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

Abstract

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.

Biological control in the microbiome era: Challenges and opportunities

“…Moreover, the taxonomical level used to describe and compare samples is crucial to spot differences. Two recent studies observed variation between sample groups only at the genus or lower taxonomical levels, while no differences were observed at the phylum level (Degrune et al, 2015;Schmidt et al, 2014a). Both publications underlined that the use of the genus or lowest possible taxonomical level could be more appropriate to detect differences in microbial communities.…”

Natural Farming Improves Soil Quality and Alters Microbial Diversity in a Cabbage Field in Japan

“…This might be due to the CF agricultural practices, including mineral fertilization and conventional tillage. Both practices have been reported to increase soil microbial size [15] and diversity [43] by increasing the availability of easily assessable nutrients and stimulating degradation of soil organic matter. Therefore, we propose that application of chemicals (e.g., pesticides) may be the main factor that alters soil microbial alpha diversity while other agricultural practices (e.g., tillage, straw mulching, and fertilization) have smaller effects on soil microbial alpha diversity at our experimental site.…”

Organic Farming Improves Soil Microbial Abundance and Diversity under Greenhouse Condition: A Case Study in Shanghai (Eastern China)

“…These investigations have identified that microbial attributes could reflect ecosystem processes such as crop productivity [3], the regulation of decomposition [4], nutrient cycling [5] and protection against soil-borne pathogens [6]. Several studies have shown that agricultural Sustainability 2018, 10, 3825 2 of 16 practices have significant influences on soil microbial communities and composition, including the tillage regime [7], fertilization [8], monoculture [9], crop residue management [10] and plant protection schemes [11]. Hence, the soil microbial community could be shifted to a positive organization for plant production and ecosystem sustainability by suitable agricultural practices [4].…”