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Ren B, Ma X, Li D, Bai L, Li J, Yu J, Meng M, Li H. Nitrogen-cycling microbial communities respond differently to nitrogen addition under two contrasting grassland soil types. Front Microbiol 2024; 15:1290248. [PMID: 38873145 PMCID: PMC11169941 DOI: 10.3389/fmicb.2024.1290248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 05/06/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction The impact of nitrogen (N) deposition on the soil N-transforming process in grasslands necessitates further investigation into how N input influences the structural composition and diversity of soil N-cycling microbial communities across different grassland types. Methods In this study, we selected two types of grassland soils in northwest Liaoning, temperate steppe and warm-temperate shrub, and conducted short-term N addition experiments using organic N, ammonium N, and nitrate N as sources with three concentration gradients to simulate N deposition. Illumina MiSeq sequencing technology was employed to sequence genes associated with N-cycling microbes including N-fixing, ammonia-oxidizing and denitrifying bacteria, and ammonia-oxidizing archaea. Results and discussion The results revealed significant alterations in the structural composition and diversity of the N-cycling microbial community due to N addition, but the response of soil microorganisms varied inconsistent among different grassland types. Ammonium transformation rates had a greater impact on soils from temperate steppes while nitrification rates were more influential for soils from warm-temperate shrubs. Furthermore, the influence of the type of N source on soil N-cycling microorganisms outweighed that of its quantity applied. The ammonium type of nitrogen source is considered the most influential driving factor affecting changes in the structure of the microbial community involved in nitrogen transformation, while the amount of low nitrogen applied primarily determines the composition of soil bacterial communities engaged in nitrogen fixation and nitrification. Different groups of N-cycling microorganisms exhibited distinct responses to varying levels of nitrogen addition with a positive correlation observed between their composition, diversity, and environmental factors examined. Overall findings suggest that short-term nitrogen deposition may sustain dominant processes such as soil-N fixation within grasslands over an extended period without causing significant negative effects on northwestern Liaoning's grassland ecosystems within the next decade.
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Sepp SK, Vasar M, Davison J, Oja J, Anslan S, Al-Quraishy S, Bahram M, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Drenkhan R, Fraser L, Garibay Oriel R, Hiiesalu I, Koorem K, Kõljalg U, Moora M, Mucina L, Öpik M, Põlme S, Pärtel M, Phosri C, Semchenko M, Vahter T, Vasco Palacios AM, Tedersoo L, Zobel M. Global diversity and distribution of nitrogen-fixing bacteria in the soil. FRONTIERS IN PLANT SCIENCE 2023; 14:1100235. [PMID: 36743494 PMCID: PMC9895822 DOI: 10.3389/fpls.2023.1100235] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria.
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Affiliation(s)
- Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C. Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Juan José Cantero
- Universidad Nacional de Córdoba, Instituto Multidisciplinario de Biología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
- Universidad Nacional de Río Cuarto, Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR CNRS 7058), Jules Verne University of Picardie, Amiens, France
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Roberto Garibay Oriel
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Perth, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Sergei Põlme
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Aida M. Vasco Palacios
- Grupo de Microbiología Ambiental y Grupo BioMicro, Escuela de Microbiología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Lv F, Zhan Y, Lu W, Ke X, Shao Y, Ma Y, Zheng J, Yang Z, Jiang S, Shang L, Ma Y, Cheng L, Elmerich C, Yan Y, Lin M. Regulation of hierarchical carbon substrate utilization, nitrogen fixation, and root colonization by the Hfq/Crc/CrcZY genes in Pseudomonas stutzeri. iScience 2022; 25:105663. [PMID: 36505936 PMCID: PMC9730152 DOI: 10.1016/j.isci.2022.105663] [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: 05/27/2022] [Revised: 09/08/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Bacteria of the genus Pseudomonas consume preferred carbon substrates in nearly reverse order to that of enterobacteria, and this process is controlled by RNA-binding translational repressors and regulatory ncRNA antagonists. However, their roles in microbe-plant interactions and the underlying mechanisms remain uncertain. Here we show that root-associated diazotrophic Pseudomonas stutzeri A1501 preferentially catabolizes succinate, followed by the less favorable substrate citrate, and ultimately glucose. Furthermore, the Hfq/Crc/CrcZY regulatory system orchestrates this preference and contributes to optimal nitrogenase activity and efficient root colonization. Hfq has a central role in this regulatory network through different mechanisms of action, including repressing the translation of substrate-specific catabolic genes, activating the nitrogenase gene nifH posttranscriptionally, and exerting a positive effect on the transcription of an exopolysaccharide gene cluster. Our results illustrate an Hfq-mediated mechanism linking carbon metabolism to nitrogen fixation and root colonization, which may confer rhizobacteria competitive advantages in rhizosphere environments.
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Affiliation(s)
- Fanyang Lv
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhua Zhan
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Lu
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiubin Ke
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yahui Shao
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiyuan Ma
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Zheng
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhimin Yang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Jiang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liguo Shang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yao Ma
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | | | - Yongliang Yan
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China,Corresponding author
| | - Min Lin
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China,Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China,Corresponding author
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Mise K, Masuda Y, Senoo K, Itoh H. Undervalued Pseudo- nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers. mSphere 2021; 6:e0078521. [PMID: 34787447 PMCID: PMC8597730 DOI: 10.1128/msphere.00785-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/03/2021] [Indexed: 12/16/2022] Open
Abstract
Nitrogen fixation, a distinct process incorporating the inactive atmospheric nitrogen into the active biological processes, has been a major topic in biological and geochemical studies. Currently, insights into diversity and distribution of nitrogen-fixing microbes are dependent upon homology-based analyses of nitrogenase genes, especially the nifH gene, which are broadly conserved in nitrogen-fixing microbes. Here, we report the pitfall of using nifH as a marker of microbial nitrogen fixation. We exhaustively analyzed genomes in RefSeq (231,908 genomes) and KEGG (6,509 genomes) and cooccurrence and gene order patterns of nitrogenase genes (including nifH) therein. Up to 20% of nifH-harboring genomes lacked nifD and nifK, which encode essential subunits of nitrogenase, within 10 coding sequences upstream or downstream of nifH or on the same genome. According to a phenotypic database of prokaryotes, no species and strains harboring only nifH possess nitrogen-fixing activities, which shows that these nifH genes are "pseudo"-nifH genes. Pseudo-nifH sequences mainly belong to anaerobic microbes, including members of the class Clostridia and methanogens. We also detected many pseudo-nifH reads from metagenomic sequences of anaerobic environments such as animal guts, wastewater, paddy soils, and sediments. In some samples, pseudo-nifH overwhelmed the number of "true" nifH reads by 50% or 10 times. Because of the high sequence similarity between pseudo- and true-nifH, pronounced amounts of nifH-like reads were not confidently classified. Overall, our results encourage reconsideration of the conventional use of nifH for detecting nitrogen-fixing microbes, while suggesting that nifD or nifK would be a more reliable marker. IMPORTANCE Nitrogen-fixing microbes affect biogeochemical cycling, agricultural productivity, and microbial ecosystems, and their distributions have been investigated intensively using genomic and metagenomic sequencing. Currently, insights into nitrogen fixers in the environment have been acquired by homology searches against nitrogenase genes, particularly the nifH gene, in public databases. Here, we report that public databases include a significant amount of incorrectly annotated nifH sequences (pseudo-nifH). We exhaustively investigated the genomic structures of nifH-harboring genomes and found hundreds of pseudo-nifH sequences in RefSeq and KEGG. Over half of these pseudo-nifH sequences belonged to members of the class Clostridia, which is supposed to be a prominent nitrogen-fixing clade. We also found that the abundance of nitrogen fixers in metagenomes could be overestimated by 1.5 to >10 times due to pseudo-nifH recorded in public databases. Our results encourage reconsideration of the prevalent use of nifH as a marker of nitrogen-fixing microbes.
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Affiliation(s)
- Kazumori Mise
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Sapporo, Hokkaido, Japan
| | - Yoko Masuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Hideomi Itoh
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido, Sapporo, Hokkaido, Japan
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