Molecular monitoring of an uncultured group of the class Actinobacteria in two terrestrial environments

Rheims, Holger; Felske, Andreas; Seufert, Stephanie; Stackebrandt, Erko

doi:10.1016/s0167-7012(99)00012-3

Cited by 51 publications

(42 citation statements)

References 27 publications

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“…The tree constructed by the relatives. Clones prefixed 'TM' were from a peat bog (Rheims et al, 1996(Rheims et al, , 1999 and strains prefixed 'Ellin' were from Australian soils (Sait et al, 2002;Joseph et al, 2003). maximum-likelihood method supported this result (data not shown).…”

Section: Phylogenetic Analysismentioning

confidence: 82%

Patulibacter minatonensis gen. nov., sp. nov., a novel actinobacterium isolated using an agar medium supplemented with superoxide dismutase, and proposal of Patulibacteraceae fam. nov.

Takahashi

Matsumoto

Morisaki

et al. 2006

International Journal of Systematic and Evolutionary Microbiology

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Patulibacter minatonensis gen. nov., sp. nov., a novel actinobacterium isolated using an agar medium supplemented with superoxide dismutase, and proposal of Patulibacteraceae fam. nov. The Kitasato Institute, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8642, JapanA novel Gram-positive bacterial strain, designated KV-614 T , was isolated from a soil sample using an agar medium supplemented with superoxide dismutase. Based on 16S rRNA gene sequence analysis, it was found that the strain represented a novel deep-rooting lineage within the class Actinobacteria and clustered with yet-uncultivated bacteria from terrestrial environments and some unidentified strains isolated by unique methods. The most closely related established genus was Conexibacter (92?4 % sequence similarity to Conexibacter woesei DSM 14684 T ). Cells of strain T were rod-shaped and motile with long flagella. The strain was catalase-positive, oxidase-negative and grew under aerobic conditions. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid and alanine and glutamic acid. The peptidoglycan acyl type was acetyl. The only detected isoprenoid quinone was demethylmenaquinone with seven isoprene units (DMK-7). Mycolic acids were not detected. The predominant cellular fatty acid was v9c-octadecenoic acid (C18 : 1v9c). Minor components were 12-methyl tetradecanoic acid (anteiso-C15 : 0) and 14-methyl hexadecanoic acid (anteiso-C17 : 0). The DNA G+C content was 72 mol%. On the basis of phenotypic and genotypic characteristics, it is proposed that strain KV-614 T represents a new genus and a novel species, Patulibacter minatonensis gen. nov., sp. nov., in the class Actinobacteria. The type strain is KV-614. The creation of the family Patulibacteraceae fam. nov. is proposed to encompass the genus Patulibacter gen. nov. INTRODUCTIONThe number of micro-organisms that have been successfully identified and cultured in vitro represents only a small portion of the total existing in nature; it has been estimated that the number of known bacteria is less than 10 % of the total number of bacterial species in the world (Whitman et al., 1998;Schleifer, 2004). For many unknown micro-organisms, the appropriate cultivation conditions have not yet been found. In the course of searching for factors which promote bacterial colony growth, we found that using an isolation agar medium supplemented with superoxide dismutases (SODs) increased the number of colonies isolated from a soil sample, a response that was further enhanced by the addition of catalase (Takahashi et al., 2003). In this paper, we report the taxonomic characterization and classification of strain T isolated from a soil sample using agar medium supplemented with SOD. METHODSIsolation and cultivation conditions. Strain KV-614 T was isolated from a soil sample collected at Minato-Ku, Tokyo, Japan, using an agar medium supplemented with SOD following the method of Takahashi et al. (2003). Glucose/peptone/meat extract (GPM) agar medium, consisting of 1 % D-glucose (Wako Pur...

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Section: Phylogenetic Analysismentioning

confidence: 82%

Patulibacter minatonensis gen. nov., sp. nov., a novel actinobacterium isolated using an agar medium supplemented with superoxide dismutase, and proposal of Patulibacteraceae fam. nov.

Takahashi

Matsumoto

Morisaki

et al. 2006

International Journal of Systematic and Evolutionary Microbiology

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“…These actinobacterial groups from soil have been designated as TM, forming three major clusters TM1, TM2 and TM3 (Rheims et al, 1996). Actinobacteria belonging to groups TM2 and TM3 in particular have been reported from various environments worldwide and with a greater abundance in low-pH environments such as peat bogs (Rheims et al, 1999). Due to their ubiquitous distribution, they are believed to be contributing to ecologically important processes (Felske et al, 1997;Rheims et al, 1999).…”

Section: Discussionmentioning

confidence: 99%

“…Actinobacteria belonging to groups TM2 and TM3 in particular have been reported from various environments worldwide and with a greater abundance in low-pH environments such as peat bogs (Rheims et al, 1999). Due to their ubiquitous distribution, they are believed to be contributing to ecologically important processes (Felske et al, 1997;Rheims et al, 1999). Studies have shown that these Actinobacteria are metabolically active (Felske et al, 1997), slow-growing and easily overgrown under enrichment conditions (Rheims et al, 1999).…”

Section: Discussionmentioning

confidence: 99%

“…Due to their ubiquitous distribution, they are believed to be contributing to ecologically important processes (Felske et al, 1997;Rheims et al, 1999). Studies have shown that these Actinobacteria are metabolically active (Felske et al, 1997), slow-growing and easily overgrown under enrichment conditions (Rheims et al, 1999). , 1996), all of which are autotrophic iron-oxidizers; however, until now the TM3 Actinobacteria lacked cultivated representatives.…”

Section: Discussionmentioning

confidence: 99%

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Chemolithotrophic nitrate-dependent Fe(II)-oxidizing nature of actinobacterial subdivision lineage TM3

et al. 2013

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Anaerobic nitrate-dependent Fe(II) oxidation is widespread in various environments and is known to be performed by both heterotrophic and autotrophic microorganisms. Although Fe(II) oxidation is predominantly biological under acidic conditions, to date most of the studies on nitrate-dependent Fe(II) oxidation were from environments of circumneutral pH. The present study was conducted in Lake Grosse Fuchskuhle, a moderately acidic ecosystem receiving humic acids from an adjacent bog, with the objective of identifying, characterizing and enumerating the microorganisms responsible for this process. The incubations of sediment under chemolithotrophic nitratedependent Fe(II)-oxidizing conditions have shown the enrichment of TM3 group of uncultured Actinobacteria. A time-course experiment done on these Actinobacteria showed a consumption of Fe(II) and nitrate in accordance with the expected stoichiometry (1:0.2) required for nitratedependent Fe(II) oxidation. Quantifications done by most probable number showed the presence of 1 Â 10 4 autotrophic and 1 Â 10 7 heterotrophic nitrate-dependent Fe(II) oxidizers per gram fresh weight of sediment. The analysis of microbial community by 16S rRNA gene amplicon pyrosequencing showed that these actinobacterial sequences correspond to B0.6% of bacterial 16S rRNA gene sequences. Stable isotope probing using 13 CO 2 was performed with the lake sediment and showed labeling of these Actinobacteria. This indicated that they might be important autotrophs in this environment. Although these Actinobacteria are not dominant members of the sediment microbial community, they could be of functional significance due to their contribution to the regeneration of Fe(III), which has a critical role as an electron acceptor for anaerobic microorganisms mineralizing sediment organic matter. To the best of our knowledge this is the first study to show the autotrophic nitrate-dependent Fe(II)-oxidizing nature of TM3 group of uncultured Actinobacteria.

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“…The low diversity of cultivated bacteria may be attributed to the simple cultivation approach chosen and a short incubation time. Most of the isolates were identified as members of the phylum Actinobacteria that includes some of the most common soil microorganisms, playing important roles in decomposition and humus formation (Felske 340 M. Ros et al / Span J Agric Res (2011) 9(1), 338-343 Rheims et al, 1999). Due to the difficult lysis of Actinobacteria cells, DNA extraction from members of this phylum is hampered (Feinstein et al, 2009), which is one possible explanation why Actinobacteria typically only display 10-16% in clone libraries from soil ecosystems, while they represent 40-100% of cultured soil bacteria (Kaiser et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

Short communication. Response of bacterial community composition to long-term applications of different composts in agricultural soils

Ros

Knapp

Peintner

et al. 1970

Span. j. agric. res.

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Differences in the bacterial community composition of agricultural soils caused by a long-term (12 year) application of different composts were identified by cultivation-dependent and -independent methods (PCR-DGGE and 16S rRNA clone libraries). The number of colony forming units indicated that the successive incorporation of organic amendments increased the bacterial abundance (6.41-5.66 log 10 cfu g -1 dry soil) compared to control and mineral soils (5.54-3.74 log 10 cfu g -1 dry soil). Isolated bacteria were dominated by Actinobacteria, whereby compost-amended soils and green compost-amended soils showed, respectively, higher number of members of Actinobacteria (100% and 64%) than control and mineral soils (50% and 40%). The 16S rRNA clone libraries were dominated by Proteobacteria (43%), Acidobacteria (21%) and Actinobacteria (13%). Proteobacteria and Actinobacteria were most abundant in compost amended soils while Acidobacteria were more frequently found in mineral fertilizer and control soils. Partial 16S rRNA gene clone libraries revealed a higher bacterial diversity than cultivation. In conclusion, we found differences of bacterial community composition with a cultivation approach and clone libraries between compost amended soils and control and mineral soil.Additional key words: 16S rRNA clone libraries; fertilizer; isolated bacteria; organic amendments. ResumenComunicación corta. Respuesta de la composición bacteriana de un suelo agrícola a la incorporación a largo plazo de diferentes composts Se estudiaron las comunidades bacterianas de suelos agrícolas enmendados durante 12 años con diferentes tipos de compost, mediante el empleo de técnicas de cultivo en placa y técnicas moleculares (PCR-DGGE y genotecas de ARNr 16S). El cultivo en placa mostró un aumento del número de bacterias en los suelos enmendado con diferentes composts (6,41-5,66 log 10 cfu g -1 suelo), respecto a los suelos no enmendados o con fertilización mineral (5,54-3,74 log 10 cfu g -1 suelo). Esta técnica reveló que las Actinobacterias componen la mayoría de las bacterias identificadas en placa, encontrando un mayor número en los suelos enmendados con diferentes compost (100%-64%) frente a los no enmendados o con fertilización mineral (50%-40%). Las genotecas permitieron identificar además de Actinobacterias (13%), la presencia de Proteobacterias (43%) y Acidobacterias (21%). En los suelos enmendados con compost predominaron Proteobacterias y Actinobacterias, mientras que en los suelos sin enmendar y con fertilización mineral predominaron las Acidobacterias. Las genotecas mostraron mayor diversidad bacteriana que el método de cultivo en placa. En conclusión, los datos obtenidos mediante cultivo en placa y con genotecas mostraron diferencias en la composición de la comunidad microbiana entre suelos enmendados con compost y aquellos sin enmendar y con fertilización mineral. Palabras clave adicionales: bacterias aisladas; enmiendas orgánicas; fertilizantes; genotecas bacterianas.

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Molecular monitoring of an uncultured group of the class Actinobacteria in two terrestrial environments

Cited by 51 publications

References 27 publications

Patulibacter minatonensis gen. nov., sp. nov., a novel actinobacterium isolated using an agar medium supplemented with superoxide dismutase, and proposal of Patulibacteraceae fam. nov.

Patulibacter minatonensis gen. nov., sp. nov., a novel actinobacterium isolated using an agar medium supplemented with superoxide dismutase, and proposal of Patulibacteraceae fam. nov.

Chemolithotrophic nitrate-dependent Fe(II)-oxidizing nature of actinobacterial subdivision lineage TM3

Short communication. Response of bacterial community composition to long-term applications of different composts in agricultural soils

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