Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA

Agnelli, Alberto; Ascher, Judith; Corti, Giacomo; Ceccherini, Maria Teresa; Nannipieri, Paolo; Pietramellara, Giacomo

doi:10.1016/j.soilbio.2004.02.004

Cited by 287 publications

(155 citation statements)

References 54 publications

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“…It is well established that MBC content decreased with increasing soil depth (Taylor et al 2002, Fierer al. , Agnelli et al 2004.…”

Section: Discussionmentioning

confidence: 98%

Biomass and catabolic diversity of microbial communities with long-term restoration, bare fallow and cropping history in Chinese Mollisols

Wang¹,

Jin²,

Chen³

et al. 2007

PLANT SOIL ENVIRON

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Microbial biomass and community catabolic diversities at three depths (0-10 cm, 20-30 cm, and 40-50 cm) in Chinese Mollisols as influenced by long-term managements of natural restoration, cropping and bare fallow were investigated. Microbial biomass was estimated from chloroform fumigation-extraction and substrate-induced respiration (SIR), and catabolic diversity was determined by using Biolog® EcoPlate. Experimental results showed that microbial biomass significantly declined with soil depth in the treatments of restoration and cropping, and not in the treatment of bare fallow, where the microbial biomass had a positive relationship with the total soil C content. The inspections into the catabolic capability of the microbial community at the same soil depth showed that the treatment of natural restoration had a relatively stronger metabolic ability than the cropping and bare fallow treatments. Shannon's diversity index, substrate richness and substrate evenness calculated from the Biolog data were higher in the treatments of natural restoration and cropping than the bare fallow treatment with the same soil depth, and with the highest values in the top soil. Principal component analysis indicated that the catabolic profiles not only varied with the soil depth in each treatment, but also differed in the three treatments within the same soil depth. The catabolic profiles of the three treatments were similar to each other in the soil depth of 0-10 cm and distinctly different in the soil depths of 20-30 cm and 40-50 cm. These results suggest that it was microbial biomass rather than community function that was influenced by the different soil management in the topsoil (0-10 cm); in the relative depths, the soil microbial community function was more easily influenced than microbial biomass.

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“…It is well established that MBC content decreased with increasing soil depth (Taylor et al 2002, Fierer al. , Agnelli et al 2004.…”

Section: Discussionmentioning

confidence: 98%

Biomass and catabolic diversity of microbial communities with long-term restoration, bare fallow and cropping history in Chinese Mollisols

Wang¹,

Jin²,

Chen³

et al. 2007

PLANT SOIL ENVIRON

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“…To this end, a database of microbial soil vertical profiles from existing literature was compiled with data from Alvarez et al (1995), Anderson and Domsch (1989), Ekelund et al (2001), Fierer et al (2003, Zhou et al (2008), Selvam et al (2010), Tsai et al (2007), Agnelli et al (2004), and Yeates et al (1997). SOM radiocarbon ( 14 C) profiles are potentially valuable tracers of the integrated suite of processes affecting vertical SOM profiles and have recently been applied to evaluate climate-scale land surface model SOM predictions (Jenkinson and Coleman, 2008;Koven et al, 2013).…”

Section: Comparison To Som and 14 C Observationsmentioning

confidence: 99%

Long residence times of rapidly decomposable soil organic matter: application of a multi-phase, multi-component, and vertically resolved model (BAMS1) to soil carbon dynamics

et al. 2014

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Abstract. Accurate representation of soil organic matter (SOM) dynamics in Earth system models is critical for future climate prediction, yet large uncertainties exist regarding how, and to what extent, the suite of proposed relevant mechanisms should be included. To investigate how various mechanisms interact to influence SOM storage and dynamics, we developed an SOM reaction network integrated in a one-dimensional, multi-phase, and multi-component reactive transport solver. The model includes representations of bacterial and fungal activity, multiple archetypal polymeric and monomeric carbon substrate groups, aqueous chemistry, aqueous advection and diffusion, gaseous diffusion, and adsorption (and protection) and desorption from the soil mineral phase. The model predictions reasonably matched observed depth-resolved SOM and dissolved organic matter (DOM) stocks and fluxes, lignin content, and fungi to aerobic bacteria ratios. We performed a suite of sensitivity analyses under equilibrium and dynamic conditions to examine the role of dynamic sorption, microbial assimilation rates, and carbon inputs. To our knowledge, observations do not exist to fully test such a complicated model structure or to test the hypotheses used to explain observations of substantial storage of very old SOM below the rooting depth. Nevertheless, we demonstrated that a reasonable combination of sorption parameters, microbial biomass and necromass dynamics, and advective transport can match observations without resorting to an arbitrary depth-dependent decline in SOM turnover rates, as is often done. We conclude that, contrary to assertions derived from existing turnover time based model formulations, observed carbon content and 14 C vertical profiles are consistent with a representation of SOM consisting of carbon compounds with relatively fast reaction rates, vertical aqueous transport, and dynamic protection on mineral surfaces.

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“…The diversity of microorganisms typically decreases with depth, whether diversity is determined by phospholipid fatty acid profiles (Fierer et al 2003), DNA fingerprinting (LaMontagne et al 2003, Agnelli et al 2004, Goberna et al 2005, 16S ribosomal RNA (rRNA) gene sequences , or internal transcribed spacer (ITS) regions of the rRNA (Baldrian et al 2012). This is due to changes in edaphic factors such as pH, moisture contents, the quality and quantity of organic matters, and O 2 concentrations throughout the soil depth profile.…”

Section: Introductionmentioning

confidence: 99%

Bacterial and fungal community composition across the soil depth profiles in a fallow field

Yoo

Yun

et al. 2017

j ecology environ

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Background: Soil microorganisms play key roles in nutrient cycling and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depths, we analyzed microbial activities and bacterial and fungal community composition in soils up to a 120 cm depth at a fallow field located in central Korea. To examine the vertical difference of microbial activities and community composition, β-1,4-glucosidase, cellobiohydrolase, β-1,4-xylosidase, β-1,4-N-acetylglucosaminidase, and acid phosphatase activities were analyzed and barcoded pyrosequencing of 16S rRNA genes (bacteria) and internal transcribed spacer region (fungi) was conducted. Results: The activity of all the soil enzymes analyzed, along with soil C concentration, declined with soil depth. For example, acid phosphatase activity was 125.9 (± 5.7 (± 1 SE)), 30.9 (± 0.9), 15.7 (± 0.6), 6.7 (± 0.9), and 3.3 (± 0.3) nmol g −1 h −1 at 0-15, 15-30, 30-60, 60-90, and 90-120 cm soil depths, respectively. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1,[15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30], and 90-120 cm soil depths, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3,[15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30], and 90-120 cm soil depths, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51. 2, 48.6, 65.7, 46.1, and 45.7% at 15, 30, 60, 90, and 120 cm depths, respectively), a dominant fungal group at this site, showed no clear trend along the soil profile. Conclusions: Our results show that soil C availability can determine soil enzyme activity at different soil depths and that bacterial communities have a clear trend along the soil depth at this study site. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of soil microbial communities and their relationship with biogeochemical factors.

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Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA

Cited by 287 publications

References 54 publications

Biomass and catabolic diversity of microbial communities with long-term restoration, bare fallow and cropping history in Chinese Mollisols

Biomass and catabolic diversity of microbial communities with long-term restoration, bare fallow and cropping history in Chinese Mollisols

Long residence times of rapidly decomposable soil organic matter: application of a multi-phase, multi-component, and vertically resolved model (BAMS1) to soil carbon dynamics

Bacterial and fungal community composition across the soil depth profiles in a fallow field

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