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Jorg Overmann - One of the best experts on this subject based on the ideXlab platform.

  • Vicinamibacteraceae fam. nov., the first described family within the subdivision 6 Acidobacteria.
    International journal of systematic and evolutionary microbiology, 2018
    Co-Authors: Katharina J. Huber, Jorg Overmann
    Abstract:

    Acidobacteria constitute a globally widespread phylum and mainly inhabit soil environments. Despite their high abundance and activity, only 60 species from seven of the 26 Acidobacterial subdivisions (sds; corresponding to class level) are (validly) described. Thus, only a low number of higher taxonomic ranks is currently distinguished within the Acidobacteria. Additionally, the distribution of the known Acidobacterial species within the described families of the Acidobacteriaceae (sd1), Bryobacteraceae (sd3), Blastocatellaceae (sd4), Pyrinomonadaceae (sd4), Holophagaceae (sd8) and Acanthopleuribacteraceae (sd8) is extremely biased as most strains are affiliated with the Acidobacteriaceae. Members of this family are characteristic for acidic soils. In contrast, culture-independent analysis of microbial communities worldwide revealed that sd6 Acidobacteria prevail in soils with neutral pH. To improve the existing Acidobacterial taxonomy, we here formally describe the first family within sd6 Acidobacteria, the Vicinamibacteraceae. Members of the Vicinamibacteraceae are aerobic, neutrophilic, psychrotolerant to mesophilic chemoheterotrophs. Their cells stain Gram-negative, do not form capsules or spores, and are non-motile. They occur as single cells or in aggregates and divide by binary fission. Growth occurs on sugars or complex proteinaceous compounds. MK-8 is the major quinone. Major fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C18 : 1ω7c or ω9c, iso-C17 : 1ω9c, C16 : 0 and iso-C17 : 0. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylglycerol are the major polar lipids. Unidentified glycolipids or unknown phospholipids might also be present. The G+C content of the DNA ranges from 64.7 to 65.9 mol%. Within the Vicinamibacteraceae fam. nov., Vicinamibacter and Luteitalea are the only genera described so far.

  • An overview of the occurrence of ether- and ester- linked iso -diabolic acid membrane lipids in microbial cultures of the Acidobacteria: Implications for brGDGT paleoproxies for temperature and pH
    Organic Geochemistry, 2018
    Co-Authors: Jaap Sinninghe S Damste, W Irene C Rijpstra, Barbel U Foesel, Jorg Overmann, Svetlana N Dedysh, Katharina J. Huber, Peter F. Dunfield, Satoshi Nakagawa, Joong Jae Kim, Laura Villanueva
    Abstract:

    Abstract 13,16-Dimethyl octacosanedioic acid (iso-diabolic acid) is a major membrane-spanning lipid of subdivisions (SDs) 1, 3 and 4 of the Acidobacteria, a highly diverse phylum within the Bacteria. It has been suggested that these lipids are potential building blocks for the orphan bacterial glycerol dialkyl glycerol tetraethers (GDGT) that occur widely in a variety of environmental settings. Here, we expand the knowledge on the occurrence of iso-diabolic acid in Acidobacteria by examining the lipid composition of six strains belonging to SDs 6, 8, 10, and 23 of the Acidobacteria, not previously analyzed for these lipids. In addition, we examined 12 new strains belonging to SDs 1, 3 and 4. Acid hydrolysis of total cell material released iso-diabolic acid in substantial quantities (25–39% of all fatty acids) from the strains of SDs 1 and 3 (except “Candidatus Solibacter usitatus”), and, for the first time, strains of SD 6 (6–25%), but not from SDs 8, 10, and 23. The monoglycerol ether derivative of iso-diabolic acid was only dominantly present in SD 4 strains (17–34%), indicating that the occurrence of ether-bound iso-diabolic acid is mainly restricted to SD 4 species. Methylated iso-diabolic acid derivatives were encountered in SDs 1, 3, 4, and 6, but only SD 4 species produced 5-methyl iso-diabolic acid derivatives, whereas the other SDs formed 6-methyl iso-diabolic acids. This suggests that the position of methylation of iso-diabolic acid may be controlled by the phylogenetic affiliation within the Acidobacteria and thus may not be a direct but an indirect response environmental to environmental conditions as inferred from the bacterial GDGT distributions in soil, peat and rivers.

  • Luteitalea pratensis gen. nov., sp. nov. a new member of subdivision 6 Acidobacteria isolated from temperate grassland soil.
    International journal of systematic and evolutionary microbiology, 2017
    Co-Authors: Selma Vieira, Manja Luckner, Gerhard Wanner, Jorg Overmann
    Abstract:

    Albeit being widespread and abundant in soils worldwide, bacteria of the phylum Acidobacteria have remained grossly understudied due to difficulties in their cultivation and isolation. To date, only 48 species have been validly described, including a single member of the phylogenetically diverse Acidobacteria subdivision 6. Here, we report the polyphasic characterization of strain HEG_-6_39T, a novel representative of Acidobacteria subdivision 6 isolated from a grassland soil in Thuringia, Germany. Cells of HEG_-6_39T are Gram-stain-negative, non-motile, non-spore-forming, non-capsulated short rods that form small dark yellow colonies. This slow growing bacterium is psychrotolerant and grows between 0 and 36 °C. It displays a narrower pH tolerance (5.3-8.3) than most Acidobacteria. The strain is an aerobe that grows chemo-organotrophically utilizing mostly sugars and proteinaceous substrates such as peptone, yeast extract, casein hydrolysate and casamino acids as substrates. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and two unknown phospholipids are identified as polar lipids. Major fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c), C18 : 1ω9c and iso-C17 : 1ω9c. The major respiratory quinone is MK-8. The G+C content of the genomic DNA is 64.7 mol%. 16S rRNA gene sequence analysis indicated that this bacterium was related to Vicinamibacter silvestris Ac_5_C6T with 93.6 % sequence similarity. Based on the present taxonomic characterization, strain HEG_-6_39T represents a new species of a novel genus for which the name Luteitalea pratensis gen. nov., sp. nov., is proposed. The type strain of the type species is HEG_-6_39T (=DSM 100886T=KCTC 52215T).

  • luteitalea pratensis gen nov sp nov a new member of subdivision 6 Acidobacteria isolated from temperate grassland soil
    International Journal of Systematic and Evolutionary Microbiology, 2017
    Co-Authors: Selma Vieira, Jorg Overmann, Gerhard Wanner, Manja Luckner
    Abstract:

    Albeit being widespread and abundant in soils worldwide, bacteria of the phylum Acidobacteria have remained grossly understudied due to difficulties in their cultivation and isolation. To date, only 48 species have been validly described, including a single member of the phylogenetically diverse Acidobacteria subdivision 6. Here, we report the polyphasic characterization of strain HEG_-6_39(T), a novel representative of Acidobacteria subdivision 6 isolated from a grassland soil in Thuringia, Germany. Cells of HEG_-6_39(T) are Gram-stain-negative, non-motile, non-spore-forming, non-capsulated short rods that form small dark yellow colonies. This slow growing bacterium is psychrotolerant and grows between 0 and 36 degrees C. It displays a narrower pH tolerance (5.3-8.3) than most Acidobacteria. The strain is an aerobe that grows chemo-organotrophically utilizing mostly sugars and proteinaceous substrates such as peptone, yeast extract, casein hydrolysate and casamino acids as substrates. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and two unknown phospholipids are identified as polar lipids. Major fatty acids are iso-C-15 : 0, summed feature 3 (C-16 : 1 omega 6c/C-16 : 1 omega 7c), C-18 : 1 omega 9c and iso-C-17 : 1 omega 9c. The major respiratory quinone is MK-8. The G+C content of the genomic DNA is 64.7 mol%. 16S rRNA gene sequence analysis indicated that this bacterium was related to Vicinamibacter silvestris Ac_5_C6(T) with 93.6% sequence similarity. Based on the present taxonomic characterization, strain HEG_-6_39(T) represents a new species of a novel genus for which the name Luteitalea pratensis gen. nov., sp. nov., is proposed. The type strain of the type species is HEG_6_39(T) (=DSM 100886(T)=KCTC 52215(T)).

  • Defining the taxonomic status of described subdivision 3 Acidobacteria: proposal of Bryobacteraceae fam. nov.
    International journal of systematic and evolutionary microbiology, 2017
    Co-Authors: Svetlana N Dedysh, Katharina J. Huber, Irina S. Kulichevskaya, Jorg Overmann
    Abstract:

    The phylum Acidobacteria represents one of the highly diverse but poorly characterized phylogenetic groups of the domain Bacteria. The taxonomically described Acidobacteria belong to 27 genera and 49 species, which represent subdivisions 1, 3, 4, 6, 8, 10 and 23 of this phylum. However, the corresponding family ranks have been defined only for some of these characterized micro-organisms. Here, we suggest the establishment of a novel family, Bryobacteraceae fam. nov., to accommodate taxonomically described members of subdivision 3 Acidobacteria. This family is characterized by Gram-stain-negative, non-spore-forming and non-motile rods, which divide by binary fission. Members of this family are mildly acidophilic, mesophilic, aerobic and facultatively anaerobic chemoheterotrophs that utilize various sugars and polysaccharides. The major fatty acids are iso-C15 : 0 and C16 : 1ω7c; the cells also contain significant amounts of 13,16-dimethyloctacosanedioic (iso-diabolic) acid. Currently, the family comprises the genera Bryobacter and Paludibaculum.

Svetlana N Dedysh - One of the best experts on this subject based on the ideXlab platform.

  • Chitinases Encoded in the Genomes of Acidobacteria: Origin and Evolution
    Microbiology, 2020
    Co-Authors: D. G. Naumoff, Svetlana N Dedysh
    Abstract:

    Acidobacteria are one of the widespread and numerically abundant groups of prokaryotes in soils and peatlands. The functional potential of these microorganisms remains poorly understood due to the limited number of cultured and characterized representatives. Acidisarcina polymorpha SBC82 is the only acidobacterium for which the ability to use chitin as a source of nitrogen and carbon has been experimentally proven. The genome of strain SBC82 encodes six proteins from the GH18 glycoside hydrolase family; each of these proteins can be considered as a representative of an independent subfamily. The present bioinformatics study shows that one of these subfamilies contains an extensive group of hypothetical chitinases from the Acidobacteria . This functional annotation was done based on the close relationship with the experimentally characterized enzyme from the proteobacterium Xylella fastidiosa . As shown by phylogenetic analysis, the studied group of Acidobacterial proteins originated due to lateral transfer of the ancestral gene from the Firmicutes . Acidobacteria subsequently served as a source for multiple lateral gene transfers to a number of bacterial phyla, including the Proteobacteria . Analysis of metagenomic datasets revealed a wide distribution of chitinase genes in Acidobacteria that inhabit wetlands and permafrost soils of the temperate and subarctic climatic zones.

  • Linking ecology and systematics of Acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils
    PloS one, 2020
    Co-Authors: Anastasia A. Ivanova, A. D. Zhelezova, Timofey Chernov, Svetlana N Dedysh
    Abstract:

    The Acidobacteria is one of the major bacterial phyla in soils and peatlands. The currently explored diversity within this phylum is assigned to 15 class-level units, five of which contain described members. The ecologically relevant traits of Acidobacteria from different classes remain poorly understood. Here, we compared the patterns of Acidobacterial diversity in sandy soils of tundra, along a gradient of increasing vegetation–unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. The Acidobacteria-affiliated 16S rRNA gene sequences retrieved from these soils comprised 11 to 33% of total bacterial reads and belonged mostly to members of the classes Acidobacteriia and Blastocatellia, which displayed opposite habitat preferences. The relative abundance of the Blastocatellia was maximal in unfixed sands and declined in soils of vegetated plots, showing positive correlation with soil pH and negative correlation with carbon and nitrogen availability. An opposite tendency was characteristic for the Acidobacteriia. Most Blastocatellia-affiliated reads belonged to as-yet-undescribed members of the family Arenimicrobiaceae, which appears to be characteristic for dry, depleted in organic matter soil habitats. The pool of Acidobacteriia-affiliated sequences, apart from Acidobacteriaceae- and Bryobacteraceae-related reads, had a large proportion of sequences from as-yet-undescribed families, which seem to specialize in degrading plant-derived organic matter. This analysis reveals sandy soils of tundra as a source of novel Acidobacterial diversity and provides an insight into the ecological preferences of different taxonomic groups within this phylum.

  • Hydrolytic Capabilities as a Key to Environmental Success: Chitinolytic and Cellulolytic Acidobacteria From Acidic Sub-arctic Soils and Boreal Peatlands.
    Frontiers in microbiology, 2018
    Co-Authors: Svetlana E. Belova, Jaap Sinninghe S Damste, Anastasia A. Ivanova, Nikolai V. Ravin, Timofey A. Pankratov, Andrey L. Rakitin, Alexey V. Beletsky, Andrey V. Mardanov, Svetlana N Dedysh
    Abstract:

    Members of the Acidobacteria are among the most efficient colonizers of acidic terrestrial habitats but the key traits underlying their environmental fitness remain to be understood. We analyzed indigenous assemblages of Acidobacteria in a lichen-covered acidic (pH 4.1) soil of forested tundra dominated by uncultivated members of subdivision 1. An isolate of these bacteria with cells occurring within saccular chambers, strain SBC82T, was obtained. The genome of strain SBC82T consists of a 7.11-Mb chromosome and four megaplasmids, and encodes a wide repertoire of enzymes involved in degradation of chitin, cellulose, and xylan. Among those, four secreted chitinases affiliated with the glycoside hydrolase family GH18 were identified. Strain SBC82T utilized amorphous chitin as a source of carbon and nitrogen; the respective enzyme activities were detected in tests with synthetic substrates. Chitinolytic capability was also confirmed for another phylogenetically related acidobacterium isolated from a Sphagnum peat bog, strain CCO287. As revealed by metatranscriptomic analysis of chitin-amended peat, 16S rRNA reads from these Acidobacteria increased in response to chitin availability. Strains SBC82T and CCO287 were assigned to a novel genus and species, Acidisarcina polymorpha gen. nov., sp. nov. Members of this genus colonize acidic soils and peatlands and specialize in degrading complex polysaccharides.

  • Refining the taxonomic structure of the phylum Acidobacteria.
    International journal of systematic and evolutionary microbiology, 2018
    Co-Authors: Svetlana N Dedysh, Pelin Yilmaz
    Abstract:

    The phylum Acidobacteria was created in 1997 in order to accommodate a large number of 16S rRNA gene sequences retrieved from various environments in cultivation-independent studies. At present, 26 major sequence clades or subdivisions (SDs) are recognized within this phylum, but only seven of them (SDs 1, 3, 4, 6, 8, 10 and 23) are commonly addressed as containing taxonomically described representatives. Here, we examined the currently explored diversity within the Acidobacteria using the candidate taxonomic unit circumscription system. Based on this analysis, 26 subdivisions were assigned to 15 class-level units, five of which contain described members. These include three earlier established classes Acidobacteriia, Blastocatellia and Holophagae, as well as two as-yet-undescribed groups defined by SDs 6 and 23, which we propose to name Vicinamibacteria classis nov. and Thermoanaerobaculia classis nov., respectively. The former assignment of Thermotomaculum hydrothermale to SD10 was found to be incorrect. This bacterium, therefore, was placed in the family Thermotomaculaceae fam. nov., order Thermotomaculales ord. nov. within the class Holophagae. We also propose establishing a number of high-level taxa to accommodate described representatives of SDs 3, 4, 6 and 23. The family Bryobacteraceae of SD3 Acidobacteria is placed in the order Bryobacterales ord. nov. within the taxonomic range of the class Acidobacteriia. The order Vicinamibacteriales ord. nov. is proposed to accommodate the family Vicinamibacteriaceae of SD6 Acidobacteria. Finally, the family Thermoanaerobaculaceae fam. nov., the order Thermoanaerobaculales ord. nov. are proposed to accommodate the only described representative of SD23, Thermoanaerobaculum aquaticum.

  • An overview of the occurrence of ether- and ester- linked iso -diabolic acid membrane lipids in microbial cultures of the Acidobacteria: Implications for brGDGT paleoproxies for temperature and pH
    Organic Geochemistry, 2018
    Co-Authors: Jaap Sinninghe S Damste, W Irene C Rijpstra, Barbel U Foesel, Jorg Overmann, Svetlana N Dedysh, Katharina J. Huber, Peter F. Dunfield, Satoshi Nakagawa, Joong Jae Kim, Laura Villanueva
    Abstract:

    Abstract 13,16-Dimethyl octacosanedioic acid (iso-diabolic acid) is a major membrane-spanning lipid of subdivisions (SDs) 1, 3 and 4 of the Acidobacteria, a highly diverse phylum within the Bacteria. It has been suggested that these lipids are potential building blocks for the orphan bacterial glycerol dialkyl glycerol tetraethers (GDGT) that occur widely in a variety of environmental settings. Here, we expand the knowledge on the occurrence of iso-diabolic acid in Acidobacteria by examining the lipid composition of six strains belonging to SDs 6, 8, 10, and 23 of the Acidobacteria, not previously analyzed for these lipids. In addition, we examined 12 new strains belonging to SDs 1, 3 and 4. Acid hydrolysis of total cell material released iso-diabolic acid in substantial quantities (25–39% of all fatty acids) from the strains of SDs 1 and 3 (except “Candidatus Solibacter usitatus”), and, for the first time, strains of SD 6 (6–25%), but not from SDs 8, 10, and 23. The monoglycerol ether derivative of iso-diabolic acid was only dominantly present in SD 4 strains (17–34%), indicating that the occurrence of ether-bound iso-diabolic acid is mainly restricted to SD 4 species. Methylated iso-diabolic acid derivatives were encountered in SDs 1, 3, 4, and 6, but only SD 4 species produced 5-methyl iso-diabolic acid derivatives, whereas the other SDs formed 6-methyl iso-diabolic acids. This suggests that the position of methylation of iso-diabolic acid may be controlled by the phylogenetic affiliation within the Acidobacteria and thus may not be a direct but an indirect response environmental to environmental conditions as inferred from the bacterial GDGT distributions in soil, peat and rivers.

Barbel U Foesel - One of the best experts on this subject based on the ideXlab platform.

  • An overview of the occurrence of ether- and ester- linked iso -diabolic acid membrane lipids in microbial cultures of the Acidobacteria: Implications for brGDGT paleoproxies for temperature and pH
    Organic Geochemistry, 2018
    Co-Authors: Jaap Sinninghe S Damste, W Irene C Rijpstra, Barbel U Foesel, Jorg Overmann, Svetlana N Dedysh, Katharina J. Huber, Peter F. Dunfield, Satoshi Nakagawa, Joong Jae Kim, Laura Villanueva
    Abstract:

    Abstract 13,16-Dimethyl octacosanedioic acid (iso-diabolic acid) is a major membrane-spanning lipid of subdivisions (SDs) 1, 3 and 4 of the Acidobacteria, a highly diverse phylum within the Bacteria. It has been suggested that these lipids are potential building blocks for the orphan bacterial glycerol dialkyl glycerol tetraethers (GDGT) that occur widely in a variety of environmental settings. Here, we expand the knowledge on the occurrence of iso-diabolic acid in Acidobacteria by examining the lipid composition of six strains belonging to SDs 6, 8, 10, and 23 of the Acidobacteria, not previously analyzed for these lipids. In addition, we examined 12 new strains belonging to SDs 1, 3 and 4. Acid hydrolysis of total cell material released iso-diabolic acid in substantial quantities (25–39% of all fatty acids) from the strains of SDs 1 and 3 (except “Candidatus Solibacter usitatus”), and, for the first time, strains of SD 6 (6–25%), but not from SDs 8, 10, and 23. The monoglycerol ether derivative of iso-diabolic acid was only dominantly present in SD 4 strains (17–34%), indicating that the occurrence of ether-bound iso-diabolic acid is mainly restricted to SD 4 species. Methylated iso-diabolic acid derivatives were encountered in SDs 1, 3, 4, and 6, but only SD 4 species produced 5-methyl iso-diabolic acid derivatives, whereas the other SDs formed 6-methyl iso-diabolic acids. This suggests that the position of methylation of iso-diabolic acid may be controlled by the phylogenetic affiliation within the Acidobacteria and thus may not be a direct but an indirect response environmental to environmental conditions as inferred from the bacterial GDGT distributions in soil, peat and rivers.

  • Pheno- and Genotyping of Hopanoid Production in Acidobacteria
    Frontiers in microbiology, 2017
    Co-Authors: Jaap Sinninghe S Damste, W Irene C Rijpstra, Barbel U Foesel, Svetlana N Dedysh, Laura Villanueva
    Abstract:

    Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium "Ca. Koribacter versatilis," but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited. We analyzed 38 different strains of seven Acidobacteria subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C30 hopenes and C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting Chloracidobacterium thermophilum), 6, 8, 10, and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated Acidobacteria. All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 Acidobacteria and C. thermophilum encode all three enzymes required for the synthesis of squalene, its cyclization (shc), and addition and modification of the extended side chain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only "Ca. K. versatilis" contained methylated hopanoids (i.e., 2,3-dimethyl bishomohopanol), although in low (

  • pheno and genotyping of hopanoid production in Acidobacteria
    Frontiers in Microbiology, 2017
    Co-Authors: Jaap Sinninghe S Damste, Irene W C Rijpstra, Barbel U Foesel, Svetlana N Dedysh, Laura Villanueva
    Abstract:

    Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium ‘Ca. Koribacter versatilis’, but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited. We analyzed 38 different strains of seven Acidobacteria subdivisions (SDs 1,3,4,6,8,10, and 23) for the presence of C30 hopenes and C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting Chloracidobacterium thermophilum),6,8,10 and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated Acidobacteria. All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 Acidobacteria and C. thermophilum encode all three enzymes required for the synthesis of squalene, its cyclization (shc), and addition and modification of the extended side chain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only ‘Ca. K. versatilis’ contained methylated hopanoids (i.e. 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes are not present in any other Acidobacterium, consistent with the absence of methylated BHPs in the other examined strains. These data are in agreement with the scattered occurrence of methylated BHPs in other bacterial phyla such as the Alpha-, Beta- and Gammaproteobacteria and the Cyanobacteria, limiting their biomarker potential. Metagenomes of Acidobacteria were also examined for the presence of genes required for hopanoid biosynthesis. The complete pathway for BHP biosynthesis was evident in SD2 Acidobacteria and a group phylogenetically related to SD1 and SD3, in line with the limited occurrence of BHPs in Acidobacterial cultures.

  • Brevitalea aridisoli, B. deliciosa and Arenimicrobium luteum, three novel species of Acidobacteria subdivision 4 (class Blastocatellia) isolated from savanna soil and description of the novel family Pyrinomonadaceae.
    International journal of systematic and evolutionary microbiology, 2016
    Co-Authors: Pia K Wust, Barbel U Foesel, Gerhard Wanner, Katharina J. Huber, Alicia Geppert, Manja Luckner, Jorg Overmann
    Abstract:

    Three novel strains of the phylum Acidobacteria (Ac_11_E3(T), Ac_12_G8(T) and Ac_16_C4(T)) were isolated from Namibian semiarid savanna soils by a high-throughput cultivation approach using low-nutrient growth media. 16S rRNA gene sequence analysis placed all three strains in the order Blastocatellales of the class Blastocatellia (Acidobacteria subdivision 4). However, 16S rRNA gene sequence similarities to their closest relative Pyrinomonas methylaliphatogenes K22(T) were

  • Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4.
    Systematic and applied microbiology, 2015
    Co-Authors: Javier Pascual, Barbel U Foesel, Pia K Wust, Katharina J. Huber, Alicia Geppert, Jorg Overmann
    Abstract:

    Despite their high phylogenetic diversity and abundance in soils worldwide, Acidobacteria represent an enigmatic bacterial phylum. Four novel Acidobacteria strains were isolated from Namibian semiarid savannah soils using low-nutrient cultivation media and extended incubation periods. 16S rRNA gene sequence analyses placed the isolates within Acidobacteria subdivision 4. Sequence identities with their closest relatives Aridibacter famidurans and Blastocatella fastidiosa were ≤94.9%. The Gram-negative, non-motile, rod-shaped, aerobic, and chemoorganotrophic bacteria grew at minimum doubling times of 5-14h and formed tiny white to pinkish colonies. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol. The major isoprenoid quinone was MK-8. The major fatty acid methyl esters comprised iso-C15:0, iso-C15:1H/C13:0 3-OH, and C16:1ω7c/C16:1ω6c. Based on a polyphasic taxonomic characterization, strain Ac_18_E7(T) (=DSM 26557(T)=LMG 28656(T)) represented a novel species and genus, Tellurimicrobium multivorans gen. nov., sp. nov. The other strains constituted three independent species of the novel genus Stenotrophobacter gen. nov., Stenotrophobacter terrae sp. nov. (Ac_28_D10(T)=DSM 26560(T)=LMG 28657(T)), S. roseus sp. nov. (Ac_15_C4(T)=DSM 29891(T)=LMG 28889(T)), and S. namibiensis sp. nov. (Ac_17_F2(T)=DSM 29893(T)=LMG 28890(T)). These isolates doubled the number of established species and permitted the description of higher taxa of Acidobacteria subdivision 4. The family Blastocatellaceae fam. nov. is proposed in order to summarize the currently known oligotrophic, slightly acidophilic to neutrophilic mesophiles from arid soils. The superordinated order Blastocatellales ord. nov. and Blastocatellia classis nov. also include the terrestrial species Pyrinomonas methylaliphatogenes and the anoxygenic photoheterotrophic species Chloracidobacterium thermophilum from microbial mats.

Werner Liesack - One of the best experts on this subject based on the ideXlab platform.

  • Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags.
    Frontiers in microbiology, 2017
    Co-Authors: Carl-eric Wegner, Werner Liesack
    Abstract:

    Acid mine drainage (AMD) and mine tailing environments are well-characterized ecosystems known to be dominated by organisms involved in iron- and sulfur-cycling. Here we examined the microbiology of industrial soft coal slags that originate from alum leaching, an ecosystem distantly related to AMD environments. Our study involved geochemical analyses, bacterial community profiling, and shotgun metagenomics. The slags still contained high amounts of alum constituents (aluminum, sulfur), which mediated direct and indirect effects on bacterial community structure. Bacterial groups typically found in AMD systems and mine tailings were not present. Instead, the soft coal slags were dominated by uncharacterized groups of Acidobacteria (DA052 [subdivision 2], KF-JG30-18 [subdivision 13]), Actinobacteria (TM214), Alphaproteobacteria (DA111), and Chloroflexi (JG37-AG-4), which have previously been detected primarily in peatlands and uranium waste piles. Shotgun metagenomics allowed us to reconstruct 13 high-quality Acidobacteria draft genomes, of which two genomes could be directly linked to dominating groups (DA052, KF-JG30-18) by recovered 16S rRNA gene sequences. Comparative genomics revealed broad carbon utilization capabilities for these two groups of elusive Acidobacteria, including polysaccharide breakdown (cellulose, xylan) and the competence to metabolize C1 compounds (ribulose monophosphate pathway) and lignin derivatives (dye-decolorizing peroxidases). Equipped with a broad range of efflux systems for metal cations and xenobiotics, DA052 and KF-JG30-18 may have a competitive advantage over other bacterial groups in this unique habitat.

  • unexpected dominance of elusive Acidobacteria in early industrial soft coal slags
    Frontiers in Microbiology, 2017
    Co-Authors: Carl-eric Wegner, Werner Liesack
    Abstract:

    Acid mine drainage (AMD) and mine tailing environments are well-characterized ecosystems known to be dominated by organisms involved in iron- and sulfur-cycling. Here we examined the microbiology of industrial soft coal slags that originate from alum leaching, an ecosystem distantly related to AMD environments. Our study involved geochemical analyses, bacterial community profiling, and targeted metagenomics. The slags still contained high amounts of alum constituents (aluminium, sulfur), which mediated direct and indirect effects on bacterial community structure. Bacterial groups typically found in AMD systems and mine tailings were not present. Instead, the soft coal slags were dominated by uncharacterized groups of Acidobacteria (DA052 [subdivision 2], KF-JG30-18 [subdivision 13]), Actinobacteria (TM214), Alphaproteobacteria (DA111) and Chloroflexi (JG37-AG-4), which have previously been detected primarily in peatlands and uranium waste piles. Shotgun metagenomics allowed us to reconstruct 13 high-quality Acidobacteria draft genomes, of which two genomes could be directly linked to dominating groups (DA052, KF-JG30-18) by recovered 16S rRNA gene sequences. Comparative genomics revealed broad carbon utilization capabilities for these two groups of elusive Acidobacteria, including polysaccharide breakdown (cellulose, xylan) and the competence to metabolize C1 compounds (ribulose monophosphate pathway) and lignin derivatives (dye-decolorizing peroxidases). Equipped with a broad range of efflux systems for metal cations and xenobiotics, DA052 and KF-JG30-18 may have a competitive advantage over other bacterial groups in this unique habitat.

  • bacterial populations and environmental factors controlling cellulose degradation in an acidic sphagnum peat
    Environmental Microbiology, 2011
    Co-Authors: Timofey A. Pankratov, Svetlana N Dedysh, Anastasia O Ivanova, Werner Liesack
    Abstract:

    Northern peatlands represent a major global carbon store harbouring approximately one-third of the global reserves of soil organic carbon. A large proportion of these peatlands consists of acidic Sphagnum-dominated ombrotrophic bogs, which are characterized by extremely low rates of plant debris decomposition. The degradation of cellulose, the major component of Sphagnum-derived litter, was monitored in long-term incubation experiments with acidic (pH 4.0) peat extracts. This process was almost undetectable at 10°C and occurred at low rates at 20°C, while it was significantly accelerated at both temperature regimes by the addition of available nitrogen. Cellulose breakdown was only partially inhibited in the presence of cycloheximide, suggesting that bacteria participated in this process. We aimed to identify these bacteria by a combination of molecular and cultivation approaches and to determine the factors that limit their activity in situ. The indigenous bacterial community in peat was dominated by Alphaproteobacteria and Acidobacteria. The addition of cellulose induced a clear shift in the community structure towards an increase in the relative abundance of the Bacteroidetes. Increasing temperature and nitrogen availability resulted in a selective development of bacteria phylogenetically related to Cytophaga hutchinsonii (94-95% 16S rRNA gene sequence similarity), which densely colonized microfibrils of cellulose. Among isolates obtained from this community only some subdivision 1 Acidobacteria were capable of degrading cellulose, albeit at a very slow rate. These Acidobacteria represent indigenous cellulolytic members of the microbial community in acidic peat and are easily out-competed by Cytophaga-like bacteria under conditions of increased nitrogen availability. Members of the phylum Firmicutes, known to be key players in cellulose degradation in neutral habitats, were not detected in the cellulolytic community enriched at low pH.

  • Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria.
    International Journal of Systematic and Evolutionary Microbiology, 2010
    Co-Authors: Irina S. Kulichevskaya, Natalia E. Suzina, Werner Liesack, Svetlana N Dedysh
    Abstract:

    Bryobacter aggregatus gen. nov., sp. nov. is proposed to accommodate three strains of slowly growing, chemo-organotrophic bacteria isolated from acidic Sphagnum peat bogs. These bacteria were strictly aerobic, Gram-negative, colourless, non-motile coccoids or short rods that multiplied by normal cell division and formed irregularly shaped cell aggregates. Strains MPL3T, MPL1011 and MOB76 were acidotolerant, mesophilic organisms capable of growth at pH 4.5–7.2 and between 4 and 33 °C (optimum growth at pH 5.5–6.5 and 22–28 °C). The preferred growth substrates were sugars, some heteropolysaccharides and galacturonic and glucuronic acids, which are released during decomposition of Sphagnum moss. The major fatty acids were iso-C15 : 0, C16 : 0 and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c); the major quinones were MK-9 and MK-10. The DNA G+C content was 55.5–56.5 mol%. Strains MPL3T, MPL1011 and MOB76 possessed nearly identical 16S rRNA gene sequences and belonged to the phylum Acidobacteria. They represent the first taxonomically characterized members of Acidobacterial subdivision 3 and display only 81.7–86.7 % 16S rRNA gene sequence similarity to other members of the Acidobacteria with validly published names. Therefore, strains MPL3T, MPL1011 and MOB76 are classified as representatives of a novel species in a new genus, for which the name Bryobacter aggregatus gen. nov., sp. nov. is proposed; strain MPL3T (=ATCC BAA-1390T =DSM 18758T) is the type strain of Bryobacter aggregatus.

  • Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria.
    International journal of systematic and evolutionary microbiology, 2009
    Co-Authors: Irina S. Kulichevskaya, Natalia E. Suzina, Werner Liesack, Svetlana N Dedysh
    Abstract:

    Bryobacter aggregatus gen. nov., sp. nov. is proposed to accommodate three strains of slowly growing, chemo-organotrophic bacteria isolated from acidic Sphagnum peat bogs. These bacteria were strictly aerobic, Gram-negative, colourless, non-motile coccoids or short rods that multiplied by normal cell division and formed irregularly shaped cell aggregates. Strains MPL3(T), MPL1011 and MOB76 were acidotolerant, mesophilic organisms capable of growth at pH 4.5-7.2 and between 4 and 33 degrees C (optimum growth at pH 5.5-6.5 and 22-28 degrees C). The preferred growth substrates were sugars, some heteropolysaccharides and galacturonic and glucuronic acids, which are released during decomposition of Sphagnum moss. The major fatty acids were iso-C(15 : 0), C(16 : 0) and summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c); the major quinones were MK-9 and MK-10. The DNA G+C content was 55.5-56.5 mol%. Strains MPL3(T), MPL1011 and MOB76 possessed nearly identical 16S rRNA gene sequences and belonged to the phylum Acidobacteria. They represent the first taxonomically characterized members of Acidobacterial subdivision 3 and display only 81.7-86.7 % 16S rRNA gene sequence similarity to other members of the Acidobacteria with validly published names. Therefore, strains MPL3(T), MPL1011 and MOB76 are classified as representatives of a novel species in a new genus, for which the name Bryobacter aggregatus gen. nov., sp. nov. is proposed; strain MPL3(T) (=ATCC BAA-1390(T) =DSM 18758(T)) is the type strain of Bryobacter aggregatus.

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  • Brevitalea aridisoli, B. deliciosa and Arenimicrobium luteum, three novel species of Acidobacteria subdivision 4 (class Blastocatellia) isolated from savanna soil and description of the novel family Pyrinomonadaceae.
    International journal of systematic and evolutionary microbiology, 2016
    Co-Authors: Pia K Wust, Barbel U Foesel, Gerhard Wanner, Katharina J. Huber, Alicia Geppert, Manja Luckner, Jorg Overmann
    Abstract:

    Three novel strains of the phylum Acidobacteria (Ac_11_E3(T), Ac_12_G8(T) and Ac_16_C4(T)) were isolated from Namibian semiarid savanna soils by a high-throughput cultivation approach using low-nutrient growth media. 16S rRNA gene sequence analysis placed all three strains in the order Blastocatellales of the class Blastocatellia (Acidobacteria subdivision 4). However, 16S rRNA gene sequence similarities to their closest relative Pyrinomonas methylaliphatogenes K22(T) were

  • The first representative of the globally widespread subdivision 6 Acidobacteria,Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil
    International journal of systematic and evolutionary microbiology, 2016
    Co-Authors: Katharina J. Huber, Pia K Wust, Gerhard Wanner, Alicia Geppert, Bärbel U. Fösel, Jorg Overmann
    Abstract:

    Members of the phylum Acidobacteria are abundant in a wide variety of soil environments. Despite this, previous cultivation attempts have frequently failed to retrieve representative phylotypes of Acidobacteria, which have, therefore, been discovered by culture-independent methods (13175 Acidobacterial sequences in the SILVA database version 123;NR99) and only 47 species have been described so far. Strain Ac_5_C6(T) represents the first isolate of the globally widespread and abundant subdivision 6 Acidobacteria and is described in the present study. Cells of strain Ac_5_C6(T) were Gram-stain-negative, immotile rods that divided by binary fission. They formed yellow, extremely cohesive colonies and stable aggregates even in rapidly shaken liquid cultures. Ac_5_C6(T) was tolerant of a wide range of temperatures (12-40 degrees C) and pH values (4.7-9.0). It grew chemoorganoheterotrophically on a broad range of substrates including different sugars, organic acids, nucleic acids and complex proteinaceous compounds. The major fatty acids of Ac_5_C6(T) were iso-C-17:1 omega 9c, C-18:1 omega 7c and iso-C-15:0. Summed feature 3 (C-16:1 omega 7c/C-16:1 omega 6c), iso-C-17:0 and C-16:0 were also detected. Phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid were identified as polar lipids. The major quinone was MK-8. The DNA G+C content of Ac_5_C6(T) was 65.9 mol%. With 16S rRNA gene sequence similarities of 83-84 %, the closest described relatives were Acidicapsa borealis KA1(T), Acidobacterium capsulatum 161(T), Granulicella pectinovorans TPB6011(T), Occallatibacter riparius 277(T) and Paludibaculum fermentans P105(T). According to the morphological, physiological and molecular characteristics, the novel genus Vicinamibacter gen. nov., and the novel species, Vicinamibacter silvestris sp. nov. (type strain Ac_5_C6(T) = DSM 29464(T) = LMG 29035(T)) are proposed.

  • Novel isolates double the number of chemotrophic species and allow the first description of higher taxa in Acidobacteria subdivision 4.
    Systematic and applied microbiology, 2015
    Co-Authors: Javier Pascual, Barbel U Foesel, Pia K Wust, Katharina J. Huber, Alicia Geppert, Jorg Overmann
    Abstract:

    Despite their high phylogenetic diversity and abundance in soils worldwide, Acidobacteria represent an enigmatic bacterial phylum. Four novel Acidobacteria strains were isolated from Namibian semiarid savannah soils using low-nutrient cultivation media and extended incubation periods. 16S rRNA gene sequence analyses placed the isolates within Acidobacteria subdivision 4. Sequence identities with their closest relatives Aridibacter famidurans and Blastocatella fastidiosa were ≤94.9%. The Gram-negative, non-motile, rod-shaped, aerobic, and chemoorganotrophic bacteria grew at minimum doubling times of 5-14h and formed tiny white to pinkish colonies. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol. The major isoprenoid quinone was MK-8. The major fatty acid methyl esters comprised iso-C15:0, iso-C15:1H/C13:0 3-OH, and C16:1ω7c/C16:1ω6c. Based on a polyphasic taxonomic characterization, strain Ac_18_E7(T) (=DSM 26557(T)=LMG 28656(T)) represented a novel species and genus, Tellurimicrobium multivorans gen. nov., sp. nov. The other strains constituted three independent species of the novel genus Stenotrophobacter gen. nov., Stenotrophobacter terrae sp. nov. (Ac_28_D10(T)=DSM 26560(T)=LMG 28657(T)), S. roseus sp. nov. (Ac_15_C4(T)=DSM 29891(T)=LMG 28889(T)), and S. namibiensis sp. nov. (Ac_17_F2(T)=DSM 29893(T)=LMG 28890(T)). These isolates doubled the number of established species and permitted the description of higher taxa of Acidobacteria subdivision 4. The family Blastocatellaceae fam. nov. is proposed in order to summarize the currently known oligotrophic, slightly acidophilic to neutrophilic mesophiles from arid soils. The superordinated order Blastocatellales ord. nov. and Blastocatellia classis nov. also include the terrestrial species Pyrinomonas methylaliphatogenes and the anoxygenic photoheterotrophic species Chloracidobacterium thermophilum from microbial mats.

  • Ether- and Ester-Bound iso-Diabolic Acid and Other Lipids in Members of Acidobacteria Subdivision 4
    Applied and environmental microbiology, 2014
    Co-Authors: Jaap Sinninghe S Damste, W Irene C Rijpstra, Ellen C Hopmans, Barbel U Foesel, Jorg Overmann, Pia K Wust, Marcus Tank, Donald A. Bryant, Peter F. Dunfield, Karen M. Houghton
    Abstract:

    Recently, iso-diabolic acid (13,16-dimethyl octacosanedioic acid) has been identified as a major membrane-spanning lipid of subdivisions 1 and 3 of the Acidobacteria, a highly diverse phylum within the Bacteria. This finding pointed to the Acidobacteria as a potential source for the bacterial glycerol dialkyl glycerol tetraethers that occur ubiquitously in peat, soil, lakes, and hot springs. Here, we examined the lipid composition of seven phylogenetically divergent strains of subdivision 4 of the Acidobacteria, a bacterial group that is commonly encountered in soil. Acid hydrolysis of total cell material released iso-diabolic acid derivatives in substantial quantities (11 to 48% of all fatty acids). In contrast to subdivisions 1 and 3 of the Acidobacteria, 6 out of the 7 species of subdivision 4 (excepting “Candidatus Chloracidobacterium thermophilum”) contained iso-diabolic acid ether bound to a glycerol in larger fractional abundance than iso-diabolic acid itself. This is in agreement with the analysis of intact polar lipids (IPLs) by high-performance liquid chromatography-mass spectrometry (HPLC-MS), which showed the dominance of mixed ether-ester glycerides. iso-Diabolic acid-containing IPLs were not identified, because these IPLs are not released with a Bligh-Dyer extraction, as observed before when studying lipid compositions of subdivisions 1 and 3 of the Acidobacteria. The presence of ether bonds in the membrane lipids does not seem to be an adaptation to temperature, because the five mesophilic isolates contained a larger amount of ether lipids than the thermophile “Ca. Chloracidobacterium thermophilum.” Furthermore, experiments with Pyrinomonas methylaliphatogenes did not reveal a major influence of growth temperature over the 50 to 69°C range.

  • Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil
    International Journal of Systematic and Evolutionary Microbiology, 2014
    Co-Authors: Katharina J. Huber, Pia K Wust, Jorg Overmann, Manfred Rohde, Barbel U Foesel
    Abstract:

    Acidobacteria constitute an abundant fraction of the soil microbial community and are currently divided into 26 subdivisions. Most cultivated members of the Acidobacteria are affiliated with subdivision 1, while only a few representatives of subdivisions 3, 4, 8, 10 and 23 have been isolated and described so far. Two novel isolates of subdivision 4 of the Acidobacteria were isolated from subtropical savannah soils and are characterized in the present work. Cells of strains A22_HD_4HT and Ac_23_E3T were immotile rods that divided by binary fission. Colonies were pink and white, respectively. The novel strains A22_HD_4HT and Ac_23_E3T were aerobic mesophiles with a broad range of tolerance towards pH (4.0–9.5 and 3.5–10.0, respectively) and temperature (15–44 and 12–47 °C, respectively). Both showed chemo-organoheterotrophic growth on some sugars, the amino sugar N-acetylgalactosamine, a few amino acids, organic acids and various complex protein substrates. Major fatty acids of A22_HD_4HT and Ac_23_E3T were iso-C15 : 0, summed feature 1 (C13 : 0 3-OH/iso-C15 : 1 H), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and anteiso-C17 : 0. The major quinone was MK-8; in addition, MK-7 occurred in small amounts. The DNA G+C contents of A22_HD_4HT and Ac_23_E3T were 53.2 and 52.6 mol%, respectively. The closest described relative was Blastocatella fastidiosa A2-16T, with 16S rRNA gene sequence identity of 93.2 and 93.3 %, respectively. Strains A22_HD_4HT and Ac_23_E3T displayed 16S rRNA gene sequence similarity of 97.4 % to each other. On the basis of the low DNA–DNA hybridization value, the two isolates represent different species. Based on morphological, physiological and molecular characteristics, the new genus Aridibacter gen. nov. is proposed, with two novel species, the type species Aridibacter famidurans sp. nov. (type strain A22_HD_4HT = DSM 26555T = LMG 27985T) and a second species, Aridibacter kavangonensis sp. nov. (type strain Ac_23_E3T = DSM 26558T = LMG 27597T).