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Bacterial diversity of Serbian agriculural soils

Authors: Gavrilović, Bojana; Adamović, Jelena; Janković, Vukašin; Ćirić, Milica; Obradović, Aleksa;

Bacterial diversity of Serbian agriculural soils

Abstract

The diversity and abundance of rhizosphere microbiota significantly influence plant growth. Interactions within this microbiota, as well as with plants, are complex and varied, ranging from beneficial to harmful. Despite increasing research on these plant-microbe relationships, much remains unknown. Our hypothesis is that rhizosphere microbiota vary across different agricultural soils and may include strains useful for plant protection. Three soil samples were collected from the open field (OF) and protected field (PF) used for vegetable production, as well as intact soil from nearby woodlands (W) in S. Palanka. Bacterial isolation and cultivation was done using complex media that favor slower growing and usually spore-forming representatives. Bacterial diversity present in 3 direct soil samples (designated as OF.D, PF.D and W.D) and in 3 cultivated samples (designated as OF.C, PF.C and W.C) was assessed by partial next-generation sequencing of the 16S rDNA using primer pair targeting V3-V4 hypervariable region of 16S rRNA gene. In direct samples, 26 (OF.D), 30 (PF.D) and 19 (W.D) bacterial phyla were detected. Over 80% of bacterial Amplicon Sequence Variants (ASVs) in all direct samples were classified to 6 phyla: Actinobacteriota, Proteobacteria, Acidobacteriota, Firmicutes, Chloroflexi and Myxococcota. Only 3 phyla (Firmicutes, Proteobacteria and Actinobacteriota) were detected in all 3 cultivated samples and >65% of all ASVs were classified to phyla Firmicutes. In these samples, 244 (OF.D), 235 (PF.D) and 148 (W.D) bacterial genera were detected, including Bacillus Rhodococcus, Streptomyces, Sphingomonas and Gaiella. In OF.D sample, besides unclassified bacteria (44.8%), most abundant genera were: Rhodococcus (9%), Nocardioides (4.6%), Bacillus (4%), Streptomyces (3.1%), Gaiella (2.6%), as well as Skermanella, Sphingomonas, Lysobacter, Rubrobacter and Gemmatimonas (with 1.2% relative abundance each). PF.D sample contained, besides unclassified bacteria (57.5%), Bacillus (5.8%), Rhodococcus (4.2%), Sphingomonas (1.9%), Gaiella (1.6%), Longispora (1.3%), Hydrogenispora (1.3%), Pedomicrobium (1.1%) and Streptomyces (1%). In W.D samples, besides unclassified bacteria (42.8%), most abundant genera, with relative abundance >1%, were: Micromonospora (10%), Streptomyces (9%), Bacillus (7.4%), Sphingomonas (4.2%), Solirubrobacter (2.1%), Bradyrhizobium (1.9%), Gaiella (1.5%), Rhodococcus (1.4%), Pseudonocardia (1.4%), Nocardioides (1.2%) and Kribbella(1.2%). In cultivated samples, 25 (OF.C), 20 (W.C) and 17 (PF.C) bacterial genera were detected. Culturing conditions drastically reduced bacterial diversity and heavily favored growth of Bacillus in all cultivated samples. Most abundant genera, with relative abundance >1%, for OF.C sample were Bacillus (80.2%), Rhodococcus (8.4%), Mitsuaria (2.7%), Paenibacillus (2.6 %) and Cupriavidus (1.3%); for PF.C sample: Bacillus (65.4%), Lysobacter (21.4%), Rhodococcus (4.1%), Ensifer (4%) and Paenibacillus (1.5%); and for W.C sample: Bacillus (62.2%), Cupriavidus (30.3%), Brevibacillus (1.9%), Paenibacillus (1.8%), Burkholderia-Caballeronia-Paraburkholderia group (1.3%) and Achromobacter (1.2%). These results showed differences in complexity of the rhizospere microbiota affected by soil type and management and will be used as a starting point for further study of bacterial population in order to select species beneficial for plant growth and protection.

Country
Serbia
Keywords

soil diversity, Serbia

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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