Analysis of bacterial communities in soil by PCR–DGGE targeting protease genes

Sakurai, Michihiko; Suzuki, Kazuyuki; Onodera, Masayuki; Shinano, Takuro; Osaki, Mitsuru

doi:10.1016/j.soilbio.2007.05.026

Cited by 60 publications

(43 citation statements)

References 44 publications

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“…pools ( Table 2). The few field studies that have measured microbial sources of proteolytic enzymes consistently identify bacteria as the dominant source (Hayano 1996;Sakurai et al 2007;Watanabe et al 2003). On average, semi-arid grasslands and shrublands had the highest pH, favoring both bacterial communities and proteolytic enzyme activity.…”

Section: Possible Drivers Of Patternsmentioning

confidence: 99%

Amino acid abundance and proteolytic potential in North American soils

et al. 2010

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Studies of nitrogen (N) cycling have traditionally focused on N mineralization as the primary process limiting plant assimilation of N. Recent evidence has shown that plants may assimilate amino acids (AAs) directly, circumventing the mineralization pathway. However, the general abundance of soil AAs and their relative importance in plant N uptake remains unclear in most ecosystems. We compared the concentrations and potential production rates of AAs and NH(4) (+), as well as the edaphic factors that influence AA dynamics, in 84 soils across the United States. Across all sites, NH(4) (+) and AA-N comprised similar proportions of the total bioavailable N pool (approximately 20%), with NO(3) (-) being the dominant form of extractable N everywhere but in tundra and boreal forest soils. Potential rates of AA production were at least comparable to those of NH(4) (+) production in all ecosystems, particularly in semi-arid grasslands, where AA production rates were six times greater than for NH(4) (+) (P < 0.01). Potential rates of proteolytic enzyme activity were greatest in bacteria-dominated soils with low NH(4) (+) concentrations, including many grassland soils. Based on research performed under standardized laboratory conditions, our continental-scale analyses suggest that soil AA and NH(4) (+) concentrations are similar in most soils and that AAs may contribute to plant and microbial N demand in most ecosystems, particularly in ecosystems with N-poor soils.

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Section: Possible Drivers Of Patternsmentioning

confidence: 99%

Amino acid abundance and proteolytic potential in North American soils

et al. 2010

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“…Different letters indicate statistically significant differences at P < 0.05 in total dry weight or total N accumulation. Madejon et al, 2001;Kandeler et al, 1999), including proteases (Sakurai et al, 2007). Kielland et al (2007) showed that soils with a high protein concentration possessed high soil protease activity.…”

Section: Resultsmentioning

confidence: 99%

“…A protease-mediated process is considered to be the ratelimiting step in degradation of organic N in soils. The protease activity in soils is considered to be derived from soil microorganisms (Sakurai et al, 2007). The apr , npr , and sub genes encode alkaline metalloprotease, neutral metalloprotease, and serine protease, respectively.…”

Section: Introductionmentioning

confidence: 99%

“…The apr , npr , and sub genes encode alkaline metalloprotease, neutral metalloprotease, and serine protease, respectively. These are the primary microbial extracellular proteases in soils (Sakurai et al, 2007;Fuka et al, 2008). Fuka et al (2008) quantified sub and npr genes in soils using realtime PCR, and found a positive relationship between the sub and npr coding genes and potential protease activity in sandy soils.…”

Section: Introductionmentioning

confidence: 99%

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Differences in Acquisition of Organic Nitrogen in Soils Between Bok Choy and Tomato

Enomoto

Sakurai²,

Okamoto

et al. 2012

Journal of Plant Nutrition

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2 Seedlings of bok choy and tomato were grown in soils with different nitrogen (N) sources [no N (−N), ammonium sulfate (AS), and cattle farmyard manure (CM)]. Comparison between soils treated with −N and CM indicated that the growth and N accumulation in bok choy were significantly enhanced by CM treatment, whereas no difference was found in tomato. In the rhizosphere soils, the highest protease activity was detected in CM treatment irrespective of species. Correlation analysis between rhizospheric protease activity and total N accumulation of plant treated with {N and CM showed a significant positive correlation only for bok choy. The determination of amino acid absorption rate in excised roots indicated that glycine was taken up at a significantly higher rate in bok choy than tomato. This study suggested that at least two possible factors affected the acquisition of organic N: rhizospheric protease activity and ability to absorb amino acids in roots.

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“…Alternatively, DGGE gels can be hybridized with taxon-specific probes that can identify one or more bands. In addition to community analysis, DGGE was also successfully used for the analysis of populations of functional genes (Gremion et al 2004, Sakurai et al 2007, Wartiainen et al 2008). There is a resolution limit with this method as only sequences with intensity higher than 0.1-1% of the total intensity can be technically assessed.…”

Section: Fingerprinting Methods To Assess the Microbial Biodiversity mentioning

confidence: 99%

Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities

Valášková¹,

Baldrián²

2009

Plant Soil Environ.

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In soil microbial ecology, the effects of environmental factors and their gradients, temporal changes or the response to specific experimental treatments of microbial communities can only be effectively analyzed using methods that address the structural differences among whole communities. Fingerprinting methods are the most appropriate technique for this task when multiple samples must be analyzed. Among the methods currently used to compare microbial communities based on nucleic acid sequences, the techniques based on differences in the melting properties of double-stranded molecules, denaturing gradient gel electrophoresis (DGGE) or temperature gradient gel electrophoresis (TGGE), are the most widely used. Their main advantage is that they provide the possibility to further analyze whole sequences contained in fingerprints using molecular methods. In addition to the analysis of microbial communities based on DNA extracted from soils, DGGE/TGGE can also be used for the assessment of the active part of the community based on the analysis of RNA-derived sequences or for the analysis of sequences of functional genes encoding for proteins involved in important soil processes.

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Analysis of bacterial communities in soil by PCR–DGGE targeting protease genes

Cited by 60 publications

References 44 publications

Amino acid abundance and proteolytic potential in North American soils

Amino acid abundance and proteolytic potential in North American soils

Differences in Acquisition of Organic Nitrogen in Soils Between Bok Choy and Tomato

Denaturing gradient gel electrophoresis as a fingerprinting method for the analysis of soil microbial communities

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