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He C, Harindintwali JD, Cui H, Yao J, Wang Z, Zhu Q, Wang F, Yang J. Warm growing season activates microbial nutrient cycling to promote fertilizer nitrogen uptake by maize. Microbiol Res 2025; 290:127936. [PMID: 39503078 DOI: 10.1016/j.micres.2024.127936] [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] [Received: 07/21/2024] [Revised: 09/16/2024] [Accepted: 10/16/2024] [Indexed: 12/12/2024]
Abstract
The influence of nitrogen (N) inputs on soil microbial communities and N uptake by plants is well-documented. Seasonal variations further impact these microbial communities and their nutrient-cycling functions, particularly within multiple cropping systems. Nevertheless, the combined effects of N fertilization and growing seasons on soil microbial communities and plant N uptake remain ambiguous, thereby constraining our comprehension of the optimal growing season for maximizing crop production. In this study, we employed 15N isotope labeling, high-throughput sequencing, and quantitative polymerase chain reaction (qPCR) techniques to investigate the effects of two distinct growing seasons on microbial communities and maize 15N uptake ratios (15NUR). Our results showed that the warm growing season (26.6 °C) increased microbial diversity, reduced network complexity but enhanced stability, decreased microbial associations, and increased modularization compared to the cool growing season (23.1 °C). Additionally, the warm growing season favored oligotrophic species and increased the abundance of microbial guilds and functional genes related to N, phosphorus, and sulfur cycling. Furthermore, alterations in the characteristics of soil microbial keystone taxa were closely linked to variations in maize 15NUR. Overall, our findings demonstrate significant seasonal variations in soil microbial diversity and functioning, with maize exhibiting higher 15NUR during the warm growing season of the double cropping system.
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Asamoto CK, Ryu Y, Eckartt KN, Kelley-Kern J, Dietrich LE, Sigman DM, Kopf SH. Stable isotopic signature of dissimilatory nitrate reduction is robust against enzyme mutation. Proc Natl Acad Sci U S A 2024; 121:e2416002121. [PMID: 39576351 PMCID: PMC11621745 DOI: 10.1073/pnas.2416002121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Accepted: 10/28/2024] [Indexed: 11/24/2024] Open
Abstract
The proportionality of oxygen-to-nitrogen isotope effects (18ε/15ε) is used as a key isotopic signature of nitrogen cycling processes in the environment. Dissimilatory nitrate reduction is observed to have an 18ε/15ε proportionality of ~0.9 in marine and ~0.6 in freshwater/terrestrial ecosystems. The origins of this difference are uncertain, with both geochemical and biological factors conceivably at play. One potential factor is variation in the isotope effect of nitrate reduction among different forms of the nitrate reductase enzyme. NarG nitrate reductases are observed to typically have an 18ε/15ε of ~0.9. However, a recent study uncovered an exception, with Bacillus NarG enzymes having an 18ε/15ε proportionality of ~0.6. This provides an opportunity to investigate genetic controls on 18ε/15ε. Furthermore, this atypical NarG signature also raises the question of whether intrinsic isotope signatures can evolve as the enzymes that produce them accumulate mutations through time. Here, we present data from site-directed mutagenesis experiments of key NarG residues, which suggest that the distinct Bacillus 18ε/15ε cannot be caused by single mutations alone and is potentially uncommon in nature. Variation in the intrinsic isotope effects of an enzyme through time may thus require more extensive evolutionary changes.
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Halverson-Kolkind KA, Caputo N, Lampi KJ, Srivastava O, David LL. Measurement of absolute abundance of crystallins in human and αA N101D transgenic mouse lenses using 15N-labeled crystallin standards. Exp Eye Res 2024; 248:110115. [PMID: 39368693 DOI: 10.1016/j.exer.2024.110115] [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] [Received: 07/21/2024] [Revised: 09/17/2024] [Accepted: 10/02/2024] [Indexed: 10/07/2024]
Abstract
Stable isotope labeled standards of all major human lens crystallins were created to measure the abundance of lens endogenous crystallins from birth to adulthood. All major human crystallins (αA, αB, βA2, βA3/A1, βA4, βB1, βB2, βB3, γA, γB, γC, γD, γS) were cloned with N-terminal 6 x His tagged SUMO for ease of purification and the ability to generate natural N-termini by SUMO protease cleavage when producing crystallins for structure/function studies. They were then expressed in 15N-enriched media, quantified by mass spectrometry, and mixed in proportions found in young human lens to act as an artificial lens standard. The absolute quantification method was tested using soluble protein from 5-day, 23-day, 18-month, and 18-year-old human lenses spiked with the 15N artificial lens standard. Proteins were trypsinized, relative ratios of light and heavy labeled peptides determined using high-resolution precursor and data independent MS2 scans, and data analysis performed using Skyline software. Crystallin abundances were measured in both human donor lenses and in transgenic mouse αA N101D cataract lenses. Technical replicates of human crystallin abundance measurements were performed with average coefficients of variation of approximately 2% across all 13 crystallins. αA crystallin comprised 27% of the soluble protein of 5-day-old lens and decreased to 16% by 18-years of age. Over this time period αB increased from 6% to 9% and the αA/αB ratio decreased from 4.5/1 to 2/1. γS-crystallin also increased nearly 2-fold from 7% to 12%, becoming the 3rd most abundant protein in adult lens, while βB1 increased from 14% to 20%, becoming the most abundant crystallin of adult lens. Minor crystallins βA2, βB3, and γA comprised only about 1% each of the newborn lens soluble protein, and their abundance dropped precipitously by adulthood. While 9 of the SUMO tagged crystallins were useful for purification of crystallins for structural studies, γA, γB, γC, and γD were resistant to cleavage by SUMO protease. The abundance of WT and N101D human αA in transgenic mouse lenses was approximately 40-fold lower than endogenous mouse αA, but the deamidation mimic human αA N101D was less soluble than human WT αA. The high content of αA and the transient abundance of βA2, βB3, and γA in young lens suggest these crystallins play a role in early lens development and growth. βB1 becoming the most abundant crystallin may result from its role in promoting higher order β-crystallin oligomerization in mature lens. The full set of human crystallin expression vectors in the Addgene repository should be a useful resource for future crystallin studies. 15N labeling of these crystallins will be useful to accurately quantify crystallins in lens anatomic regions, as well as measure the composition of insoluble light scattering crystallin aggregates. The standards will also be useful to measure the abundance of crystallins expressed in transgenic animal models.
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Wannicke N, Stüeken EE, Bauersachs T, Gehringer MM. Exploring the influence of atmospheric CO 2 and O 2 levels on the utility of nitrogen isotopes as proxy for biological N 2 fixation. Appl Environ Microbiol 2024; 90:e0057424. [PMID: 39320082 PMCID: PMC11497790 DOI: 10.1128/aem.00574-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 08/26/2024] [Indexed: 09/26/2024] Open
Abstract
Biological N2 fixation (BNF) is traced to the Archean. The nitrogen isotopic fractionation composition (δ15N) of sedimentary rocks is commonly used to reconstruct the presence of ancient diazotrophic ecosystems. While δ15N has been validated mostly using organisms grown under present-day conditions; it has not under the pre-Cambrian conditions, when atmospheric pO2 was lower and pCO2 was higher. Here, we explore δ15N signatures under three atmospheres with (i) elevated CO2 and no O2 (Archean), (ii) present-day CO2, and O2 and (iii) future elevated CO2, in marine and freshwater, heterocytous cyanobacteria. Additionally, we augment our data set from literature for more generalized dependencies of δ15N and the associated fractionation factor epsilon (ε = δ15Nbiomass - δ15NN2) during BNF in Archaea and Bacteria, including cyanobacteria, and habitats. The ε ranges between 3.70‰ and -4.96‰ with a mean ε value of -1.38 ± 0.95‰, for all bacteria, including cyanobacteria, across all tested conditions. The expanded data set revealed correlations of isotopic fractionation of BNF with CO2 concentrations, toxin production, and light, although within 1‰. Moreover, correlation showed significant dependency of ε to species type, C/N ratios and toxin production in cyanobacteria, albeit it within a small range (-1.44 ± 0.89‰). We therefore conclude that δ15N is likely robust when applied to the pre-Cambrian-like atmosphere, stressing the strong cyanobacterial bias. Interestingly, the increased fractionation (lower ε) observed in the toxin-producing Nodularia and Nostoc spp. suggests a heretofore unknown role of toxins in modulating nitrogen isotopic signals that warrants further investigation.IMPORTANCENitrogen is an essential element of life on Earth; however, despite its abundance, it is not biologically accessible. Biological nitrogen fixation is an essential process whereby microbes fix N2 into biologically usable NH3. During this process, the enzyme nitrogenase preferentially uses light 14N, resulting in 15N depleted biomass. This signature can be traced back in time in sediments on Earth, and possibly other planets. In this paper, we explore the influence of pO2 and pCO2 on this fractionation signal. We find the signal is stable, especially for the primary producers, cyanobacteria, with correlations to CO2, light, and toxin-producing status, within a small range. Unexpectedly, we identified higher fractionation signals in toxin-producing Nodularia and Nostoc species that offer insight into why some organisms produce these N-rich toxic secondary metabolites.
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Mantha OL, Mahé M, Mahéo K, Fromont G, Guéguinou M, Tea I, Hankard R, De Luca A. Understanding natural isotopic variations in cultured cancer cells. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9878. [PMID: 39117991 DOI: 10.1002/rcm.9878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 06/14/2024] [Accepted: 07/15/2024] [Indexed: 08/10/2024]
Abstract
RATIONALE Natural variations in the abundance of the stable isotopes of nitrogen (δ15N) and carbon (δ13C) offer valuable insights into metabolic fluxes. In the wake of strong interest in cancer metabolism, recent research has revealed δ15N and δ13C variations in cancerous compared to non-cancerous tissues and cell lines. However, our understanding of natural isotopic variations in cultured mammalian cells, particularly in relation to metabolism, remains limited. This study aims to start addressing this gap using metabolic modulations in cells cultured under controlled conditions. METHODS Prostate cancer cells (PC3) were cultured in different conditions and their δ15N and δ13C were measured using isotope ratio mass spectrometry. Isotopic variations during successive cell culture passages were assessed and two widely used cell culture media (RPMI and DMEM) were compared. Metabolism was modulated through glutamine deprivation and hypoxia. RESULTS Successive cell culture passages generally resulted in reproducible δ15N and δ13C values. The impact of culture medium composition on δ15N and δ13C of the cells highlights the importance of maintaining a consistent medium composition across conditions whenever possible. Glutamine deprivation and hypoxia induced a lower δ13C in bulk cell samples, with only the former affecting δ15N. Gaps between theory and experiments were bridged and the lessons learned throughout the process are provided. CONCLUSIONS Exposing cultured cancer cells to hypoxia allowed us to further investigate the relation between metabolic modulations and natural isotopic variations, while mitigating the confounding impact of changing culture medium composition. This study highlights the potential of natural δ13C variations for studying substrate fluxes and nutrient allocation in reproducible culture conditions. Considering cell yield and culture medium composition is pivotal to the success of this approach.
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Doby JR, Siniscalchi CM, Pajuelo M, Krigbaum J, Soltis DE, Guralnick RP, Folk RA. Elemental and isotopic analysis of leaves predicts nitrogen-fixing phenotypes. Sci Rep 2024; 14:20065. [PMID: 39209870 PMCID: PMC11362558 DOI: 10.1038/s41598-024-70412-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Nitrogen (N)-fixing symbiosis is critical to terrestrial ecosystems, yet possession of this trait is known for few plant species. Broader presence of the symbiosis is often indirectly determined by phylogenetic relatedness to taxa investigated via manipulative experiments. This data gap may ultimately underestimate phylogenetic, spatial, and temporal variation in N-fixing symbiosis. Still needed are simpler field or collections-based approaches for inferring symbiotic status. N-fixing plants differ from non-N-fixing plants in elemental and isotopic composition, but previous investigations have not tested predictive accuracy using such proxies. Here we develop a regional field study and demonstrate a simple classification model for fixer status using nitrogen and carbon content measurements, and stable isotope ratios (δ15N and δ13C), from field-collected leaves. We used mixed models and classification approaches to demonstrate that N-fixing phenotypes can be used to predict symbiotic status; the best model required all predictors and was 80-94% accurate. Predictions were robust to environmental context variation, but we identified significant variation due to native vs. non-native (exotic) status and phylogenetic affinity. Surprisingly, N content-not δ15N-was the strongest predictor, suggesting that future efforts combine elemental and isotopic information. These results are valuable for understudied taxa and ecosystems, potentially allowing higher-throughput field-based N-fixer assessments.
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Helmer M, Helmer D, Yohannes E, Newton J, Dietrich DR, Martin-Creuzburg D. Dissolved nitrogen uptake versus nitrogen fixation: Mode of nitrogen acquisition affects stable isotope signatures of a diazotrophic cyanobacterium and its grazer. PLoS One 2024; 19:e0306173. [PMID: 39088456 PMCID: PMC11293670 DOI: 10.1371/journal.pone.0306173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/12/2024] [Indexed: 08/03/2024] Open
Abstract
Field studies suggest that changes in the stable isotope ratios of phytoplankton communities can be used to track changes in the utilization of different nitrogen sources, i.e., to detect shifts from dissolved inorganic nitrogen (DIN) uptake to atmospheric nitrogen (N2) fixation by diazotrophic cyanobacteria as an indication of nitrogen limitation. We explored changes in the stable isotope signature of the diazotrophic cyanobacterium Trichormus variabilis in response to increasing nitrate (NO3-) concentrations (0 to 170 mg L-1) under controlled laboratory conditions. In addition, we explored the influence of nitrogen utilization at the primary producer level on trophic fractionation by studying potential changes in isotope ratios in the freshwater model Daphnia magna feeding on the differently grown cyanobacteria. We show that δ 15N values of the cyanobacterium increase asymptotically with DIN availability, from -0.7 ‰ in the absence of DIN (suggesting N2 fixation) to 2.9 ‰ at the highest DIN concentration (exclusive DIN uptake). In contrast, δ 13C values of the cyanobacterium did not show a clear relationship with DIN availability. The stable isotope ratios of the consumer reflected those of the differently grown cyanobacteria but also revealed significant trophic fractionation in response to nitrogen utilization at the primary producer level. Nitrogen isotope turnover rates of Daphnia were highest in the absence of DIN as a consequence of N2 fixation and resulting depletion in 15N at the primary producer level. Our results highlight the potential of stable isotopes to assess nitrogen limitation and to explore diazotrophy in aquatic food webs.
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Hu CC, Liu XY, Driscoll AW, Kuang YW, Brookshire ENJ, Lü XT, Chen CJ, Song W, Mao R, Liu CQ, Houlton BZ. Global distribution and drivers of relative contributions among soil nitrogen sources to terrestrial plants. Nat Commun 2024; 15:6407. [PMID: 39079989 PMCID: PMC11289379 DOI: 10.1038/s41467-024-50674-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
Soil extractable nitrate, ammonium, and organic nitrogen (N) are essential N sources supporting primary productivity and regulating species composition of terrestrial plants. However, it remains unclear how plants utilize these N sources and how surface-earth environments regulate plant N utilization. Here, we establish a framework to analyze observational data of natural N isotopes in plants and soils globally, we quantify fractional contributions of soil nitrate (fNO3-), ammonium (fNH4+), and organic N (fEON) to plant-used N in soils. We find that mean annual temperature (MAT), not mean annual precipitation or atmospheric N deposition, regulates global variations of fNO3-, fNH4+, and fEON. The fNO3- increases with MAT, reaching 46% at 28.5 °C. The fNH4+ also increases with MAT, achieving a maximum of 46% at 14.4 °C, showing a decline as temperatures further increase. Meanwhile, the fEON gradually decreases with MAT, stabilizing at about 20% when the MAT exceeds 15 °C. These results clarify global plant N-use patterns and reveal temperature rather than human N loading as a key regulator, which should be considered in evaluating influences of global changes on terrestrial ecosystems.
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Kinslow CJ, Ll MB, Cai Y, Yan J, Lorkiewicz PK, Al-Attar A, Tan J, Higashi RM, Lane AN, Fan TWM. Stable isotope-resolved metabolomics analyses of metabolic phenotypes reveal variable glutamine metabolism in different patient-derived models of non-small cell lung cancer from a single patient. Metabolomics 2024; 20:87. [PMID: 39068202 PMCID: PMC11317205 DOI: 10.1007/s11306-024-02126-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/02/2024] [Indexed: 07/30/2024]
Abstract
INTRODUCTION Stable isotope tracers have been increasingly used in preclinical cancer model systems, including cell culture and mouse xenografts, to probe the altered metabolism of a variety of cancers, such as accelerated glycolysis and glutaminolysis and generation of oncometabolites. Comparatively little has been reported on the fidelity of the different preclinical model systems in recapitulating the aberrant metabolism of tumors. OBJECTIVES We have been developing several different experimental model systems for systems biochemistry analyses of non-small cell lung cancer (NSCLC1) using patient-derived tissues to evaluate appropriate models for metabolic and phenotypic analyses. METHODS To address the issue of fidelity, we have carried out a detailed Stable Isotope-Resolved Metabolomics study of freshly resected tissue slices, mouse patient derived xenografts (PDXs), and cells derived from a single patient using both 13C6-glucose and 13C5,15N2-glutamine tracers. RESULTS Although we found similar glucose metabolism in the three models, glutamine utilization was markedly higher in the isolated cell culture and in cell culture-derived xenografts compared with the primary cancer tissue or direct tissue xenografts (PDX). CONCLUSIONS This suggests that caution is needed in interpreting cancer biochemistry using patient-derived cancer cells in vitro or in xenografts, even at very early passage, and that direct analysis of patient derived tissue slices provides the optimal model for ex vivo metabolomics. Further research is needed to determine the generality of these observations.
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Su X, Huang X, Zhang Y, Yang L, Wen T, Yang X, Zhu G, Zhang J, Tang Y, Li Z, Ding J, Li R, Pan J, Chen X, Huang F, Rillig MC, Zhu YG. Nitrifying niche in estuaries is expanded by the plastisphere. Nat Commun 2024; 15:5866. [PMID: 38997249 PMCID: PMC11245476 DOI: 10.1038/s41467-024-50200-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
The estuarine plastisphere, a novel ecological habitat in the Anthropocene, has garnered global concerns. Recent geochemical evidence has pointed out its potential role in influencing nitrogen biogeochemistry. However, the biogeochemical significance of the plastisphere and its mechanisms regulating nitrogen cycling remain elusive. Using 15N- and 13C-labelling coupled with metagenomics and metatranscriptomics, here we unveil that the plastisphere likely acts as an underappreciated nitrifying niche in estuarine ecosystems, exhibiting a 0.9 ~ 12-fold higher activity of bacteria-mediated nitrification compared to surrounding seawater and other biofilms (stone, wood and glass biofilms). The shift of active nitrifiers from O2-sensitive nitrifiers in the seawater to nitrifiers with versatile metabolisms in the plastisphere, combined with the potential interspecific cooperation of nitrifying substrate exchange observed among the plastisphere nitrifiers, collectively results in the unique nitrifying niche. Our findings highlight the plastisphere as an emerging nitrifying niche in estuarine environment, and deepen the mechanistic understanding of its contribution to marine biogeochemistry.
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Villamarín F, Jardine TD, Bunn SE, Malvasio A, Piña CI, Jacobi CM, Araújo DD, de Brito ES, de Moraes Carvalho F, da Costa ID, Verdade LM, Lara N, de Camargo PB, Miorando PS, Portelinha TCG, Marques TS, Magnusson WE. Body size predicts ontogenetic nitrogen stable-isotope (δ 15N) variation, but has little relationship with trophic level in ectotherm vertebrate predators. Sci Rep 2024; 14:14102. [PMID: 38890338 PMCID: PMC11189434 DOI: 10.1038/s41598-024-61969-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
Large predators have disproportionate effects on their underlying food webs. Thus, appropriately assigning trophic positions has important conservation implications both for the predators themselves and for their prey. Large-bodied predators are often referred to as apex predators, implying that they are many trophic levels above primary producers. However, theoretical considerations predict both higher and lower trophic position with increasing body size. Nitrogen stable isotope values (δ15N) are increasingly replacing stomach contents or behavioral observations to assess trophic position and it is often assumed that ontogenetic dietary shifts result in higher trophic positions. Intraspecific studies based on δ15N values found a positive relationship between size and inferred trophic position. Here, we use datasets of predatory vertebrate ectotherms (crocodilians, turtles, lizards and fishes) to show that, although there are positive intraspecific relationships between size and δ15N values, relationships between stomach-content-based trophic level (TPdiet) and size are undetectable or negative. As there is usually no single value for 15N trophic discrimination factor (TDF) applicable to a predator species or its prey, estimates of trophic position based on δ15N in ectotherm vertebrates with large size ranges, may be inaccurate and biased. We urge a reconsideration of the sole use of δ15N values to assess trophic position and encourage the combined use of isotopes and stomach contents to assess diet and trophic level.
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Gan HY, Hohberg K, Schneider C, Ebner M, Marais E, Miranda T, Lehmitz R, Maggs-Kölling G, Bocherens H. The hidden oases: unveiling trophic dynamics in Namib's fog plant ecosystem. Sci Rep 2024; 14:13334. [PMID: 38858480 PMCID: PMC11164947 DOI: 10.1038/s41598-024-61796-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/09/2024] [Indexed: 06/12/2024] Open
Abstract
The Namib Desert is a hyperarid coastal desert where fog is a major moisture source. We hypothesized that the fog-harvesting grass Stipagrostis sabulicola establishes an important ecological niche, termed the "Fog-Plant-Oases" (FPOs), and serves as the primary carbon source for the invertebrate community. To determine this, we measured the natural variations of the stable carbon and nitrogen isotopes (δ13C and δ15N) of invertebrates as well as that of plant biomass and belowground detritus and estimated the contributions of the fog plants in their diets. Our findings revealed a complex trophic structure and demonstrated that S. sabulicola fuels carbon flow from lower to higher trophic levels in the aboveground food web. The distinct δ13C values of bacterial- and fungal-feeding nematodes indicated however the separation of the aboveground niche, which is primarily sustained by S. sabulicola, from the belowground niche, where wind-blown sediments may serve as the main energy source for the soil biota. Our findings further accentuate the critical role of S. sabulicola FPOs in establishing complex trophic dynamics and a distinctive food web within the hyperarid Namib dunes.
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Fan KT, Xu Y, Hegeman AD. Elevated Temperature Effects on Protein Turnover Dynamics in Arabidopsis thaliana Seedlings Revealed by 15N-Stable Isotope Labeling and ProteinTurnover Algorithm. Int J Mol Sci 2024; 25:5882. [PMID: 38892074 PMCID: PMC11172382 DOI: 10.3390/ijms25115882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024] Open
Abstract
Global warming poses a threat to plant survival, impacting growth and agricultural yield. Protein turnover, a critical regulatory mechanism balancing protein synthesis and degradation, is crucial for the cellular response to environmental changes. We investigated the effects of elevated temperature on proteome dynamics in Arabidopsis thaliana seedlings using 15N-stable isotope labeling and ultra-performance liquid chromatography-high resolution mass spectrometry, coupled with the ProteinTurnover algorithm. Analyzing different cellular fractions from plants grown under 22 °C and 30 °C growth conditions, we found significant changes in the turnover rates of 571 proteins, with a median 1.4-fold increase, indicating accelerated protein dynamics under thermal stress. Notably, soluble root fraction proteins exhibited smaller turnover changes, suggesting tissue-specific adaptations. Significant turnover alterations occurred with redox signaling, stress response, protein folding, secondary metabolism, and photorespiration, indicating complex responses enhancing plant thermal resilience. Conversely, proteins involved in carbohydrate metabolism and mitochondrial ATP synthesis showed minimal changes, highlighting their stability. This analysis highlights the intricate balance between proteome stability and adaptability, advancing our understanding of plant responses to heat stress and supporting the development of improved thermotolerant crops.
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Gao F, Li Y, Fan H, Luo D, Chapman SJ, Yao H. 15N-DNA stable isotope probing reveals niche differentiation of ammonia oxidizers in paddy soils. Appl Microbiol Biotechnol 2024; 108:342. [PMID: 38789552 PMCID: PMC11126484 DOI: 10.1007/s00253-024-13170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/14/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
Chemoautotrophic canonical ammonia oxidizers (ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB)) and complete ammonia oxidizers (comammox Nitrospira) are accountable for ammonia oxidation, which is a fundamental process of nitrification in terrestrial ecosystems. However, the relationship between autotrophic nitrification and the active nitrifying populations during 15N-urea incubation has not been totally clarified. The 15N-labeled DNA stable isotope probing (DNA-SIP) technique was utilized in order to study the response from the soil nitrification process and the active nitrifying populations, in both acidic and neutral paddy soils, to the application of urea. The presence of C2H2 almost completely inhibited NO3--N production, indicating that autotrophic ammonia oxidation was dominant in both paddy soils. 15N-DNA-SIP technology could effectively distinguish active nitrifying populations in both soils. The active ammonia oxidation groups in both soils were significantly different, AOA (NS (Nitrososphaerales)-Alpha, NS-Gamma, NS-Beta, NS-Delta, NS-Zeta and NT (Ca. Nitrosotaleales)-Alpha), and AOB (Nitrosospira) were functionally active in the acidic paddy soil, whereas comammox Nitrospira clade A and Nitrosospira AOB were functionally active in the neutral paddy soil. This study highlights the effective discriminative effect of 15N-DNA-SIP and niche differentiation of nitrifying populations in these paddy soils. KEY POINTS: • 15N-DNA-SIP technology could effectively distinguish active ammonia oxidizers. • Comammox Nitrospira clade A plays a lesser role than canonical ammonia oxidizers. • The active groups in the acidic and neutral paddy soils were significantly different.
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Abu-Zied RH, Orif MI, Bantan RA, Al-Farawati R, Ghandourah MA, Aljahdali MH. Sources and pathways of carbon and nitrogen of macrophytes and sediments using stable isotopes in Al-Kharrar Lagoon, eastern Red Sea coast, Saudi Arabia. PLoS One 2024; 19:e0299562. [PMID: 38662683 PMCID: PMC11045092 DOI: 10.1371/journal.pone.0299562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/13/2024] [Indexed: 04/28/2024] Open
Abstract
Elemental ratios (δ13C, δ15N and C/N) and carbon and nitrogen concentrations in macrophytes, sediments and sponges of the hypersaline Al-Kharrar Lagoon (KL), central eastern Red Sea coast, were measured to distinguish their sources, pathways and see how they have been influenced by biogeochemical processes and terrestrial inputs. The mangroves and halophytes showed the most depleted δ13C values of -27.07±0.2 ‰ and -28.34±0.4 ‰, respectively, indicating their preferential 12C uptake, similar to C3-photosynthetic plants, except for the halophytes Atriplex sp. and Suaeda vermiculata which showed δ13C of -14.31±0.6 ‰, similar to C4-plants. Macroalgae were divided into A and B groups based on their δ13C values. The δ13C of macroalgae A averaged -15.41±0.4 ‰, whereas macroalgae B and seagrasses showed values of -7.41±0.8 ‰ and -7.98 ‰, suggesting uptake of HCO3- as a source for CO2 during photosynthesis. The δ13C of sponges was -10.7±0.3 ‰, suggesting that macroalgae and seagrasses are their main favoured diets. Substrates of all these taxa showed δ13C of -15.52±0.8 ‰, suggesting the KL is at present a macroalgae-dominated lagoon. The δ15N in taxa/sediments averaged 1.68 ‰, suggesting that atmospheric N2-fixation is the main source of nitrogen in/around the lagoon. The heaviest δ15N (10.58 ‰) in halophytes growing in algal mats and sabkha is possibly due to denitrification and ammonia evaporation. The macrophytes in the KL showed high C %, N %, and C/N ratios, but this is not indicated in their substrates due possibly to a rapid turnover of dense, hypersaline waters carrying most of the detached organic materials out into the Red Sea. The δ13C allowed separation of subaerial from aquatic macrophytes, a proxy that could be used when interpreting paleo-sea level or paleoclimatic changes from the coastal marine sediments.
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van Oordt F, Cuba A, Choy ES, Elliott JE, Elliott KH. Amino acid-specific isotopes reveal changing five-dimensional niche segregation in Pacific seabirds over 50 years. Sci Rep 2024; 14:7899. [PMID: 38570566 PMCID: PMC10991557 DOI: 10.1038/s41598-024-57339-w] [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] [Received: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/05/2024] Open
Abstract
Hutchison's niche theory suggests that coexisting competing species occupy non-overlapping hypervolumes, which are theoretical spaces encompassing more than three dimensions, within an n-dimensional space. The analysis of multiple stable isotopes can be used to test these ideas where each isotope can be considered a dimension of niche space. These hypervolumes may change over time in response to variation in behaviour or habitat, within or among species, consequently changing the niche space itself. Here, we use isotopic values of carbon and nitrogen of ten amino acids, as well as sulphur isotopic values, to produce multi-isotope models to examine niche segregation among an assemblage of five coexisting seabird species (ancient murrelet Synthliboramphus antiquus, double-crested cormorant Phalacrocorax auritus, Leach's storm-petrel Oceanodrama leucorhoa, rhinoceros auklet Cerorhinca monocerata, pelagic cormorant Phalacrocorax pelagicus) that inhabit coastal British Columbia. When only one or two isotope dimensions were considered, the five species overlapped considerably, but segregation increased in more dimensions, but often in complex ways. Thus, each of the five species occupied their own isotopic hypervolume (niche), but that became apparent only when factoring the increased information from sulphur and amino acid specific isotope values, rather than just relying on proxies of δ15N and δ13C alone. For cormorants, there was reduction of niche size for both species consistent with a decline in their dominant prey, Pacific herring Clupea pallasii, from 1970 to 2006. Consistent with niche theory, cormorant species showed segregation across time, with the double-crested demonstrating a marked change in diet in response to prey shifts in a higher dimensional space. In brief, incorporating multiple isotopes (sulfur, PC1 of δ15N [baselines], PC2 of δ15N [trophic position], PC1 and PC2 of δ13C) metrics allowed us to infer changes and differences in food web topology that were not apparent from classic carbon-nitrogen biplots.
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Wasserfurth P, Huelsemann F, Koehler K. Changes in urinary stable nitrogen isotope ratios during controlled short-term energy deficit: a proof-of-principle analysis. Eur J Nutr 2024; 63:919-926. [PMID: 38243136 PMCID: PMC10948555 DOI: 10.1007/s00394-023-03320-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/29/2023] [Indexed: 01/21/2024]
Abstract
PURPOSE Stable isotope ratios of nitrogen (δ15N) have previously been shown to increase in human hair during periods of catabolism. The goal of this study was to assess changes in δ15N in urinary urea (δ15Nurea) and Δ15N during a short-term controlled energy deficit. METHODS We analyzed samples from 6 recreationally active men (25 ± 1 years, BMI: 23.5 ± 0.6 kg/m2) who participated in a repeated measures cross-over study involving 4 days of energy deficit (ED, ~ 15 kcal/kg FFM) without and with exercise (ED-EX, ED + EX) and control conditions in energy balance (CON-EX, CON + EX). δ15Nurea was analyzed from urine samples, and Δ15N was calculated as δ15Nurea-δ15Ndiet, with δ15Ndiet obtained from diet prescriptions. RESULTS δ15Nurea was significantly elevated in ED-EX (4.4 ± 0.2‰) when compared to CON-EX (3.7 ± 0.1‰; p = 0.026) and CON + EX (3.34 ± 0.13‰, p = 0.001). As a consequence, Δ15N was positive in ED-EX (0.2 ± 0.2‰) and remained negative in ED + EX (- 0.6 ± 0.5‰), CON-EX (- 1.0 ± 0.2) and CON + EX (- 1.1 ± 0.2). Differences in Δ15N were significant between ED-EX and CON-EX (p = 0.005) and ED-EX and CON + EX (p = 0.006). CONCLUSION Our results suggest that δ15Nurea and subsequently Δ15N are responsive to a short-term energy deficit, likely due to increased amino acid oxidation to meet energy demands and preferable elimination of 14N.
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Muñoz-Lechuga R, Lino PG, González-Ortegón E. Interspecific, ontogenetic and temporal variations in stable isotopes of small tuna species in the northeast Atlantic Ocean. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2024; 60:13-31. [PMID: 38127307 DOI: 10.1080/10256016.2023.2289956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/16/2023] [Indexed: 12/23/2023]
Abstract
In order to study the trophic level of small tuna species and their contribution to the carbon flow in pelagic food webs, an analysis of carbon and nitrogen stable isotopes was carried out. The investigation was focused on four small tuna species (Auxis rochei, Auxis thazard, Euthynnus alletteratus and Sarda sarda) commonly harvested in the northeast Atlantic Ocean. The isotope analysis showed how the results for S. sarda are different from the rest of the species analysed, with a higher trophic level, similar to other major tuna species. The greatest niche overlap in δ13C and δ15N occurs among A. rochei, A. thazard and E. alletteratus. Auxis rochei and E. alletteratus showed a size-dependent variability in δ15N, and in δ13C for S. sarda. The small tuna S. sarda exhibits the highest migration rates among various geographical areas in comparison to other small pelagic tunas, and the seasonal variability of isotope values in the area studied can be attributed to the incorporation of larger individuals with a higher lipid content. The results of this work provide new information on the ecological role played by small tuna in food webs, which is more complex and varied than currently thought. This knowledge is essential for a more effective management of fisheries.
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Martocello DE, Wankel SD. Physiological Influence of Fe and Cu Availability on Nitrogen Isotope Fractionation during Ammonia Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:421-431. [PMID: 38147309 DOI: 10.1021/acs.est.3c05964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Microbially mediated cycling processes play central roles in regulating the speciation and availability of nitrogen, a vital nutrient with wide implications for agriculture, water quality, wastewater treatment, ecosystem health, and climate change. Ammonia oxidation, the first and rate-limiting step of nitrification, is carried out by bacteria (AOB) and archaea (AOA) that require the trace metal micronutrients copper (Cu) and iron (Fe) for growth and metabolic catalysis. While stable isotope analyses for constraining nitrogen cycling are commonly used, it is unclear whether metal availability may modulate expression of stable isotope fractionation during ammonia oxidation, by varying growth or through regulation of metabolic metalloenzymes. We present the first study examining the influence of Fe and Cu availability on the kinetic nitrogen isotope effect in ammonia oxidation (15εAO). We report a general independence of 15εAO from the growth rate in AOB, except at a low temperature (10 °C). With AOA Nitrosopumilus maritimus SCM1, however, 15εAO decreases nonlinearly at lower oxidation rates. We examine assumptions involved in the interpretation of 15εAO values and suggest these dynamics may arise from physiological constraints that push the system toward isotopic equilibrium. These results suggest important links between isotope fractionation and environmental constraints on physiology in these key N cycling microorganisms.
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Charteris AF, Knowles TDJ, Mead A, Reay MK, Michaelides K, Evershed RP. The differential assimilation of nitrogen fertilizer compounds by soil microorganisms. FEMS Microbiol Lett 2024; 371:fnae041. [PMID: 38849295 PMCID: PMC11223579 DOI: 10.1093/femsle/fnae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 03/14/2024] [Accepted: 06/06/2024] [Indexed: 06/09/2024] Open
Abstract
The differential soil microbial assimilation of common nitrogen (N) fertilizer compounds into the soil organic N pool is revealed using novel compound-specific amino acid (AA) 15N-stable isotope probing. The incorporation of fertilizer 15N into individual AAs reflected the known biochemistry of N assimilation-e.g. 15N-labelled ammonium (15NH4+) was assimilated most quickly and to the greatest extent into glutamate. A maximum of 12.9% of applied 15NH4+, or 11.7% of 'retained' 15NH4+ (remaining in the soil) was assimilated into the total hydrolysable AA pool in the Rowden Moor soil. Incorporation was lowest in the Rowden Moor 15N-labelled nitrate (15NO3-) treatment, at 1.7% of applied 15N or 1.6% of retained 15N. Incorporation in the 15NH4+ and 15NO3- treatments in the Winterbourne Abbas soil, and the 15N-urea treatment in both soils was between 4.4% and 6.5% of applied 15N or 5.2% and 6.4% of retained 15N. This represents a key step in greater comprehension of the microbially mediated transformations of fertilizer N to organic N and contributes to a more complete picture of soil N-cycling. The approach also mechanistically links theoretical/pure culture derived biochemical expectations and bulk level fertilizer immobilization studies, bridging these different scales of understanding.
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Jiang YY, Zeng YH, Lu RF, Guan KL, Qi XM, Feng Q, Long L, Zhang YT, Zheng X, Luo XJ, Mai BX. Trophic Transfer of Halogenated Organic Pollutants in a Wetland Food Web: Insights from Compound-Specific Nitrogen Isotope of Amino Acids and Food Source Analysis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16585-16594. [PMID: 37842981 DOI: 10.1021/acs.est.3c05844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
A trophic position (TP) model (TPmix model) that simultaneously considered trophic discrimination factor and βGlu/Phe variations was developed in this study and was first applied to investigate the trophic transfer of halogenated organic pollutants (HOPs) in wetland food webs. The TPmix model characterized the structure of the wetland food web more accurately and significantly improved the reliability of TMF compared to the TPbulk, TPAAs, and TPsimmr models, which were calculated based on the methods of stable nitrogen isotope analysis of bulk, traditional AAs-N-CSIA, and weighted βGlu/Phe, respectively. Food source analysis revealed three interlocking food webs (kingfisher, crab, and frogs) in this wetland. The highest HOP biomagnification capacities (TMFmix) were found in the kingfisher food web (0.24-82.0), followed by the frog (0.08-34.0) and crab (0.56-11.7) food webs. The parabolic trends of TMFmix across combinations of log KOW in the frog food web were distinct from those of aquatic food webs (kingfisher and crab), which may be related to differences in food web composition and HOP bioaccumulation behaviors between aquatic and terrestrial organisms. This study provides a new tool to accurately study the trophic transfer of contaminants in wetlands and terrestrial food webs with diverse species and complex feeding relationships.
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Kuwae T, Hosoya J, Ichimi K, Watanabe K, Drever MC, Moriya T, Elner RW, Hobson KA. Using stable isotope (δ 13C, δ 15N) values from feces and breath to infer shorebird diets. Oecologia 2022; 200:23-35. [PMID: 36123584 PMCID: PMC9547797 DOI: 10.1007/s00442-022-05257-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 09/05/2022] [Indexed: 12/03/2022]
Abstract
The use of stable isotopes of carbon (δ13C) and nitrogen (δ15N) from feces and breath offers potential as non-destructive tools to assess diets and nutrition. How stable isotope values derived from breath and feces compare with those from commonly used tissues, such as blood fractions and liver, remains uncertain, including understanding the metabolic routing of dietary nutrients. Here, we measured δ13C and δ15N from feces and δ13C of breath from captive Red-necked Stints (Calidris ruficollis) and 26 species of wild-caught migratory shorebirds (n = 259 individuals) and compared them against isotopic values from blood and feathers. For captive birds fed either cereal- or fish-based diets, differences in δ13C between feces and lipid-free diet were small, - 0.2 ± 0.5‰ and 0.1 ± 0.3‰, respectively, and differences in δ15N, - 0.7 ± 0.5‰ and - 0.5 ± 0.5‰, respectively. Hence, δ13C and δ15N values from feces can serve as proxies for ingested proteinaceous tissues and non-soluble carbohydrates because isotopic discrimination can be considered negligible. Stable isotope values in plasma and feces were strongly correlated in wild-caught shorebirds, indicating feces can be used to infer assimilated macronutrients. Breath δ13C was 1.6 ± 0.8‰ to 5.6 ± 1.2‰ lower than bulk food sources, and breath C derived from lipids was estimated at 47.5% (cereal) to 96.1% (fish), likely underlining the importance of dietary lipids for metabolism. The findings validate the use of stable isotope values of feces and breath in isotopic assays to better understand the dietary needs of shorebirds.
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Zhu G, Cheng D, Wang X, Guo Q, Zhang Q, Zhang J, Tu Q, Li W. Free amino acids, carbon and nitrogen isotopic compositions responses to cadmium stress in two castor (Ricinus communis L.) species. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 184:40-46. [PMID: 35623112 DOI: 10.1016/j.plaphy.2022.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/27/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) toxicity induce various disturbances in metabolic processes and impair plant establishment. The composition of carbon and nitrogen stable isotopes (δ13C and δ15N) and free amino acids (FAAs) can reflect the response of plants to environmental stress. In the present study, a solution culture experiment was carried out, and the secretion characteristics of FAAs as well as δ13C and δ15N were evaluated as indicative of the functional performance of two castor species (Zibo-3 and Zibo-9) under various Cd concentrations stress (0, 1, 2, and 5 mg L-1). The results indicated that: 1) The treatment of the plants with 5 mg L-1 of a Cd solution resulted in a significant decline of biomasses by 22.4% and 11.6% in Zibo-3 and Zibo-9, respectively, relative to controls; additionally, the accumulation levels for Cd in Zibo-9 were higher than those in Zibo-3, thus Zibo-9 showed higher tolerance and enrichment ability to Cd. 2) The exposure of castor to Cd treatments results in significant modifications in individual FAAs, suggesting a differential sensitivity of each biosynthetic pathway to this stress; however, a positive correlation was found between the accumulation of total FAAs and Cd treatment dosages; higher proportion of asparagine and glutamate in total amino acids for Zibo-9, and abundant secretion of arginine in Cd treated Zibo-9 may be associated with the higher Cd-tolerance and Cd-accumulation in Zibo-9. 3) Cd stress increased leaf δ13C and δ15N values regardless of the castor species; δ13C and δ15N could be used as monitoring tools for heavy metal stress in plants.
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Svennerstam H, Jämtgård S. Timing is everything - obtaining accurate measures of plant uptake of amino acids. THE NEW PHYTOLOGIST 2022; 234:311-318. [PMID: 35023179 PMCID: PMC9303729 DOI: 10.1111/nph.17964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Plants are known to have the capacity to take up and utilise amino acids for growth. The significance of this uptake, however, remains elusive, partly due to methodological challenges and biological implications associated with acquiring and interpreting data. This study compared bulk stable isotope analysis and compound-specific liquid chromatography-mass spectrometry, two established methods for determining amino acid uptake. Root amino acid uptake was assayed using U-13 C5 -15 N2 -l-glutamine and axenically grown Arabidopsis thaliana. After 15-120 min of exposure, the content of intact glutamine measured in the roots was constant, whilst the 15 N and 13 C content increased over time, resulting in very different estimated uptake rates. The 13 C : 15 N ratio in roots declined with time, suggesting a loss of glutamine carbon of up to 15% within 120 min. The results presented indicate that, regardless of method used, time is a crucial factor when determining plant amino acid uptake. Due to post-uptake metabolism, compound-specific methods should primarily be used in experiments with a time frame of minutes rather than hours or days. Post-uptake metabolism in plants may account for significant loss of carbon, suggesting that it is not just pre-uptake metabolism by microbes that accounts for the 15 N-13 C mismatch reported in ecological studies, but also post-uptake metabolism in the plant.
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Fischer-Rush J, Rochette R, Paton E, Dickey A, Hayden B. An arithmetic correction for the effect of lipid on carbon stable isotope ratios in muscle and digestive glands of the American lobster (Homarus americanus). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9204. [PMID: 34549474 DOI: 10.1002/rcm.9204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
RATIONALE Lipid correction models use elemental carbon-to-nitrogen ratios to estimate the effect of lipids on δ13 C values and provide a fast and inexpensive alternative to chemically removing lipids. However, the performance of these models varies, especially in whole-body invertebrate samples. The generation of tissue-specific lipid correction models for American lobsters, both an ecologically and an economically important species in eastern North America, will aid ecological research of this species and our understanding of the function of these models in invertebrates. METHOD We determined the δ13 C and δ15 N values before and after lipid extraction in muscle and digestive glands of juvenile and adult lobster. We assessed the performance of four commonly used models (nonlinear, linear, natural logarithm (LN) and generalized linear model (GLM)) at estimating lipid-free δ13 C values based on the non-lipid-extracted δ13 C values and elemental C:N ratios. The accuracy of model predictions was tested using paired t-tests, and the performance of the different models was compared using the Akaike information criterion score. RESULTS Lipid correction models accurately estimated post-lipid-extraction δ13 C values in both tissues. The nonlinear model was the least accurate for both tissues. In muscle, the three other models performed well, and in digestive glands, the LN model provided the most accurate estimates throughout the range of C:N values. In both tissues, the GLM estimates were not independent of the post-lipid-extraction δ13 C values, thus reducing their transferability to other datasets. CONCLUSIONS Whereas previous work found that whole-body models poorly estimated the effect of lipids in invertebrates, we show that tissue-specific lipid correction models can generate accurate and precise estimates of lipid-free δ13 C values in lobster. We suggest that the tissue-specific logarithmic models presented here are the preferred models for accounting for the effect of lipid on lobster isotope ratios.
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