Bacterial populations assimilating carbon from 13C-labeled plant residue in soil: Analysis by a DNA-SIP approach

Lee, Chol Gyu; Watanabe, Takeshi; Satō, Yutaka; Murase, Jun; Asakawa, Susumu; Kimura, Makoto

doi:10.1016/j.soilbio.2010.12.016

Cited by 69 publications

(56 citation statements)

References 26 publications

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“…The DNA was the same DNA fractionates in which Lee et al (2011) elucidated bacterial communities that assimilated dried callus C. The DNA was obtained from an upland soil microcosm that incubated for 56 d after addition of dried cells of 13 C-labeled rice callus.…”

Section: Methodsmentioning

confidence: 99%

“…Details of callus preparation were described by Lee et al (2011). The plow layer soil sample was adjusted to 55% of the maximum water holding capacity, and three treatments were prepared by amending dried rice callus as follows: 1) soil without rice callus (referred to as noncallus treatment), 2) soil with unlabeled callus ( 12 C-callus treatment), and 3) soil with 13 C-callus ( 13 C-callus treatment).…”

Section: Methodsmentioning

confidence: 99%

“…Ten g of soil from each treatment were placed into a test tube and closed with a silicon plug. Test tubes were placed in a completely dark room at 25 C for 56 d (Lee et al 2011). The soil samples from 12 C-and 13 C-callus treatments were used in this study.…”

Section: Methodsmentioning

confidence: 99%

“…Details of DNA extraction and isopycnic centrifugation were described by Lee et al (2011). Briefly, DNA was extracted with a FastDNA SPIN kit for soil (MP Biochemicals; Solon, OH, USA).…”

Section: Dna Extraction and Isopycnic Centrifugationmentioning

confidence: 99%

“…This study aimed to elucidate the heterotrophic growth of cyanobacteria and the microbial loop mediated by cyanophages (cyanobacteria-cyanophages-DOC) in soil using carbon-13 ( 13 C)-labeled dried rice callus cells as a model material of plant residues (Lee et al 2011). This study used the stable isotope probing (SIP) method for this purpose.…”

Section: Introductionmentioning

confidence: 99%

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Heterotrophic growth of cyanobacteria and phage-mediated microbial loop in soil: Examination by stable isotope probing (SIP) method

Lee

Watanabe

Fujita

et al. 2012

Soil Science and Plant Nutrition

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Cyanobacteria play an important role in maintaining soil fertility in rice fields. Some cyanobacterial members can grow heterotrophically under dark conditions, which might be an important trait for the survival of cyanobacteria during the drained period after harvest. This study aimed to elucidate the heterotrophic growth of cyanobacteria and the microbial loop mediated by cyanophages (cyanobacteria-cyanophagesdissolved organic carbon) in soil using carbon-13 ( 13 C)-labeled dried callus cells as a model material of plant residues. This study used the stable isotope probing (SIP) method coupled with denaturing gradient gel electrophoresis (DGGE). Although heterotrophic growth of cyanobacteria in soil was not observed, the phage-mediated microbial loop in the transformation of callus carbon was elucidated from the detection of 13 C-labeled g20 genes in the heaviest fractions (buoyant density: 1.754 g mL À1). The closest relatives of eleven sequenced DGGE bands from the heaviest fractions were uncultured cyanophage g20 clones that had been obtained from rice field soils in Japan. Proliferation of bacteriophages having cyanophage-related g20 genes with no detectable heterotrophic growth of cyanobacteria strongly indicates that bacteriophages having these g20 genes infected bacteria other than cyanobacteria.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…Details of DNA extraction and isopycnic centrifugation were described by Lee et al (2011). Briefly, DNA was extracted with a FastDNA SPIN kit for soil (MP Biochemicals; Solon, OH, USA).…”

Section: Dna Extraction and Isopycnic Centrifugationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Heterotrophic growth of cyanobacteria and phage-mediated microbial loop in soil: Examination by stable isotope probing (SIP) method

Lee

Watanabe

Fujita

et al. 2012

Soil Science and Plant Nutrition

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Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California

Baker

Khalili

Martiny

et al. 2018

Ecology

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Microbial decomposers mediate the return of CO to the atmosphere by producing extracellular enzymes to degrade complex plant polymers, making plant carbon available for metabolism. Determining if and how these decomposer communities are constrained in their ability to degrade plant litter is necessary for predicting how carbon cycling will be affected by future climate change. We analyzed mass loss, litter chemistry, microbial biomass, extracellular enzyme activities, and enzyme temperature sensitivities in grassland litter transplanted along a Mediterranean climate gradient in southern California. Microbial community composition was manipulated by caging litter within bags made of nylon membrane that prevent microbial immigration. To test whether grassland microbes were constrained by climate history, half of the bags were inoculated with local microbial communities native to each gradient site. We determined that temperature and precipitation likely interact to limit microbial decomposition in the extreme sites along our gradient. Despite their unique climate history, grassland microbial communities were not restricted in their ability to decompose litter under different climate conditions across the gradient, although microbial communities across our gradient may be restricted in their ability to degrade different types of litter. We did find some evidence that local microbial communities were optimized based on climate, but local microbial taxa that proliferated after inoculation into litterbags did not enhance litter decomposition. Our results suggest that microbial community composition does not constrain C-cycling rates under climate change in our system, but optimization to particular resource environments may act as more general constraints on microbial communities.

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Glucose triggers strong taxon‐specific responses in microbial growth and activity: insights from DNA and RNA qSIP

Papp

Hungate

Schwartz

2019

Ecology

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Growth of soil microorganisms is often described as carbon limited, and adding labile carbon to soil often results in a transient and large increase in respiration. In contrast, soil microbial biomass changes little, suggesting that growth and respiration are decoupled in response to a carbon pulse. Alternatively, measuring bulk responses of the entire community (total respiration and biomass) could mask ecologically important variation among taxa in response to the added carbon. Here, we assessed taxon‐specific variation in cellular growth (measured as DNA synthesis) and metabolic activity (measured as rRNA synthesis) following glucose addition to soil using quantitative stable isotope probing with H218O. We found that glucose addition altered rates of DNA and rRNA synthesis, but the effects were strongly taxon specific: glucose stimulated growth and rRNA transcription for some taxa, and suppressed these for others. These contrasting taxon‐specific responses could explain the small and transient changes in total soil microbial biomass. Responses to glucose were not well predicted by a priori assignments of taxa into copiotrophic or oligotrophic categories. Across all taxa, rates of DNA and rRNA synthesis changed in parallel, indicating that growth and activity were coupled, and the degree of coupling was unaffected by glucose addition. This pattern argues against the idea that labile carbon addition causes a large reduction in metabolic growth efficiency; rather, the large pulse of respiration observed with labile substrate addition is more likely to be the result of rapid turnover of microbial biomass, possibly due to trophic interactions. Our results support a strong connection between rRNA synthesis and bacterial growth, and indicate that taxon‐specific responses among soil bacteria can buffer responses at the scale of the whole community.

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Bacterial populations assimilating carbon from 13C-labeled plant residue in soil: Analysis by a DNA-SIP approach

Cited by 69 publications

References 26 publications

Heterotrophic growth of cyanobacteria and phage-mediated microbial loop in soil: Examination by stable isotope probing (SIP) method

Heterotrophic growth of cyanobacteria and phage-mediated microbial loop in soil: Examination by stable isotope probing (SIP) method

Microbial decomposers not constrained by climate history along a Mediterranean climate gradient in southern California

Glucose triggers strong taxon‐specific responses in microbial growth and activity: insights from DNA and RNA qSIP

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