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Bellanger M, Figueroa JL, Tiemann L, Friesen ML, III RW. NF ixDB (Nitrogen Fixation DataBase)-a comprehensive integrated database for robust 'omics analysis of diazotrophs. NAR Genom Bioinform 2024; 6:lqae063. [PMID: 38846350 PMCID: PMC11155484 DOI: 10.1093/nargab/lqae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Biological nitrogen fixation is a fundamental biogeochemical process that transforms molecular nitrogen into biologically available nitrogen via diazotrophic microbes. Diazotrophs anaerobically fix nitrogen using the nitrogenase enzyme which is arranged in three different gene clusters: (i) molybdenum nitrogenase (nifHDK) is the most abundant, followed by it's alternatives, (ii) vanadium nitrogenase (vnfHDK) and (iii) iron nitrogenase (anfHDK). Multiple databases have been constructed as resources for diazotrophic 'omics analysis; however, an integrated database based on whole genome references does not exist. Here, we present NFixDB (Nitrogen Fixation DataBase), a comprehensive integrated whole genome based database for diazotrophs, which includes all nitrogenases (nifHDK, vnfHDK, anfHDK) and nitrogenase-like enzymes (e.g. nflHD) linked to ribosomal RNA operons (16S-5S-23S). NFixDB was computed using Hidden Markov Models (HMMs) against the entire whole genome based Genome Taxonomy Database (GTDB R214), providing searchable reference HMMs for all nitrogenase and nitrogenase-like genes, complete ribosomal RNA operons, both GTDB and NCBI/RefSeq taxonomy, and an SQL database for querying matches. We compared NFixDB to nifH databases from Buckley, Zehr, Mise and FunGene finding extensive evidence of nifH, in addition to vnfH and nflH. NFixDB contains >4000 verified nifHDK sequences contained on 50 unique phyla of bacteria and archaea. NFixDB provides the first comprehensive nitrogenase database available to researchers unlocking diazotrophic microbial potential.
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Affiliation(s)
- Madeline Bellanger
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 N Research Campus Dr, Kannapolis, NC 28081, USA
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
| | - Jose L Figueroa
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 N Research Campus Dr, Kannapolis, NC 28081, USA
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
| | - Lisa Tiemann
- Department of Plant, Soil and Microbial Sciences, Michigan State University, Plant and Soil Sciences Building, 1066 Bogue St Room A286, East Lansing, MI 48824, USA
| | - Maren L Friesen
- Department of Plant Pathology, Washington State University, Clark Hall, 2040 Ellis Way, Pullman, WA 99163, USA
| | - Richard Allen White III
- North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 150 N Research Campus Dr, Kannapolis, NC 28081, USA
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
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Xiao D, Hong T, Chen M, He X, Wang K. Assessing the Effect of Slope Position on the Community Assemblage of Soil Diazotrophs and Root Arbuscular Mycorrhizal Fungi. J Fungi (Basel) 2023; 9:jof9040394. [PMID: 37108849 PMCID: PMC10145487 DOI: 10.3390/jof9040394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/02/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Considering the crucial role of soil diazotrophs and root arbuscular mycorrhizal fungi (AMF) in soil nutrient cycling during ecosystem restoration, diazotroph and AMF communities may be determined by slope position. However, the effect of slope position on diazotroph and AMF abundance, diversity, and community composition of karst ecosystems remains unknown. In this study, soil diazotrophs and root AMF characteristics on varying slope positions were assessed in a karst shrub ecosystem. The results displayed that the abundance of soil diazotrophs and root AMF diversity were significantly affected by slope position. Diazotroph abundance accompanied by soil nutrient and plant richness was higher on the lower slopes than the upper slopes, whereas root AMF diversity displayed the opposite trend. The soil diazotroph and root AMF community composition differed among the upper, middle, and lower slopes. The dominant taxa of soil diazotrophs and root AMF at the order level were Rhizobiales and Glomerales, respectively. Moreover, the diazotroph order of Nostocales and the AMF order of Paraglomerales were richer on the upper slopes than on the lower slopes. The slope position directly affected the plant diversity and soil nutrient distribution, indirectly affecting the diazotroph and AMF communities. Increased available nitrogen on the lower slope caused great diazotroph abundance by stimulating plant growth with sufficient carbohydrates. However, low soil nutrients and plant diversity but high plant root biomass induced more root AMF diversity on the upper slope than on the lower slope. Therefore, this study expands the knowledge of soil diazotroph and root AMF ecological functions along different slope positions during vegetation recovery for the successive stages of grass and shrub in the karst region.
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Affiliation(s)
- Dan Xiao
- Pingguo Guangxi, Karst Ecosystem, National Observation and Research Station, Pingguo 531400, China
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, Ministry of Natural Resources, Institute of Karst Geology, CAGS, Guilin 541004, China
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
| | - Tao Hong
- Pingguo Guangxi, Karst Ecosystem, National Observation and Research Station, Pingguo 531400, China
- Key Laboratory of Karst Ecosystem and Treatment of Rocky Desertification, Ministry of Natural Resources, Institute of Karst Geology, CAGS, Guilin 541004, China
| | - Meifeng Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
| | - Xunyang He
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
- Guangxi Industrial Technology Research Institute for Karst Rocky Desertification Control, Nanning 530001, China
- Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, China
| | - Kelin Wang
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Huanjiang Observation and Research Station for Karst Ecosystems, Chinese Academy of Sciences, Huanjiang 547100, China
- Guangxi Industrial Technology Research Institute for Karst Rocky Desertification Control, Nanning 530001, China
- Guangxi Key Laboratory of Karst Ecological Processes and Services, Huanjiang 547100, China
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Wang Z, Li D, Sun X, Chen H, Xiao K, Wang K. Effects of Lithology on Asymbiotic N2 Fixation in Subtropical Secondary Forests, Southwest China. Ecosystems 2023. [DOI: 10.1007/s10021-023-00824-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Flores BM, Staal A. Feedback in tropical forests of the Anthropocene. GLOBAL CHANGE BIOLOGY 2022; 28:5041-5061. [PMID: 35770837 PMCID: PMC9542052 DOI: 10.1111/gcb.16293] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 04/06/2022] [Accepted: 05/31/2022] [Indexed: 05/27/2023]
Abstract
Tropical forests are complex systems containing myriad interactions and feedbacks with their biotic and abiotic environments, but as the world changes fast, the future of these ecosystems becomes increasingly uncertain. In particular, global stressors may unbalance the feedbacks that stabilize tropical forests, allowing other feedbacks to propel undesired changes in the whole ecosystem. Here, we review the scientific literature across various fields, compiling known interactions of tropical forests with their environment, including the global climate, rainfall, aerosols, fire, soils, fauna, and human activities. We identify 170 individual interactions among 32 elements that we present as a global tropical forest network, including countless feedback loops that may emerge from different combinations of interactions. We illustrate our findings with three cases involving urgent sustainability issues: (1) wildfires in wetlands of South America; (2) forest encroachment in African savanna landscapes; and (3) synergistic threats to the peatland forests of Borneo. Our findings reveal an unexplored world of feedbacks that shape the dynamics of tropical forests. The interactions and feedbacks identified here can guide future qualitative and quantitative research on the complexities of tropical forests, allowing societies to manage the nonlinear responses of these ecosystems in the Anthropocene.
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Affiliation(s)
- Bernardo M. Flores
- Graduate Program in EcologyFederal University of Santa CatarinaFlorianopolisBrazil
| | - Arie Staal
- Copernicus Institute of Sustainable DevelopmentUtrecht UniversityUtrechtThe Netherlands
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Increasing calcium scarcity along Afrotropical forest succession. Nat Ecol Evol 2022; 6:1122-1131. [PMID: 35788708 DOI: 10.1038/s41559-022-01810-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/24/2022] [Indexed: 11/09/2022]
Abstract
Secondary forests constitute an increasingly important component of tropical forests worldwide. Although cycling of essential nutrients affects recovery trajectories of secondary forests, the effect of nutrient limitation on forest regrowth is poorly constrained. Here we use three lines of evidence from secondary forest succession sequences in central Africa to identify potential nutrient limitation in regrowing forests. First, we show that atmospheric phosphorus supply exceeds demand along forest succession, whereas forests rely on soil stocks to meet their base cation demands. Second, soil nutrient metrics indicate that available phosphorus increases along the succession, whereas available cations decrease. Finally, fine root, foliar and litter stoichiometry show that tissue calcium concentrations decline relative to those of nitrogen and phosphorus during succession. Taken together, these observations suggest that calcium becomes an increasingly scarce resource in central African forests during secondary succession. Furthermore, ecosystem calcium storage shifts from soil to woody biomass over succession, making it a vulnerable nutrient in the wake of land-use change scenarios that involve woody biomass export. Our results thus call for a broadened focus on elements other than nitrogen and phosphorus regarding tropical forest biogeochemical cycles and identify calcium as a scarce and potentially limiting nutrient in an increasingly disturbed and dynamic tropical forest landscape.
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Permin A, Horwath AB, Metcalfe DB, Priemé A, Rousk K. ‘High nitrogen‐fixing rates associated with ground‐covering mosses in a tropical mountain cloud forest will decrease drastically in a future climate’. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Aya Permin
- Terrestrial Ecology Section, Department of Biology University of Copenhagen Copenhagen Denmark
- Center for Permafrost (CENPERM) University of Copenhagen Copenhagen Denmark
| | - Aline B. Horwath
- Biological and Environmental Sciences, Faculty of Natural Sciences University of Stirling Stirling UK
| | - Daniel B. Metcalfe
- Department of Physical Geography and Ecosystem Science Lund University SE Lund Sweden
- Department of Ecology and Environmental Science SE Umeå Sweden
| | - Anders Priemé
- Center for Permafrost (CENPERM) University of Copenhagen Copenhagen Denmark
- Section of Microbiology, Department of Biology University of Copenhagen Copenhagen Denmark
| | - Kathrin Rousk
- Terrestrial Ecology Section, Department of Biology University of Copenhagen Copenhagen Denmark
- Center for Permafrost (CENPERM) University of Copenhagen Copenhagen Denmark
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Seasonal and long-term effects of nutrient additions and liming on the nifH gene in cerrado soils under native vegetation. iScience 2021; 24:102349. [PMID: 33870141 PMCID: PMC8044383 DOI: 10.1016/j.isci.2021.102349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/02/2020] [Accepted: 03/18/2021] [Indexed: 11/20/2022] Open
Abstract
Biological nitrogen fixation (BNF) represents the main input source of N in tropical savannas. BNF could be particularly important for Brazilian savannas (known as Cerrado) that show a highly conservative N cycle. We evaluated the effects of seasonal precipitation and nutrient additions on the nifH gene abundance in soils from a long-term fertilization experiment in a Cerrado's native area. The experiment consists of five treatments: (1) control, (2) liming, (3) nitrogen (N), (4) nitrogen + phosphorus (NP), and (5) phosphorus (P) additions. The nifH gene sequence was related to Bradyrhizobium members. Seasonal effects on N-fixing potential were observed by a decrease in the nifH relative abundance from rainy to dry season in control, N, and NP treatments. A significant reduction in nifH abundance was found in the liming treatment in both seasons. The findings evidenced the multiple factors controlling the potential N-fixing by free-living diazotrophs in these nutrient-limited and seasonally dry ecosystems.
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Wong MY, Neill C, Marino R, Silvério D, Howarth RW. Molybdenum, phosphorus, and pH do not constrain nitrogen fixation in a tropical forest in the southeastern Amazon. Ecology 2020; 102:e03211. [PMID: 32981087 DOI: 10.1002/ecy.3211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 07/06/2020] [Accepted: 08/06/2020] [Indexed: 01/09/2023]
Abstract
High rates of biological nitrogen fixation (BNF) are commonly reported for tropical forests, but most studies have been conducted in regions that receive substantial inputs of molybdenum (Mo) from atmospheric dust and sea-salt aerosols. Even in these regions, the low availability of Mo can constrain free-living BNF catalyzed by heterotrophic bacteria and archaea. We hypothesized that in regions where atmospheric inputs of Mo are low and soils are highly weathered, such as the southeastern Amazon, Mo would constrain BNF. We also hypothesized that the high soil acidity, characteristic of the Amazon Basin, would further constrain Mo availability and therefore soil BNF. We conducted two field experiments across the wet and dry seasons, adding Mo, phosphorus (P), and lime alone and in combination to the forest floor in the southeastern Amazon. We sampled soils and litter immediately, and then weeks and months after the applications, and measured Mo and P availability through resin extractions and BNF with the acetylene reduction assay. The experimental additions of Mo and P increased their availability and the lime increased soil pH. While the combination of Mo and P increased BNF at some time points, BNF rates did not increase strongly or consistently across the study as a whole, suggesting that Mo, P, and soil pH are not the dominant controls over BNF. In a separate short-term laboratory experiment, BNF did not respond strongly to Mo and P even when labile carbon was added. We postulate that high nitrogen (N) availability in this area of the Amazon, as indicated by the stoichiometry of soils and vegetation and the high nitrate soil stocks, likely suppresses BNF at this site. These patterns may also extend across highly weathered soils with high N availability in other topographically stable regions of the tropics.
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Affiliation(s)
- Michelle Y Wong
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA
| | | | - Roxanne Marino
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Divino Silvério
- Instituto de Pesquisa Ambiental da Amazônia (IPAM), Canarana, Mato Grosso, 78640-000, Brazil.,Departamento de Biologia, Universidade Federal Rural da Amazônia-UFRA, Capitão Poço, Pará, 68650-000, Brazil
| | - Robert W Howarth
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA.,Woods Hole Research Center, Falmouth, Massachusetts, 02450, USA
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Verryckt LT, Ellsworth DS, Vicca S, Van Langenhove L, Peñuelas J, Ciais P, Posada JM, Stahl C, Coste S, Courtois EA, Obersteiner M, Chave J, Janssens IA. Can light‐saturated photosynthesis in lowland tropical forests be estimated by one light level? Biotropica 2020. [DOI: 10.1111/btp.12817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - David S. Ellsworth
- Hawkesbury Institute for the Environment Western Sydney University Penrith NSW Australia
| | - Sara Vicca
- Department of Biology University of Antwerp Wilrijk Belgium
| | | | - Josep Peñuelas
- CREAF Barcelona Spain
- CSIC Global Ecology CREAF‐CSIC‐UAB Barcelona Spain
| | - Philippe Ciais
- Laboratoire des Sciences du Climat et de l’Environnement CEA‐CNRS‐UVSQ Gif‐sur‐Yvette France
| | - Juan M. Posada
- Biology Department Faculty of Natural Sciences Universidad del Rosario Bogotá, D.C. Colombia
| | - Clément Stahl
- INRA UMR Ecofog AgroParisTech CNRS Cirad Université des AntillesUniversité de Guyane Kourou France
| | - Sabrina Coste
- UMR Ecofog AgroParisTech CNRS Cirad INRA Université de GuyaneUniversité des Antilles Kourou France
| | - Elodie A. Courtois
- Laboratoire Ecologie, évolution, interactions des systèmes amazoniens (LEEISA) CNRS IFREMER Université de Guyane Cayenne French Guiana
| | - Michael Obersteiner
- International Institute for Applied Systems Analysis (IIASA) Laxenburg Austria
| | - Jérôme Chave
- UMR 5174 Laboratoire Evolution et Diversité Biologique CNRS Université Paul Sabatier Toulouse France
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