Amino acid dynamics across a grassland altitudinal gradient

Farrell, Mark; Macdonald, Lynne M.; Hill, Paul W.; Wanniarachchi, Sudas D.; Farrar, J. F.; Bardgett, Richard D.; Jones, Davey L.

doi:10.1016/j.soilbio.2014.05.015

Cited by 37 publications

(14 citation statements)

References 16 publications

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“…This raises the question: why are these residues more abundant? The intrinsic chemical recalcitrance of individual AAs themselves does not predict abundance in SOM because the half-lives of AAs added to soils do not correlate with the abundances of the old hydrolysable pools observed here (see Farrell et al., 2014 ). These discrepancies could be due to increased recalcitrance through biogenic association (e.g.…”

Section: Discussionmentioning

confidence: 68%

Soil organic matter and the extracellular microbial matrix show contrasting responses to C and N availability

Redmile-Gordon

Evershed

Hirsch

et al. 2015

Soil Biology and Biochemistry

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An emerging paradigm in soil science suggests microbes can perform ‘N mining’ from recalcitrant soil organic matter (SOM) in conditions of low N availability. However, this requires the production of extracellular structures rich in N (including enzymes and structural components) and thus defies stoichiometric expectation. We set out to extract newly synthesised peptides from the extracellular matrix in soil and compare the amino acid (AA) profiles, N incorporation and AA dynamics in response to labile inputs of contrasting C/N ratio. Glycerol was added both with and without an inorganic source of N (10% 15N labelled NH4NO3) to a soil already containing a large pool of refractory SOM and incubated for 10 days. The resulting total soil peptide (TSP) and extracellular pools were compared using colorimetric methods, gas chromatography, and isotope ratio mass spectrometry. N isotope compositions showed that the extracellular polymeric substance (EPS) contained a greater proportion of products formed de novo than did TSP, with hydrophobic EPS-AAs (leucine, isoleucine, phenylalanine, hydroxyproline and tyrosine) deriving substantially more N from the inorganic source provided. Quantitative comparison between extracts showed that the EPS contained greater relative proportions of alanine, glycine, proline, phenylalanine and tyrosine. The greatest increases in EPS-peptide and EPS-polysaccharide concentrations occurred at the highest C/N ratios. All EPS-AAs responded similarly to treatment whereas the responses of TSP were more complex. The results suggest that extracellular investment of N (as EPS peptides) is a microbial survival mechanism in conditions of low N/high C which, from an evolutionary perspective, must ultimately lead to the tendency for increased N returns to the microbial biomass. A conceptual model is proposed that describes the dynamics of the extracellular matrix in response to the C/N ratio of labile inputs.

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Section: Discussionmentioning

confidence: 68%

Soil organic matter and the extracellular microbial matrix show contrasting responses to C and N availability

Redmile-Gordon

Evershed

Hirsch

et al. 2015

Soil Biology and Biochemistry

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“…The turnover time of FAAs in our study indicates a longer residence time than results from 15 N labelling studies in forest litter and agricultural soils (0.5 to 1.5 h in Wanek et al, 2010;3.5 h in Geisseler et al, 2012). Moreover, studies using 14 C methodologies suggest a maximum turnover of 12 h Farrell et al, 2014;Wilkinson et al, 2014). The gross FAA production rates quantified in the current study can be considered as an indicator for total depolymerization, as the rates are only based on five AAs.…”

Section: Discussionmentioning

confidence: 85%

Amino acid and N mineralization dynamics in heathland soil after long-term warming and repetitive drought

Andresen¹,

Bodé²,

Tietema³

et al. 2014

Preprint

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Abstract. Monomeric organic nitrogen (N) such as free amino acids (fAA) is an important resource for both plants and soil microorganisms and is, furthermore, a source of ammonium (NH4+) via microbial fAA mineralization. We compared gross fAA dynamics with gross N mineralization in a Dutch heathland soil using 15N labelling. A special focus was made on the effects of climate change factors warming and drought, followed by rewetting. Our aims were to: (1) compare fAA mineralization (NH4+ production from fAAs) with gross N mineralization, (2) assess gross fAA production rate (depolymerization) and turnover time relative to gross N mineralization rate, and (3) assess the effects of warming and drought on these rates. The turnover of fAA in the soil was ca. 3 h, which is almost two orders of magnitude faster than that of NH4+ (i.e. ca. 4 days). This suggests that fAAs is an extensively used resource by soil microorganisms. In control soil (i.e. no climatic treatment), the gross N mineralization rate (10 ± 2.9 μg N g−1 day−1) was eight-times smaller than the summed gross fAA production rate of five AAs (alanine, valine, leucine, isoleucine, proline: 127.4 to 25.0 μg N g−1 day−1). Gross fAA mineralization (3.4 ± 0.2 μg N g−1 day−1) contributed by 34% to the gross N mineralization rate and is, thus, an important component of N mineralization. In the drought treatment, gross fAA production was reduced by 65% and gross fAA mineralization by 41%, compared to control. On the other hand, gross N mineralization was unaffected by drought, indicating an increased mineralization of other soil organic nitrogen (SON) components. Warming did not significantly affect N transformations, even though that gross fAA production was more than halved. Overall our results suggest that heathland soil exposed to droughts has a shift in the composition of the SON being mineralized. Furthermore, compared to agricultural soils, fAA mineralization was relatively less important in the investigated heathland. This indicates a more complex mineralization dynamics in semi-natural ecosystems.

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“…We note that each of the amino acids that we have identified as osmoprotectants has been detected in the soil (8)(9)(10)47), one of the prime habitats of B. subtilis (1). High-affinity transport systems should allow their scavenging from scarce environmental resources.…”

Section: Discussionmentioning

confidence: 87%

“…Both proteogenic and nonproteogenic amino acids can be found in the soil (8,10), and they exhibit a high degree of turnover, a process to which microorganisms contribute substantially (47). We wondered whether the uptake of amino acids other than proline (25,26) would aid B. subtilis in its process of adjustment to high-salinity surroundings.…”

Section: Resultsmentioning

confidence: 99%

Uptake of Amino Acids and Their Metabolic Conversion into the Compatible Solute Proline Confers Osmoprotection to Bacillus subtilis

Zaprasis

Bleisteiner

Kerres

et al. 2015

Appl Environ Microbiol

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bThe data presented here reveal a new facet of the physiological adjustment processes through which Bacillus subtilis can derive osmostress protection. We found that the import of proteogenic (Glu, Gln, Asp, Asn, and Arg) and of nonproteogenic (Orn and Cit) amino acids and their metabolic conversion into proline enhances growth under otherwise osmotically unfavorable conditions. Osmoprotection by amino acids depends on the functioning of the ProJ-ProA-ProH enzymes, but different entry points into this biosynthetic route are used by different amino acids to finally yield the compatible solute proline. Glu, Gln, Asp, and Asn are used to replenish the cellular pool of glutamate, the precursor for proline production, whereas Arg, Orn, and Cit are converted into ␥-glutamic semialdehyde/⌬ 1 -pyrroline-5-carboxylate, an intermediate in proline biosynthesis. The import of Glu, Gln, Asp, Asn, Arg, Orn, and Cit did not lead to a further increase in the size of the proline pool that is already present in osmotically stressed cells. Hence, our data suggest that osmoprotection of B. subtilis by this group of amino acids rests on the savings in biosynthetic building blocks and energy that would otherwise have to be devoted either to the synthesis of the proline precursor glutamate or of proline itself. Since glutamate is the direct biosynthetic precursor for proline, we studied its uptake and found that GltT, an Na ؉ -coupled symporter, is the main uptake system for both glutamate and aspartate in B. subtilis. Collectively, our data show how effectively B. subtilis can exploit environmental resources to derive osmotic-stress protection through physiological means. Bacillus subtilis is a resident of the upper layers of the soil and of the rhizosphere, and it can also efficiently colonize root surfaces (1-3). The blueprint of its genome (4) bears the hallmarks of a bacterium that can exploit many plant-produced compounds for its growth. Accordingly, a considerable portion of the coding capacity of the B. subtilis chromosome (5) is devoted to highaffinity import systems (6) that allow the scavenging of a wide spectrum of nutrients. Reoccurring and persisting high osmolarity in the soil ecosystem (7) is a situation in which B. subtilis can take advantage of the import of plant-produced compounds (8-10) for its physiological adjustment to these unfavorable environmental conditions (7, 11).As in many bacterial species (11-13), cellular adaptation of B. subtilis to both sudden and sustained increases in the external osmolarity involves a two-stage process (7,14). It initially encompasses the uptake of large quantities of potassium as an emergency stress reaction to curb water efflux (14, 15) and, subsequently, the replacement of part of this ion by organic osmolytes, such as proline (Pro) and glycine betaine (GB), to decrease the ionic strength of the cytoplasm and to optimize its solvent properties (14,(16)(17)(18)(19). These organic osmolytes, commonly referred to as compatible solutes, are highly compliant with cellular physiolog...

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Amino acid dynamics across a grassland altitudinal gradient

Cited by 37 publications

References 16 publications

Soil organic matter and the extracellular microbial matrix show contrasting responses to C and N availability

Soil organic matter and the extracellular microbial matrix show contrasting responses to C and N availability

Amino acid and N mineralization dynamics in heathland soil after long-term warming and repetitive drought

Uptake of Amino Acids and Their Metabolic Conversion into the Compatible Solute Proline Confers Osmoprotection to Bacillus subtilis

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