Differential acquisition of amino acid and peptide enantiomers within the soil microbial community and its implications for carbon and nitrogen cycling in soil

Broughton, Richard; Newsham, Kevin K.; Hill, Paul W.; Stott, Alistair W.; Jones, Davey L.

doi:10.1016/j.soilbio.2015.05.003

Cited by 34 publications

(14 citation statements)

References 41 publications

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“…In this study, amino acid contents revealed treatments response similar to that for total microbial PLFAs, bacterial PLFAs and G+ve bacterial PLFAs, as found earlier by Broughton et al (2015). Some other studies also revealed a positive correlation between soil amino acids and microbial N (Geisseler & Horwath, 2008;Hofmockel et al, 2010).…”

Section: Discussionsupporting

confidence: 88%

Organic and mineral fertilizers sway the nitrogen availability to plants via microbial diversity – long-term impact

Bibi¹,

Ding²,

Jilani³

et al. 2019

PAK.J.BOT.

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Continued application of organic matter and inorganic synthetic fertilizers to soil influences the nutrient dynamics and diversity of microbial communities. A single site field study (plot size of 9.5 m × 5 m used in each treatment) encompassing 23 years compared the impact of organic and NPK fertilizers for exploring amino acids as indicators of nitrogen fate, and phospholipid fatty acids (PLFA) as biomarkers of microbial diversity in North China Plain field. Treatments in quadruplicated RCBD experiment were: whole N from organic manure (OM); half N from OM + half N from chemical fertilizer (HOM); chemical NPK fertilizers (NPK), NP, NK, PK, and no fertilizer control or check (CK) applied to raise wheat and maize crops continuously. To each crop, N was applied at the rate of 150 kg N ha-1 through organic manure and/or chemical fertilizer urea in two splits (90 + 60 kg N ha-1). Calcium superphosphate (150 kg P2O5 ha-1) and potassium sulfate (150 kg K2O ha-1) were applied basally in respective treatments. Soil samples were drawn from each treatment after 23 years of experimentation. These fertilization amendments exhibited that contents of total nitrogen and amino acids were significantly (p≤0.05) higher under OM and HOM compared to NPK and CK treatments. Total amino acids determination revealed that N and P included treatments among mineral fertilizers mainly contributed to amino acids residues in soil. The PLFA profiling exhibited that increased amino acids under OM and HOM correlated significantly (p≤0.05) and positively with an increase of Gram-positive (G+ve) bacteria and fungi, negatively with actinomycetes, and non-significantly with Gram-negative (G-ve) bacteria. These results suggest that accrual of organic and microbial residues (G+ve bacterial and fungal) enhance the N stabilization in surface soil, which ultimately could increase the plant growth and yield of crops.

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Section: Discussionsupporting

confidence: 88%

Organic and mineral fertilizers sway the nitrogen availability to plants via microbial diversity – long-term impact

Bibi¹,

Ding²,

Jilani³

et al. 2019

PAK.J.BOT.

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“…The microbial utilization of D -amino acids has been studied mainly in soils and is regarded as common in soil microorganisms (e.g., Hill et al, 2011 ; Broughton et al, 2015 ; Radkov et al, 2016 ). D -amino acid utilization by marine microbiota has also been studied (e.g., Perez et al, 2003 ; Azúa et al, 2014 ; Shelford et al, 2014 ); however, only a few D -amino acid utilizers have been isolated.…”

Section: Introductionmentioning

confidence: 99%

Enhanced Bacterial Growth and Gene Expression of D-Amino Acid Dehydrogenase With D-Glutamate as the Sole Carbon Source

et al. 2018

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In a search for life-supporting, not life-assisting, D-amino acid metabolism, an environmental strain that grows better with D-glutamate as the sole carbon source was isolated from an ordinary river. The strain, designated as A25, exhibited a faster growth rate and greater cell yield with D-glutamate than with L-glutamate. Conversely, the D/L ratio of total cellular glutamate was as low as 4/96, which suggests that D-glutamate is more likely catabolized than anabolized. Strain A25 was phylogenetically most closely related to the gamma-proteobacterial species Raoultella ornithinolytica, with a 16S rRNA gene sequence similarity of 100%. A standard strain, R. ornithinolytica JCM 6096T, also showed similarly enhanced growth with D-glutamate, which was proven for the first time. Gene expression of the enzymes involved in D-amino acid metabolism was assayed by reverse-transcription quantitative PCR (RT-qPCR) using specifically designed primers. The targets were the genes encoding D-amino acid dehydrogenase (DAD; EC 1.4.99.1), glutamate racemase (EC 5.1.1.3), D-glutamate oxidase (EC 1.4.3.7 or EC 1.4.3.15), and UDP-N-acetyl-α-D-muramoyl-L-alanyl-D-glutamate ligase (EC 6.3.2.9). As a result, the growth of strains A25 and R. ornithinolytica JCM 6096T on D-glutamate was conspicuously associated with the enhanced expression of the DAD gene (dadA) in the exponential phase compared with the other enzyme genes. Pseudomonas aeruginosa is also known to grow on D-glutamate as the sole carbon source but to a lesser degree than with L-glutamate. A standard strain of P. aeruginosa, JCM 5962T, was tested for gene expression of the relevant enzymes by RT-qPCR and also showed enhanced dadA expression, but in the stationary phase. Reduction of ferricyanide with D-glutamate was detected in cell extracts of the tested strains, implying probable involvement of DAD in the D-glutamate catabolizing activity. DAD-mediated catalysis may have advantages in the one-step production of α-keto acids and non-production of H2O2 over other enzymes such as racemase and D-amino acid oxidase. The physiological and biochemical importance of DAD in D-amino acid metabolism is discussed.

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“…Amino acids in both and L-and D-forms can be considered as organic nitrogen and carbon sources for soil microbes [38,39] that can lead to an increase in respiration in soil [40]. However, studies reveal that L-amino acids are more readily taken up by gram-positive bacteria in soil than their D form [38].…”

Section: Discussionmentioning

confidence: 99%

Amino Acid: Its Dual Role as Nutrient and Scavenger of Free Radicals in Soil

et al. 2017

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Ascorbic acid is a bacteriostatic agent; one of the many ways by which ascorbic acid hampers bacterial growth is by the production of hydrogen peroxide, which further converts into hydroxyl free radicals. Certain amino acids can counteract the inhibitory effect of hydroxyl free radicals by checking their oxidizing effect. Though ascorbic acid is bacteriostatic in nature, it facilitates prokaryotic respiration by decarboxylation. This study was carried out to understand how microbes from different horizons of the forest soil respond to the addition of a bacteriostatic agent (ascorbic acid) and growth promoting agent (amino acids), with respect to the soil respiration. We observed that the addition of either ascorbic acid or a combination of it with amino acid consistently results in increased soil respiration, and this increase is different for different soil types depending on soil composition and origin. Furthermore, we also found that beta alanine-induced maximum respiration in basic soils and L-glutamic in acidic soils. This study is significant because it can be used to explain how a strong reducing sugar, i.e., ascorbic acid, affects the soil respiration mediated via soil microbes. To the best of our knowledge, it is the first report that demonstrates the effect of bacteriostatic and the growth promoting agent together on microbe-mediated soil respiration.

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Differential acquisition of amino acid and peptide enantiomers within the soil microbial community and its implications for carbon and nitrogen cycling in soil

Cited by 34 publications

References 41 publications

Organic and mineral fertilizers sway the nitrogen availability to plants via microbial diversity – long-term impact

Organic and mineral fertilizers sway the nitrogen availability to plants via microbial diversity – long-term impact

Enhanced Bacterial Growth and Gene Expression of D-Amino Acid Dehydrogenase With D-Glutamate as the Sole Carbon Source

Amino Acid: Its Dual Role as Nutrient and Scavenger of Free Radicals in Soil

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