Cropping Systems Management, Soil Microbial Communities, and Soil Biological Fertility

Nelson, Alison; Spaner, Dean

doi:10.1007/978-90-481-8741-6_8

Cited by 16 publications

(14 citation statements)

References 128 publications

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“…In this light, the ability to manage the soil microbiome for the presence of beneficial and absence of detrimental organisms could offer a promising approach to improve sustainable agricultural production. Effects of agricultural management on the soil microbiome are, however, complex and diverse ( Bünemann et al , 2006 ; Nelson and Spaner, 2010 ), and retrieving universally valid conclusions on organic and conventional farming systems is difficult. In general, it has been reported that low-input farming systems promote higher abundance and diversity of most organisms, and although the positive effects on the macrobiota are largely consistent across studies, the impact on the microbiota seems less clear ( Hole et al , 2005 ; Postma-Blaauw et al , 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Distinct soil microbial diversity under long-term organic and conventional farming

et al. 2014

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Low-input agricultural systems aim at reducing the use of synthetic fertilizers and pesticides in order to improve sustainable production and ecosystem health. Despite the integral role of the soil microbiome in agricultural production, we still have a limited understanding of the complex response of microbial diversity to organic and conventional farming. Here we report on the structural response of the soil microbiome to more than two decades of different agricultural management in a long-term field experiment using a high-throughput pyrosequencing approach of bacterial and fungal ribosomal markers. Organic farming increased richness, decreased evenness, reduced dispersion and shifted the structure of the soil microbiota when compared with conventionally managed soils under exclusively mineral fertilization. This effect was largely attributed to the use and quality of organic fertilizers, as differences became smaller when conventionally managed soils under an integrated fertilization scheme were examined. The impact of the plant protection regime, characterized by moderate and targeted application of pesticides, was of subordinate importance. Systems not receiving manure harboured a dispersed and functionally versatile community characterized by presumably oligotrophic organisms adapted to nutrient-limited environments. Systems receiving organic fertilizer were characterized by specific microbial guilds known to be involved in degradation of complex organic compounds such as manure and compost. The throughput and resolution of the sequencing approach permitted to detect specific structural shifts at the level of individual microbial taxa that harbours a novel potential for managing the soil environment by means of promoting beneficial and suppressing detrimental organisms.

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Section: Introductionmentioning

confidence: 99%

Distinct soil microbial diversity under long-term organic and conventional farming

et al. 2014

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“…There is usually a dynamic interaction between plant and microorganisms in different agricultural ecosystems [2]. Agricultural management effects on the soil microbial communities are complex and diverse [3,4] and retrieving comprehensively effective explanations on organic and conventional farming systems is thought-provoking. Management practices influence soil microbial community structure [5] hence, intensive farming practices may undermine the welfare of natural habitats leading to disruption of ecosystem services [6].…”

Section: Introductionmentioning

confidence: 99%

Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya

et al. 2020

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Management practices such as tillage, crop rotation, irrigation, organic and inorganic inputs application are known to influence diversity and function of soil microbial populations. In this study, we investigated the effect of conventional versus organic farming systems at low and high input levels on structure and diversity of prokaryotic microbial communities. Soil samples were collected from the ongoing long-term farming system comparison trials established in 2007 at Chuka and Thika in Kenya. Physicochemical parameters for each sample were analyzed. Total DNA and RNA amplicons of variable region (V4-V7) of the 16S rRNA gene were generated on an Illumina platform using the manufacturer's instructions. Diversity indices and statistical analysis were done using QIIME2 and R packages, respectively. A total of 29,778,886 high quality reads were obtained and assigned to 16,176 OTUs at 97% genetic distance across both 16S rDNA and 16S rRNA cDNA datasets. The results pointed out a histrionic difference in OTUs based on 16S rDNA and 16S rRNA cDNA. Precisely, while 16S rDNA clustered by site, 16S rRNA cDNA clustered by farming systems. In both sites and systems, dominant phylotypes were affiliated to phylum Actinobacteria, Proteobacteria and Acidobacteria. Conventional farming systems showed a higher species richness and diversity compared to organic farming systems, whilst 16S rRNA cDNA datasets were similar. Physiochemical factors were associated differently depending on rRNA and rDNA. Soil pH, electrical conductivity, organic carbon, nitrogen, potassium, aluminium, zinc, iron, boron and micro-aggregates showed a significant influence on the observed microbial diversity. The observed higher species diversity in the conventional farming systems can be attributed to the integration of synthetic and organic agricultural inputs. These results show that the type of inputs used in a farming system not only affect the soil chemistry but also the microbial population dynamics and eventually the functional roles of these microbes.

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“…Farming practices have been proven to influence the composition of soil bacterial communities. Agricultural management had complex and diverse effects on the soil microbiome 16 17 . Arriving at universally valid conclusions about organic and conventional farming systems is difficult because of the complexity of the soil microbial community and the limitations imposed by the resolution of analytical methods.…”

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confidence: 99%

Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River

Wang

Hui

Feng

et al. 2016

Sci Rep

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Soil microorganisms play a crucial role in the biogeochemical cycling of nutrient elements and maintaining soil health. We aimed to investigate the response of bacteria communities to organic farming over different crops (rice, tea and vegetable) along the middle and lower reaches of the Yangtze River of China. Compared with conventional farming, organic farming significantly increased soil nutrients, soil enzyme activities, and bacterial richness and diversity. A Venn diagram and principal component analysis revealed that the soils with 3 different crops under organic farming have more number and percent of shared OTUs (operational taxonomic units), and shared a highly similar microbial community structure. Under organic farming, several predominant guilds and major bacterial lineages (Rhizobiales, Thiotrichaceae, Micromonosporaceae, Desulfurellaceae and Myxococcales) contributing to nutrient (C, N, S and P) cycling were enriched, whereas the relative abundances of acid and alkali resistant microorganisms (Acidobacteriaceae and Sporolactobacillaceae) were increased under conventional farming practices. Our results indicated that, for all three crops, organic farming have a more stable microflora and the uniformity of the bacterial community structure. Organic agriculture significantly increased the abundance of some nutrition-related bacteria, while reducing some of the abundance of acid and alkali resistant bacteria.

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Cropping Systems Management, Soil Microbial Communities, and Soil Biological Fertility

Cited by 16 publications

References 128 publications

Distinct soil microbial diversity under long-term organic and conventional farming

Distinct soil microbial diversity under long-term organic and conventional farming

Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya

Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River

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