamics in Response to Long-Term Nitrogen Fertilization. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19052732. [PMID: 35270425 PMCID: PMC8910298 DOI: 10.3390/ijerph19052732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 11/16/2022]
Abstract
Ammonia oxidizing archaea (AOA) and bacteria (AOB) mediate a crucial step in nitrogen (N) metabolism. The effect of N fertilizer rates on AOA and AOB communities is less studied in the wheat-fallow system from semi-arid areas. Based on a 17-year wheat field experiment, we explored the effect of five N fertilizer rates (0, 52.5, 105, 157.5, and 210 kg ha-1 yr-1) on the AOA and AOB community composition. This study showed that the grain yield of wheat reached the maximum at 105 kg N ha-1 (49% higher than control), and no further significant increase was observed at higher N rates. With the increase of N, AOA abundance decreased in a regular trend from 4.88 × 107 to 1.05 × 107 copies g-1 dry soil, while AOB abundance increased from 3.63 × 107 up to a maximum of 8.24 × 107 copies g-1 dry soil with the N105 treatment (105 kg N ha-1 yr-1). Application rates of N fertilizer had a more significant impact on the AOB diversity than on AOA diversity, and the highest AOB diversity was found under the N105 treatment in this weak alkaline soil. The predominant phyla of AOA and AOB were Thaumarchaeota and Proteobacteria, respectively, and higher N treatment (N210) resulted in a significant decrease in the relative abundance of genus Nitrosospira. In addition, AOA and AOB communities were significantly associated with grain yield of wheat, soil potential nitrification activity (PNA), and some soil physicochemical parameters such as pH, NH4-N, and NO3-N. Among them, soil moisture was the most influential edaphic factor for structuring the AOA community and NH4-N for the AOB community. Overall, 105 kg N ha-1 yr-1 was optimum for the AOB community and wheat yield in the semi-arid area.
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Zhang K, Li M, Yan Z, Li M, Kang E, Yan L, Zhang X, Li Y, Wang J, Yang A, Niu Y, Kang X. Changes in precipitation regime lead to acceleration of the N cycle and dramatic N 2O emission. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:152140. [PMID: 34864035 DOI: 10.1016/j.scitotenv.2021.152140] [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: 08/23/2021] [Revised: 11/03/2021] [Accepted: 11/28/2021] [Indexed: 06/13/2023]
Abstract
Alpine meadows on the Qinghai-Tibetan Plateau are sensitive to climate change. The precipitation regime in this region has undergone major changes, "repackaging" precipitation from more frequent, smaller events to less frequent, larger events. Nitrous oxide (N2O) is an important indicator of responses to global change in alpine meadow ecosystems. However, little information is available describing the mechanisms driving the response of N2O emissions to changes in the precipitation regime. In this study, a manipulative field experiment was conducted to investigate N2O flux, soil properties, enzyme activity, and gene abundance in response to severe and moderate changes in precipitation regime over two years. Severe changes in precipitation regime led to a 12.6-fold increase in N2O fluxes (0.0068 ± 0.0018 mg m-2 h-1) from Zoige alpine meadows relative to natural conditions (0.0005 ± 0.0029 mg m-2 h-1). In addition, severe changes in precipitation regime significantly suppressed the activities of leucine amino peptidase (LAP) and peroxidase (PEO), affected ecoenzymatic stoichiometry, and increased the abundances of gdhA, narI and nirK genes, which significantly promoted organic nitrogen (N) decomposition, denitrification, and anammox processes. The increase in abundance of these genes could be ascribed to changes in the abundance of several dominant bacterial taxa (i.e., Actinobacteria and Proteobacteria) as a result of the altered precipitation regime. Decreases in nitrate and soil moisture caused by severe changes in precipitation may exacerbate N limitation and water deficit, lead to a suppression of soil enzyme activity, and change the structure of microorganism community. The N cycle of the alpine meadow ecosystem may accelerate by increasing the abundance of key N functional genes. This would, in turn, lead to increased N2O emission. This study provided insights into how precipitation regimes changes affect N cycling, and may also improve prediction of N2O fluxes in response to changes in precipitation regime.
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Affiliation(s)
- Kerou Zhang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, Sichuan, China
| | - Mingxu Li
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhongqing Yan
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, Sichuan, China
| | - Meng Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, Sichuan, China
| | - Enze Kang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, Sichuan, China
| | - Liang Yan
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, Sichuan, China
| | - Xiaodong Zhang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, Sichuan, China
| | - Yong Li
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, Sichuan, China
| | - Jinzhi Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, Sichuan, China
| | - Ao Yang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, Sichuan, China
| | - Yuechuan Niu
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoming Kang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; Beijing Key Laboratory of Wetland Services and Restoration, Beijing 100091, China; Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, 624500, Sichuan, China.
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Laparoscopic sleeve gastrectomy for morbid obesity improves gut microbiota balance, increases colonic mucosal-associated invariant T cells and decreases circulating regulatory T cells. Surg Endosc 2022; 36:7312-7324. [PMID: 35182212 DOI: 10.1007/s00464-022-09122-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: 12/11/2021] [Accepted: 02/07/2022] [Indexed: 01/06/2023]
Abstract
BACKGROUND Laparoscopic sleeve gastrectomy (LSG) for morbid obesity may improve gut microbiota balance and decrease chronic inflammation. This study examines the changes in gut microbiota and immune environment, including mucosal-associated invariant T cells (MAIT cells) and regulatory T cells (Treg cells) caused by LSG. METHODS Ten morbidly obese patients underwent LSG at our institution between December 2018 and March 2020. Flow cytometry for Th1/Th2/Th17 cells, Treg cells and MAIT cells in peripheral blood and colonic mucosa and 16S rRNA analysis of gut microbiota were performed preoperatively and then 12 months postoperatively. RESULTS Twelve months after LSG, the median percent total weight loss was 30.3% and the median percent excess weight loss was 66.9%. According to laboratory data, adiponectin increased, leptin decreased, and chronic inflammation improved after LSG. In the gut microbiota, Bacteroidetes and Fusobacteria increased after LSG, and indices of alpha diversity increased after LSG. In colonic mucosa, the frequency of MAIT cells increased after LSG. In peripheral blood, the frequency of Th1 cells and effector Treg cells decreased after LSG. CONCLUSIONS After LSG for morbid obesity, improvement in chronic inflammation in obesity is suggested by change in the constituent bacterial species, increase in the diversity of gut microbiota, increase in MAIT cells in the colonic mucosa, and decrease in effector Treg cells in the peripheral blood.
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Shi B, Cheng C, Zhang Y, Du Z, Zhu L, Wang J, Wang J, Li B. Effects of 3,6-dichlorocarbazole on microbial ecology and its degradation in soil. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127315. [PMID: 34601412 DOI: 10.1016/j.jhazmat.2021.127315] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/18/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
The emerging contaminants polyhalogenated carbazoles (PHCZs) have been verified to be present in soils and sediments globally, and they show dioxin-like toxicity. However, there is a lack of soil ecological risk assessments on PHCZs despite their high detection rate and concentration in soils. The present study investigated the degradation and soil microbial influence of 3,6-dichlorocarbazole (3,6-DCCZ, a frequently detected PHCZ) in soil. The results showed that the half-lives of 3,6-DCCZ at concentrations of 0.100 mg/kg and 1.00 mg/kg were 7.75 d and 16.73 d, respectively. We found that 3,6-DCCZ was transformed into 3-chlorocarbazole (3-CCZ) by dehalogenation in soil. Additionally, intermediate products with higher molecular weights were detected, presumably because the -H on the carbazole ring was replaced by -CH3, -CH2-O-CH3, or -CH2-O-CH2CH3. 3,6-DCCZ exposure slightly increased the soil bacterial abundance and diversity and clearly changed the soil bacterial community structure. Through a comprehensive analysis of FAPROTAX, functional gene qPCR and soil enzyme tests, we concluded that 3,6-DCCZ exposure inhibited nitrification and nitrogen fixation but promoted denitrification, carbon dioxide fixation and hydrocarbon degradation processes in soil. This study provides valuable data for clarifying the PHCZ ecological risk in soil.
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Affiliation(s)
- Baihui Shi
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian 271018, PR China.
| | - Chao Cheng
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian 271018, PR China.
| | - Yuanqing Zhang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian 271018, PR China.
| | - Zhongkun Du
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian 271018, PR China.
| | - Lusheng Zhu
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian 271018, PR China.
| | - Jun Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian 271018, PR China.
| | - Jinhua Wang
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian 271018, PR China.
| | - Bing Li
- College of Resources and Environment, Shandong Agricultural University, Key Laboratory of Agricultural Environment in Universities of Shandong, 61 Daizong Road, Taian 271018, PR China.
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Huérfano X, Estavillo JM, Torralbo F, Vega-Mas I, González-Murua C, Fuertes-Mendizábal T. Dimethylpyrazole-based nitrification inhibitors have a dual role in N 2O emissions mitigation in forage systems under Atlantic climate conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150670. [PMID: 34610408 DOI: 10.1016/j.scitotenv.2021.150670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/13/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
Nitrogen fertilization is the most important factor increasing nitrous oxide (N2O) emissions from agriculture, which is a powerful greenhouse gas. These emissions are mainly produced by the soil microbial processes of nitrification and denitrification, and the application of nitrification inhibitors (NIs) together with an ammonium-based fertilizer has been proved as an efficient way to decrease them. In this work the NIs dimethylpyrazole phosphate (DMPP) and dimethylpyrazole succinic acid (DMPSA) were evaluated in a temperate grassland under environmental changing field conditions in terms of their efficiency reducing N2O emissions and their effect on the amount of nitrifying and denitrifying bacterial populations responsible of these emissions. The stimulation of nitrifying bacteria induced by the application of ammonium sulphate as fertilizer was efficiently avoided by the application of both DMPP and DMPSA whatever the soil water content. The denitrifying bacteria population capable of reducing N2O up to N2 was also enhanced by both NIs provided that sufficiently high soil water conditions and low nitrate content were occurring. Therefore, both NIs showed the capacity to promote the denitrification process up to N2 as a mechanism to mitigate N2O emissions. DMPSA proved to be a promising NI, since it showed a more significant effect than DMPP in decreasing N2O emissions and increasing ryegrass yield.
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Affiliation(s)
- Ximena Huérfano
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain
| | - José M Estavillo
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain
| | - Fernando Torralbo
- Division of Plant Science, University of Missouri, Columbia, MO 65201, USA
| | - Izargi Vega-Mas
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain
| | - Carmen González-Murua
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain
| | - Teresa Fuertes-Mendizábal
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Apdo. 644, E-48080 Bilbao, Spain.
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Li J, Yang H, Qin K, Wei L, Xia X, Zhu F, Tan X, Xue C, Zhao Q. Effect of pig manure-derived sulfadiazine on species distribution and bioactivities of soil ammonia-oxidizing microorganisms after fertilization. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:126994. [PMID: 34481384 DOI: 10.1016/j.jhazmat.2021.126994] [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: 06/14/2021] [Revised: 08/07/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
To evaluate the effect of pig manure-derived sulfadiazine (SDZ) on the species distribution and bioactivities of ammonia-oxidizing microorganisms (AOMs), ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and complete ammonia oxidizer (comammox) within the soil were investigated pre- and post-fertilization. Kinetic modeling and linear regression results demonstrated that the DT50 value of different SDZ fractions under initial SDZ concentrations of 50 and 100 mg·kg-1 exhibited the following trend: total SDZ>CaCl2-extractable SDZ>MeOH-extractable SDZ, whereas their inhibiting effect on AOMs showed an opposite trend. qPCR analysis suggested that comammox was the predominant ammonia oxidizer in soils regardless of SDZ addition, accounting for as much as 77.2-94.7% of the total amoA, followed by AOA (5.3-22.5%), whereas AOB (<0.5%) was the lowest. The SDZ exhibited a significant effect on the AOM abundance. Specifically, SDZ exerted the highest inhibitory effect on comammox growth, followed by AOA, whereas negligible for AOB. The community diversity of AOMs within the pig manure-fertilized soils was affected by SDZ, and AOA Nitrososphaera cluster 3 played a key role in potential ammonia oxidation capacity (PAO) maintenance. This study provides new insights into the inhibition mechanisms of pig manure-derived antibiotics on AOMs within the fertilized soil.
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Affiliation(s)
- Jianju Li
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Haizhou Yang
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kena Qin
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Liangliang Wei
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Xinhui Xia
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Fengyi Zhu
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xuefei Tan
- College of Materials and Chemical Engineering, Heilongjiang Institute of Technology, Harbin 100050, China
| | - Chonghua Xue
- Beijing Advanced Innovation Center for Future Urban Design, Beijing University of Civil Engineering and Architecture, Beijing 100044, China
| | - Qingliang Zhao
- State Key Laboratory of Urban Water Resources and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
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Ding L, Zhou J, Li Q, Tang J, Chen X. Effects of Land-Use Type and Flooding on the Soil Microbial Community and Functional Genes in Reservoir Riparian Zones. MICROBIAL ECOLOGY 2022; 83:393-407. [PMID: 33893533 DOI: 10.1007/s00248-021-01746-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Ecological processes (e.g., nutrient cycling) in riparian zones are often affected by land-use type and flooding. The extent to which land-use types and flooding conditions affect soil microorganisms and their ecological functions in riparian zones is not well known. By using high-throughput sequencing and quantitative PCR (q-PCR), we tested the effects of three land-use types (i.e., forest, wetland, and grassland) and two flooding conditions (i.e., landward locations and waterward locations within the land-use types) on soil microbial communities and microbial functional genes in the riparian zones of a reservoir. Land-use type but not flooding significantly affected soil microbial community composition at the phylum level, while both land-use type and flooding significantly affected the orders Nitrosotaleales and Nitrososphaerales. Alpha diversity was higher in the wetland and forest regardless of flooding conditions. Functional gene abundance differed among the three land-use types. Archaeal amoA (AOA) and nirS genes were more abundant in the wetland than in the grassland or forest. Bacterial amoA (AOB), nirK, nirS, and nosZ genes were more abundant in the waterward location than in the landward location but only in the wetland. Soil pH, moisture, and concentrations of soil organic matter and total soil nitrogen were significantly associated with the composition of archaeal and bacterial communities as well as with their gene abundance. This study revealed that soil microorganisms putatively involved in nitrogen cycling in riparian zones were more affected by land-use type than flooding.
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Affiliation(s)
- Lilian Ding
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Jingyi Zhou
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Qiyao Li
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China
| | - Jianjun Tang
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China.
| | - Xin Chen
- College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang Province, China.
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Pan J, Liu Y, Yang Y, Cheng Z, Lan X, Hu W, Shi G, Zhang Q, Feng H. Slope aspect determines the abundance and composition of nitrogen-cycling microbial communities in an alpine ecosystem. Environ Microbiol 2022; 24:3598-3611. [PMID: 35048487 DOI: 10.1111/1462-2920.15900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 01/11/2022] [Indexed: 11/28/2022]
Abstract
Slope aspect is an important topographic feature that can influence local environmental conditions. While strong effects of slope aspect on aboveground and belowground communities have been frequently elucidated, how slope aspect affects soil nitrogen (N) cycling microbes remains unclear. Here, we characterized the communities of soil N-cycling microbes on south- and north-facing slopes in an alpine ecosystem, by quantifying (qPCR) and high-throughput sequencing six genes involved in N-fixation (nifH), nitrification (archaeal and bacterial amoA) and denitrification (nirK, nirS and nosZ). We found that the abundance, diversity and community composition of major N-cycling microbes differed dramatically between the two slope aspects, and these variances could be well explained by the aspect-driven differences in environmental conditions, especially soil temperature and moisture. The response patterns of different N-cycling groups to slope aspect were much inconsistent, especially for those with similar functions (i.e. ammonia-oxidizing archaea vs. bacteria, nirK- vs. nirS-reducers), indicating strong niche differentiation between these counterparts. We also observed strong preferences and distinct co-occurrence patterns of N-cycling microbial taxa for the two slope aspects. These findings highlight the importance of slope aspect in determining the abundance, species distribution and community structure of N-cycling microbes, and consequently influencing N-cycling processes and ecosystem functioning. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jianbin Pan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yongjun Liu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.,State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730000, China
| | - Yue Yang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhongxia Cheng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaomei Lan
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Weigang Hu
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Guoxi Shi
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui, 741000, China
| | - Qi Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Huyuan Feng
- School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.,Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China
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Hu J, Richwine JD, Keyser PD, Li L, Yao F, Jagadamma S, DeBruyn JM. Ammonia-oxidizing bacterial communities are affected by nitrogen fertilization and grass species in native C 4 grassland soils. PeerJ 2022; 9:e12592. [PMID: 35003922 PMCID: PMC8684740 DOI: 10.7717/peerj.12592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background Fertilizer addition can contribute to nitrogen (N) losses from soil by affecting microbial populations responsible for nitrification. However, the effects of N fertilization on ammonia oxidizing bacteria under C4 perennial grasses in nutrient-poor grasslands are not well studied. Methods In this study, a field experiment was used to assess the effects of N fertilization rate (0, 67, and 202 kg N ha−1) and grass species (switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii)) on ammonia-oxidizing bacterial (AOB) communities in C4 grassland soils using quantitative PCR, quantitative reverse transcription-PCR, and high-throughput amplicon sequencing of amoA genes. Results Nitrosospira were dominant AOB in the C4 grassland soil throughout the growing season. N fertilization rate had a stronger influence on AOB community composition than C4 grass species. Elevated N fertilizer application increased the abundance, activity, and alpha-diversity of AOB communities as well as nitrification potential, nitrous oxide (N2O) emission and soil acidity. The abundance and species richness of AOB were higher under switchgrass compared to big bluestem. Soil pH, nitrate, nitrification potential, and N2O emission were significantly related to the variability in AOB community structures (p < 0.05).
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Affiliation(s)
- Jialin Hu
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jonathan D Richwine
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Patrick D Keyser
- Department of Forestry, Wildlife and Fisheries, University of Tennessee, Knoxville, TN, United States of America
| | - Lidong Li
- Agroecosystem Management Research Unit, USDA-Agricultural Research Service, Lincoln, NE, United States of America
| | - Fei Yao
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Sindhu Jagadamma
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN, United States of America
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Romdhane S, Spor A, Banerjee S, Breuil MC, Bru D, Chabbi A, Hallin S, van der Heijden MGA, Saghai A, Philippot L. Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity. ENVIRONMENTAL MICROBIOME 2022; 17:1. [PMID: 34991714 PMCID: PMC8740439 DOI: 10.1186/s40793-021-00396-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 12/23/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. RESULTS We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. CONCLUSIONS Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification.
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Affiliation(s)
- Sana Romdhane
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - Aymé Spor
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - Samiran Banerjee
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Biological Sciences, North Dakota State University, Fargo, 58102, USA
| | - Marie-Christine Breuil
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - David Bru
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France
| | - Abad Chabbi
- ECOSYS, UMR INRAE, AgroParisTech, Thiverval-Grignon, France
- CNRS, Institute of Ecology and Environmental Sciences-Paris (iEES-Paris, UMR Sorbonne Université, CNRS, INRAE), Thiverval-Grignon, France
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marcel G A van der Heijden
- Agroscope, Plant-Soil Interactions Group, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Aurélien Saghai
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Laurent Philippot
- Department of Agroecology, University Bourgogne Franche Comte, INRAE, AgroSup Dijon, Dijon, France.
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129
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Farooq MS, Uzair M, Maqbool Z, Fiaz S, Yousuf M, Yang SH, Khan MR. Improving Nitrogen Use Efficiency in Aerobic Rice Based on Insights Into the Ecophysiology of Archaeal and Bacterial Ammonia Oxidizers. FRONTIERS IN PLANT SCIENCE 2022; 13:913204. [PMID: 35769304 PMCID: PMC9234532 DOI: 10.3389/fpls.2022.913204] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/16/2022] [Indexed: 05/22/2023]
Abstract
The abundance and structural composition of nitrogen (N) transformation-related microbial communities under certain environmental conditions provide sufficient information about N cycle under different soil conditions. This study aims to explore the major challenge of low N use efficiency (NUE) and N dynamics in aerobic rice systems and reveal the agronomic-adjustive measures to increase NUE through insights into the ecophysiology of ammonia oxidizers. Water-saving practices, like alternate wetting and drying (AWD), dry direct seeded rice (DDSR), wet direct seeding, and saturated soil culture (SSC), have been evaluated in lowland rice; however, only few studies have been conducted on N dynamics in aerobic rice systems. Biological ammonia oxidation is majorly conducted by two types of microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). This review focuses on how diversified are ammonia oxidizers (AOA and AOB), whose factors affect their activities and abundance under different soil conditions. It summarizes findings on pathways of N cycle, rationalize recent research on ammonia oxidizers in N-cycle, and thereby suggests adjustive agronomic measures to reduce N losses. This review also suggests that variations in soil properties significantly impact the structural composition and abundance of ammonia oxidizers. Nitrification inhibitors (NIs) especially nitrapyrin, reduce the nitrification rate and inhibit the abundance of bacterial amoA without impacting archaeal amoA. In contrast, some NIs confine the hydrolysis of synthetic N and, therefore, keep low NH4 +-N concentrations that exhibit no or very slight impact on ammonia oxidizers. Variations in soil properties are more influential in the community structure and abundance of ammonia oxidizers than application of synthetic N fertilizers and NIs. Biological nitrification inhibitors (BNIs) are natural bioactive compounds released from roots of certain plant species, such as sorghum, and could be commercialized to suppress the capacity of nitrifying soil microbes. Mixed application of synthetic and organic N fertilizers enhances NUE and plant N-uptake by reducing ammonia N losses. High salt concentration promotes community abundance while limiting the diversity of AOB and vice versa for AOA, whereas AOA have lower rate for potential nitrification than AOB, and denitrification accounts for higher N2 production. Archaeal abundance, diversity, and structural composition change along an elevation gradient and mainly depend on various soil factors, such as soil saturation, availability of NH4 +, and organic matter contents. Microbial abundance and structural analyses revealed that the structural composition of AOA was not highly responsive to changes in soil conditions or N amendment. Further studies are suggested to cultivate AOA and AOB in controlled-environment experiments to understand the mechanisms of AOA and AOB under different conditions. Together, this evaluation will better facilitate the projections and interpretations of ammonia oxidizer community structural composition with provision of a strong basis to establish robust testable hypotheses on the competitiveness between AOB and AOA. Moreover, after this evaluation, managing soils agronomically for potential utilization of metabolic functions of ammonia oxidizers would be easier.
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Affiliation(s)
- Muhammad Shahbaz Farooq
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Zubaira Maqbool
- Institute of Soil Science, Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
- *Correspondence: Seung Hwan Yang,
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
- Muhammad Ramzan Khan,
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130
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Joos L, De Tender C. Soil under stress: The importance of soil life and how it is influenced by (micro)plastic pollution. Comput Struct Biotechnol J 2022; 20:1554-1566. [PMID: 35422972 PMCID: PMC8991314 DOI: 10.1016/j.csbj.2022.03.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/31/2022] [Accepted: 03/31/2022] [Indexed: 11/03/2022] Open
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131
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Asad NI, Tremblay J, Dozois J, Mukula E, L'Espérance E, Constant P, Yergeau E. Predictive microbial-based modelling of wheat yields and grain baking quality across a 500km transect in Québec. FEMS Microbiol Ecol 2021; 97:6458360. [PMID: 34888659 DOI: 10.1093/femsec/fiab160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/07/2021] [Indexed: 11/14/2022] Open
Abstract
Crops yield and quality are difficult to predict using soil physico-chemical parameters. Because of their key roles in nutrient cycles, we hypothesized that there is an untapped predictive potential in the soil microbial communities. To test our hypothesis, we sampled soils across 80 wheat fields of the province of Quebec at the beginning of the growing season in May-June. We used a wide array of methods to characterize the microbial communities, their functions, and activities, including: 1) amplicon sequencing, 2) real-time PCR quantification, and 3) community-level substrate utilization. We also measured grain yield and quality at the end of the growing season, and key soil parameters at sampling. The diversity of fungi, the abundance of nitrification genes, and the use of specific organic carbon sources were often the best predictors for wheat yield and grain quality. Using 11 or less parameters, we were able to explain 64 to 90% of the variation in wheat yield and grain and flour quality across the province of Quebec. Microbial-based regression models outperformed basic soil-based models for predicting wheat quality indicators. Our results suggest that the measurement of microbial parameters early in the season could help predict accurately grain quality and quantity.
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Affiliation(s)
- Numan Ibne Asad
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Julien Tremblay
- National Research Council Canada, Energy Mining and Environment, 6100 Royalmount Ave., Montreal, QC, H4P 2R2, Canada
| | - Jessica Dozois
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Eugenie Mukula
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Emmy L'Espérance
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Philippe Constant
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Etienne Yergeau
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
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132
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Marushchak ME, Kerttula J, Diáková K, Faguet A, Gil J, Grosse G, Knoblauch C, Lashchinskiy N, Martikainen PJ, Morgenstern A, Nykamb M, Ronkainen JG, Siljanen HMP, van Delden L, Voigt C, Zimov N, Zimov S, Biasi C. Thawing Yedoma permafrost is a neglected nitrous oxide source. Nat Commun 2021; 12:7107. [PMID: 34876586 PMCID: PMC8651752 DOI: 10.1038/s41467-021-27386-2] [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: 03/12/2021] [Accepted: 11/15/2021] [Indexed: 11/21/2022] Open
Abstract
In contrast to the well-recognized permafrost carbon (C) feedback to climate change, the fate of permafrost nitrogen (N) after thaw is poorly understood. According to mounting evidence, part of the N liberated from permafrost may be released to the atmosphere as the strong greenhouse gas (GHG) nitrous oxide (N2O). Here, we report post-thaw N2O release from late Pleistocene permafrost deposits called Yedoma, which store a substantial part of permafrost C and N and are highly vulnerable to thaw. While freshly thawed, unvegetated Yedoma in disturbed areas emit little N2O, emissions increase within few years after stabilization, drying and revegetation with grasses to high rates (548 (133–6286) μg N m−2 day−1; median with (range)), exceeding by 1–2 orders of magnitude the typical rates from permafrost-affected soils. Using targeted metagenomics of key N cycling genes, we link the increase in in situ N2O emissions with structural changes of the microbial community responsible for N cycling. Our results highlight the importance of extra N availability from thawing Yedoma permafrost, causing a positive climate feedback from the Arctic in the form of N2O emissions. During permafrost thaw, nitrogen can be released as the greenhouse gas nitrous oxide, but the magnitude of this flux is unknown. Nitrous oxide emissions from ice-rich permafrost deposits are reported here, showing that emissions increase after thawing and stabilization and could represent an unappreciated positive climate feedback in the Arctic.
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Affiliation(s)
- M E Marushchak
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland. .,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
| | - J Kerttula
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - K Diáková
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland.,Department of Soil Biogeochemistry, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - A Faguet
- Trofimuk Institute of Petroleum Geology and Geophysics, Novosibirsk, Russia
| | - J Gil
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland.,Department of Integrative Biology, Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, USA
| | - G Grosse
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany.,Institute of Geosciences, University of Potsdam, Potsdam, Germany
| | - C Knoblauch
- Institute of Soil Science, Universität Hamburg, Hamburg, Germany.,Center for Earth System Research and Sustainability, Universität Hamburg, Hamburg, Germany
| | - N Lashchinskiy
- Trofimuk Institute of Petroleum Geology and Geophysics, Novosibirsk, Russia.,Central Siberian Botanical Garden, Novosibirsk, Russia
| | - P J Martikainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - A Morgenstern
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - M Nykamb
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - J G Ronkainen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - H M P Siljanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland.,Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - L van Delden
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - C Voigt
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland.,Department of Geography, University of Montreal, Montreal, QC, Canada
| | - N Zimov
- North-East Scientific Station, Pacific Institute for Geography, Far-East Branch, Russian Academy of Sciences, Cherskii, Russia
| | - S Zimov
- North-East Scientific Station, Pacific Institute for Geography, Far-East Branch, Russian Academy of Sciences, Cherskii, Russia
| | - C Biasi
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
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133
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Full Genome Sequence of a Methanomassiliicoccales Representative Enriched from Peat Soil. Microbiol Resour Announc 2021; 10:e0044321. [PMID: 34854727 PMCID: PMC8638594 DOI: 10.1128/mra.00443-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The full genome of a Methanomassiliicoccales strain, U3.2.1, was obtained from enrichment cultures of percolation fen peat soil under methanogenic conditions, with methanol and hydrogen as the electron acceptor and donor, respectively. Metagenomic assembly of combined long-read and short-read sequences resulted in a 1.51-Mbp circular genome.
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134
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Destan E, Yuksel B, Tolar BB, Ayan E, Deutsch S, Yoshikuni Y, Wakatsuki S, Francis CA, DeMirci H. Structural insights into bifunctional thaumarchaeal crotonyl-CoA hydratase and 3-hydroxypropionyl-CoA dehydratase from Nitrosopumilus maritimus. Sci Rep 2021; 11:22849. [PMID: 34819551 PMCID: PMC8613188 DOI: 10.1038/s41598-021-02180-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/08/2021] [Indexed: 11/08/2022] Open
Abstract
The ammonia-oxidizing thaumarchaeal 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle is one of the most energy-efficient CO2 fixation cycles discovered thus far. The protein encoded by Nmar_1308 (from Nitrosopumilus maritimus SCM1) is a promiscuous enzyme that catalyzes two essential reactions within the thaumarchaeal 3HP/4HB cycle, functioning as both a crotonyl-CoA hydratase (CCAH) and 3-hydroxypropionyl-CoA dehydratase (3HPD). In performing both hydratase and dehydratase activities, Nmar_1308 reduces the total number of enzymes necessary for CO2 fixation in Thaumarchaeota, reducing the overall cost for biosynthesis. Here, we present the first high-resolution crystal structure of this bifunctional enzyme with key catalytic residues in the thaumarchaeal 3HP/4HB pathway.
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Affiliation(s)
- Ebru Destan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Busra Yuksel
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, CA, 94305, USA
| | - Esra Ayan
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey
| | - Sam Deutsch
- Nutcracker Therapeutics, Inc 5858 Horton Street, Suite 540, Emeryville, CA, 94608, USA
| | - Yasuo Yoshikuni
- The US Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, Palo Alto, CA, 94305, USA.
- Biosciences Division, SLAC National Laboratory, Menlo Park, CA, 94025, USA.
| | | | - Hasan DeMirci
- Department of Molecular Biology and Genetics, Koc University, 34450, Istanbul, Turkey.
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA, 94025, USA.
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135
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Saghaï A, Banjeree S, Degrune F, Edlinger A, García-Palacios P, Garland G, van der Heijden MGA, Herzog C, Maestre FT, Pescador DS, Philippot L, Rillig MC, Romdhane S, Hallin S. Diversity of archaea and niche preferences among putative ammonia-oxidizing Nitrososphaeria dominating across European arable soils. Environ Microbiol 2021; 24:341-356. [PMID: 34796612 DOI: 10.1111/1462-2920.15830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 08/28/2021] [Accepted: 10/27/2021] [Indexed: 01/04/2023]
Abstract
Archaeal communities in arable soils are dominated by Nitrososphaeria, a class within Thaumarchaeota comprising all known ammonia-oxidizing archaea (AOA). AOA are key players in the nitrogen cycle and defining their niche specialization can help predicting effects of environmental change on these communities. However, hierarchical effects of environmental filters on AOA and the delineation of niche preferences of nitrososphaerial lineages remain poorly understood. We used phylogenetic information at fine scale and machine learning approaches to identify climatic, edaphic and geomorphological drivers of Nitrososphaeria and other archaea along a 3000 km European gradient. Only limited insights into the ecology of the low-abundant archaeal classes could be inferred, but our analyses underlined the multifactorial nature of niche differentiation within Nitrososphaeria. Mean annual temperature, C:N ratio and pH were the best predictors of their diversity, evenness and distribution. Thresholds in the predictions could be defined for C:N ratio and cation exchange capacity. Furthermore, multiple, independent and recent specializations to soil pH were detected in the Nitrososphaeria phylogeny. The coexistence of widespread ecophysiological differences between closely related soil Nitrososphaeria highlights that their ecology is best studied at fine phylogenetic scale.
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Affiliation(s)
- Aurélien Saghaï
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Florine Degrune
- Institute of Biology, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Anna Edlinger
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gina Garland
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Soil Quality and Use Group, Agroscope, Zurich, Switzerland.,Department of Environmental System Sciences, Soil Resources Group, ETH Zurich, Zurich, Switzerland
| | - Marcel G A van der Heijden
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Chantal Herzog
- Plant-Soil Interactions Group, Agroscope, Zurich, Switzerland.,Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Alicante, Spain.,Departamento de Ecología, Universidad de Alicante, Alicante, Spain
| | - David S Pescador
- Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Escuela Superior de Ciencias Experimentales y Tecnología, Móstoles, Spain
| | - Laurent Philippot
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Matthias C Rillig
- Institute of Biology, Freie Universität Berlin, Berlin, Germany.,Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany
| | - Sana Romdhane
- Department of Agroecology, University of Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Dijon, France
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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136
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Yuan D, Zheng L, Tan Q, Wang X, Xing Y, Wang H, Wang S, Zhu G. Comammox activity dominates nitrification process in the sediments of plateau wetland. WATER RESEARCH 2021; 206:117774. [PMID: 34757282 DOI: 10.1016/j.watres.2021.117774] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
The recent discovery of complete ammonia oxidation (comammox) has increased our understanding of nitrification. Although comammox has been shown to play an important role in plain wetland ecosystems, studies of comammox contribution are still limited in plateau wetland ecosystems. Here, we analyzed the abundance, activity, community and biogeochemical mechanisms of the comammox bacteria in Yunnan-kweichow and Qinghai-Tibet plateau wetlands from elevations of 1000-5000 m. Comammox bacteria were widely distributed in all 16 sediment samples with abundances higher than 0.96 ± 0.26 × 107 copies g-1 (n = 16). Comammox showed high activity (1.18 ± 0.17 to 1.98 ± 0.08 mg N kg-1 d-1) at high-elevation (3000-5000 m) and dominated the nitrification process (activity contribution: 37.20 - 60.62%). The activity contribution of ammonia-oxidizing bacteria (1.07 ± 0.08 to 2.79 ± 0.35 mg N kg-1 d-1) dominated the nitrification process (44.55 - 64.15%) in low-elevation (1000-3000 m) samples. All detected comammox Nitrospira belonged to clade A, while clade B was not detected. Elevation always had a strongest effect on key comammox species. Thus, we infer that elevation may drive the high relative abundance of the species Candidatus Nitrospira nitrificans (avg. 12.40%) and the low relative abundance of the species Nitrospira sp. SG-bin2 (avg. 4.75%) in high-elevation samples that showed a high comammox activity (avg. 1.62 mg N kg-1 d-1) and high contribution (avg. 46.08%) to the nitrification process. These results indicate that comammox may be an important and currently underestimated microbial nitrification process in plateau wetland ecosystems.
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Affiliation(s)
- Dongdan Yuan
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Lei Zheng
- College of Water Sciences, Beijing Normal University, Beijing 100875, China.
| | - Qiuyang Tan
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Xue Wang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Yuzi Xing
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Huipeng Wang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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137
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Yao T, Liu L, Tan S, Li H, Liu X, Zeng A, Pan L, Li X, Bai L, Liu K, Xing B. Can the multi-walled carbon nanotubes be used to alleviate the phytotoxicity of herbicides in soils? CHEMOSPHERE 2021; 283:131304. [PMID: 34467944 DOI: 10.1016/j.chemosphere.2021.131304] [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: 04/29/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
Herbicides are commonly used globally. However, residual herbicides in soils for ages often result in phytotoxicity and serious yield loss to subsequent crops. In this paper, the multi-walled carbon nanotubes (MWCNTs) were utilized to amend the herbicide polluted soil, and the adsorption performance of herbicides to MWCNTs amended soil was studied. Results indicate efficient alleviation of herbicide-induced phytotoxicity to rice and tobacco due to MWCNTs amendment. When 0.4% MWCNTs were applied, the concentration of sulfentrazone that inhibited the same rice height by 50% (IC50) increased to more than 3 times that of pure soil. When the MWCNTs were used to alleviate the phytotoxicity of quinclorac to tobacco, the MWCNTs not only alleviated the phytotoxicity of quinclorac but also promoted the growth of tobacco. The MWCNTs amended soil significantly increased the adsorption of herbicide to soil than biochar. The soil microbial analysis shows that MWCNTs had no significant effect on soil microbial community diversity, but the long-term exposure to MWCNTs could change the structure of the soil microbial community. Above all, our results highlighted the potential implication of the MWCNTs to ensure crop production by promoting crop growth and reducing the residual bioavailability of herbicides.
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Affiliation(s)
- Ting Yao
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Lejun Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Shuo Tan
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Hui Li
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, United States
| | - Xiangying Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China; Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha, 410125, PR China
| | - Aiping Zeng
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Lang Pan
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Xiaogang Li
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China
| | - Lianyang Bai
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China; Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Science, Changsha, 410125, PR China
| | - Kailin Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, PR China; Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, United States.
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, 01003, United States
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138
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Gallarotti N, Barthel M, Verhoeven E, Pereira EIP, Bauters M, Baumgartner S, Drake TW, Boeckx P, Mohn J, Longepierre M, Mugula JK, Makelele IA, Ntaboba LC, Six J. In-depth analysis of N 2O fluxes in tropical forest soils of the Congo Basin combining isotope and functional gene analysis. THE ISME JOURNAL 2021; 15:3357-3374. [PMID: 34035444 PMCID: PMC8528805 DOI: 10.1038/s41396-021-01004-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/14/2021] [Accepted: 04/30/2021] [Indexed: 02/04/2023]
Abstract
Primary tropical forests generally exhibit large gaseous nitrogen (N) losses, occurring as nitric oxide (NO), nitrous oxide (N2O) or elemental nitrogen (N2). The release of N2O is of particular concern due to its high global warming potential and destruction of stratospheric ozone. Tropical forest soils are predicted to be among the largest natural sources of N2O; however, despite being the world's second-largest rainforest, measurements of gaseous N-losses from forest soils of the Congo Basin are scarce. In addition, long-term studies investigating N2O fluxes from different forest ecosystem types (lowland and montane forests) are scarce. In this study we show that fluxes measured in the Congo Basin were lower than fluxes measured in the Neotropics, and in the tropical forests of Australia and South East Asia. In addition, we show that despite different climatic conditions, average annual N2O fluxes in the Congo Basin's lowland forests (0.97 ± 0.53 kg N ha-1 year-1) were comparable to those in its montane forest (0.88 ± 0.97 kg N ha-1 year-1). Measurements of soil pore air N2O isotope data at multiple depths suggests that a microbial reduction of N2O to N2 within the soil may account for the observed low surface N2O fluxes and low soil pore N2O concentrations. The potential for microbial reduction is corroborated by a significant abundance and expression of the gene nosZ in soil samples from both study sites. Although isotopic and functional gene analyses indicate an enzymatic potential for complete denitrification, combined gaseous N-losses (N2O, N2) are unlikely to account for the missing N-sink in these forests. Other N-losses such as NO, N2 via Feammox or hydrological particulate organic nitrogen export could play an important role in soils of the Congo Basin and should be the focus of future research.
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Affiliation(s)
- Nora Gallarotti
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Matti Barthel
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Elizabeth Verhoeven
- grid.4391.f0000 0001 2112 1969College of Agricultural Sciences, Oregon State University, Corvallis, OR USA
| | - Engil Isadora Pujol Pereira
- grid.449717.80000 0004 5374 269XSchool of Earth, Environmental, and Marine Sciences, University of Texas Rio Grande Valley, Edinburg, TX USA
| | - Marijn Bauters
- grid.5342.00000 0001 2069 7798Isotope Bioscience Laboratory, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium ,grid.5342.00000 0001 2069 7798Computational and Applied Vegetation Ecology Lab, Department of Environment, Ghent University, Ghent, Belgium
| | - Simon Baumgartner
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland ,grid.7942.80000 0001 2294 713XEarth and Life Institute, Université Catholique de Louvain, Louvain, Belgium
| | - Travis W. Drake
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Pascal Boeckx
- grid.5342.00000 0001 2069 7798Isotope Bioscience Laboratory, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Joachim Mohn
- grid.7354.50000 0001 2331 3059Laboratory for Air Pollution/Environmental Technology, Swiss Federal Laboratories of Materials Science and Technology, Empa Dubendorf, Switzerland
| | - Manon Longepierre
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - John Kalume Mugula
- grid.442836.f0000 0004 7477 7760Département de Biologie, Université Officielle de Bukavu, Bukavu, Democratic Republic of Congo
| | - Isaac Ahanamungu Makelele
- grid.442836.f0000 0004 7477 7760Département de Biologie, Université Officielle de Bukavu, Bukavu, Democratic Republic of Congo ,grid.5342.00000 0001 2069 7798Department of Green Chemistry and Technology, Ghent University, Ghent, Belgium
| | - Landry Cizungu Ntaboba
- grid.442834.d0000 0004 6011 4325Département d’ Agronomie, Université Catholique de Bukavu, Bukavu, Democratic Republic of Congo
| | - Johan Six
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
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139
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Sun P, Zhao Z, Fan P, Chen W, Ruan Y, Wang Q. Ammonia- and Nitrite-Oxidizing Bacteria are Dominant in Nitrification of Maize Rhizosphere Soil Following Combined Application of Biochar and Chemical Fertilizer. Front Microbiol 2021; 12:715070. [PMID: 34675894 PMCID: PMC8524134 DOI: 10.3389/fmicb.2021.715070] [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: 05/26/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Autotrophic nitrification is regulated by canonical ammonia-oxidizing archaea (AOA) and bacteria (AOB) and nitrite-oxidizing bacteria (NOB). To date, most studies have focused on the role of canonical ammonia oxidizers in nitrification while neglecting the NOB. In order to understand the impacts of combined biochar and chemical fertilizer addition on nitrification and associated nitrifiers in plant rhizosphere soil, we collected rhizosphere soil from a maize field under four different treatments: no fertilization (CK), biochar (B), chemical nitrogen (N) + phosphorus (P) + potassium (K) fertilizers (NPK), and biochar + NPK fertilizers (B + NPK). The potential nitrification rate (PNR), community abundances, and structures of AOA, AOB, complete ammonia-oxidizing bacteria (Comammox Nitrospira clade A), and Nitrobacter- and Nitrospira-like NOB were measured. Biochar and/or NPK additions increased soil pH and nutrient contents in rhizosphere soil. B, NPK, and B + NPK treatments significantly stimulated PNR and abundances of AOB, Comammox, and Nitrobacter- and Nitrospira-like NOB, with the highest values observed in the B + NPK treatment. Pearson correlation and random forest analyses predicted more importance of AOB, Comammox Nitrospira clade A, and Nitrobacter- and Nitrospira-like NOB abundances over AOA on PNR. Biochar and/or NPK additions strongly altered whole nitrifying community structures. Redundancy analysis (RDA) showed that nitrifying community structures were significantly affected by pH and nutrient contents. This research shows that combined application of biochar and NPK fertilizer has a positive effect on improving soil nitrification by affecting communities of AOB and NOB in rhizosphere soil. These new revelations, especially as they related to understudied NOB, can be used to increase efficiency of agricultural land and resource management.
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Affiliation(s)
- Ping Sun
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Ziting Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Pingshan Fan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Wei Chen
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Yunze Ruan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
| | - Qing Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, China
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140
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Gallego S, Montemurro N, Béguet J, Rouard N, Philippot L, Pérez S, Martin-Laurent F. Ecotoxicological risk assessment of wastewater irrigation on soil microorganisms: Fate and impact of wastewater-borne micropollutants in lettuce-soil system. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 223:112595. [PMID: 34390984 DOI: 10.1016/j.ecoenv.2021.112595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 06/13/2023]
Abstract
The implementation of the new Water Reuse regulation in the European Union brings to the forefront the need to evaluate the risks of using wastewater for crop irrigation. Here, a two-tier ecotoxicological risk assessment was performed to evaluate the fate of wastewater-borne micropollutants in soil and their ecotoxicological impact on plants and soil microorganisms. To this end, two successive cultivation campaigns of lettuces were irrigated with wastewater (at agronomical dose (not spiked) and spiked with a mixture of 14 pharmaceuticals at 10 and 100 µg/L each) in a controlled greenhouse experiment. Over the two cultivation campaigns, an accumulation of PPCPs was observed in soil microcosms irrigated with wastewater spiked with 100 μg/L of PPCPs with the highest concentrations detected for clarithromycin, hydrochlorothiazide, citalopram, climbazole and carbamazepine. The abundance of bacterial and fungal communities remained stable over the two cultivation campaigns and was not affected by any of the irrigation regimes applied. Similarly, no changes were observed in the abundance of ammonium oxidizing archaea (AOA) and bacteria (AOB), nor in clade A of commamox no matter the cultivation campaign or the irrigation regime considered. Only a slight increase was detected in clade B of commamox bacteria after the second cultivation campaign. Sulfamethoxazole-resistant and -degrading bacteria were not impacted either. The irrigation regimes had only a limited effect on the bacterial evenness. However, in response to wastewater irrigation the structure of soil bacterial community significantly changed the relative abundance of Acidobacteria, Chloroflexi, Verrucomicrobia, Beta-, Gamma- and Deltaprotebacteria. Twenty-eight operational taxonomic units (OTUs) were identified as responsible for the changes observed within the bacterial communities of soils irrigated with wastewater or with water. Interestingly, the relative abundance of these OTUs was similar in soils irrigated with either spiked or non-spiked irrigation solutions. This indicates that under both agronomical and worst-case scenario the mixture of fourteen PPCPs had no effect on soil bacterial community.
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Affiliation(s)
- Sara Gallego
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Agroécologie, Dijon, France
| | - Nicola Montemurro
- ENFOCHEM, Environmental Chemistry Department, IDAEA-CSIC, c/Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Jérémie Béguet
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Agroécologie, Dijon, France
| | - Nadine Rouard
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Agroécologie, Dijon, France
| | - Laurent Philippot
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, INRAE, Agroécologie, Dijon, France
| | - Sandra Pérez
- ENFOCHEM, Environmental Chemistry Department, IDAEA-CSIC, c/Jordi Girona 18-26, 08034 Barcelona, Spain
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141
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Wei W, Isobe K, Shiratori Y, Yano M, Toyoda S, Koba K, Yoshida N, Shen H, Senoo K. Revisiting the involvement of ammonia oxidizers and denitrifiers in nitrous oxide emission from cropland soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 287:117494. [PMID: 34182387 DOI: 10.1016/j.envpol.2021.117494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/05/2021] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Nitrous oxide (N2O), an ozone-depleting greenhouse gas, is generally produced by soil microbes, particularly NH3 oxidizers and denitrifiers, and emitted in large quantities after N fertilizer application in croplands. N2O can be produced via multiple processes, and reduced, with the involvement of more diverse microbes with different physiological constraints than previously thought; therefore, there is a lack of consensus on the production processes and microbes involved under different agricultural practices. In this study, multiple approaches were applied, including N2O isotopocule analyses, microbial gene transcript measurements, and selective inhibition assays, to revisit the involvement of NH3 oxidizers and denitrifiers, including the previously-overlooked taxa, in N2O emission from a cropland, and address the biological and environmental factors controlling the N2O production processes. Then, we synthesized the results from those approaches and revealed that the overlooked denitrifying bacteria and fungi were more involved in N2O production than the long-studied ones. We also demonstrated that the N2O production processes and soil microbes involved were different based on fertilization practices (plowing or surface application) and fertilization types (manure or urea). In particular, we identified the following intensified activities: (1) N2O production by overlooked denitrifying fungi after manure fertilization onto soil surface; (2) N2O production by overlooked denitrifying bacteria and N2O reduction by long-studied N2O-reducing bacteria after manure fertilization into the plowed layer; and (3) N2O production by NH3-oxidizing bacteria and overlooked denitrifying bacteria and fungi when urea fertilization was applied into the plowed layer. We finally propose the conceptual scheme of N flow after fertilization based on distinct physiological constraints among the diverse NH3 oxidizers and denitrifiers, which will help us understand the environmental context-dependent N2O emission processes.
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Affiliation(s)
- Wei Wei
- School of Agricultural Engineering, Jiangsu University, Jiangsu, 212013, China; Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Kazuo Isobe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan.
| | - Yutaka Shiratori
- Niigata Agricultural Research Institute, Niigata, 940-0826, Japan
| | - Midori Yano
- Center for Ecological Research, Kyoto University, Shiga, 5202113, Japan
| | - Sakae Toyoda
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Keisuke Koba
- Center for Ecological Research, Kyoto University, Shiga, 5202113, Japan
| | - Naohiro Yoshida
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, 226-8503, Japan; Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8550, Japan; National Institute of Information and Communications Technology, Tokyo, 184-8795, Japan
| | - Haoyang Shen
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Keishi Senoo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan
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142
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Zhang D, Cheng H, Hao B, Li Q, Wu J, Zhang Y, Fang W, Yan D, Li Y, Wang Q, Jin X, He L, Cao A. Fresh chicken manure fumigation reduces the inhibition time of chloropicrin on soil bacteria and fungi and increases beneficial microorganisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117460. [PMID: 34438480 DOI: 10.1016/j.envpol.2021.117460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/22/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Chloropicrin (CP) controls soil-borne plant diseases caused by pathogenic microbes, increases crop yield, but has a long-term inhibitory effect on beneficial soil microorganisms. Therefore, we evaluated the effects of biofumigation material fresh chicken manure (FCM) on soil microorganisms, and the duration of those effects in this experiment. Our results showed that in the laboratory, FCM significantly increased substrate-induced respiration (SIR) of soil microorganisms by 2.2-3.2 times at 80 d compared to the control, however, CP significantly inhibited the SIR of soil microorganisms. FCM and CP increased NH4+-N concentration within 40 days which then returned to the control level. FCM increased NO3--N by 2.82-5.78 times by 80 days, compared with the control, while the concentration of NO3--N in the CP treatment was not significantly different from the control at the 80 day. Although in the laboratory FCM inhibited the relative abundance of 16 S rRNA and the nitrogen cycle functional genes AOA amoA, AOB amoA, nirK and nosZ over a 40-day period, the taxonomic diversity of soil bacteria and fungi in the FCM treatment were restored to unfumigated level within 90 days in the field. However, CP treatment has a strong inhibitory effect on soil microorganisms after 90 days. Importantly, the relative abundance of some beneficial microorganisms that control soil-borne pathogenic microbes or degrade pollutants increased significantly in FCM, including Bacillus, Pseudomonas and Streptomyces bacterial genera and Chaetomium and Mycothermus fungal genera. Noteworthy, like CP, FCM still had a strong inhibitory effect on Fusarium at 90 d. Our results indicated that FCM not only increased the content of inorganic nitrogen and improved the respiration rate of soil microorganisms, but it also shortened the recovery time of beneficial soil microorganisms and increased taxonomic diversity. Our previous reports showed that FCM and CP treatments had the same effect in disease control and crop growth. Combined with the results of this experiment, we believe that FCM has the potential to replace CP, which would eliminate CP's detrimental environmental impact, improve farmer safety and promote sustainable crop production.
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Affiliation(s)
- Daqi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongyan Cheng
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Baoqiang Hao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingjie Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jiajia Wu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yi Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wensheng Fang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dongdong Yan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qiuxia Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xi Jin
- Hebei Technology Innovation Center for Green Management of Soil-borne Diseases Baoding University, Baoding, Hebei, 071000, China
| | - Lin He
- College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Aocheng Cao
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China; Hebei Technology Innovation Center for Green Management of Soil-borne Diseases Baoding University, Baoding, Hebei, 071000, China.
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143
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Ritter CD, Forster D, Azevedo JAR, Antonelli A, Nilsson RH, Trujillo ME, Dunthorn M. Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding. MICROBIAL ECOLOGY 2021; 82:746-760. [PMID: 33604703 PMCID: PMC8463405 DOI: 10.1007/s00248-021-01719-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here, we used DNA metabarcoding data from litter and mineral soils collected from a longitudinal transect in Amazonia to explore patterns of co-occurrence. We compared data from different Amazonian habitat types, each with a characteristic biota and environmental conditions. These included non-flooded rainforests (terra-firme), forests seasonally flooded by fertile white waters (várzeas) or by unfertile black waters (igapós), and open areas associated with white sand soil (campinas). We ran co-occurrence network analyses based on null models and Spearman correlation for all samples and for each habitat separately. We found that one third of all operational taxonomic units (OTUs) were bacteria and two thirds were eukaryotes. The resulting networks were nevertheless mostly composed of bacteria, with fewer fungi, protists, and metazoans. Considering the functional traits of the OTUs, there is a combination of metabolism modes including respiration and fermentation for bacteria, and a high frequency of saprotrophic fungi (those that feed on dead organic matter), indicating a high turnover of organic material. The organic carbon and base saturation indices were important in the co-occurrences in Amazonian networks, whereas several other soil properties were important for the co-exclusion. Different habitats had similar network properties with some variation in terms of modularity, probably associated with flooding pulse. We show that Amazonian microorganism communities form highly interconnected co-occurrence and co-exclusion networks, which highlights the importance of complex biotic and abiotic interactions in explaining the outstanding biodiversity of the region.
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Affiliation(s)
- Camila Duarte Ritter
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5 S05 R04 H83, D-45141, Essen, Germany.
| | - Dominik Forster
- Department of Ecology, University of Kaiserslautern, D-67663, Kaiserslautern, Germany
| | - Josue A R Azevedo
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, 69060-000, Brazil
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
- Royal Botanic Gardens, Kew, TW9 3AE, Richmond, Surrey, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Micah Dunthorn
- Eukaryotic Microbiology, University of Duisburg-Essen, Universitätsstrasse 5 S05 R04 H83, D-45141, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
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144
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Lahlali R, Ibrahim DS, Belabess Z, Kadir Roni MZ, Radouane N, Vicente CS, Menéndez E, Mokrini F, Barka EA, Galvão de Melo e Mota M, Peng G. High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects. Heliyon 2021; 7:e08142. [PMID: 34693062 PMCID: PMC8515249 DOI: 10.1016/j.heliyon.2021.e08142] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 08/08/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022] Open
Abstract
Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.
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Affiliation(s)
- Rachid Lahlali
- Plant Pathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknes, BP S/40, 50001, Meknes, Morocco
| | - Dina S.S. Ibrahim
- Department of Nematodes Diseases and Central Lab of Biotechnology, Plant Pathology Research Institute, Agricultural Research Center (ARC), 12619, Egypt
| | - Zineb Belabess
- Plant Protection Laboratory. Regional Center of Agricultural Research of Oujda, National Institute of Agricultural Research, Avenue Mohamed VI, BP428 60000 Oujda, Morocco
| | - Md Zohurul Kadir Roni
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences (JIRCAS), 1091-1 Maezato-Kawarabaru, Ishigaki, Okinawa, 907-0002, Japan
| | - Nabil Radouane
- Plant Pathology Unit, Department of Plant Protection, Ecole Nationale d’Agriculture de Meknes, BP S/40, 50001, Meknes, Morocco
- Department of Biology, Laboratory of Functional Ecology and Environmental Engineering, FST-Fez, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Cláudia S.L. Vicente
- MED – Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research (IIFA), Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
- INIAV, I.P. - Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, 2780-159 Oeiras, Portugal
| | - Esther Menéndez
- INIAV, I.P. - Instituto Nacional de Investigação Agrária e Veterinária, Quinta do Marquês, 2780-159 Oeiras, Portugal
- Department of Microbiology and Genetics / Spanish-Portuguese Institute for Agricultural Research (CIALE). University of Salamanca, 37007, Salamanca, Spain
| | - Fouad Mokrini
- Plant Protection Laboratory, INRA, Centre Régional de la Recherche Agronomique (CRRA), Rabat, Morocco
| | - Essaid Ait Barka
- Unité de Recherche Résistance Induite et Bio-protection des Plantes, EA 4707, USC, INRAe1488, Université de Reims Champagne-Ardenne, France
| | - Manuel Galvão de Melo e Mota
- NemaLab, MED – Mediterranean Institute for Agriculture, Environment and Development & Department of Biology, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Gary Peng
- Saskatoon Research Development Centre, Agriculture and Agri-Food, Saskatchewan, Canada
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145
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Shen LD, Yang YL, Liu JQ, Hu ZH, Liu X, Tian MH, Yang WT, Jin JH, Wang HY, Wang YY, Wu HS. Different responses of ammonia-oxidizing archaea and bacteria in paddy soils to elevated CO 2 concentration. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 286:117558. [PMID: 34119867 DOI: 10.1016/j.envpol.2021.117558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/30/2021] [Accepted: 06/06/2021] [Indexed: 06/12/2023]
Abstract
The elevated atmospheric CO2 concentration is well known to have an important effect on soil nutrient cycling. Ammonia oxidation, mediated by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), is the rate-limiting step in soil nitrification, which controls the availability of two key soil nutrients (ammonium and nitrate) for crops. Until now, how the AOA and AOB communities in paddy soils respond to elevated CO2 remains largely unknown. Here, we examined the communities of AOA and AOB and nitrification potential at both surface (0-5 cm) and subsurface (5-10 cm) soil layers of paddy fields under three different CO2 treatments, including CK (ambient CO2 concentration), LT (CK + 160 ppm of CO2) and HT (CK + 200 ppm of CO2). The elevated CO2 was found to have a greater impact on the community structure of AOB than that of AOA in surface soils as revealed by high-throughput sequencing of their amoA genes. However, no obvious variation of AOA or AOB communities was observed in subsurface soils among different CO2 treatments. The abundance of AOA and AOB, and nitrification potential were significantly increased in surface soils under elevated CO2. The variation of AOB abundance correlated well with the variation of nitrification potential. The soil water content and dissolved organic carbon content had important impacts on the dynamic of AOB communities and nitrification potential. Overall, our results showed different responses of AOA and AOB communities to elevated CO2 in paddy ecosystems, and AOB were more sensitive to the rising CO2 concentration.
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Affiliation(s)
- Li-Dong Shen
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China.
| | - Yu-Ling Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jia-Qi Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Zheng-Hua Hu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Xin Liu
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Mao-Hui Tian
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Wang-Ting Yang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Jing-Hao Jin
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Hao-Yu Wang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Yuan-Yuan Wang
- Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters, Institute of Ecology, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Hong-Sheng Wu
- Department of Agricultural Resources and Environment, School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing, 210044, China
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146
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Cha G, Meinhardt KA, Orellana LH, Hatt JK, Pannu MW, Stahl DA, Konstantinidis KT. The influence of alfalfa-switchgrass intercropping on microbial community structure and function. Environ Microbiol 2021; 23:6828-6843. [PMID: 34554631 DOI: 10.1111/1462-2920.15785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 09/17/2021] [Indexed: 11/30/2022]
Abstract
The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching and emissions of N2 O, a potent greenhouse gas. Intercropping with nitrogen-fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. We analysed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared with the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, ammonia-oxidizing archaea and bacteria increased in abundance with intercropping and fertilization. However, only betaproteobacterial ammonia-oxidizing bacteria abundance in fertilized plots significantly correlated to N2 O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization.
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Affiliation(s)
- Gyuhyon Cha
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Kelley A Meinhardt
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Manmeet W Pannu
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
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147
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Wang X, Bai J, Xie T, Wang W, Zhang G, Yin S, Wang D. Effects of biological nitrification inhibitors on nitrogen use efficiency and greenhouse gas emissions in agricultural soils: A review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 220:112338. [PMID: 34015632 DOI: 10.1016/j.ecoenv.2021.112338] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 05/27/2023]
Abstract
To maintain and increase crop yields, large amounts of nitrogen fertilizers have been applied to farmland. However, the nitrogen use efficiency (NUE) of chemical fertilizer remains very low, which may lead to serious environmental problems, including nitrate pollution, air quality degradation and greenhouse gas (GHG) emissions. Nitrification inhibitors can alleviate nitrogen loss by inhibiting nitrification; thus, biological nitrification inhibition by plants has gradually attracted increasing attention due to its low cost and environmental friendliness. Research progress on BNI is reviewed in this article, including the source, mechanisms, influencing factors and application of BNIs. In addition, the impact of BNI on agriculture and GHG emissions is summarized from the perspective of agricultural production and environmental protection, and the key future research prospects of BNIs are also noted.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Tian Xie
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Wei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Shuo Yin
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Dawei Wang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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148
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Gottshall EY, Bryson SJ, Cogert KI, Landreau M, Sedlacek CJ, Stahl DA, Daims H, Winkler M. Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria. WATER RESEARCH 2021; 202:117426. [PMID: 34274897 DOI: 10.1016/j.watres.2021.117426] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The discovery of anaerobic ammonia-oxidizing bacteria (Anammox) and, more recently, aerobic bacteria common in many natural and engineered systems that oxidize ammonia completely to nitrate (Comammox) have significantly altered our understanding of the global nitrogen cycle. A high affinity for ammonia (Km(app),NH3 ≈ 63nM) and oxygen place Comammox Nitrospira inopinata, the first described isolate, in the same trophic category as organisms such as some ammonia-oxidizing archaea. However, N. inopinata has a relatively low affinity for nitrite (Km,NO2 ≈ 449.2μM) suggesting it would be less competitive for nitrite than other nitrite-consuming aerobes and anaerobes. We examined the ecological relevance of the disparate substrate affinities by coupling it with the Anammox bacterium Candidatus Brocadia anammoxidans. Synthetic communities of the two were established in hydrogel granules in which Comammox grew in the aerobic outer layer to provide Anammox with nitrite in the inner anoxic core to form dinitrogen gas. This spatial organization was confirmed with FISH imaging, supporting a mutualistic or commensal relationship. The functional significance of interspecies spatial organization was informed by the hydrogel encapsulation format, broadening our limited understanding of the interplay between these two species. The resulting low nitrate formation and the competitiveness of Comammox over other aerobic ammonia- and nitrite-oxidizers sets this ecological cooperation apart and points to potential biotechnological applications. Since nitrate is an undesirable product of wastewater treatment effluents, the Comammox-Anammox symbiosis may be of economic and ecological importance to reduce nitrogen contamination of receiving waters.
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Affiliation(s)
- Ekaterina Y Gottshall
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States.
| | - Sam J Bryson
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States
| | - Kathryn I Cogert
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States
| | - Matthieu Landreau
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States
| | - Christopher J Sedlacek
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1010, Austria
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States
| | - Holger Daims
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1010, Austria; The Comammox Research Platform. University of Vienna, 1010, Austria
| | - Mari Winkler
- Civil and Environmental Engineering, University of Washington, Seattle, WA 98165, United States
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149
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Clark IM, Hughes DJ, Fu Q, Abadie M, Hirsch PR. Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils. Sci Rep 2021; 11:15905. [PMID: 34354121 PMCID: PMC8342464 DOI: 10.1038/s41598-021-95100-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022] Open
Abstract
The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted field plots under contrasting management regimes-permanent bare fallow, grassland, and arable (wheat) cultivation maintained for more than 50 years. Metagenome and metatranscriptome analysis indicated nitrite oxidizing bacteria (NOB) were more abundant than ammonia oxidizing archaea (AOA) and bacteria (AOB) in all soils. The most abundant AOA and AOB in the metagenomes were, respectively, Nitrososphaera and Ca. Nitrososcosmicus (family Nitrososphaeraceae) and Nitrosospira and Nitrosomonas (family Nitrosomonadaceae). The most abundant NOB were Nitrospira including the comammox species Nitrospira inopinata, Ca. N. nitrificans and Ca. N. nitrosa. Anammox bacteria were also detected. Nitrospira and the AOA Nitrososphaeraceae showed most transcriptional activity in arable soil. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome; AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Nitrification potential assessed in soil from the experimental sites (microcosms amended or not with DCD at concentrations inhibitory to AOB but not AOA), was highest in arable samples and lower in all assays containing DCD, indicating AOB were responsible for oxidizing ammonium fertilizer added to these soils.
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Affiliation(s)
- Ian M Clark
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - David J Hughes
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Qingling Fu
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, Hubei Province, People's Republic of China
| | - Maïder Abadie
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Penny R Hirsch
- Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK.
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150
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Hu J, Zhao Y, Yao X, Wang J, Zheng P, Xi C, Hu B. Dominance of comammox Nitrospira in soil nitrification. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 780:146558. [PMID: 33765470 DOI: 10.1016/j.scitotenv.2021.146558] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/09/2021] [Accepted: 03/14/2021] [Indexed: 06/12/2023]
Abstract
The first and limiting step of nitrification is catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB). Recently, complete ammonia oxidizers (comammox Nitrospira) have been discovered to perform complete nitrification in one cell, yet their role in soil nitrification is still unclear. This study investigated the abundance and contribution of aerobic ammonia oxidizers in typical soil habitats, and assessed the role of comammox Nitrospira in ammonia-oxidizing communities. The results showed that comammox Nitrospira were dominant in 70% of the samples and their abundance displayed a significant positive correlation with nitrification potential. The median amoA gene transcription level of comammox Nitrospira exceeded that of AOA and AOB in in-situ soils. The abundance of comammox Nitrospira was negatively correlated with soil pH, dominating in 84% of soil samples with pH < 6.17. The results challenge the role of AOA and AOB in soils, highlighting the importance of comammox Nitrospira in soil nitrification, especially in acid soils. This work supports better understanding and regulation of the soil nitrogen cycle.
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Affiliation(s)
- Jiajie Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Yuxiang Zhao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Ping Zheng
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Chuanwu Xi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China.
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