Actinobacterial community dominated by a distinct clade in acidic soil of a waterlogged deciduous forest

Kopecký, Jan; Kyselková, Martina; Omelka, Marek; Čermák, Ladislav; Novotná, Jitka; Grundmann, G. L.; Moënne‐Loccoz, Yvan; Sagova‐Mareckova, Marketa

doi:10.1111/j.1574-6941.2011.01173.x

Cited by 54 publications

(29 citation statements)

References 59 publications

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“…However, higher number of detected compounds was found in acidic soils and even though this result is based only on a small dataset, we think that acidic soils may harbor novel actinobacterial diversity. That result is supported by our previous description of high erm gene variability and of a new suborder of actinobacteria dominating actinobacterial communities at both of the studied acidic sites (Trebon - [20,50]; Zakopana - [17]).…”

Section: Discussionsupporting

confidence: 88%

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria

et al. 2015

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BackgroundDistribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions.ResultsNinety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene.ConclusionsThe type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite scaffolds occurring more likely in taxonomically distant producers but suggest that the antibiotic selection of gene pools is also influenced by site conditions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0416-6) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 88%

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria

et al. 2015

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“…The Proteobacteria phylum includes many of the bacteria responsible for nitrogen fixation (Chen et al 2003; Wang et al 2015) and a wide variety of pathogens (Tsolis 2002). Actinobacteria play an important role in the decomposition and humus formation processes (Kopecky et al 2011). The ecology and metabolism of Acidobacteria is not well understood because the majority of these bacteria have not been cultured (Sun et al 2014).…”

Section: Discussionmentioning

confidence: 99%

Isolation and characterization of phosphofungi, and screening of their plant growth-promoting activities

Wang

Sui

et al. 2018

AMB Expr

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Rhizospheric microorganisms can increase phosphorus availability in the soil. In this regard, the ability of phosphofungi to dissolve insoluble phosphorus compounds is greater than that of phosphate-solubilizing bacteria. The aim of the current study was to identify efficient phosphofungi that could be developed as commercial microbial agents. Among several phosphate-solubilizing fungal isolates screened, strain CS-1 showed the highest phosphorus-solubilization ability. Based on phylogenetic analysis of the internal transcribed spacer region sequence, it was identified as Aspergillus niger. High-performance liquid chromatography analysis revealed that the mechanism of phosphorus solubilization by CS-1 involved the synthesis and secretion of organic acids, mainly oxalic, tartaric, and citric acids. Furthermore, strain CS-1 exhibited other growth-promoting abilities, including efficient potassium release and degradation of crop straw cellulose. These properties help to returning crop residues to the soil, thereby increasing nutrient availability and sustaining organic matter concentration therein. A pot experiment revealed that CS-1 apparently increased the assessed biometric parameters of wheat seedlings, implying the potential of this strain to be developed as a commercial microbial agent. We used Illumina MiSeq sequencing to investigate the microbial community composition in the rhizosphere of uninoculated wheat plants and wheat plants inoculated with the CS-1 strain to obtain insight into the effect of the CS-1 strain inoculation. The data clearly demonstrated that CS-1 significantly reduced the content of pathogenic fungi, including Gibberella, Fusarium, Monographella, Bipolaris, and Volutella, which cause soil-borne diseases in various crops. Strain CS-1 may hence be developed into a microbial agent for plant growth improvement.Electronic supplementary materialThe online version of this article (10.1186/s13568-018-0593-4) contains supplementary material, which is available to authorized users.

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“…At the Z site, the most diverse bacterial communities (based on the number of T-RFs) and nonproducer type erm genes suggested that the diversification of bacteria was conditioned by large amounts of recalcitrant litter (16). The Z site conditions selected for a small but very specific actinobacterial community (lowest richness and lowest percentage of actinobacteria in the community by quantity), which consisted of Acidimicrobidae and sequences related to the recently described Trebon clade occurring in low-pH soil (33). At the M and D sites, the recalcitrant litter led to relatively high C content and corresponded with high abundance of both bacteria and actinobacteria (41) and also with the highest proportion of actinobacteria in the bacterial community.…”

Section: Discussionmentioning

confidence: 99%

Microbial Communities Show Parallels at Sites with Distinct Litter and Soil Characteristics

Sagova‐Mareckova

Omelka

Čermák

et al. 2011

Appl Environ Microbiol

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Plant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecularweight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated by erm resistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.

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Actinobacterial community dominated by a distinct clade in acidic soil of a waterlogged deciduous forest

Cited by 54 publications

References 59 publications

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria

Isolation and characterization of phosphofungi, and screening of their plant growth-promoting activities

Microbial Communities Show Parallels at Sites with Distinct Litter and Soil Characteristics

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