Short- and long-term effects of continuous compost amendment on soil microbiome community

Judith Kraut-Cohen; Avihai Zolti; Nativ Rotbart; Asher Bar-Tal; Yael Laor; Shlomit Medina; Raneen Shawahna; Ibrahim Saadi; Michael Raviv; Stefan J Green; Uri Yermiyahu; Dror Minz

doi:10.1016/j.csbj.2023.05.030

Short- and long-term effects of continuous compost amendment on soil microbiome community

Comput Struct Biotechnol J. 2023 May 31:21:3280-3292. doi: 10.1016/j.csbj.2023.05.030. eCollection 2023.

Authors

Judith Kraut-Cohen¹, Avihai Zolti^{1

2}, Nativ Rotbart^{1

3}, Asher Bar-Tal¹, Yael Laor⁴, Shlomit Medina⁴, Raneen Shawahna¹, Ibrahim Saadi⁴, Michael Raviv⁵, Stefan J Green⁶, Uri Yermiyahu⁷, Dror Minz¹

Affiliations

¹ Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel.
² Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
³ Shamir Research Institute, University of Haifa, Qatzrin, Israel.
⁴ Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Institute, Newe Ya'ar Research Center, Ramat Yishai 30095, Israel.
⁵ Institute of Plant Science, Agricultural Research Organization - Volcani Institute, Newe Ya'ar Research Center, Ramat Yishai 30095, Israel.
⁶ Genomics and Microbiome Core Facility, Rush University, Chicago, IL, USA.
⁷ Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Gilat Research Center, Israel.

Abstract

Organic amendment, and especially the use of composts, is a well-accepted sustainable agricultural practice. Compost increases soil carbon and microbial biomass, changes enzymatic activity, and enriches soil carbon and nitrogen stocks. However, relatively little is known about the immediate and long-term temporal dynamics of agricultural soil microbial communities following repeated compost applications. Our study was conducted at two field sites: Newe Ya'ar (NY, Mediterranean climate) and Gilat (G, semi-arid climate), both managed organically over 4 years under either conventional fertilization (0, zero compost) or three levels of compost amendment (20, 40 and 60 m³/ha or 2, 4, 6 L/m²). Microbial community dynamics in the soils was examined by high- and low-time-resolution analyses. Annual community composition in compost-amended soils was significantly affected by compost amendment levels in G (first, second and third years) and in NY (third year). Repeated sampling at high resolution (9-10 times over 1 year) showed that at both sites, compost application initially induced a strong shift in microbial communities, lasting for up to 1 month, followed by a milder response. Compost application significantly elevated alpha diversity at both sites, but differed in the compost-dose correlation effect. We demonstrate higher abundance of taxa putatively involved in organic decomposition and characterized compost-related indicator taxa and a compost-derived core microbiome at both sites. Overall, this study describes temporal changes in the ecology of soil microbiomes in response to compost vs. conventional fertilization.

Keywords: Compost amendment; Microbial community; Organic agriculture; Soil ecology; Soil fertility; Soil microbiome.