Modification of the terminal restriction fragment length polymorphism analysisfor assessment of a specific taxonomic group within a soil microbial community

Kopecký, Jan; Novotná, Gabriela Balíková; Ságová-Marečková, Markéta

doi:10.17221/1012-pse

Cited by 3 publications

(3 citation statements)

References 24 publications

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“…For double-color T-RFLP, purified PCR products of bacterial amplicon obtained with forward primer labelled with HEX and of actinobacterial amplicon labeled with FAM were combined in a proportion 2:1 for simultaneous cleavage by AluI. Details are given in [30]. Fragment analysis was performed at the Genomac International (Prague, Czech Republic, with a 96-capillary sequencer (Applied Biosystems, Foster City, CA).…”

Section: Terminal Restriction Fragment Length Polymorphism Analysis Amentioning

confidence: 99%

Bacterial diversity and abundance of a creek valley sites reflected soil pH and season

et al. 2015

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The effect of environmental factors on bacterial and actinobacterial communities was assessed to predict microbial community structure in natural gradients. Bacterial and actinobacterial communities were studied at four sites differing in vegetation and water regime: creek sediment, wet meadow, dry meadow and deciduous forest located in a shallow valley. The vegetation structure was assessed by phytocoenological releves. T-RFLP and quantitative PCR were used to determine community composition and abundances. Significant relationships between bacterial community structure and selected soil traits at sites located relatively close to each other (within 200 m) were demonstrated. Both the quantity and structure of bacterial communities were significantly influenced by organic matter content, soil moisture and pH. Bacterial diversity was higher in summer, while that of actinobacteria increased in winter. The Simpson’s evenness E was significantly correlated with soil organic matter content. Soil pH had the greatest influence on bacterial community structure showing higher within-site variability in summer than in winter.

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Section: Terminal Restriction Fragment Length Polymorphism Analysis Amentioning

confidence: 99%

Bacterial diversity and abundance of a creek valley sites reflected soil pH and season

et al. 2015

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“…Double-color T-RFLP was used for the bacterial community analysis (32). Briefly, PCR amplicons of the 16S rRNA gene region with primers labeled with the fluorescent dye hexachlorofluorescein (HEX) for bacteria and 6-carboxyfluorescein (FAM) for actinobacteria were mixed in ratio of 2:1 and cleaved by AluI.…”

Section: Vol 77 2011 Microbial Communities At Distinct Sites 7561mentioning

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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“…Mound-building ants of the genus Formica are common in Northern Eurasia, including Finland (Collingwood, 1979;Czechowski et al, 2002;Kopecký et al, 2009). Our study species, the ant Formica exsecta, occupies meadows, forest clearings and rocky outcrops, where they build perennial nest mounds (Sundstrom & Vitikainen, 2022;Vitikainen et al, 2011;Vitikainen et al, 2015).…”

Section: Study Site and Study Organismmentioning

confidence: 99%

Microbial communities of the antFormica exsectaand its nest material

Lindström

Timonen

Sundström

2023

European J Soil Science

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In this study, we investigated the bacterial and fungal microbiomes of the ant Formica exsecta (Hymenoptera, Formicidae), and assessed whether the microbial communities inside the ants differ from those in their nest material. Furthermore, we investigated whether the microbial communities inside the ants are conserved across time. To achieve this, we sequenced the bacterial 16S rRNA, and the fungal ITS region in entire adult worker ants and their nest material by Illumina MiSeq. We found that both the bacterial, and the fungal microbiomes form communities discrete from those in the surrounding nest material. In addition to the differences in species composition, we also found that bacterial species diversity, species richness, ζ diversity, and evenness were lower in ants than in the nest material. For fungi, only species richness was lower in the ants than in the nest material. The rate of within‐colony species turnover across sampling events was not statistically significant for bacteria, but highly significant for fungi. This suggests that the fungal communities in the ants are less stable than the bacterial ones. Four bacterial taxa (Alphaproteobacteria, Proteobacteria, Staphylococcus, and Streptococcus), and two fungal taxa (Davidiella and Cryptococcus) formed a core microbiome, being consistently present and more abundant in the ants, but absent in the nest material. In all other cases differences in community composition and structure were due to taxa that were more consistently present and more abundant in the nest material, and frequently absent in the ants. Furthermore, we found 36 unique OTUs identified as Proteobacteria, and 82 unique OTUs identified as Alphaproteobacteria in the ants, representing 2.5% and 5.8% of all bacterial OTUs and 24.6% and 41% of the total number of bacterial sequences. This suggests that F. exsecta harbours a considerable bacterial diversity that so far remains unexplored.

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Modification of the terminal restriction fragment length polymorphism analysisfor assessment of a specific taxonomic group within a soil microbial community

Cited by 3 publications

References 24 publications

Bacterial diversity and abundance of a creek valley sites reflected soil pH and season

Bacterial diversity and abundance of a creek valley sites reflected soil pH and season

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

Microbial communities of the antFormica exsectaand its nest material

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