Bacterial community structure in fumigated soil

Domínguez-Mendoza, Cristina A.; Bello–López, Juan Manuel; Navarro‐Noya, Yendi E.; León-Lorenzana, Arit S. de; Delgado–Balbuena, Laura; Gómez-Acata, Selene; Ruíz-Valdiviezo, Víctor Manuel; Ramírez-Villanueva, Daniel Alejandro; Luna‐Guido, Marco; Dendooven, Luc

doi:10.1016/j.soilbio.2014.02.012

Cited by 26 publications

(11 citation statements)

References 49 publications

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“…Strongest reduction in relative abundance of OTUs after soil disinfestation was seen for Acidobacteria . A recent study showed that Acidobacteria were one of the groups that were most sensitive to a strongly disturbing soil treatment (fumigation) (Domínguez-Mendoza et al, 2014 ). Earlier studies have shown that changes in land use, fertilization and management caused shifts in relative abundance of Acidobacteria and its different subgroups (Jones et al, 2009 ; Barnard et al, 2013 ; Navarrete et al, 2013 ).…”

Section: Discussionmentioning

confidence: 99%

Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles

Agtmaal

Hol

et al. 2015

Front. Microbiol.

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There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the suggested importance of microbial VOCs in the natural buffer of soils against diseases caused by soil-borne pathogens.

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Section: Discussionmentioning

confidence: 99%

Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles

Agtmaal

Hol

et al. 2015

Front. Microbiol.

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“…Details of the aerobic incubation experiment and the measurement of the CO 2 emitted can be found in Domínguez‐Mendoza et al . (). The metabolic quotient q CO 2 was defined as the ratio between respiration (CO 2 emission after 1 day) and microbial biomass.…”

Section: Methodsmentioning

confidence: 97%

Deforestation and Cultivation with Maize (Zea mays L.) has a Profound Effect on the Bacterial Community Structure in Soil

et al. 2014

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In this study, the effect of deforestation and cultivation of maize (Zea mays L.) on the physicochemical characteristics and the bacterial community structure in soil were studied at the national park Área de Protección de Flora y Fauna Nevado de Toluca in Mexico. Soil was sampled from three forested areas in the national park, from three deforested areas grazed by animals and from three areas cultivated with maize. The soil was characterized chemically and biologically, whilst the bacterial community structure was investigated through 454 pyrosequencing of the 16S rRNA gene. The pH in the forest soil decreased from 6·1 to 5·3 in the maize-cultivated soil, whilst the soil organic C content decreased 1·4 times in the arable soil compared with the forest soil. The microbial biomass C decreased 2·9 times in the arable soil compared with the forest soil, but the metabolic quotient qCO 2 (ratio basal respiration to microbial biomass C) nearly doubled. Deforestation and maize cultivation reduced the abundance of Proteobacteria, Actinobacteria and Bacteroidetes, whereas Acidobacteria, Chloroflexi, Gemmatimonadetes and Firmicutes were resistant to these changes. It was found that soil characteristics were affected negatively by deforestation and nearly half of the organic matter was lost, and on these sloped fields, erosion will be high, further decreasing soil fertility. Although the relative abundance of a number of bacterial groups was reduced by deforestation, others were not affected by land-use change.key words: bacterial community structure; metabolic quotient qCO 2 ; microbial biomass C and N; soil organic matter; resistance of the bacterial community to land-use change

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“…Most of the fungal population was eliminated and remained low for many weeks. Other work, using modern molecular methods (Dominguez-Mendoza et al, 2014;Chen et al, 2015), also showed that there are distinctly different microbial community structures in fumigated and non-fumigated soils.…”

Section: Controversy Over the Control In The Fi Methodsmentioning

confidence: 97%

“…However, Chen et al (2015) showed that the much diminished soil microbial biomass in the fumigated soil has a much smaller diversity (survivors mainly belong to the classes Bacilli, Eurotiomycetes and Sordariomycetes). Others have also shown vast differences in the community structure of pre-and post-fumigation populations (Reber, 1967;Dominguez-Mendoza et al, 2014). This suggests that the basal (or underlying) rate of SOC mineralisation is unrelated to the size, community structure or activity of the soil microbial biomass.…”

Section: Why Is Som So Stable? the Regulatory Gate Hypothesismentioning

confidence: 99%