Control of common scab disease can be reached by resistant cultivars or suppressive soils. Both mechanisms are likely to translate into particular potato microbiome profiles, but the relative importance of each is not known. Here, microbiomes of bulk and tuberosphere soil and of potato periderm were studied in one resistant and one susceptible cultivar grown in a conducive and a suppressive field. Disease severity was suppressed similarly by both means yet, the copy numbers of txtB gene (coding for a pathogenicity determinant) were similar in both soils but higher in periderms of the susceptible cultivar from conducive soil. Illumina sequencing of 16S rRNA genes for bacteria (completed by 16S rRNA microarray approach) and archaea, and of 18S rRNA genes for micro-eukarytes showed that in bacteria, the more important was the effect of cultivar and diversity decreased from resistant cultivar to bulk soil to susceptible cultivar. The major changes occurred in proportions of Actinobacteria, Chloroflexi, and Proteobacteria. In archaea and micro-eukaryotes, differences were primarily due to the suppressive and conducive soil. The effect of soil suppressiveness × cultivar resistance depended on the microbial community considered, but differed also with respect to soil and plant nutrient contents particularly in N, S and Fe.
- MeSH
- Actinobacteria klasifikace genetika růst a vývoj patogenita MeSH
- Archaea klasifikace genetika růst a vývoj patogenita MeSH
- Chloroflexi klasifikace genetika růst a vývoj patogenita MeSH
- dusík metabolismus farmakologie MeSH
- eukaryotické buňky metabolismus MeSH
- faktory virulence genetika metabolismus MeSH
- genotypizační techniky MeSH
- mikrobiota genetika MeSH
- náchylnost k nemoci imunologie MeSH
- nemoci rostlin imunologie mikrobiologie MeSH
- odolnost vůči nemocem účinky léků MeSH
- Proteobacteria klasifikace genetika růst a vývoj patogenita MeSH
- půdní mikrobiologie * MeSH
- RNA ribozomální 16S genetika MeSH
- RNA ribozomální 18S genetika MeSH
- síra metabolismus farmakologie MeSH
- Solanum tuberosum účinky léků imunologie mikrobiologie MeSH
- železo metabolismus farmakologie MeSH
- zemědělské plodiny MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The dark ocean microbiota represents the unknown majority in the global ocean waters. The SAR202 cluster belonging to the phylum Chloroflexi was the first microbial lineage discovered to specifically inhabit the aphotic realm, where they are abundant and globally distributed. The absence of SAR202 cultured representatives is a significant bottleneck towards understanding their metabolic capacities and role in the marine environment. In this work, we use a combination of metagenome-assembled genomes from deep-sea datasets and publicly available single-cell genomes to construct a genomic perspective of SAR202 phylogeny, metabolism and biogeography. Our results suggest that SAR202 cluster members are medium sized, free-living cells with a heterotrophic lifestyle, broadly divided into two distinct clades. We present the first evidence of vertical stratification of these microbes along the meso- and bathypelagic ocean layers. Remarkably, two distinct species of SAR202 cluster are highly abundant in nearly all deep bathypelagic metagenomic datasets available so far. SAR202 members metabolize multiple organosulfur compounds, many appear to be sulfite-oxidizers and are predicted to play a major role in sulfur turnover in the dark water column. This concomitantly suggests an unsuspected availability of these nutrient sources to allow for the high abundance of these microbes in the deep sea.
- MeSH
- Chloroflexi klasifikace genetika izolace a purifikace metabolismus MeSH
- fylogeneze MeSH
- genomika MeSH
- metagenom MeSH
- metagenomika MeSH
- mikrobiota MeSH
- mořská voda mikrobiologie MeSH
- oceány a moře MeSH
- síra metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- oceány a moře MeSH
A novel nitrite-oxidizing bacterium (NOB), strain Lb(T), was isolated from a nitrifying bioreactor with a high loading of ammonium bicarbonate in a mineral medium with nitrite as the energy source. The cells were oval (lancet-shaped) rods with pointed edges, non-motile, Gram-positive (by staining and from the cell wall structure) and non-spore-forming. Strain Lb(T) was an obligately aerobic, chemolitoautotrophic NOB, utilizing nitrite or formate as the energy source and CO2 as the carbon source. Ammonium served as the only source of assimilated nitrogen. Growth with nitrite was optimal at pH 6.8-7.5 and at 40 °C (maximum 46 °C). The membrane lipids consisted of C20 alkyl 1,2-diols with the dominant fatty acids being 10MeC18 and C(18 : 1)ω9. The peptidoglycan lacked meso-DAP but contained ornithine and lysine. The dominant lipoquinone was MK-8. Phylogenetic analyses of the 16s rRNA gene sequence placed strain Lb(T) into the class Thermomicrobia of the phylum Chloroflexi with Sphaerobacter thermophilus as the closest relative. On the basis of physiological and phylogenetic data, it is proposed that strain Lb(T) represents a novel species of a new genus, with the suggested name Nitrolancea hollandica gen. nov., sp. nov. The type strain of the type species is Lb(T) ( = DSM 23161(T) = UNIQEM U798(T)).
- MeSH
- bioreaktory mikrobiologie MeSH
- chemoautotrofní růst MeSH
- Chloroflexi klasifikace genetika izolace a purifikace ultrastruktura MeSH
- DNA bakterií genetika MeSH
- dusitany metabolismus MeSH
- fylogeneze * MeSH
- mastné kyseliny chemie MeSH
- molekulární sekvence - údaje MeSH
- nitrifikace MeSH
- oxidace-redukce MeSH
- peptidoglykan chemie MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- vitamin K 2 analogy a deriváty chemie MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Nizozemsko MeSH
