Relative impacts of tillage, residue management and crop-rotation on soil bacterial communities in a semi-arid agroecosystem

Navarro‐Noya, Yendi E.; Gómez-Acata, Selene; Montoya‐Ciriaco, Nina; Rojas-Valdez, Aketzally; Suárez-Arriaga, Mayra C.; Valenzuela‐Encinas, César; Jiménez‐Bueno, Norma G.; Verhulst, Nele; Govaerts, Bram; Dendooven, Luc

doi:10.1016/j.soilbio.2013.05.009

Cited by 243 publications

(167 citation statements)

References 54 publications

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“…We found that the phyla Proteobacteria, Actinobacteria, and Acidobacteria were the most abundant in the samples, which was consistent with several other studies (Nacke et al 2011;Navarro-Noya et al 2013). Furthermore, the phylum Firmicutes were highly abundant in the zero and chisel plow tillage soils (Fig.…”

Section: Effects Of Different Tillage Protocols On Soil Bacterial Taxsupporting

confidence: 91%

Conservation tillage increases soil bacterial diversity in the dryland of northern China

Wang

Lü

Chen

et al. 2016

Agron. Sustain. Dev.

123

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Agricultural practices change soil's physical and chemical properties, therefore modifying soil microbial communities. Conservation tillage is widely used to improve the soil texture and nutrient status in the dryland regions of northern China. However, little is known about the influence of soil properties on microbes, in particular on the effect of conservation tillage on soil bacterial communities. Here, we studied the effect of a 5-year tillage treatment on soil properties and soil bacterial communities in the dryland regions of northern China using a high-throughput sequencing technology and quantitative PCR of 16S rRNA genes. We compared the changes in soil bacterial diversity, and composition was measured for conservation tillage, including zero plow or chisel plow, and for conventional tillage using plow. Our results show that conservation tillage increased the Simpson index by 378 % and exhibited significantly dissimilar polygenetic diversity, with r of 1, and taxonomic diversity, of r higher than 0.49, compared to conventional tillage. This finding demonstrates that conservation tillage modifies soil bacterial diversity. Chisel plow and zero tillage increase the abundance of the genus Bacillus, including 85 % of the phylum Firmicutes, and of Rhizobiales belonging to the Alphaproteobacteria. Overall conservation tillage increased the abundance of profitable functional bacteria species.

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Section: Effects Of Different Tillage Protocols On Soil Bacterial Taxsupporting

confidence: 91%

Conservation tillage increases soil bacterial diversity in the dryland of northern China

Wang

Lü

Chen

et al. 2016

Agron. Sustain. Dev.

123

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“…Aggregates are broken and the organic matter is released and available for bacterial activity (Cheeke et al 2012). Our results are consistent with those of Lienhard et al (2013) and Navarro-Noya et al (2013), showing an increase in bacterial diversity with increased soil disturbance and cropping intensity. In addition, Siciliano et al (2014) have shown soil fertility, including nitrates and organic matter, to be the most important factor influencing bacterial and fungal richness and diversity indexes.…”

Section: Analysis Of Alpha Diversity In Relation To Soil Treatmentsupporting

confidence: 91%

“…2a). These phyla are often dominant in very diverse agricultural soils (Janssen 2006;Lienhard et al 2013;Navarro-Noya et al 2013). We also showed that the most abundant fungal phyla for each combination were Ascomycota (74-86 %) and Basidiomycota (12-25 %), which are saprotrophic soil fungi (de Boer et al 2005) frequently dominant in soil ecosystems (Lienhard et al 2013;Buée et al 2009) (Fig.…”

Section: Phylum Composition Of Microbial Communitiesmentioning

confidence: 54%

“…The most recent surveys based on massive DNA sequencing and multivariate analysis, aiming to detect microbial patterns in an agricultural context, have focused on a high taxonomic level, i.e., class or phylum (Lienhard et al 2013;CejaNavarro et al 2010;Navarro-Noya et al 2013). Such studies allow a coarse assessment of the variability of large microbial groups in relation to agricultural practices.…”

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confidence: 99%

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A novel sub-phylum method discriminates better the impact of crop management on soil microbial community

Degrune

Dufrêne

Colinet

et al. 2015

Agron. Sustain. Dev.

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Soil microorganisms such as mycorrhizae and plant-growth-promoting rhizobacteria have beneficial effects on crop productivity. Agricultural practices are known to impact soil microbial communities, but past studies examining this impact have focused mostly on one or two taxonomic levels, such as phylum and class, thus missing potentially relevant information from lower levels. Therefore, we propose here an original, sub-phylum method for studying how agricultural practices modify microbial communities. This method involves exploiting the available sequence information at the lowest taxonomic level attainable for each operational taxonomic unit. In order to validate this novel method, we assessed microbial community composition using 454 pyrosequencing of 16S and 28S rRNA genes, and then we compared the results with results of a phylum-level analysis. Agricultural practices included conventional tillage, reduced tillage, residue removal, and residue retention. Results show that, at the lowest taxonomic level attainable, tillage is the main factor influencing both bacterial community composition, accounting for 13 % of the variation, and fungal community composition, accounting for 18 % of the variation. On the other hand, phylum-level analysis failed to reveal any effect of soil practice on bacterial community composition and missed the fact that different members of the same phylum responded differently to tillage practice. For instance, the fungal phylum Chytridiomycota showed no impact of soil treatment, while sub-phylum-level analysis revealed an impact of tillage practice on the Chytridiomycota sub-groups Gibberella, which includes a notorious wheat pathogen, and Trichocomaceae. This clearly demonstrates the necessity of exploiting the information obtainable at sub-phylum level when assessing the effects of agricultural practice on microbial communities.

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“…Therefore, it requires complex operation, long cycles and high costs. High-throughput sequencing technology requires no cloning construction and presents high throughput, in which the 454 sequencing technique presents the longest sequence reads, opening the door to the comprehensive and efficient understanding of the information of microflora in fermented food (Navarro-Noya et al, 2013;Poulsen et al, 2013;Sul et al, 2013;Yu et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Analysis of the Microbiota in Naturally Fermented Cabbage of Northeastern Part of China by High-throughput Sequencing of the V3-V4 Regions of the 16S rRNA Gene

Li¹,

Yue²

2016

IJAB

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To cite this paper: Li, X. and X. Yue, 2016. Analysis of the microbiota in naturally fermented cabbage of northeastern part of China by high-throughput sequencing of the V3-V4 regions of the 16S rRNA gene. AbstractIn order to explore the microbiota in naturally fermented cabbage of northeastern part of China, the sequencing of the V3-V4 regions of the 16S rRNA gene of the microbiota in naturally fermented cabbage of northeastern part of China was made in this experiment by using the 454 FLX+ platform. A total of 302,327 valid sequences of 16 samples were obtained by 454 pyrosequencing. Evaluation of the richness of microflora of the samples by calculating Chao1 index showed that the microbiota of the samples from Daqing presented a higher richness. Beta diversity analysis showed species overlap with a very low content in the samples from Heilongjiang, Jilin and Liaoning. Heat-map showed significant differences among the dominant bacteria of different provinces. The results of sample analysis based on microbiota showed that the Lactobacilli content of the samples from Daqing, Heihe and Songyuan was more than 50%, and that from Heihe was up to 69.6%. In addition, Wohlfahrtiimonas was found for the first time in fermented food in this experiment, revealing the security risks of traditional methods.

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Relative impacts of tillage, residue management and crop-rotation on soil bacterial communities in a semi-arid agroecosystem

Cited by 243 publications

References 54 publications

Conservation tillage increases soil bacterial diversity in the dryland of northern China

Conservation tillage increases soil bacterial diversity in the dryland of northern China

A novel sub-phylum method discriminates better the impact of crop management on soil microbial community

Analysis of the Microbiota in Naturally Fermented Cabbage of Northeastern Part of China by High-throughput Sequencing of the V3-V4 Regions of the 16S rRNA Gene

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