Coexisting Curtobacterium Bacterium Promotes Growth of White-Rot Fungus Stereum sp.

Kamei, Ichiro; Yoshida, Takehito; Enami, Daisuke; Meguro, Sadatoshi

doi:10.1007/s00284-011-0050-y

Cited by 26 publications

(20 citation statements)

References 21 publications

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“…Bacterial mycophagy has also been described in different environments (Leveau and Preston, 2008). Under controlled conditions, some bacterial strains have been proven capable of promoting (Kamei et al, 2012;Bontemps et al, 2013) or inhibiting (Radtke et al, 1994) the growth of white-rot fungi. More specifically, from a functional point of view, it has been suggested that bacterial-fungal interactions during the wood decay process might be beneficial for both partners through a series of enzymatic reactions.…”

Section: Introductionmentioning

confidence: 99%

Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay

Hervé

Roux

Uroz

et al. 2013

Environmental Microbiology

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Wood recycling is key to forest biogeochemical cycles, largely driven by microorganisms such as white-rot fungi which naturally coexist with bacteria in the environment. We have tested whether and to what extent the diversity of the bacterial community associated with wood decay is determined by wood and/or by white-rot fungus Phanerochaete chrysosporium. We combined a microcosm approach with an enrichment procedure, using beech sawdust inoculated with or without P.chrysosporium. During 18 weeks, we used 16S rRNA gene-based pyrosequencing to monitor the forest bacterial community inoculated into these microcosms. We found bacterial communities associated with wood to be substantially less diverse than the initial forest soil inoculum. The presence of most bacterial operational taxonomic units (OTUs) varied over time and between replicates, regardless of their treatment, suggestive of the stochastic processes. However, we observed two OTUs belonging to Xanthomonadaceae and Rhizobium, together representing 50% of the relative bacterial abundance, as consistently associated with the wood substrate, regardless of fungal presence. Moreover, after 12 weeks, the bacterial community composition based on relative abundance was significantly modified by the presence of the white-rot fungus. Effectively, members of the Burkholderia genus were always associated with P.chrysosporium, representing potential taxonomic bioindicators of the white-rot mycosphere.

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Section: Introductionmentioning

confidence: 99%

Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay

Hervé

Roux

Uroz

et al. 2013

Environmental Microbiology

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“…It is assumed that the colonizing of vegetative structures of fungi by bacteria is used as a mechanism for a move to novel microhabitats and to occupy new niches [10]. Another study has shown that coexisting bacteria living with wood-decaying basidiomycetes significantly promoted the mycelial growth of its fungal host by mechanisms unclear until now [11]. Moreover, Pseudomonas species can interact with fungi and fungi-like organisms in plants directly.…”

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confidence: 99%

PPZPMs - a Novel Group of Cyclic Lipodepsipeptides Produced by thePhytophthora alniAssociated StrainPseudomonassp. JX090307 -the Missing Link between the Viscosin and Amphisin Group

Weißhoff

Hentschel

Zaspel

et al. 2014

Natural Product Communications

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The closely related to the Pseudomonas orientalis strain Pseudomonas sp. acc. no. JX090307 was isolated from hyphae of the phytopathogenic oomycete Phytophthora alni spp. alni. In in-vitro antagonistic tests, the living bacterium JX090307 and its cell extract showed antibiosis activity against different fungal pathogens of forest tree species, particularly against Verticillium dahliae and some strains of P. alni ssp. alni. Investigating the cell extract of JX090307 by means of LC-ESI-Q-TOF-MS and-MS/MS techniques, more than 30 cyclic lipodepsipeptids (CLPs) were found. 24 of them belong to a novel group of CLPs named PPZPM. The cyclic lipodepsidecapeptides PPZPMs are composed of a β-hydroxy fatty acid linked to a peptide part comprising 10 amino acids, where 8 of them are organized in a cyclic structure. PPZPMs differ from members of the Viscosin and Amphisin group by the number of amino acids forming the cyclic structure. The two main components, PPZPM-1a and PPZPM-2a, were investigated additionally by means of NMR spectroscopy.

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“…It is well known that many fungal species are involved in the degradation of wood. More recently it has been recognized that bacteria might collaboratively work with fungal species to accelerate wood decay [50]. Emerging molecular techniques are expanding our knowledge of the diversity of wood inhabiting organisms [51, 52].…”

Section: Resultsmentioning

confidence: 99%

Census-based rapid and accurate metagenome taxonomic profiling

et al. 2014

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BackgroundUnderstanding the taxonomic composition of a sample, whether from patient, food or environment, is important to several types of studies including pathogen diagnostics, epidemiological studies, biodiversity analysis and food quality regulation. With the decreasing costs of sequencing, metagenomic data is quickly becoming the preferred typed of data for such analysis.ResultsRapidly defining the taxonomic composition (both taxonomic profile and relative frequency) in a metagenomic sequence dataset is challenging because the task of mapping millions of sequence reads from a metagenomic study to a non-redundant nucleotide database such as the NCBI non-redundant nucleotide database (nt) is a computationally intensive task. We have developed a robust subsampling-based algorithm implemented in a tool called CensuScope meant to take a ‘sneak peak’ into the population distribution and estimate taxonomic composition as if a census was taken of the metagenomic landscape. CensuScope is a rapid and accurate metagenome taxonomic profiling tool that randomly extracts a small number of reads (based on user input) and maps them to NCBI’s nt database. This process is repeated multiple times to ascertain the taxonomic composition that is found in majority of the iterations, thereby providing a robust estimate of the population and measures of the accuracy for the results.ConclusionCensuScope can be run on a laptop or on a high-performance computer. Based on our analysis we are able to provide some recommendations in terms of the number of sequence reads to analyze and the number of iterations to use. For example, to quantify taxonomic groups present in the sample at a level of 1% or higher a subsampling size of 250 random reads with 50 iterations yields a statistical power of >99%. Windows and UNIX versions of CensuScope are available for download at https://hive.biochemistry.gwu.edu/dna.cgi?cmd=censuscope. CensuScope is also available through the High-performance Integrated Virtual Environment (HIVE) and can be used in conjunction with other HIVE analysis and visualization tools.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-918) contains supplementary material, which is available to authorized users.

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Coexisting Curtobacterium Bacterium Promotes Growth of White-Rot Fungus Stereum sp.

Cited by 26 publications

References 21 publications

Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay

Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay

PPZPMs - a Novel Group of Cyclic Lipodepsipeptides Produced by thePhytophthora alniAssociated StrainPseudomonassp. JX090307 -the Missing Link between the Viscosin and Amphisin Group

Census-based rapid and accurate metagenome taxonomic profiling

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