Laor, Y. | Search bioRxiv

bioRxiv2026

Site, Fertilization and Season Structure the Soil Microbiome and its Interactions with Bdellovibrio and Like Organisms Predators

The contribution of predation between bacteria to microbial community dynamics in agricultural fields has hardly been investigated. Here. dynamics of general prokaryotes (GEP) and of the predators Bdellovibrionales (Bd) and Bacteriovoracales (Bac) (Bdellovibrio-and-Like Organisms, BALOs) were studied in two agricultural fields differing in organic and mineral input regimes, for one year. Season, but not fertilization, affected absolute sizes of GEP and of BALO communities. 16S rRNA gene community analysis identified numerous novel Bd and Bac lineages, with none of the dominant BALOs related to characterized isolates. A few dominant BALO amplicon sequence variants (ASVs) persisted year-round, whereas others showed seasonal- or treatment specific responses. GEP, Bd, and Bac ASV -diversity was mostly influenced by season, with some changes due to fertilization in Bd, and Bac communities. Seasonal changes, site, and fertilization regimes influenced {beta}-diversity of GEP, Bd and Bac communities and determined the structure of BALO-gram-negative bacteria interaction networks, signaling that niche segregation acts at the microbiome-BALO interface. Accordingly, we suggest that shifts in GEP community structure triggered by environmental changes and agricultural practices cascade to BALO predators, in turn affecting BALO-microbiome interactions. These dynamics may be harnessed to manipulate the soil microbiome to benefit sustainable environmental and agricultural outcomes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/735237v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@ee25dcorg.highwire.dtl.DTLVardef@f79940org.highwire.dtl.DTLVardef@16e48a2org.highwire.dtl.DTLVardef@1628c9e_HPS_FORMAT_FIGEXP M_FIG The soil microbiome and the microbial predators Bdellovibrio and Like Organisms (BALOs) are influenced by environmental parameters (season) and agricultural practice (fertilization) in their population dynamics, diversity and interactions. BALO diversity is high, and novel clades are found with BALOs differing in abundance and persistence. Microbiome-BALO interactions suggest environment and agricultural practice-dependence of niche segregation in BALOs. BALOs - and other micro-predators-may thus be integrated in the development of soil microbiome manipulations for environmental and agricultural applications. C_FIG

microbiology↗

bioRxiv2023

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

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 Yaar (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. HighlightsO_LIDose-dependent changes in soil microbiome structure by manure compost application C_LIO_LIDynamic short-and long-term changes in soil microbiomes by compost amendment C_LIO_LIClimate, soil properties and management influence compost-amendment effects C_LIO_LIImmediate and temporal cumulative effects of compost on soil and {beta} diversity C_LI

microbiology↗