scholarly journals Depth-related Variability of Biological Nitrogen Fixation and Diazotrophic Communities in Mangrove Sediments

2021 ◽  
Author(s):  
Zhiwen Luo ◽  
Qiuping Zhong ◽  
Xingguo Han ◽  
Ruiwen Hu ◽  
Xingyu Liu ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Biological Nitrogen Fixation ◽  
Carbon Fixation ◽  
Metagenomic Sequencing ◽  
Low Oxygen ◽  
Mangrove Sediments ◽  
Available Nitrogen ◽  
Fixation Rate ◽  
Denitrification Genes ◽  
Biological Nitrogen

Abstract Background: Nitrogen-fixing microorganisms (diazotrophs) provide biological available nitrogen and play a pivotal role in nitrogen cycling of mangrove sediments. However, most studies on diazotrophs have been restricted to easily accessible surface sediments, while the diversity, structure and ecological function of diazotrophic communities at the in-depth profile of mangrove sediments are largely unknown. Here, we investigated how biological nitrogen fixation vary with depth of mangrove sediments from the perspective of both NFR and diazotrophic communities.Results: Through acetylene reduction assay, nifH gene amplicon and metagenomic sequencing, we found that the nitrogen fixation rate (NFR) increased but the diversity of diazotrophic community decreased with the depth of mangrove sediments. The structure of diazotrophic communities at different depths was largely driven by salinity, and exhibited a clear divergence at the partition depth of 50 cm. Agrobacterium and Azotobacter were specifically enriched at 50-100 cm sediments, while aerobic diazotrophs such as Methylomonas had a higher abundance at 0-30 cm. Consistent with the higher NFR, metagenomic analysis indicated the elevated abundance of nitrogen fixation genes (nifH/D/K) in deeper sediment layers, where nitrification genes (amoA/B/C) and denitrification genes (nirK and norB) became less abundant. Three metagenome-assembled genomes (MAGs) of diazotrophs from deep mangrove sediments indicated their facultative anaerobic and amphitrophic lifestyles as they contained genes for low-oxygen-dependent metabolism, hydrogenotrophic respiration, carbon fixation and pyruvate fermentation.Conclusions: Together, this study determines the depth-related variability of NFR and diazotrophs, which potentially contribute to nitrogen sinks and relieve nitrogen limitation, especially in the deep sediments of mangrove ecosystems.

Early response of biological nitrogen fixation in a mature oak dominated forest to elevated atmospheric CO2 fumigation at BIFoR-FACE

2020 ◽  
Author(s):  
Sami Ullah ◽  
Ernesto Saiz Val ◽  
Fotis Sgouridis ◽  
Falko Drijfhout
Keyword(s):  
Carbon Dioxide ◽  
Nitrogen Fixation ◽  
Biological Nitrogen Fixation ◽  
Early Years ◽  
Available Nitrogen ◽  
Preliminary Results ◽  
Hypnum Cupressiforme ◽  
Feather Moss ◽  
Feather Mosses ◽  
Biological Nitrogen

<p>Elevated atmospheric carbon dioxide concentrations are stimulating photosynthesis and carbon sequestration. However, the extent of photosynthetic stimulation in forests under future climates is highly uncertain given that nutrient limitation in soils may constrain the CO<sub>2</sub> fertilization effect. The Birmingham Institute of Forest Research (BIFoR), University of Birmingham established the only global mature temperate deciduous forests Free Air Carbon Dioxide Enrichment (FACE) experiment to study the response of forests to future climates. Fumigation of the forest with ~550 ppm CO<sub>2</sub> started in 2017 and will continue until at least 2026. Soil nutrients cycling including nitrogen transformation in response to elevated atmospheric CO<sub>2</sub> (eCO<sub>2</sub>) fumigation is currently investigated to determine the role of nutrient availability in carbon capture by forests. In this paper, we show preliminary results of the response of asymbiotic biological nitrogen fixation (BNF) in soils and epiphytic bryophytes at BIFoR-FACE following a year of eCO<sub>2</sub> fumigation. It is hypothesized that the demand for available nitrogen by trees will increase under eCO<sub>2</sub> and that competition of roots and soil microbes for available nitrogen will enhance asymbiotic BNF to at least meet microbial metabolic nitrogen demands in the long run. Surface soils (0-5 cm) and epiphytic feather moss (Hypnum cupressiforme) growing on oak tree stems in the FACE site were  collected during the second year of eCO<sub>2</sub> fumigation for the quantification of BNF activity using the <sup>15</sup>N<sub>2</sub> assimilation methods (Saiz et al. 2019). Samples were incubated in 50 mL serum bottles under in situ conditions, followed by the analysis of soil and tissue samples for <sup>15</sup>N signature on an Isotope Ratio Mass Spectrometer for the quantification of BNF activity.</p><p>The BNF activity under eCO<sub>2</sub> were 369% higher than in soils under ambient atmospheric CO<sub>2</sub>. BNF rates associated with feather mosses (Hypnum cupressiforme) did not differ between the eCO<sub>2</sub> and control plots; however, rates under eCO<sub>2</sub> on average were 60% lower than in the control plots. Unlike soils, the moisture of feather mosses correlated significantly (R<sup>2</sup> = 51%) with BNF activity. Among nutrients in soil with implications for BNF activity, the concentrations of Mg, K, Co and Ni were significantly lower in soils under eCO<sub>2</sub> than in the control plots, while in feather moss tissues no differences were observed.  Our preliminary results show that eCO<sub>2</sub> fumigation primed asymbiotic BNF activity in soils. An enhancement of BNF together with the observation of a relatively low nutrient content under eCO<sub>2</sub> points to important changes in nitrogen cycling processes in the early years of CO<sub>2</sub> fumigation. Further detailed studies are underway to fully disentangle controls on nitrogen availability to trees under future climates.</p><p><strong> </strong></p><p><strong>Reference</strong></p><p>Saiz, E, Sgouridis, F, Drifjhout, F & Ullah, S. 2019. Biological nitrogen fixation in peatlands: comparison between acetylene reduction assay and <sup>15</sup>N<sub>2</sub> assimilation methods. Soil Biol. Biochem:131:157-165</p>

scholarly journals Impacts of biological nitrogen fixation on N<sub>2</sub>O emissions from global natural terrestrial ecosystem soils: An Analysis with a process-based biogeochemistry model

2019 ◽  
Author(s):  
Tong Yu ◽  
Qianlai Zhuang
Keyword(s):  
Nitrogen Fixation ◽  
Biological Nitrogen Fixation ◽  
Terrestrial Ecosystem ◽  
Terrestrial Ecosystems ◽  
Climatic Conditions ◽  
N2o Emissions ◽  
Emission Model ◽  
Fixation Rate ◽  
Observational Site ◽  
Biological Nitrogen

Abstract. Biological nitrogen fixation plays an important role in the global nitrogen cycle. However, the fixation rate has been usually measured or estimated at a particular observational site. To quantify the fixation amount at the global scale, a process-based model is needed. This study develops a biological nitrogen fixation model and couples it with an extant biogeochemistry model of N2O emissions to examine the fixation rate and its effects on N2O emissions. The revised N2O emission model better matches the observed data in comparison with our previous model that has not considered the fixation effects. The new model estimates that tropical forests have the highest fixation rate among all ecosystem types, and decrease from the equator to the polar region. The estimated nitrogen fixation in global terrestrial ecosystems is 61.5 Tg N yr−1 with a range of 19.8–107.9 Tg N yr−1 in the 1990s. Our estimates are relatively low compared to some early estimates using empirical approaches, but comparable to more recent estimates that involve more detailed processes in their modeling. Furthermore, we estimate that the fixation contributes to −5 % to 20 % changes in N2O emissions compared to our previous estimates, depending on ecosystem types and climatic conditions. This study highlights that there are relatively large effects of the biological nitrogen fixation on ecosystem nitrogen cycling and soil N2O emissions and calls for more comprehensive understanding of biological nitrogen fixation and more observational data for different ecosystems to improve future quantification of the fixation and its impacts.

scholarly journals Modeling biological nitrogen fixation in global natural terrestrial ecosystems

2020 ◽  
Vol 17 (13) ◽  
pp. 3643-3657
Author(s):  
Tong Yu ◽  
Qianlai Zhuang
Keyword(s):  
Nitrogen Fixation ◽  
Nitrogen Cycle ◽  
Biological Nitrogen Fixation ◽  
Terrestrial Ecosystems ◽  
Global Scale ◽  
Climatic Conditions ◽  
Fixation Rate ◽  
Observational Site ◽  
Biological Nitrogen ◽  
Global Nitrogen Cycle

Abstract. Biological nitrogen fixation plays an important role in the global nitrogen cycle. However, the fixation rate has been usually measured or estimated at a particular observational site. To quantify the fixation amount at the global scale, process-based models are needed. This study develops a biological nitrogen fixation model to quantitatively estimate the nitrogen fixation rate by plants in a natural environment. The revised nitrogen module better simulates the nitrogen cycle in comparison with our previous model that has not considered the fixation effects. The new model estimates that tropical forests have the highest fixation rate among all ecosystem types, which decreases from the Equator to the polar region. The estimated nitrogen fixation in global terrestrial ecosystems is 61.5 Tg N yr−1 with a range of 19.8–107.9 Tg N yr−1 in the 1990s. Our estimates are relatively low compared to some early estimates using empirical approaches but comparable to more recent estimates that involve more detailed processes in their modeling. Furthermore, the contribution of nitrogen made by biological nitrogen fixation depends on ecosystem type and climatic conditions. This study highlights that there are relatively large effects of biological nitrogen fixation on ecosystem nitrogen cycling. and the large uncertainty of the estimation calls for more comprehensive understanding of biological nitrogen fixation. More direct observational data for different ecosystems are in need to improve future quantification of fixation and its impacts.

scholarly journals Functional analysis of multiple nifB genes of Paenibacillus strains in synthesis of Mo-, Fe- and V-nitrogenases

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Qin Li ◽  
Haowei Zhang ◽  
Liqun Zhang ◽  
Sanfeng Chen
Keyword(s):  
Functional Analysis ◽  
Nitrogen Fixation ◽  
Gene Cluster ◽  
Biological Nitrogen Fixation ◽  
Deletion Analysis ◽  
Phylogeny Analysis ◽  
Biological Nitrogen

Abstract Background Biological nitrogen fixation is catalyzed by Mo-, V- and Fe-nitrogenases that are encoded by nif, vnf and anf genes, respectively. NifB is the key protein in synthesis of the cofactors of all nitrogenases. Most diazotrophic Paenibacillus strains have only one nifB gene located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV). But some Paenibacillus strains have multiple nifB genes and their functions are not known. Results A total of 138 nifB genes are found in the 116 diazotrophic Paenibacillus strains. Phylogeny analysis shows that these nifB genes fall into 4 classes: nifBI class including the genes (named as nifB1 genes) that are the first gene within the compact nif gene cluster, nifBII class including the genes (named as nifB2 genes) that are adjacent to anf or vnf genes, nifBIII class whose members are designated as nifB3 genes and nifBIV class whose members are named as nifB4 genes are scattered on genomes. Functional analysis by complementation of the ∆nifB mutant of P. polymyxa which has only one nifB gene has shown that both nifB1 and nifB2 are active in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Deletion analysis also has revealed that nifB1 of Paenibacillus sabinae T27 is involved in synthesis of Mo-nitrogenase, while nifB3 and nifB4 genes are not. Complementation of the P. polymyxa ∆nifBHDK mutant with the four reconstituted operons: nifB1anfHDGK, nifB2anfHDGK, nifB1vnfHDGK and nifB2vnfHDGK, has shown both that nifB1 and nifB2 were able to support synthesis of Fe- or V-nitrogenases. Transcriptional results obtained in the original Paenibacillus strains are consistent with the complementation results. Conclusions The multiple nifB genes of the diazotrophic Paenibacillus strains are divided into 4 classes. The nifB1 located in a compact nif gene cluster (nifBHDKENX(orf1)hesAnifV) and the nifB2 genes being adjacent to nif or anf or vnf genes are active in synthesis of Mo-, Fe and V-nitrogenases, but nifB3 and nifB4 are not. The reconstituted anf system comprising 8 genes (nifBanfHDGK and nifXhesAnifV) and vnf system comprising 10 genes (nifBvnfHDGKEN and nifXhesAnifV) support synthesis of Fe-nitrogenase and V-nitrogenase in Paenibacillus background, respectively.

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