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Qin J, Yang J, Zhang J, Liu X, Yu J, Wang Z, Li Y, Guan B, Wang X, Zhao W. Effects of tidal hydrology on soil phosphorus forms in the Yellow River estuary wetland: A field study of soil core translocation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171360. [PMID: 38428613 DOI: 10.1016/j.scitotenv.2024.171360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/03/2024] [Accepted: 02/27/2024] [Indexed: 03/03/2024]
Abstract
Phosphorus (P) forms in soil are related to the P cycle and play an important role in maintaining the productivity and function of wetlands. Tidal hydrology is a key factor controlling soil P forms in estuary wetlands; however, the response of soil P forms to tidal hydrological changes remains unclear. A translocation experiment in the Yellow River Estuary wetland was conducted to study the effect of hydrological changes on P forms in the soil, in which freshwater marsh soils in the supratidal zone were translocated to salt marshes in different intertidal zones (up-high-tidal zone, high-tidal zone, and middle-tidal zone). Over a 23-month experiment, soil properties showed varying changes under different tidal hydrology conditions, with an increase in pH, salinity, Ca2+ and salt ions and a decrease in iron oxide and nutrients. Compared with the control, the content of different forms of phosphorus (total phosphorus, inorganic phosphorus, organic phosphorus, and calcium-bound phosphorus) in the cultured soil cores decreased from 3.3 % to 67.0 % in the intertidal zones, whereas the content of ferrum‑aluminum-bound phosphorus increased from 58.9 % to 65.1 % at the end of the experiment. According to the partial least squares structural equation model, P forms are influenced by tidal hydrology mainly through the mediation of salt ions and nutrient levels. These results suggest that seawater intrusion promotes the release of P in the supratidal zone soil of estuary wetlands.
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Affiliation(s)
- Jifa Qin
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Jisong Yang
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China; Dongying Academy of Agricultural Sciences, Dongying, China.
| | - Jiapeng Zhang
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Xue Liu
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Junbao Yu
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Zhikang Wang
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Yunzhao Li
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Bo Guan
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Xuehong Wang
- Institute for Advanced Study in Coastal Ecology, School of Resource and Environmental Engineering, Ludong University, Yantai, China
| | - Wei Zhao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, China.
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Lidbury IDEA, Hitchcock A, Groenhof SRM, Connolly AN, Moushtaq L. New insights in bacterial organophosphorus cycling: From human pathogens to environmental bacteria. Adv Microb Physiol 2024; 84:1-49. [PMID: 38821631 DOI: 10.1016/bs.ampbs.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
In terrestrial and aquatic ecosystems, phosphorus (P) availability controls primary production, with consequences for climate regulation and global food security. Understanding the microbial controls on the global P cycle is a prerequisite for minimising our reliance on non-renewable phosphate rock reserves and reducing pollution associated with excessive P fertiliser use. This recognised importance has reinvigorated research into microbial P cycling, which was pioneered over 75 years ago through the study of human pathogenic bacteria-host interactions. Immobilised organic P represents a significant fraction of the total P pool. Hence, microbes have evolved a plethora of mechanisms to transform this fraction into labile inorganic phosphate, the building block for numerous biological molecules. The 'genomics era' has revealed an extraordinary diversity of organic P cycling genes exist in the environment and studies going 'back to the lab' are determining how this diversity relates to function. Through this integrated approach, many hitherto unknown genes and proteins that are involved in microbial P cycling have been discovered. Not only do these fundamental discoveries push the frontier of our knowledge, but several examples also provide exciting opportunities for biotechnology and present possible solutions for improving the sustainability of how we grow our food, both locally and globally. In this review, we provide a comprehensive overview of bacterial organic P cycling, covering studies on human pathogens and how this knowledge is informing new discoveries in environmental microbiology.
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Affiliation(s)
- Ian D E A Lidbury
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom.
| | - Andrew Hitchcock
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom; Plants, Photosynthesis, and Soil, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Sophie R M Groenhof
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Alex N Connolly
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
| | - Laila Moushtaq
- Molecular Microbiology - Biochemistry and Disease, School of Biosciences, The University of Sheffield, Sheffield, United Kingdom
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Garaycochea S, Altier NA, Leoni C, Neal AL, Romero H. Abundance and phylogenetic distribution of eight key enzymes of the phosphorus biogeochemical cycle in grassland soils. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:352-369. [PMID: 37162018 PMCID: PMC10472533 DOI: 10.1111/1758-2229.13159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Grassland biomes provide valuable ecosystem services, including nutrient cycling. Organic phosphorus (Po) represents more than half of the total P in soils. Soil microorganisms release organic P through enzymatic processes, with alkaline phosphatases, acid phosphatases and phytases being the key P enzymes involved in the cycling of organic P. This study analysed 74 soil metagenomes from 17 different grassland biomes worldwide to evaluate the distribution and abundance of eight key P enzymes (PhoD, PhoX, PhoA, Nsap-A, Nsap-B, Nsap-C, BPP and CPhy) and their relationship with environmental factors. Our analyses showed that alkaline phosphatase phoD was the dataset's most abundant P-enzyme encoding genes, with a wide phylogenetic distribution. Followed by the acid phosphatases Nsap-A and Nsap-C showed similar abundance but a different distribution in their respective phylogenetic trees. Multivariate analyses revealed that pH, Tmax , SOC and soil moisture were associated with the abundance and diversity of all genes studied. PhoD and phoX genes strongly correlated with SOC and clay, and the phoX gene was more common in soils with low to medium SOC and neutral pH. In particular, P-enzyme genes tended to respond in a positively correlated manner among them, suggesting a complex relationship of abundance and diversity among them.
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Affiliation(s)
- Silvia Garaycochea
- Instituto Nacional de Investigación Agropecuaria (INIA)Estación Experimental INIA Las BrujasCanelonesUruguay
| | - Nora Adriana Altier
- Instituto Nacional de Investigación Agropecuaria (INIA)Estación Experimental INIA Las BrujasCanelonesUruguay
| | - Carolina Leoni
- Instituto Nacional de Investigación Agropecuaria (INIA)Estación Experimental INIA Las BrujasCanelonesUruguay
| | - Andrew L. Neal
- Net‐Zero and Resilient FarmingRothamsted Research, North WykeOkehamptonUK
| | - Héctor Romero
- Laboratorio de Organización y Evolución del Genoma/Genómica Evolutiva, Departamento de Ecología y Evolución, Facultad de Ciencias/CUREUniversidad de la RepúblicaMaldonadoUruguay
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4
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Liu S, Zeng J, Yu H, Wang C, Yang Y, Wang J, He Z, Yan Q. Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils. THE ISME JOURNAL 2023:10.1038/s41396-023-01445-6. [PMID: 37270585 DOI: 10.1038/s41396-023-01445-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 05/14/2023] [Accepted: 05/24/2023] [Indexed: 06/05/2023]
Abstract
Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.
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Affiliation(s)
- Shengwei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jiaxiong Zeng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Huang Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, 100084, Beijing, China
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510006, China.
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Li HP, Han QQ, Liu QM, Gan YN, Rensing C, Rivera WL, Zhao Q, Zhang JL. Roles of phosphate-solubilizing bacteria in mediating soil legacy phosphorus availability. Microbiol Res 2023; 272:127375. [PMID: 37058784 DOI: 10.1016/j.micres.2023.127375] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/16/2023]
Abstract
Phosphorus (P), an essential macronutrient for all life on Earth, has been shown to be a vital limiting nutrient element for plant growth and yield. P deficiency is a common phenomenon in terrestrial ecosystems across the world. Chemical phosphate fertilizer has traditionally been employed to solve the problem of P deficiency in agricultural production, but its application has been limited by the non-renewability of raw materials and the adverse influence on the ecological health of the environment. Therefore, it is imperative to develop efficient, economical, environmentally friendly and highly stable alternative strategies to meet the plant P demand. Phosphate-solubilizing bacteria (PSB) are able to improve plant productivity by increasing P nutrition. Pathways to fully and effectively use PSB to mobilize unavailable forms of soil P for plants has become a hot research topic in the fields of plant nutrition and ecology. Here, the biogeochemical P cycling in soil systems are summarized, how to make full use of soil legacy P via PSB to alleviate the global P resource shortage are reviewed. We highlight the advances in multi-omics technologies that are helpful for exploring the dynamics of nutrient turnover and the genetic potential of PSB-centered microbial communities. Furthermore, the multiple roles of PSB inoculants in sustainable agricultural practices are analyzed. Finally, we project that new ideas and techniques will be continuously infused into fundamental and applied research to achieve a more integrated understanding of the interactive mechanisms of PSB and rhizosphere microbiota/plant to maximize the efficacy of PSB as P activators.
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Affiliation(s)
- Hui-Ping Li
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Center for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Qing-Qing Han
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Center for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Qiong-Mei Liu
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Center for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Ya-Nan Gan
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Center for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Windell L Rivera
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, The Philippines
| | - Qi Zhao
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Center for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
| | - Jin-Lin Zhang
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Center for Grassland Microbiome, State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
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6
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Stimulation of Distinct Rhizosphere Bacteria Drives Phosphorus and Nitrogen Mineralization in Oilseed Rape under Field Conditions. mSystems 2022; 7:e0002522. [PMID: 35862821 PMCID: PMC9426549 DOI: 10.1128/msystems.00025-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Advances in DNA sequencing technologies have drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Important ecological interactions being performed by microbes can be investigated by analyzing the extracellular protein fraction. Here, we combined a unique protein extraction method and an iterative bioinformatics pipeline to capture and identify extracellular proteins (metaexoproteomics) synthesized in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analyzed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1,885 plant, insect, and microbial proteins were identified across bulk and rhizosphere samples. Metaexoproteomics identified a significant shift in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This included stimulation of rhizosphere-specialized bacteria, such as Gammaproteobacteria, Betaproteobacteria, and Flavobacteriia, and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralization. Our metaproteomic assessment of the “active” plant microbiome at the field-scale demonstrates the importance of moving beyond metagenomics to determine ecologically important plant-microbe interactions underpinning plant health. IMPORTANCE Plant-microbe interactions are critical to ecosystem function and crop production. While significant advances have been made toward understanding the structure of the plant microbiome, learning about its full functional role is still in its infancy. This is primarily due to an incomplete ability to determine in situ plant-microbe interactions actively operating under field conditions. Proteins are the functional entities of the cell. Therefore, their identification and relative quantification within a microbial community provide the best proxy for which microbes are the most metabolically active and which are driving important plant-microbe interactions. Here, we provide the first metaexoproteomics assessment of the plant microbiome using field-grown oilseed rape as the model crop species, identifying key taxa responsible for specific ecological interactions. Gaining a mechanistic understanding of the plant microbiome is central to developing engineered plant microbiomes to improve sustainable agricultural approaches and reduce our reliance on nonrenewable resources.
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Zeng J, Tu Q, Yu X, Qian L, Wang C, Shu L, Liu F, Liu S, Huang Z, He J, Yan Q, He Z. PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes. MICROBIOME 2022; 10:101. [PMID: 35787295 PMCID: PMC9252087 DOI: 10.1186/s40168-022-01292-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/12/2022] [Indexed: 05/29/2023]
Abstract
BACKGROUND Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database. RESULTS In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments. CONCLUSIONS We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.
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Affiliation(s)
- Jiaxiong Zeng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237 China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Lu Qian
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Longfei Shu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Fei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Shengwei Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Zhijian Huang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Jianguo He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510006 China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128 China
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Wang M, Wu Y, Zhao J, Liu Y, Chen Z, Tang Z, Tian W, Xi Y, Zhang J. Long-term fertilization lowers the alkaline phosphatase activity by impacting the phoD-harboring bacterial community in rice-winter wheat rotation system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153406. [PMID: 35092777 DOI: 10.1016/j.scitotenv.2022.153406] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/16/2022] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
PhoD-harboring bacteria and the secreted alkaline phosphatases (ALP) are crucial in the regulation of soil phosphorus (P) cycling. However, the influential factors of these crucial indicators and their internal interactions remain controversial. Here, a long-term field experiment containing different fertilization regimes was conducted (chemical, organic, and no fertilizer applied). The results indicated that the richness and diversity of phoD-harboring bacterial community were significantly decreased after long-term fertilization. The applied fertilizer promoted the growth of competitive species, while phoD-harboring bacteria lost the advantage to outcompete other microorganisms after long-term fertilization. The decreased ALP activity was caused by the declined phoD gene abundance, which is attributed to the comprehensive effects of soil organic C (SOC), total nitrogen (TN), and various forms of P. The random forest models identified SOC, TN, and available P (AP) to be the dominant environmental factors in shaping the phoD-harboring bacterial community. In addition, some other forms of P such as organic P (Po), inorganic P (Pi) or total P (TP) also exerted significant effects. Different fertilization regimes changed the keystone genera that contributed significantly to soil ALP activities, while Pseudolabrys and Pseudomonas were predicted to be the most important genera regardless of different fertilization regimes. This study extends the understanding of the main process and mechanisms of P mobilization in response to different fertilization regimes.
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Affiliation(s)
- Mengmeng Wang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Yuncheng Wu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Jiayin Zhao
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Yu Liu
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Zhe Chen
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Zhaoyang Tang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Wei Tian
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China.
| | - Yunguan Xi
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Jibing Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
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9
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A widely distributed phosphate-insensitive phosphatase presents a route for rapid organophosphorus remineralization in the biosphere. Proc Natl Acad Sci U S A 2022; 119:2118122119. [PMID: 35082153 PMCID: PMC8812569 DOI: 10.1073/pnas.2118122119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2021] [Indexed: 11/24/2022] Open
Abstract
At several locations across the globe, terrestrial and marine primary production, which underpin global food security, biodiversity, and climate regulation, are limited by inorganic phosphate availability. A major fraction of the total phosphorus pool exists in organic form, requiring mineralization to phosphate by enzymes known as phosphatases prior to incorporation into cellular biomolecules. Phosphatases are typically synthesized in response to phosphate depletion, assisting with phosphorus acquisition. Here, we reveal that a unique bacterial phosphatase, PafA, is widely distributed in the biosphere and has a distinct functional role in carbon acquisition, releasing phosphate as a by-product. PafA, therefore, represents an overlooked mechanism in the global phosphorus cycle and a hitherto cryptic route for the regeneration of bioavailable phosphorus in nature. The regeneration of bioavailable phosphate from immobilized organophosphorus represents a key process in the global phosphorus cycle and is facilitated by enzymes known as phosphatases. Most bacteria possess at least one of three phosphatases with broad substrate specificity, known as PhoA, PhoX, and PhoD, whose activity is optimal under alkaline conditions. The production and activity of these phosphatases is repressed by phosphate availability. Therefore, they are only fully functional when bacteria experience phosphorus-limiting growth conditions. Here, we reveal a previously overlooked phosphate-insensitive phosphatase, PafA, prevalent in Bacteroidetes, which is highly abundant in nature and represents a major route for the regeneration of environmental phosphate. Using the enzyme from Flavobacterium johnsoniae, we show that PafA is highly active toward phosphomonoesters, is fully functional in the presence of excess phosphate, and is essential for growth on phosphorylated carbohydrates as a sole carbon source. These distinct properties of PafA may expand the metabolic niche of Bacteroidetes by enabling the utilization of abundant organophosphorus substrates as C and P sources, providing a competitive advantage when inhabiting zones of high microbial activity and nutrient demand. PafA, which is constitutively synthesized by soil and marine flavobacteria, rapidly remineralizes phosphomonoesters releasing bioavailable phosphate that can be acquired by neighboring cells. The pafA gene is highly diverse in plant rhizospheres and is abundant in the global ocean, where it is expressed independently of phosphate availability. PafA therefore represents an important enzyme in the context of global biogeochemical cycling and has potential applications in sustainable agriculture.
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10
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Park Y, Solhtalab M, Thongsomboon W, Aristilde L. Strategies of organic phosphorus recycling by soil bacteria: acquisition, metabolism, and regulation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:3-24. [PMID: 35001516 PMCID: PMC9306846 DOI: 10.1111/1758-2229.13040] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Critical to meeting cellular phosphorus (P) demand, soil bacteria deploy a number of strategies to overcome limitation in inorganic P (Pi ) in soils. As a significant contributor to P recycling, soil bacteria secrete extracellular enzymes to degrade organic P (Po ) in soils into the readily bioavailable Pi . In addition, several Po compounds can be transported directly via specific transporters and subsequently enter intracellular metabolic pathways. In this review, we highlight the strategies that soil bacteria employ to recycle Po from the soil environment. We discuss the diversity of extracellular phosphatases in soils, the selectivity of these enzymes towards various Po biomolecules and the influence of the soil environmental conditions on the enzyme's activities. Moreover, we outline the intracellular metabolic pathways for Po biosynthesis and transporter-assisted Po and Pi uptake at different Pi availabilities. We further highlight the regulatory mechanisms that govern the production of phosphatases, the expression of Po transporters and the key metabolic changes in P metabolism in response to environmental Pi availability. Due to the depletion of natural resources for Pi , we propose future studies needed to leverage bacteria-mediated P recycling from the large pools of Po in soils or organic wastes to benefit agricultural productivity.
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Affiliation(s)
- Yeonsoo Park
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Mina Solhtalab
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Wiriya Thongsomboon
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Chemistry, Faculty of ScienceMahasarakham UniversityMahasarakham44150Thailand
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
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11
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Gaiero JR, Tosi M, Bent E, Boitt G, Khosla K, Turner BL, Richardson AE, Condron LM, Dunfield KE. Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand. FEMS Microbiol Ecol 2021; 97:6145523. [PMID: 33609120 DOI: 10.1093/femsec/fiab034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/18/2021] [Indexed: 01/04/2023] Open
Abstract
The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2).
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Affiliation(s)
- Jonathan R Gaiero
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Elizabeth Bent
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Gustavo Boitt
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Kamini Khosla
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Benjamin L Turner
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Republic of Panama
| | | | - Leo M Condron
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, Canterbury, New Zealand
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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12
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Niche-adaptation in plant-associated Bacteroidetes favours specialisation in organic phosphorus mineralisation. THE ISME JOURNAL 2021; 15:1040-1055. [PMID: 33257812 PMCID: PMC8115612 DOI: 10.1038/s41396-020-00829-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
Bacteroidetes are abundant pathogen-suppressing members of the plant microbiome that contribute prominently to rhizosphere phosphorus mobilisation, a frequent growth-limiting nutrient in this niche. However, the genetic traits underpinning their success in this niche remain largely unknown, particularly regarding their phosphorus acquisition strategies. By combining cultivation, multi-layered omics and biochemical analyses we first discovered that all plant-associated Bacteroidetes express constitutive phosphatase activity, linked to the ubiquitous possession of a unique phosphatase, PafA. For the first time, we also reveal a subset of Bacteroidetes outer membrane SusCD-like complexes, typically associated with carbon acquisition, and several TonB-dependent transporters, are induced during Pi-depletion. Furthermore, in response to phosphate depletion, the plant-associated Flavobacterium used in this study expressed many previously characterised and novel proteins targeting organic phosphorus. Collectively, these enzymes exhibited superior phosphatase activity compared to plant-associated Pseudomonas spp. Importantly, several of the novel low-Pi-inducible phosphatases and transporters, belong to the Bacteroidetes auxiliary genome and are an adaptive genomic signature of plant-associated strains. In conclusion, niche adaptation to the plant microbiome thus appears to have resulted in the acquisition of unique phosphorus scavenging loci in Bacteroidetes, enhancing their phosphorus acquisition capabilities. These traits may enable their success in the rhizosphere and also present exciting avenues to develop sustainable agriculture.
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13
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Udaondo Z, Duque E, Daddaoua A, Caselles C, Roca A, Pizarro-Tobias P, Ramos JL. Developing robust protein analysis profiles to identify bacterial acid phosphatases in genomes and metagenomic libraries. Environ Microbiol 2020; 22:3561-3571. [PMID: 32564477 DOI: 10.1111/1462-2920.15138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022]
Abstract
Phylogenetic analysis of more than 4000 annotated bacterial acid phosphatases was carried out. Our analysis enabled us to sort these enzymes into the following three types: (1) class B acid phosphatases, which were distantly related to the other types, (2) class C acid phosphatases and (3) generic acid phosphatases (GAP). Although class B phosphatases are found in a limited number of bacterial families, which include known pathogens, class C acid phosphatases and GAP proteins are found in a variety of microbes that inhabit soil, fresh water and marine environments. As part of our analysis, we developed three profiles, named Pfr-B-Phos, Pfr-C-Phos and Pfr-GAP, to describe the three groups of acid phosphatases. These sequence-based profiles were then used to scan genomes and metagenomes to identify a large number of formerly unknown acid phosphatases. A number of proteins in databases annotated as hypothetical proteins were also identified by these profiles as putative acid phosphatases. To validate these in silico results, we cloned genes encoding candidate acid phosphatases from genomic DNA or recovered from metagenomic libraries or genes synthesized in vitro based on protein sequences recovered from metagenomic data. Expression of a number of these genes, followed by enzymatic analysis of the proteins, further confirmed that sequence similarity searches using our profiles could successfully identify previously unknown acid phosphatases.
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Affiliation(s)
- Zulema Udaondo
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain.,Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA
| | - Estrella Duque
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
| | - Abdelali Daddaoua
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Carlos Caselles
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
| | | | | | - Juan L Ramos
- Estación Experimental del Zaidín, CSIC, Granada, E-18008, Spain
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14
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Pfahler V, Macdonald A, Mead A, Smith AC, Tamburini F, Blackwell MSA, Granger SJ. Changes of oxygen isotope values of soil P pools associated with changes in soil pH. Sci Rep 2020; 10:2065. [PMID: 32034236 PMCID: PMC7005815 DOI: 10.1038/s41598-020-59103-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/20/2020] [Indexed: 12/05/2022] Open
Abstract
Field data about the effect of soil pH on phosphorus (P) cycling is limited. A promising tool to study P cycling under field conditions is the 18O:16O ratio of phosphate (δ18OP). In this study we investigate whether the δ18OP can be used to elucidate the effect of soil pH on P cycling in grasslands. Soils and plants were sampled from different fertilisation and lime treatments of the Park Grass long term experiment at Rothamsted Research, UK. The soils were sequentially extracted to isolate different soil P pools, including available P and corresponding δ18OP values were determined. We did not observe changes in plant δ18OP value, but soil P δ18OP values changed, and lower δ18OP values were associated with higher soil pH values. At sites where P was not limiting, available P δ18OP increased by up to 3‰ when lime was applied. We show that the δ18OP method is a useful tool to investigate the effect of pH on soil P cycling under field conditions as it highlights that different soil processes must govern P availability as pH shifts. The next challenge is now to identify these underlying processes, enabling better management of soil P at different pH.
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Affiliation(s)
- Verena Pfahler
- Rothamsted Research, Sustainable Agriculture Sciences North Wyke, Okehampton, Devon, EX20 2SB, UK.
| | - Andy Macdonald
- Rothamsted Research, Sustainable Agriculture Sciences Harpenden, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Andrew Mead
- Rothamsted Research, Computational and Analytical Sciences, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Andrew C Smith
- NERC Isotope Geoscience Laboratory, British Geological Survey, Nottingham, NG12 5GG, UK
| | - Federica Tamburini
- Department of Environmental System Sciences, ETH Zurich, Eschikon 33, 8315, Lindau, Switzerland
| | - Martin S A Blackwell
- Rothamsted Research, Sustainable Agriculture Sciences North Wyke, Okehampton, Devon, EX20 2SB, UK
| | - Steven J Granger
- Rothamsted Research, Sustainable Agriculture Sciences North Wyke, Okehampton, Devon, EX20 2SB, UK
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15
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Ozaki K, Thompson KJ, Simister RL, Crowe SA, Reinhard CT. Anoxygenic photosynthesis and the delayed oxygenation of Earth's atmosphere. Nat Commun 2019; 10:3026. [PMID: 31289261 PMCID: PMC6616575 DOI: 10.1038/s41467-019-10872-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/28/2019] [Indexed: 12/03/2022] Open
Abstract
The emergence of oxygenic photosynthesis created a new niche with dramatic potential to transform energy flow through Earth's biosphere. However, more primitive forms of photosynthesis that fix CO2 into biomass using electrons from reduced species like Fe(II) and H2 instead of water would have competed with Earth's early oxygenic biosphere for essential nutrients. Here, we combine experimental microbiology, genomic analyses, and Earth system modeling to demonstrate that competition for light and nutrients in the surface ocean between oxygenic phototrophs and Fe(II)-oxidizing, anoxygenic photosynthesizers (photoferrotrophs) translates into diminished global photosynthetic O2 release when the ocean interior is Fe(II)-rich. These results provide a simple ecophysiological mechanism for inhibiting atmospheric oxygenation during Earth's early history. We also find a novel positive feedback within the coupled C-P-O-Fe cycles that can lead to runaway planetary oxygenation as rising atmospheric pO2 sweeps the deep ocean of the ferrous iron substrate for photoferrotrophy.
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Affiliation(s)
- Kazumi Ozaki
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- NASA Astrobiology Institute, Alternative Earths Team, Riverside, CA, USA
- NASA Postdoctoral Program, Universities Space Research Association, Columbia, MD, 21046, USA
- Department of Environmental Science, Toho University, Funabashi, Chiba, 274-8510, Japan
| | - Katharine J Thompson
- Departments of Microbiology & Immunology and Earth, Ocean, & Atmospheric Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Rachel L Simister
- Departments of Microbiology & Immunology and Earth, Ocean, & Atmospheric Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Sean A Crowe
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Departments of Microbiology & Immunology and Earth, Ocean, & Atmospheric Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Christopher T Reinhard
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- NASA Astrobiology Institute, Alternative Earths Team, Riverside, CA, USA.
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16
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Skouri-Panet F, Benzerara K, Cosmidis J, Férard C, Caumes G, De Luca G, Heulin T, Duprat E. In Vitro and in Silico Evidence of Phosphatase Diversity in the Biomineralizing Bacterium Ramlibacter tataouinensis. Front Microbiol 2018; 8:2592. [PMID: 29375498 PMCID: PMC5768637 DOI: 10.3389/fmicb.2017.02592] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/12/2017] [Indexed: 11/13/2022] Open
Abstract
Microbial phosphatase activity can trigger the precipitation of metal-phosphate minerals, a process called phosphatogenesis with global geochemical and environmental implications. An increasing diversity of phosphatases expressed by diverse microorganisms has been evidenced in various environments. However, it is challenging to link the functional properties of genomic repertoires of phosphatases with the phosphatogenesis capabilities of microorganisms. Here, we studied the betaproteobacterium Ramlibacter tataouinensis (Rta), known to biomineralize Ca-phosphates in the environment and the laboratory. We investigated the functional repertoire of this biomineralization process at the cell, genome and molecular level. Based on a mineralization assay, Rta is shown to hydrolyse the phosphoester bonds of a wide range of organic P molecules. Accordingly, its genome has an unusually high diversity of phosphatases: five genes belonging to two non-homologous families, phoD and phoX, were detected. These genes showed diverse predicted cis-regulatory elements. Moreover, they encoded proteins with diverse structural properties according to molecular models. Heterologously expressed PhoD and PhoX in Escherichia coli had different profiles of substrate hydrolysis. As evidenced for Rta cells, recombinant E. coli cells induced the precipitation of Ca-phosphate mineral phases, identified as poorly crystalline hydroxyapatite. The phosphatase genomic repertoire of Rta (containing phosphatases of both the PhoD and PhoX families) was previously evidenced as prevalent in marine oligotrophic environments. Interestingly, the Tataouine sand from which Rta was isolated showed similar P-depleted, but Ca-rich conditions. Overall, the diversity of phosphatases in Rta allows the hydrolysis of a broad range of organic P substrates and therefore the release of orthophosphates (inorganic phosphate) under diverse trophic conditions. Since the release of orthophosphates is key to the achievement of high saturation levels with respect to hydroxyapatite and the induction of phosphatogenesis, Rta appears as a particularly efficient driver of this process as shown experimentally.
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Affiliation(s)
- Fériel Skouri-Panet
- Centre National de la Recherche Scientifique, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, UMR 7590, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, IRD 206, Paris, France
| | - Karim Benzerara
- Centre National de la Recherche Scientifique, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, UMR 7590, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, IRD 206, Paris, France
| | - Julie Cosmidis
- Department of Geological Sciences, University of Colorado, Boulder, CO, United States
| | - Céline Férard
- Centre National de la Recherche Scientifique, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, UMR 7590, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, IRD 206, Paris, France
| | - Géraldine Caumes
- Centre National de la Recherche Scientifique, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, UMR 7590, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, IRD 206, Paris, France
| | - Gilles De Luca
- Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Aix Marseille Univ, Centre National de la Recherche Scientifique, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Saint-Paul-lez-Durance, France
| | - Thierry Heulin
- Laboratoire d'Écologie Microbienne de la Rhizosphère et Environnements Extrêmes, UMR 7265, Aix Marseille Univ, Centre National de la Recherche Scientifique, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Saint-Paul-lez-Durance, France
| | - Elodie Duprat
- Centre National de la Recherche Scientifique, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Universités, UMR 7590, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, IRD 206, Paris, France
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17
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Lidbury IDEA, Fraser T, Murphy ARJ, Scanlan DJ, Bending GD, Jones AME, Moore JD, Goodall A, Tibbett M, Hammond JP, Wellington EMH. The 'known' genetic potential for microbial communities to degrade organic phosphorus is reduced in low-pH soils. Microbiologyopen 2017; 6:e00474. [PMID: 28419748 PMCID: PMC5552915 DOI: 10.1002/mbo3.474] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/01/2017] [Accepted: 02/16/2017] [Indexed: 11/29/2022] Open
Abstract
In soil, bioavailable inorganic orthophosphate is found at low concentrations and thus limits biological growth. To overcome this phosphorus scarcity, plants and bacteria secrete numerous enzymes, namely acid and alkaline phosphatases, which cleave orthophosphate from various organic phosphorus substrates. Using profile hidden Markov modeling approaches, we investigated the abundance of various non specific phosphatases, both acid and alkaline, in metagenomes retrieved from soils with contrasting pH regimes. This analysis uncovered a marked reduction in the abundance and diversity of various alkaline phosphatases in low-pH soils that was not counterbalanced by an increase in acid phosphatases. Furthermore, it was also discovered that only half of the bacterial strains from different phyla deposited in the Integrated Microbial Genomes database harbor alkaline phosphatases. Taken together, our data suggests that these 'phosphatase lacking' isolates likely increase in low-pH soils and future research should ascertain how these bacteria overcome phosphorus scarcity.
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Affiliation(s)
| | - Tandra Fraser
- School of Agriculture, Policy, and DevelopmentUniversity of ReadingWhiteknightsUnited Kingdom
| | - Andrew R. J. Murphy
- School of Life SciencesUniversity of WarwickCoventryWest MidlandsUnited Kingdom
| | - David J. Scanlan
- School of Life SciencesUniversity of WarwickCoventryWest MidlandsUnited Kingdom
| | - Gary D. Bending
- School of Life SciencesUniversity of WarwickCoventryWest MidlandsUnited Kingdom
| | | | - Jonathan D. Moore
- The Genome Analysis CentreNorwich Research ParkNorwichUnited Kingdom
| | - Andrew Goodall
- School of Agriculture, Policy, and DevelopmentUniversity of ReadingWhiteknightsUnited Kingdom
| | - Mark Tibbett
- School of Agriculture, Policy, and DevelopmentUniversity of ReadingWhiteknightsUnited Kingdom
| | - John P. Hammond
- School of Agriculture, Policy, and DevelopmentUniversity of ReadingWhiteknightsUnited Kingdom
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreAustralia
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