A DGGE analysis shows that crop rotation systems influence the bacterial and fungal communities in soils

Suzuki, Carlos Kenichi; Takenaka, Mikihito; Oka, Norikuni; Nagaoka, Kazunari; Karasawa, Toshihiko

doi:10.1080/00380768.2012.694119

Cited by 29 publications

(14 citation statements)

References 26 publications

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“…From here, we define microbial community "assemblage" as the community composition with respect to other. Similar analysis of DGGE banding patterns have been previously used in other studies (Anderson et al, 2003;Cleary et al, 2012;Flores-Rentería et al, 2015;Gafan et al, 2005;Suzuki et al, 2012;Vaz-Moreira et al, 2013).…”

Section: Soil Community Structurementioning

confidence: 73%

Agricultural matrix affects differently the alpha and beta structural and functional diversity of soil microbial communities in a fragmented Mediterranean holm oak forest

Flores‐Rentería

Rincón

Valladares

et al. 2016

Soil Biology and Biochemistry

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Given the increase in habitat fragmentation in the Mediterranean forests, understanding its impacts over the ecology of soil microbial communities, responsible for many ecosystem functions, and their capacity to metabolize different substrates from soil organic matter, is of upmost importance. We evaluated how the influence of the agricultural matrix, as one of the main consequences of forest fragmentation, may affect both the composition and the functioning of soil microbial communities in Mediterranean holm oak forests. We determined structural and functional alpha and beta-diversity of microbial communities, as well as microbial assemblages and metabolic profiles, by using a commonly used fingerprinting technique (Denaturing Gel Gradient Electrophoresis) and a community level physiological profiles (CLPP) technique (EcoPlate). Key drivers of soil microbial structure and metabolism were evaluated by using structural equation models (SEM) and multivariate ordination (envfit) approaches. Our results pointed out that forest fragmentation affects microbial community structure and functioning through a complex cascade of causal-effect interactions with the plant-soil system, which ultimately affects the nutrient cycling and functioning of forest soils. We also found a strong scale-dependency effect of forest fragmentation over the ecology of microbial communities: fragmentation increases the local (alpha) diversity, but affected negatively microbial diversity at the landscape scale (beta diversity). This homogenization of the microbial communities and their metabolism at landscape scale resulting from habitat fragmentation may have unknown potential consequences on the capacity of these communities, and hence these ecosystems, to respond to the climate change. Finally, we found a consistent relation between the structure and functional diversity of bacterial community, which further 3 showed the important role that the assemblage of microbial communities might have over their functioning.

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Section: Soil Community Structurementioning

confidence: 73%

Agricultural matrix affects differently the alpha and beta structural and functional diversity of soil microbial communities in a fragmented Mediterranean holm oak forest

Flores‐Rentería

Rincón

Valladares

et al. 2016

Soil Biology and Biochemistry

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“…In a recent meta-analysis of 122 studies, McDaniel et al (2014b) showed that crop rotations increase microbial biomass by an average 21%. Changes in microbial community structure with differences in rotational diversity have also been reported (Alvey et al 2003;Johnson et al 2003;Yin et al 2010); in particular, rotational diversity increases microbial community diversity and the relative abundance of fungi vs. bacteria (Bunemann et al 2004;Gonz alez-Ch avez et al 2010;Suzuki et al 2012). These changes are important because microbial community diversity is linked to functional resilience or resistance to disturbance (Griffiths et al 2000).…”

Section: Introductionmentioning

confidence: 85%

“…; Suzuki et al . ). These changes are important because microbial community diversity is linked to functional resilience or resistance to disturbance (Griffiths et al .…”

Section: Introductionmentioning

confidence: 97%

Crop rotational diversity enhances belowground communities and functions in an agroecosystem

et al. 2015

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Biodiversity loss, an important consequence of agricultural intensification, can lead to reductions in agroecosystem functions and services. Increasing crop diversity through rotation may alleviate these negative consequences by restoring positive aboveground-belowground interactions. Positive impacts of aboveground biodiversity on belowground communities and processes have primarily been observed in natural systems. Here, we test for the effects of increased diversity in an agroecosystem, where plant diversity is increased over time through crop rotation. As crop diversity increased from one to five species, distinct soil microbial communities were related to increases in soil aggregation, organic carbon, total nitrogen, microbial activity and decreases in the carbon-to-nitrogen acquiring enzyme activity ratio. This study indicates positive biodiversity-function relationships in agroecosystems, driven by interactions between rotational and microbial diversity. By increasing the quantity, quality and chemical diversity of residues, high diversity rotations can sustain soil biological communities, with positive effects on soil organic matter and soil fertility.

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“…Principal component analysis (PCA) was conducted to reduce the n-dimensional DGGE data obtained for each sample into linear axes explaining the maximum amount of variance, using the relative intensity of the bands obtained from the DGGE. We used the first two principal components of the PCA to define the structure of bacterial and fungal communities [58].…”

Section: Discussionmentioning

confidence: 99%

“…The number and pixel intensity of bands in a particular sample were considered comparative proxies of richness and proportional abundance of fungal or bacterial OTUs, respectively [55]. Similar analysis of DGGE banding patterns have been previously used in other studies [52,[54][55][56][57][58].…”

Section: Soil Microbial Community Activity and Fingerprinting Profilesmentioning

confidence: 99%

Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests

et al. 2015

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Ecological transformations derived from habitat fragmentation have led to increased threats to above-ground biodiversity. However, the impacts of forest fragmentation on soils and their microbial communities are not well understood. We examined the effects of contrasting fragment sizes on the structure and functioning of soil microbial communities from holm oak forest patches in two bioclimatically different regions of Spain. We used a microcosm approach to simulate the annual summer drought cycle and first autumn rainfall (rewetting), evaluating the functional response of a plant-soil-microbial system. Forest fragment size had a significant effect on physicochemical characteristics and microbial functioning of soils, although the diversity and structure of microbial communities were not affected. The response of our plant-soil-microbial systems to drought was strongly modulated by the bioclimatic conditions and the fragment size from where the soils were obtained. Decreasing fragment size modulated the effects of drought by improving local environmental conditions with higher water and nutrient availability. However, this modulation was stronger for plant-soil-microbial systems built with soils from the northern region (colder and wetter) than for those built with soils from the southern region (warmer and drier) suggesting that the responsiveness of the soil-plant-microbial system to habitat fragmentation was strongly dependent on both the physicochemical characteristics of soils and the historical adaptation of soil microbial communities to specific bioclimatic conditions. This interaction challenges our understanding of future global change scenarios in Mediterranean ecosystems involving drier conditions and increased frequency of forest fragmentation.

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A DGGE analysis shows that crop rotation systems influence the bacterial and fungal communities in soils

Cited by 29 publications

References 26 publications

Agricultural matrix affects differently the alpha and beta structural and functional diversity of soil microbial communities in a fragmented Mediterranean holm oak forest

Agricultural matrix affects differently the alpha and beta structural and functional diversity of soil microbial communities in a fragmented Mediterranean holm oak forest

Crop rotational diversity enhances belowground communities and functions in an agroecosystem

Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests

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