Acidobacteria in Fens: Phylogenetic Diversity and Genome Analysis of the Key Representatives

Dedysh, Svetlana N.; Ivanova, Anastasia A.; Begmatov, Shahjahon; Beletsky, Alexey V.; Rakitin, Andrey L.; Mardanov, Andrey V.; Philippov, Dmitriy; Ravin, Nikolai V.

doi:10.1134/s0026261722601440

Cited by 8 publications

(5 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is known that acidobacteria of the class Acidobacteriia are abundant in acidic ombrotrophic peatlands [19,22,70]. In fens (Vologda Oblast, Russia), the communities of acidobacteria were dominated by other classes of acidobacteria-Vicinamibacteria and Blastocatellia [70]. However, in the fen profile studied by us, the abundance of these families was low.…”

Section: Discussionmentioning

confidence: 63%

“…In the catotelm, the proportion of these families was lower due to a decrease in the proportion of bacteria of the order Acidobacteriales, but the proportions of acidobacteria SD13 (16%-38%) and SD18 (3%-9%) and the class Holophagae (3%-7%) became more significant. It is known that acidobacteria of the class Acidobacteriia are abundant in acidic ombrotrophic peatlands [19,22,70]. In fens (Vologda Oblast, Russia), the communities of acidobacteria were dominated by other classes of acidobacteria-Vicinamibacteria and Blastocatellia [70].…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Diversity and Functional Potential of Prokaryotic Communities in Depth Profile of Boreo-Nemoral Minerotrophic Pine Swamp (European Russia)

Golovchenko,

Dobrovolskaya,

Sokolova

et al. 2023

Forests

View full text Add to dashboard Cite

Natural peatlands represent a wide range of habitats that contribute to the conservation of biodiversity, including microbial biodiversity. Molecular biological methods make it possible to significantly increase the accounting of microbial diversity compared to the cultivation methods. The studies on microbial diversity in minerotrophic peatlands using molecular biological methods lag significantly behind such studies for ombrotrophic peatlands. In this work, we characterized the taxonomic composition and functional potential of the prokaryotic community of the minerotrophic pine swamp (fen) in the Tver region of northwestern Russia using high-throughput sequencing of 16S rRNA gene fragments. This study is unique, since it was carried out not in individual horizons but across the entire fen profile, taking into account the differentiation of the profile into the acrotelm and catotelm. The composition and dominants of bacterial and archaeal communities were determined not only at the level of phyla but also at the level of classes, families, and cultivated genera. The prokaryotic community of the studied fen was shown to have a high taxonomic diversity (28 bacterial and 10 archaeal phyla were identified). The profile differentiation of the taxonomic composition of prokaryotic communities is most clearly manifested in the analysis of the acrotelm and catotelm. In the bacterial communities of the acrotelm, the top three phyla included Acidobacteriota, Alphaproteobacteria, and Actinomycetota, in the catotelm—Betaproteobacteria, Bacteroidota, and Chloroflexota. In archaeal communities of the acrotelm, we discovered the monodominance of Nitrososphaerota, in the catotelm—the dominance of Bathyarchaeota and subdominance of Thermoplasmatota, Halobacterota, and Aenigmarchaeota. The hot spots of microbial diversity in the studied fen profile were found to be the 0–20 cm layer of the acrotelm and the 150–200 cm layer of the catotelm. In contrast to the taxonomic composition, the functional profiles of the prokaryotic communities of the acrotelm and catotelm were generally similar, except for methane metabolism, which was primarily carried out in the catotelm.

show abstract

Section: Discussionmentioning

confidence: 63%

Section: Discussionmentioning

confidence: 99%

Diversity and Functional Potential of Prokaryotic Communities in Depth Profile of Boreo-Nemoral Minerotrophic Pine Swamp (European Russia)

Golovchenko,

Dobrovolskaya,

Sokolova

et al. 2023

Forests

View full text Add to dashboard Cite

show abstract

“…Bacteria of the order Vicinamibacteriales were reported to be the main population in soils and peatlands, and they are especially abundant in acidic peat bogs. The genome of a bacterium of the class Vicinamibacteria contained a set of genes encoding bacterial microcompartments (metabolosomes) that have not previously been described in acidobacteria and are probably involved in the metabolism of L-rhamnose ( Dedysh et al, 2022 ). Bacteria from the order Vicinamibacteriales involved in P solubilization was also proven by a genome-centric metagenomics approach ( Wu et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Recruitment of beneficial cucumber rhizosphere microbes mediated by amino acid secretion induced by biocontrol Bacillus subtilis isolate 1JN2

Yang,

Li,

Yan

et al. 2024

Front. Microbiol.

View full text Add to dashboard Cite

IntroductionAt present, the use of beneficial microorganisms to control cucumber Fusarium wilt is a widely used method, and the rhizosphere microecological reset is one of the mechanisms involved. However, how biocontrol strains reshape cucumber rhizosphere microecology remains to be further studied.MethodsThe composition changes of cucumber root exudates induced by biocontrol strain 1JN2, the microbial ecology of cucumber rhizosphere and the colonization ability of biocontrol strain 1JN2 in cucumber rhizosphere were analyzed through UHPLC-MS/MS analysis, Illumina high-throughput sequencing and SEM, respectively.ResultsFirst, cucumber plants treated with biocontrol Bacillus 1JN2 reduced the disease severity of Fusarium wilt by 60%. Significant changes in cucumber root exudates were found after 1JN2 inoculation and the contents of four amino acids including glutamine, tryptophan, glycine and glutamic acid were significantly increased. Second, It was found that the bacterial diversity in the rhizosphere of cucumber was significantly increased in both the strain treatment group and the amino acid mixture treatment group, The number of Bacillus was the largest in all dominant populations, exceeded 20% in all treatment groups. The bacteria of Hydrogenispora and Vicinamibacteria were significantly increased after treatment.DiscussionOverall, the results demonstrated that amino acid substances in cucumber root exudates induced by biocontrol strain 1JN2 can shift the cucumber root microenvironment and prevent the occurrence of Fusarium wilt disease.

show abstract

“…The available information about the functional role of Acidobacteria in soil ecosystems includes data on their involvement in the destruction of various biopolymers, as well as participation in the global carbon, iron and hydrogen cycles [12].…”

Section: Discussionmentioning

confidence: 99%

Metagenomics analysis of therapeutical peats samples mined from the deposits of the “Puścizna Wielka” peat bog in Poland

Łukasz,

Marta,

Mazańska

et al. 2023

Preprint

View full text Add to dashboard Cite

Therapeutic values of therapeutical peats have been appreciated for centuries. Although microbiological criteria for therapeutical peats used in therapies exists in Poland, this source is still “terra incognita” in terms of microbiological diversity. Many authors studying peats indicate that microorganisms inhabiting this niches possess abilities allowing their application in biotechnology and various fields of industry, economy, and medicine. The aim of this research was to explore this ecosystem and reveal microbiological potential for commercial use. Samples of peats were collected from protected deposits of the Czarny Dunajec in Poland to perform metagenomics analysis. Moreover, for better samples characteristics, physicochemical properties were performed. In all testes samples, the most abundant phylum was Acidobacteriota, its percentage ranged from 46.42% to 60.02%. Second the most predominant phylum was Proteobacteria, present in all samples in the range of 20.75% to 35.34%. Proteobacteriais a large group of Gram-negative bacilli and cocci. This phylum is divided into five classes, among which the OTUs of Alphaproteobacteria and Gammaproteobacteriawere identified in tested samples. Other phyla present in each tested sample were Verrucomicrobiota (1.97% – 7.72%), Desulfobacterota (0.83% - 6.04%) and Actinobacteriota (1.97% - 3.38%). “Puścizna Wielka” peat bog possess a great microbiological potential and can be a source of bacteria that could be used in industry or biotechnology. Many articles published over the past few years describe isolates of new species and their individual features. In next step authors plan to isolate and test strains using various media and conditions.

show abstract

Acidobacteria in Fens: Phylogenetic Diversity and Genome Analysis of the Key Representatives

Cited by 8 publications

References 52 publications

Diversity and Functional Potential of Prokaryotic Communities in Depth Profile of Boreo-Nemoral Minerotrophic Pine Swamp (European Russia)

Diversity and Functional Potential of Prokaryotic Communities in Depth Profile of Boreo-Nemoral Minerotrophic Pine Swamp (European Russia)

Recruitment of beneficial cucumber rhizosphere microbes mediated by amino acid secretion induced by biocontrol Bacillus subtilis isolate 1JN2

Metagenomics analysis of therapeutical peats samples mined from the deposits of the “Puścizna Wielka” peat bog in Poland

Contact Info

Product

Resources

About