Composition of hydrolysable amino acids in soil organic matter and soil microbial biomass

Friedel, Jürgen K.; Scheller, Edwin

doi:10.1016/s0038-0717(01)00185-7

Cited by 131 publications

(92 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…U. copiosus genome implies that these compounds can be acquired from the soil environment. Several studies have shown that free amino acids and oligopeptides are present in soil 45,46 . The enrichment of proteases and amino acid and peptide importers in the Ca.…”

Section: Lifestyles (Supplementarymentioning

confidence: 99%

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

et al. 2016

View full text Add to dashboard Cite

Although bacteria within the Verrucomicrobia phylum are pervasive in soils around the world, they are under-represented in both isolate collections and genomic databases. Here, we describe a single verrucomicrobial group within the class Spartobacteria that is not closely related to any previously described taxa. We examined more than 1,000 soils and found this spartobacterial phylotype to be ubiquitous and consistently one of the most abundant soil bacterial phylotypes, particularly in grasslands, where it was typically the most abundant. We reconstructed a nearly complete genome of this phylotype from a soil metagenome for which we propose the provisional name ‘Candidatus Udaeobacter copiosus’. The Ca. U. copiosus genome is unusually small for a cosmopolitan soil bacterium, estimated by one measure to be only 2.81 Mbp, compared to the predicted effective mean genome size of 4.74 Mbp for soil bacteria. Metabolic reconstruction suggests that Ca. U. copiosus is an aerobic heterotroph with numerous putative amino acid and vitamin auxotrophies. The large population size, relatively small genome and multiple putative auxotrophies characteristic of Ca. U. copiosus suggest that it may be undergoing streamlining selection to minimize cellular architecture, a phenomenon previously thought to be restricted to aquatic bacteria. Although many soil bacteria need relatively large, complex genomes to be successful in soil, Ca. U. copiosus appears to use an alternative strategy, sacrificing metabolic versatility for efficiency to become dominant in the soil environment.

show abstract

Section: Lifestyles (Supplementarymentioning

confidence: 99%

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

et al. 2016

View full text Add to dashboard Cite

show abstract

“…Elemental composition: N ≥ 1; H/C = 1.0 to 2.2; O/C = 0.1 to 0.67. Typical amino acid distributions in forest soils indicate a protein fraction with average H/C = 1.7 and O/C = 0.4 (Friedel and Scheller 2002).…”

Section: Hockaday Et Al Characterization Of Organic Matter In Naturamentioning

confidence: 99%

Electrospray and photoionization mass spectrometry for the characterization of organic matter in natural waters: a qualitative assessment

Hockaday

Purcell

Marshall

et al. 2009

Limnology & Ocean Methods

255

214

View full text Add to dashboard Cite

Fourier‐transform ion cyclotron resonance mass spectrometry (MS) has demonstrated potential to revolutionize the fields of limnology and chemical oceanography by identifying the individual molecular components of organic matter in natural waters. The use of MS for this purpose is made possible by the electrospray technique which successfully ionizes polar, nonvolatile organic molecules. Another recently developed ion source, atmospheric pressure photoionization (APPI), extends MS capabilities to less polar molecules. This article presents early results on the application of APPI MS to natural organic matter. We compare APPI MS and electrospray MS data for dissolved organic matter from Lake Drummond (Virginia, USA). Collectively, electrospray and APPI MS identify more than 6000 molecular species to which we assign unique molecular formulas. Fewer than 1000 molecular species are common to both electrospray and APPI mass spectra, indicating that the techniques are highly complementary in the types of molecules they ionize. Access to a broad range of molecules provided by combining APPI and electrospray has prompted a qualitative analysis. The goal is to assess the extent to which molecular MS data correspond with elemental (CHNOS) and structural characteristics determined by combustion elemental analyses and 13C nuclear magnetic resonance (NMR). Because the data obtained by these different methods are not directly comparable, we propose a novel data analysis procedure that facilitates their comparison. The bulk elemental composition calculated from electrospray MS data are in close agreement (± 15%) with values determined by combustion elemental analysis. APPI and electrospray MS detect protein contributions in agreement with 13C NMR (6 wt %) but underestimate carbohydrates relative to 13C NMR. Nevertheless, MS results agree with NMR on the relative proportions of noncarbohydrate compounds in the organic matter: lignins > lipids > peptides. Finally, we use a molecular mixing model to simulate a 13C NMR spectrum from the MS datasets. The correspondence of the simulated and measured 13C NMR signals (74%) suggests that, collectively, the molecular species identified by APPI and electrospray MS comprise a large portion of the organic matter in Lake Drummond. These results add credibility to electrospray and APPI MS in limnology and oceanography applications, but further characterization of ion source behavior is fundamental to the accurate interpretation of MS data.

show abstract

“…The costs of enzyme production include the metabolic energy required for protein synthesis and excretion, as well as the C and nutrient content of the enzymes themselves. For example, between 50 and 70% of N acquired by microbes may be allocated to amino acids that are the building blocks of enzymes (Friedel and Scheller 2002), and extracellular enzyme production has been reported to consume 1-5% of C and N assimilation by bacteria (Frankena et al 1988).…”

mentioning

confidence: 99%

Evolutionary-Economic Principles as Regulators of Soil Enzyme Production and Ecosystem Function

et al. 2010

View full text Add to dashboard Cite

Composition of hydrolysable amino acids in soil organic matter and soil microbial biomass

Cited by 131 publications

References 34 publications

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

Electrospray and photoionization mass spectrometry for the characterization of organic matter in natural waters: a qualitative assessment

Evolutionary-Economic Principles as Regulators of Soil Enzyme Production and Ecosystem Function

Contact Info

Product

Resources

About