Cattle impact on composition of archaeal, bacterial, and fungal communities by comparative fingerprinting of total and extracellular DNA

• Published in: Biology and fertility of soils 2013-04, Vol.49 (3), p.351-361
• Main Authors: Chroňáková, A., Ascher, J., Jirout, J., Ceccherini, M. T., Elhottová, D., Pietramellara, G., Šimek, M.
• Format: Article
• Language: English
• Subjects: Agriculture; Agronomy. Soil science and plant productions; Animal husbandry; Archaea; Bacteria; Biochemistry and biology; Biological and medical sciences; Biomedical and Life Sciences; Cattle; Chemical, physicochemical, biochemical and biological properties; Community ecology; Community structure; Deoxyribonucleic acid; DNA; Environmental DNA; Feces; Fundamental and applied biological sciences. Psychology; Grasslands; Life Sciences; Microbial activity; Microbiology; Microorganisms; Original Paper; Overwintering; Physics, chemistry, biochemistry and biology of agricultural and forest soils; Soil microorganisms; Soil science; Soil Science & Conservation; Soil sciences; Soils
• ISSN: 0178-2762; 1432-0789
• DOI: 10.1007/s00374-012-0726-x

The aim of the study was to evaluate the impact of cattle overwintering husbandry on composition of upland grassland soil archaeal, bacterial, and fungal communities by comparative fingerprinting (SSU rRNA denaturing gradient gel electrophoresis (DGGE)) of total (tDNA) and extracellular DNA (eDNA) extracted from three differently impacted soils (severely, moderately, and non-impacted soil) and cattle excrements. Cattle excrements carried a significant amount of viable microorganisms and eDNA, and as a result of its high external returns, the amounts of extractable eDNA in soil increased with cattle impact, being positively correlated with soil microbial biomass and activity. The soil eDNA fraction (2.8 to 5.7 μg g −1  dw) significantly contributed to the soil metagenome, representing 18–31 % of soil tDNA. The largest shift in soil community structure was observed for Archaea, followed by fungi and bacteria, indicating that soil bacteria possess the highest resilience to cattle-induced changes. Cattle excrements showed more diverse bacterial than archaeal and fungal communities. The specific DGGE bands of cattle excrements were also observed in community profiles of cattle-impacted soils, confirming the effect of cattle husbandry on composition of soil microbial communities, probably as a result of introduced rumen-borne microbes. Similar changes were also reflected in the eDNA-derived DGGE profiles, suggesting a higher contribution of bacteria to soil extracellular metagenome than Archaea and fungi. This study provided first evidences about the extracellular mobilome in cattle-impacted soils, carrying also genetic information of Archaea, and its susceptibility to impact by outdoor cattle husbandry.