Endophytic bacteria of Sphagnum mosses as promising objects of agricultural microbiology

Shcherbakov, Andrey; Bragina, Anastasia; Kuzmina, E. Yu.; Berg, Christian; Muntyan, A. N.; Макарова, Н. В.; Malfanova, Natalia; Cardinale, Massimiliano; Berg, Gabriele; Chebotar, Vladimir; Тихонович, И. А.

doi:10.1134/s0026261713030107

Cited by 55 publications

(45 citation statements)

References 27 publications

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“…37) Some are also characterized as xylanolytic and laminarinolytic bacteria highly associated with the degradation of peat bogs to provide carbon sources to other heterotrophs. 38,39) Among the bacteria isolated from the culture, three isolates of Burkholderia, SF-A1, SF-C1, and SF-E2, were relatively active in N 2 O emission (Fig. S1).…”

Section: Resultsmentioning

confidence: 96%

Nitrous oxide emission potentials of Burkholderia species isolated from the leaves of a boreal peat moss *Sphagnum fuscum**

Nie

Wang

et al. 2015

Bioscience, Biotechnology, and Biochemistry

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Using a culture-based nitrous oxide (N2O) emission assay, three active N2O emitters were isolated from Sphagnum fuscum leaves and all identified as members of Burkholderia. These isolates showed N2O emission in the medium supplemented with [Formula: see text] but not with [Formula: see text], and Burkholderia sp. SF-E2 showed the most efficient N2O emission (0.20 μg·vial(-1)·day(-1)) at 1.0 mM KNO3. In Burkholderia sp. SF-E2, the optimum pH for N2O production was 5.0, close to that of the phyllosphere of Sphagnum mosses, while the optimum temperature was uniquely over 30 °C. The stimulating effect of additional 1.5 mM sucrose on N2O emission was ignorable, but Burkholderia sp. SF-E2 upon exposure to 100 mg·L(-1) E-caffeic acid showed uniquely 67-fold higher N2O emission. All of the three N2O emitters were negative in both acetylene inhibition assay and PCR assay for nosZ-detection, suggesting that N2O reductase or the gene itself is missing in the N2O-emitting Burkholderia.

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Section: Resultsmentioning

confidence: 96%

Nitrous oxide emission potentials of Burkholderia species isolated from the leaves of a boreal peat moss *Sphagnum fuscum**

Nie

Wang

et al. 2015

Bioscience, Biotechnology, and Biochemistry

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“…Here, we analysed the core rather than entire microbiome of the bog vegetation, for which many more differences are expected. (Vandamme et al 2007;Shcherbakov et al 2013). For Sphagnum mosses, associated B. bryophila was shown to be vertically transmitted and independent of the geographic region (Bragina et al 2013b).…”

Section: Discussionmentioning

confidence: 94%

“…; Shcherbakov et al . ). For Sphagnum mosses, associated B. bryophila was shown to be vertically transmitted and independent of the geographic region (Bragina et al .…”

Section: Discussionmentioning

confidence: 97%

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity

Bragina

Berg

2015

Molecular Ecology

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Bog ecosystems fulfil important functions in Earth's carbon and water turnover. While plant communities and their keystone species Sphagnum have been well studied, less is known about the microbial communities associated with them. To study our hypothesis that bog plants share an essential core of their microbiome despite their different phylogenetic origins, we analysed four plant community plots with 24 bryophytes, vascular plants and lichen species in two Alpine bogs in Austria by 16S rDNA amplicon sequencing followed by bioinformatic analyses. The overall bog microbiome was classified into 32 microbial phyla, while Proteobacteria (30.8%), Verrucomicrobia (20.3%) and Planctomycetes (15.1%) belonged to the most abundant groups. Interestingly, the archaeal phylum Euryarcheota represented 7.2% of total microbial abundance. However, a high portion of micro-organisms remained unassigned at phylum and class level, respectively. The core microbiome of the bog vegetation contained 177 operational taxonomic units (OTUs) (150 526 seq.) and contributed to 49.5% of the total microbial abundance. Only a minor portion of associated core micro-organisms was host specific for examined plant groups (5.9-11.6%). Using our new approach to analyse plant-microbial communities in an integral framework of ecosystem, vegetation and microbiome, we demonstrated that bog vegetation harboured a core microbiome that is shared between plants and lichens over the whole ecosystem and formed a transkingdom metacommunity. All micro- and macro-organisms are connected to keystone Sphagnum mosses via set of microbial species, for example Burkholderia bryophila which was found associated with a wide spectrum of host plants and is known for a beneficial plant-microbe interaction.

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“…Siderophore production and antibiotic or antifungal activity have been detected in many bacteria isolated from Sphagnum spp. (5,6,28,29), although no microbial bioactive compounds have been isolated so far. Toxins, siderophores, and antibiotics are commonly synthetized by NRPS and PKS systems (30).…”

Section: Discussionmentioning

confidence: 99%

Mining for Nonribosomal Peptide Synthetase and Polyketide Synthase Genes Revealed a High Level of Diversity in the Sphagnum Bog Metagenome

Müller

Oberauner-Wappis

Peyman

et al. 2015

Appl Environ Microbiol

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c Sphagnum bog ecosystems are among the oldest vegetation forms harboring a specific microbial community and are known to produce an exceptionally wide variety of bioactive substances. Although the Sphagnum metagenome shows a rich secondary metabolism, the genes have not yet been explored. To analyze nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), the diversity of NRPS and PKS genes in Sphagnum-associated metagenomes was investigated by in silico data mining and sequence-based screening (PCR amplification of 9,500 fosmid clones). The in silico Illumina-based metagenomic approach resulted in the identification of 279 NRPSs and 346 PKSs, as well as 40 PKS-NRPS hybrid gene sequences. The occurrence of NRPS sequences was strongly dominated by the members of the Protebacteria phylum, especially by species of the Burkholderia genus, while PKS sequences were mainly affiliated with Actinobacteria. Thirteen novel NRPS-related sequences were identified by PCR amplification screening, displaying amino acid identities of 48% to 91% to annotated sequences of members of the phyla Proteobacteria, Actinobacteria, and Cyanobacteria. Some of the identified metagenomic clones showed the closest similarity to peptide synthases from Burkholderia or Lysobacter, which are emerging bacterial sources of as-yet-undescribed bioactive metabolites. This report highlights the role of the extreme natural ecosystems as a promising source for detection of secondary compounds and enzymes, serving as a source for biotechnological applications.T he plant microbiome has established itself in recent years as an important player in the field of plant health and agricultural productivity (1). Mosses, especially Sphagnum species, are a phylogenetically old group of land plants in bog ecosystems, which are unique extreme habitats displaying high acidity, low temperature, and water saturation, together with extremely low concentrations of mineral nutrients (2). Sphagnum bogs in particular are of enormous importance because of their approved role in the global carbon cycle and have therefore been used globally as an indicator of climate change (3). The role of Sphagnum mosses as an important model for examining plant-microbe interactions as well as the ecology of plant-associated bacteria has been reported previously (4). Sphagnum mosses in particular are characterized by a specific but diverse microbial community (4, 5-7) whose members fulfil important functions in cooperation with the host, promoting plant growth by enhancing nutrient supply and showing antagonistic activity against plant pathogens (4, 8). In fact, high abundances of functional systems that are responsible for oxidative and drought stress responses and genetic exchange were detected recently by metagenomic analysis of the Sphagnum microbiome (4). The biological activity of bryophytes and their traditional use in medicine and agriculture are well known (9). It has been shown that Sphagnum species produce bioactive secondary metabolites which influence their micr...

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Endophytic bacteria of Sphagnum mosses as promising objects of agricultural microbiology

Cited by 55 publications

References 27 publications

Nitrous oxide emission potentials of Burkholderia species isolated from the leaves of a boreal peat moss *Sphagnum fuscum**

Nitrous oxide emission potentials of Burkholderia species isolated from the leaves of a boreal peat moss *Sphagnum fuscum**

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity

Mining for Nonribosomal Peptide Synthetase and Polyketide Synthase Genes Revealed a High Level of Diversity in the Sphagnum Bog Metagenome

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Endophytic bacteria of Sphagnum mosses as promising objects of agricultural microbiology

Cited by 55 publications

References 27 publications

Nitrous oxide emission potentials of Burkholderia species isolated from the leaves of a boreal peat moss Sphagnum fuscum*

Nitrous oxide emission potentials of Burkholderia species isolated from the leaves of a boreal peat moss Sphagnum fuscum*

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity

Mining for Nonribosomal Peptide Synthetase and Polyketide Synthase Genes Revealed a High Level of Diversity in the Sphagnum Bog Metagenome

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Nitrous oxide emission potentials of Burkholderia species isolated from the leaves of a boreal peat moss *Sphagnum fuscum**

Nitrous oxide emission potentials of Burkholderia species isolated from the leaves of a boreal peat moss *Sphagnum fuscum**