Soil actinobacteria tend to have neutral interactions with other co‐occurring microorganisms, especially under oligotrophic conditions

Abstract

Summary Actinobacteria produce a variety of secondary metabolites that can influence the survival or behaviour of other organisms. The understanding of the ecological roles of actinobacteria has significantly improved in the past decades, but a systematic insight into the interactions between actinobacteria and other microbes in nature is warranted. Here, we studied the pairwise effects of actinobacteria on other microbes isolated from red soils under different nutritional conditions. We found that neutral effects dominated the interactions, accounting for 68.1% of the interactions in eutrophic conditions and for a significantly higher proportion (86.2%) in oligotrophic conditions. High nutrient levels boosted active metabolism of actinobacteria and generally made them more aggressive, supporting the stress gradient hypothesis. The secondary metabolites produced by actinobacteria played a pivotal role in interference competition with other microbes, of which the role of desferrioxamine siderophores could not be ignored. Niche overlap seemed to be another cause of competition, notably under oligotrophic conditions. Moreover, the large‐scale phylogeny had a much greater impact on the interaction than the location origin of the microbes. These results provide an understanding of the coexistence of actinobacteria with other microbes in nature and suggest neutrality as a key mechanism for maintaining microbial diversity in soils.

Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions

“…The directionality itself is the qualitative outcome, i.e., the sign of the effect of one microorganism on another. Microbes can have net negative, neutral, or positive effect on one another and sometimes qualitative information of directionality may be sufficient to categorize interactions into relationship types and observe patterns (Yan et al, 2021). However, the strength, that is the quantitative magnitude of these effects, can vary and have important implications for the biodiversity and stability of microbial communities (Ratzke et al, 2020).…”

Intra-Species Interactions in Streptococcus pneumoniae Biofilms

“…Neutral interactions among bacteria are not frequently described. Nevertheless, a recent study reported dominance of neutral interactions among actinobacteria in the soil ecosystem (Yan et al, 2021), particularly in oligotrophic conditions, i.e., in nutrient poor conditions that resulted from obtained for each strain in each condition (single-strain or dual-strain biofilm). The detailed results obtained for biological replica are presented in Figure 3 and Figure S2.…”

Activation of Secondary Metabolism in Red Soil-Derived Streptomycetes via Co-Culture with Mycolic Acid-Containing Bacteria

“…Therefore, the above four strains of MACB were chosen for subsequent co-culture. In addition, based on the antimicrobial activity and 16S rRNA gene similarity of the red soil-derived Streptomyces strains [19,24], 44 bioactive streptomycetes with abundant diversity were preferentially selected for this study (Table S1). The selected MACB and streptomycetes thus formed 176 (4 × 44) co-culture pairs.…”

“…The strains used in this work are listed in Table S1. Eight MACB were isolated from soils collected in Haixi Mongolian and Tibetan Autonomous Prefecture, China [23], and two MACB and all Streptomyces strains were from red soils collected in Jiangxi Province, China [19,24]. All these strains were preliminarily identified by 16S rRNA gene sequencing in our previous studies [19,23,24].…”

“…Eight MACB were isolated from soils collected in Haixi Mongolian and Tibetan Autonomous Prefecture, China [23], and two MACB and all Streptomyces strains were from red soils collected in Jiangxi Province, China [19,24]. All these strains were preliminarily identified by 16S rRNA gene sequencing in our previous studies [19,23,24]. Three indicator strains from different phyla were used for antimicrobial activity assay: Micrococcus luteus CGMCC 1.2567 (Gram-positive bacterium) and Trichoderma viride CGMCC 3.1913 (fungus) were obtained from the China General Microbiological Culture Collection Center (CGMCC), and extended-spectrum β-lactamase (ESBL)-producing Escherichia coli 4-1 (Gram-negative bacterium) was obtained from the Weifang Medical University, Shandong Province, China.…”