Changes in composition and activity of soil microbial communities in peach and kiwifruit Mediterranean orchards under an innovative management system

Soil Research ◽  
2010 ◽  
Vol 48 (3) ◽  
pp. 266 ◽  
Author(s):  
Adriano Sofo ◽  
Giuseppe Celano ◽  
Patrizia Ricciuti ◽  
Maddalena Curci ◽  
Bartolomeo Dichio ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Cover Crops ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Diversity Index ◽  
Soil Depth ◽  
Soil Microbial Communities ◽  
Soil Management ◽  
Organic Input ◽  
Soil Microbial ◽  
Peach Orchard

The aim of this work was to evaluate the effects of 2 soil management systems, so called ‘innovative’ (INN) and ‘conventional’ (CON), on genetic and metabolic diversity of soil microbial communities of peach and kiwifruit orchards. INN system included minimum tillage, organic matter inputs from compost and cover crops, winter pruning, and adequate irrigation and fertilisation. CON system was characterised by conventional tillage, zero organic input, empirical pruning, strong chemical fertilisation, and excessive irrigation. After 4 years of treatments, soil samples were collected in different orchard sites. In peach and kiwifruit INN orchards, average fruit yields were significantly higher than in CON. INN orchards had a significantly higher total number of bacteria. The patterns of denaturing gradient gel electrophoresis of bacterial 16S rDNA/RNA from peach orchard showed differences between soils under drip emitters and along the inter-rows, whereas those from kiwifruit orchard clearly distinguished between INN and CON for both bacteria (16S rRNA) and fungi (18S rDNA/RNA). Shannon’s substrate diversity index, evaluated by Biolog® metabolic assay, was affected by soil treatment in peach orchard and by soil depth in kiwifruit orchard. Principal component analysis of Biolog® values clearly discriminated INN and CON soils of both orchards. The results revealed qualitative and quantitative changes of soil microbial communities in response to an innovative and sustainable soil management.

scholarly journals Comparison of Drivers of Soil Microbial Communities Developed in Karst Ecosystems with Shallow and Deep Soil Depths

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 173
Author(s):  
Huiling Guan ◽  
Jiangwen Fan ◽  
Haiyan Zhang ◽  
Warwick Harris
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Soil Depth ◽  
Phospholipid Fatty Acid ◽  
Soil Microbial Communities ◽  
Deep Soil ◽  
Soil System ◽  
Soil Microbial ◽  
Total Soil ◽  
Karst Ecosystems

Soil erosion is prevalent in karst areas, but few studies have compared the differences in the drivers for soil microbial communities among karst ecosystems with different soil depths, and most studies have focused on the local scale. To fill this research gap, we investigated the upper 20 cm soil layers of 10 shallow–soil depth (shallow–SDC, total soil depth less than 100 cm) and 11 deep–soil depth communities (deep–SDC, total soil depth more than 100 cm), covering a broad range of vegetation types, soils, and climates. The microbial community characteristics of both the shallow–SDC and deep–SDC soils were tested by phospholipid fatty acid (PLFAs) analysis, and the key drivers of the microbial communities were illustrated by forward selection and variance partitioning analysis. Our findings demonstrated that more abundant soil nutrients supported higher fungal PLFA in shallow–SDC than in deep–SDC (p < 0.05). Furthermore, stronger correlation between the microbial community and the plant–soil system was found in shallow–SDC: the pure plant effect explained the 43.2% of variance in microbial biomass and 57.8% of the variance in the ratio of Gram–positive bacteria to Gram–negative bacteria (G+/G−), and the ratio of fungi to total bacteria (F/B); the pure soil effect accounted for 68.6% variance in the microbial diversity. The ratio of microbial PLFA cyclopropyl to precursors (Cy/Pr) and the ratio of saturated PLFA to monounsaturated PLFA (S/M) as indicators of microbial stress were controlled by pH, but high pH was not conducive to microorganisms in this area. Meanwhile, Cy/Pr in all communities was >0.1, indicating that microorganisms were under environmental stress. Therefore, the further ecological restoration of degraded karst communities is needed to improve their microbial communities.

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

2009 ◽  
Vol 55 (No. 10) ◽  
pp. 413-423 ◽  
Author(s):  
V. Valášková ◽  
P. Baldrian
Keyword(s):  
Microbial Communities ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Genes Encoding ◽  
Gradient Gel Electrophoresis ◽  
Temperature Gradient Gel Electrophoresis ◽  
Experimental Treatments ◽  
Multiple Samples

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.

scholarly journals Continuous monocropping highly affect the composition and diversity of microbial communities in peanut (Arachis hypogaea L.)

2021 ◽  
Vol 49 (4) ◽  
pp. 12532
Author(s):  
Ali I. MALLANO ◽  
Xianli ZHAO ◽  
Yanling SUN ◽  
Guangpin JIANG ◽  
Huang CHAO
Keyword(s):  
Microbial Communities ◽  
Management Practices ◽  
Rhizosphere Soil ◽  
Diversity Index ◽  
Cropping Systems ◽  
Soil Microbial Communities ◽  
Pathogenic Fungi ◽  
Continuous Cropping ◽  
Bacterial Phyla ◽  
Soil Microbial

Continuous cropping systems are the leading cause of decreased soil biological environments in terms of unstable microbial population and diversity index. Nonetheless, their responses to consecutive peanut monocropping cycles have not been thoroughly investigated. In this study, the structure and abundance of microbial communities were characterized using pyrosequencing-based approach in peanut monocropping cycles for three consecutive years. The results showed that continuous peanut cultivation led to a substantial decrease in soil microbial abundance and diversity from initial cropping cycle (T1) to later cropping cycle (T3). Peanut rhizosphere soil had Actinobacteria, Protobacteria, and Gemmatimonadetes as the major bacterial phyla. Ascomycota, Basidiomycota were the major fungal phylum, while Crenarchaeota and Euryarchaeota were the most dominant phyla of archaea. Several bacterial, fungal and archaeal taxa were significantly changed in abundance under continuous peanut cultivation. Bacterial orders, Actinomycetales, Rhodospirillales and Sphingomonadales showed decreasing trends from T1>T2>T3. While, pathogenic fungi Phoma was increased and beneficial fungal taxa Glomeraceae decreased under continuous monocropping. Moreover, Archaeal order Nitrososphaerales observed less abundant in first two cycles (T1&T2), however, it increased in third cycle (T3), whereas, Thermoplasmata exhibit decreased trends throughout consecutive monocropping. Taken together, we have shown the taxonomic profiles of peanut rhizosphere communities that were affected by continuous peanut monocropping. The results obtained from this study pave ways towards a better understanding of the peanut rhizosphere soil microbial communities in response to continuous cropping cycles, which could be used as bioindicator to monitor soil quality, plant health and land management practices.

scholarly journals Evaluation of functional diversity of soil microbial communities – a case study

2011 ◽  
Vol 50 (No. 4) ◽  
pp. 141-148 ◽  
Author(s):  
J. Hofman ◽  
J. Švihálek ◽  
I. Holoubek
Keyword(s):  
Microbial Communities ◽  
Functional Diversity ◽  
Diversity Index ◽  
Soil Microbial Communities ◽  
Natural Area ◽  
Multivariate Statistical ◽  
Soil Microbial ◽  
Routine Monitoring ◽  
Best Parameter

In our case study, we measured the functional diversity of the microbial communities of twelve soils from the small natural area to assess if this assay is suitable for routine monitoring of soil biological quality. We found the BIOLOG assay meets especially practical benefits in routine monitoring of soils being simple and quick assay. However, we confirmed the ambiguity about the most appropriate analysis of the BIOLOG multivariate data and about the best parameter, which can be derived from the assay. The different analyses of the data were examined and various parameters derived from the BIOLOG assay were comparatively used to contribute to the discussion of how the data should be evaluated. We showed that not-normalized raw absorbances or trapezoid areas should be used for calculation of diversity index if the inoculum was standardized. There was no single answer to what parameter provided more correct results in the multivariate statistical analysis. Evaluating at least one not-normalized (e.g. trapezoid area) and one normalized parameter (e.g. absorbances read in fixed AWCD) was strongly suggested keeping in mind that they reveal different information.

scholarly journals Effects of Wildfire and Harvest Disturbances on Forest Soil Bacterial Communities

2007 ◽  
Vol 74 (1) ◽  
pp. 216-224 ◽  
Author(s):  
Nancy R. Smith ◽  
Barbara E. Kishchuk ◽  
William W. Mohn
Keyword(s):  
Microbial Biomass ◽  
Microbial Communities ◽  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Biomass Carbon ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Microbial Biomass Nitrogen ◽  
Soil Microbial

ABSTRACT Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH4 + and NO3 − due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments. Gamma- and Alphaproteobacteria were highly characteristic of the unburned treatments, while Betaproteobacteria and members of Bacillus were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.

Functional and molecular responses of soil microbial communities under differing soil management practices

2004 ◽  
Vol 36 (11) ◽  
pp. 1873-1883 ◽  
Author(s):  
Carmine Crecchio ◽  
Antonio Gelsomino ◽  
Roberto Ambrosoli ◽  
José Luis Minati ◽  
Pacifico Ruggiero
Keyword(s):  
Microbial Communities ◽  
Management Practices ◽  
Soil Microbial Communities ◽  
Soil Management ◽  
Molecular Responses ◽  
Soil Microbial

scholarly journals Cover crop-driven shifts in soil microbial communities could modulate tomato early crop growth via plant-soil feedbacks

2021 ◽  
Author(s):  
Micaela Tosi ◽  
John Drummelsmith ◽  
Dasiel Obregón ◽  
Inderjot Chahal ◽  
Laura L. Van Eerd ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Cover Crops ◽  
Cover Crop ◽  
Crop Residues ◽  
Management Strategies ◽  
Soil Microbial Communities ◽  
Crop Productivity ◽  
Residue Management ◽  
Soil Microbial ◽  
Plant Soil

Abstract Sustainable agricultural practices such as crop diversification, cover crops and residue retention are increasingly applied to counteract detrimental effects of agriculture on natural resources. Since part of their effects occur via changes soil microbial communities, it is critical to understand how these respond to different practices. Our study analyzed five cover crop (cc) treatments (oat, rye, radish, rye-radish mixture and no-cc control) and two crop residue management strategies (retention/R+ or removal/R-) in an 8-year diverse horticultural crop rotation trial from ON, Canada. Cc effects were small but stronger than those of residue management. Radish-based cover crops tended to be the most beneficial for both microbial abundance and richness, yet detrimental for fungal evenness. Cc species, in particular radish, also shaped fungal and, to a lesser extent, prokaryotic community composition. Crop residues modulated cc effects on bacterial abundance and fungal evenness (i.e., more sensitive in R- than R+), as well as microbial taxa. Several microbial structure features, some affected by cc, were correlated with early tomato growth in the following spring (e.g., composition, taxa within Actinobacteria, Firmicutes and Ascomycota). Our study suggests that, whereas mid-term cc effects were small, they need to be better understood as they could be influencing crop productivity via plant-soil feedbacks.

Sign in / Sign up

Export Citation Format

Share Document