DNA‐based stable isotope probing enables the identification of active bacterial endophytes in potatoes

Rasche, Frank; Lueders, Tillmann; Schloter, Michael; Schaefer, Sabine; Buegger, Franz; Gattinger, Andreas; Hood‐Nowotny, Rebecca; Sessitsch, Angela

doi:10.1111/j.1469-8137.2008.02744.x

Cited by 50 publications

(21 citation statements)

References 35 publications

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“…The high abundance of Acinetobacter sp. in a potato phytosphere has also been reported in a series of previous studies (3, 43, 52). These studies demonstrated that Acinetobacter spp.…”

Section: Discussionsupporting

confidence: 79%

“…Indeed, the representative sequences of OTUs (AP1, AP2, AP3, AP4, and AP5) for Sphingomonas sp. showed high identity to Sphingomonas faeni or Sphingomonas melonis , both of which have been reported for the association with above-ground tissues of plants (43, 59). In addition, interestingly, an isolate in OTU AP6 showed plant growth-promoting activity to potato seedlings (data not shown).…”

Section: Discussionsupporting

confidence: 58%

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Molecular Characterization of the Bacterial Community in a Potato Phytosphere

et al. 2013

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The bacterial community of a potato phytosphere at the flowering stage was examined using both culture-dependent and -independent methods. Tissues (leaves, stems, roots and tubers) were sampled from field-grown potato plants (cultivar Matilda), and the clone libraries of 16S rRNA genes and the isolate collections using R2A medium were constructed. By analyzing the combined data set of 16S rRNA gene sequences from both clone libraries and isolate collections, 82 genera from 8 phyla were found and 237 OTUs (≥97% identity) at species level were identified across the potato phytosphere. The statistical analyses of clone libraries suggested that stems harbor the lowest diversity among the tissues examined. The phylogenetic analyses revealed that the most dominant phylum was shown to be Proteobacteria for all tissues (62.0%–89.7% and 57.7%–72.9%, respectively), followed by Actinobacteria (5.0%–10.7% and 14.6%–39.4%, respectively). The results of principal coordinates analyses of both clone libraries and isolate collections indicated that distinct differences were observed between above- and below-ground tissues for bacterial community structures. The results also revealed that leaves harbored highly similar community structures to stems, while the tuber community was shown to be distinctly different from the stem and root communities.

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“…The high abundance of Acinetobacter sp. in a potato phytosphere has also been reported in a series of previous studies (3, 43, 52). These studies demonstrated that Acinetobacter spp.…”

Section: Discussionsupporting

confidence: 79%

Section: Discussionsupporting

confidence: 58%

Molecular Characterization of the Bacterial Community in a Potato Phytosphere

et al. 2013

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“…In particular, those enabling the recognition and catabolism of plant compounds such as the uptake and degradation of plant-derived polysaccharides have been described to be involved in this process (Fouts et al, 2008). Recent work by Rasche et al (2009) further showed that endophytes have the capacity to metabolize photosynthetic plant products.…”

Section: Root Endophytic Colonizationmentioning

confidence: 99%

Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

Compant

Clément

Sessitsch

2010

Soil Biology and Biochemistry

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1,837

1,013

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In both managed and natural ecosystems, beneficial plant-associated bacteria play a key role in supporting and/or increasing plant health and growth. Plant growth-promoting bacteria (PGPB) can be applied in agricultural production or for the phytoremediation of pollutants. However, because of their capacity to confer plant beneficial effects, efficient colonization of the plant environment is of utmost importance. The majority of plant-associated bacteria derives from the soil environment. They may migrate to the rhizosphere and subsequently the rhizoplane of their hosts before they are able to show beneficial effects. Some rhizoplane colonizing bacteria can also penetrate plant roots, and some strains may move to aerial plant parts, with a decreasing bacterial density in comparison to rhizosphere or root colonizing populations. A better understanding on colonization processes has been obtained mostly by microscopic visualisation as well as by analysing the characteristics of mutants carrying disfunctional genes potentially involved in colonization. In this review we describe the individual steps of plant colonization and survey the known mechanisms responsible for rhizosphere and endophytic competence. The understanding of colonization processes is important to better predict how bacteria interact with plants and whether they are likely to establish themselves in the plant environment after field application as biofertilisers or biocontrol agents.

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“…Labeled and unlabeled microbial RNA can be separated by density gradient centrifugation in order to identify the microbial communities using plant carbon. This approach has been used to identify archaea (18,21), bacteria (19,(25)(26)(27), and fungi (26) incorporating root carbon, as well as to identify bacterial endophytes of plant shoots (28). In particular, the combination of RNA-SIP with 454 pyrosequencing represents a powerful molecular tool for the sensitive detection of labeled microorganisms (29).…”

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confidence: 99%

Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon

Hernández

Dumont

Yuan

et al. 2015

Appl Environ Microbiol

120

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Microorganisms associated with the roots of plants have an important function in plant growth and in soil carbon sequestration. Rice cultivation is the second largest anthropogenic source of atmospheric CH 4 , which is a significant greenhouse gas. Up to 60% of fixed carbon formed by photosynthesis in plants is transported below ground, much of it as root exudates that are consumed by microorganisms. A stable isotope probing (SIP) approach was used to identify microorganisms using plant carbon in association with the roots and rhizosphere of rice plants. Rice plants grown in Italian paddy soil were labeled with 13 CO 2 for 10 days. RNA was extracted from root material and rhizosphere soil and subjected to cesium gradient centrifugation followed by 16S rRNA amplicon pyrosequencing to identify microorganisms enriched with 13 C. Thirty operational taxonomic units (OTUs) were labeled and mostly corresponded to Proteobacteria (13 OTUs) and Verrucomicrobia (8 OTUs). These OTUs were affiliated with the Alphaproteobacteria, Betaproteobacteria, and Deltaproteobacteria classes of Proteobacteria and the "Spartobacteria" and Opitutae classes of Verrucomicrobia. In general, different bacterial groups were labeled in the root and rhizosphere, reflecting different physicochemical characteristics of these locations. The labeled OTUs in the root compartment corresponded to a greater proportion of the 16S rRNA sequences (ϳ20%) than did those in the rhizosphere (ϳ4%), indicating that a proportion of the active microbial community on the roots greater than that in the rhizosphere incorporated plant-derived carbon within the time frame of the experiment. The interaction between plants and microorganisms within the root and in the rhizosphere is complex and poorly understood. Early studies focused on specific plant growth-promoting bacteria (1, 2) and more recently on characterizing the rhizosphere microbial community (3). For example, studies with Arabidopsis thaliana, a model plant species, have shown that the root endophytic microbial communities are highly specific (4, 5). In rice, the microbial communities associated with the rhizosphere and the phyllosphere have been characterized by a metaproteogenomic approach (6), and a metagenomic approach was used to characterize the endophytic root community in rice (7).A variety of factors act to shape the microbial community within the roots and in the rhizosphere, including the volume and nature of carbon substrates transported by the plant to the roots (8) and highly evolved signaling and interaction mechanisms between plants and microbes and the plant immune system (9). Plants actively recruit and sustain microorganisms in the root environment in part by the translocation of organic compounds from the leaves to the roots and into the rhizosphere that serve as growth substrates. In annual plants, this has been shown to account for 30 to 60% of net fixed carbon, 40 to 90% of which is excreted by the root and ultimately sequestered or respired by the root-associated microorganisms (10)....

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DNA‐based stable isotope probing enables the identification of active bacterial endophytes in potatoes

Cited by 50 publications

References 35 publications

Molecular Characterization of the Bacterial Community in a Potato Phytosphere

Molecular Characterization of the Bacterial Community in a Potato Phytosphere

Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization

Different Bacterial Populations Associated with the Roots and Rhizosphere of Rice Incorporate Plant-Derived Carbon

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