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1.
BMC Microbiol ; 23(1): 46, 2023 02 21.
Artículo en Inglés | MEDLINE | ID: mdl-36809988

RESUMEN

BACKGROUND: Elevated carbon dioxide concentrations (eCO2), one of the main causes of climate change, have several consequences for both vine and cover crops in vineyards and potentially also for the soil microbiome. Hence soil samples were taken from a vineyard free-air CO2 enrichment (VineyardFACE) study in Geisenheim and examined for possible changes in the soil active bacterial composition (cDNA of 16S rRNA) using a metabarcoding approach. Soil samples were taken from the areas between the rows of vines with and without cover cropping from plots exposed to either eCO2 or ambient CO2 (aCO2). RESULTS: Diversity indices and redundancy analysis (RDA) demonstrated that eCO2 changed the active soil bacterial diversity in grapevine soil with cover crops (p-value 0.007). In contrast, the bacterial composition in bare soil was unaffected. In addition, the microbial soil respiration (p-values 0.04-0.003) and the ammonium concentration (p-value 0.003) were significantly different in the samples where cover crops were present and exposed to eCO2. Moreover, under eCO2 conditions, qPCR results showed a significant decrease in 16S rRNA copy numbers and transcripts for enzymes involved in N2 fixation and NO2- reduction were observed using qPCR. Co-occurrence analysis revealed a shift in the number, strength, and patterns of microbial interactions under eCO2 conditions, mainly represented by a reduction in the number of interacting ASVs and the number of interactions. CONCLUSIONS: The results of this study demonstrate that eCO2 concentrations changed the active soil bacterial composition, which could have future influence on both soil properties and wine quality.


Asunto(s)
Microbiota , Suelo , Dióxido de Carbono , ARN Ribosómico 16S , Productos Agrícolas , Bacterias
2.
Curr Microbiol ; 80(7): 234, 2023 Jun 06.
Artículo en Inglés | MEDLINE | ID: mdl-37278851

RESUMEN

One gram-negative strain designated Bb-Pol-6 T was isolated from birch (Betula pendula) pollen at Giessen area, Germany. The analysis of 16S rRNA gene-based phylogenies indicated the next-relative genera were Robbsia, Chitinasiproducens, Pararobbsia and Paraburkholderia (96-95.6%). Further comparative genome analysis and phylogenetic tree-based methods revealed its phylogenetic position under the genus Robbsia. The genome of strain Bb-Pol-6 T was 5.04 Mbp with 4401 predicted coding sequences and a G + C content of 65.31 mol%. Average amino acid identity, average nucleotide identity, digital DNA-DNA hybridization and percentage of conserved proteins values to Robbsia andropogonis DSM 9511 T were 68.0, 72.5, 22.7 and 65.85%, respectively. Strain Bb-Pol-6 T was rod-shaped, non-motile, facultative anaerobic and grew optimally at 28 °C and pH 6-7. Ubiquinone 8 was the major respiratory quinone and the major cellular fatty acids were C16:0, C19:0 cyclo ω7c, C17:0 cyclo ω7c and C17:1 ω6c. The dominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. Based on the genomic physiological and phenotypic characteristics, strain Bb-Pol-6 T was considered a novel species under the genus Robbsia, for which the name Robbsia betulipollinis sp. nov. was proposed. The type strain is Bb-Pol-6 T (= LMG 32774 T = DSM 114812 T).


Asunto(s)
Betula , Fosfolípidos , Fosfolípidos/química , Betula/genética , Filogenia , ARN Ribosómico 16S/genética , Técnicas de Tipificación Bacteriana , Ácidos Grasos/química , Polen/química , ADN , ADN Bacteriano/genética , Análisis de Secuencia de ADN
3.
Curr Microbiol ; 80(12): 384, 2023 Oct 23.
Artículo en Inglés | MEDLINE | ID: mdl-37872440

RESUMEN

The obligate biotrophic fungal pathogen Blumeria graminis causes the powdery mildew disease of cereals, which results in large crop losses. Control of B. graminis in barley is mainly achieved by fungicide treatment and by breeding resistant varieties. Vampyrellid amoebae, just like mycophagous protists, are able to consume a variety of fungi. To reveal the impact of some selected fungus-consuming protists on Blumeria graminis f. sp. hordei (Bgh), and to evaluate the possibility of using these protists as biological agents in the future, their feeding behaviour on B. graminis spores on barley leaves was investigated. An experiment was carried out with five different protist isolates (Leptophrys vorax, Platyreta germanica, Theratromyxa weberi U 11, Theratromyxa weberi G7.2 and Acanthamoeba castellanii) and four matched controls, including the food sources of the cultures and the medium. Ten-day-old leaves of barley (Hordeum vulgare cv. Golden Promise) were first inoculated with Blumeria graminis (f. sp. hordei race A6) spores, then treated with protists and fungal colonies on the leaf surfaces were counted under the microscope after 5 days. The isolates L. vorax, P. germanica, and T. weberi U11 did not show a significant reduction in the number of powdery mildew colonies whereas the isolates T. weberi G7.2 and A. castellanii significantly reduced the number of powdery mildew colonies on the leaf surfaces compared to their respective controls. This indicates that these two isolates are capable of reducing B. graminis colonies on barley leaves and are suitable candidates for further investigation for possible use as biological agents. Nevertheless, the susceptibility to dryness and the cell division rate should be considered during the optimisation of the next steps like application procedure and whole plant treatment.


Asunto(s)
Ascomicetos , Hordeum , Hordeum/microbiología , Hojas de la Planta/microbiología , Factores Biológicos , Enfermedades de las Plantas/prevención & control , Enfermedades de las Plantas/microbiología
4.
Arch Microbiol ; 204(7): 363, 2022 Jun 04.
Artículo en Inglés | MEDLINE | ID: mdl-35661258

RESUMEN

Kitchen sponges are particularly well known to harbor a high number and diversity of bacteria, including pathogens. Viruses, archaea, and eukaryotes in kitchen sponges, however, have not been examined in detail so far. To increase knowledge on the non-bacterial kitchen sponge microbiota and its potential hygienic relevance, we investigated five used kitchen sponges by means of metagenomic shot-gun sequencing. Viral particles were sought to be enriched by a filter step during DNA extraction from the sponges. Data analysis revealed that ~ 2% of the sequences could be assigned to non-bacterial taxa. Each sponge harbored different virus (phage) species, while the present archaea were predominantly affiliated with halophilic taxa. Among the eukaryotic taxa, besides harmless algae, or amoebas, mainly DNA from food-left-overs was found. The presented work offers new insights into the complex microbiota of used kitchen sponges and contributes to a better understanding of their hygienic relevance.


Asunto(s)
Microbiota , Poríferos , Animales , Archaea/genética , Bacterias/genética , Metagenoma , Metagenómica , Microbiota/genética , Filogenia , Poríferos/genética
5.
Microb Ecol ; 83(3): 619-634, 2022 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-34148108

RESUMEN

Elevated levels of atmospheric CO2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO2 enrichment (Gi-FACE) experiment on a permanent grassland site near Giessen, Germany. The aim was to assess the effects of increased C supply into the soil, due to elevated CO2, on the active soil microbiome composition. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and the obtained data were processed for a compositional data analysis calculating diversity indices and differential abundance analyses. The structure of the metabolic active microbiome in the rhizospheric soil showed a clear separation between elevated and ambient CO2 (p = 0.002); increased atmospheric CO2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO2 had no major influence on the structure of the bulk soil microbiome (p = 0.097). Differential abundance results demonstrated that 42 bacterial genera were stimulated under elevated CO2. The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO2 increase of climate change will significantly shift the microbiome structure in the rhizosphere.


Asunto(s)
Microbiota , Rizosfera , Dióxido de Carbono/metabolismo , Microbiota/genética , ARN Ribosómico 16S/genética , Suelo/química , Microbiología del Suelo
6.
Artículo en Inglés | MEDLINE | ID: mdl-33300859

RESUMEN

A Gram-stain-negative bacterium, designated I-24T, was isolated from soil of a natural salt meadow. Strain I-24T was aerobic, non-motile, rod-shaped, catalase-positive, oxidase-positive and grew optimally at pH 7 and 25 °C. Comparative 16S rRNA gene analysis indicated that strain I-24T has closest similarities to Spirosoma agri KCTC 52727T (95.9 %) and Spirosoma terrae KCTC 52035T (95.5 %). Strain I-24T contained summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C16 : 1 ω5c as the major fatty acids, the predominant respiratory quinone was menaquinone MK-7, and the major polar lipids were phosphatidylethanolamine as well as an unidentified phosphoaminolipid. The draft genome of strain I-24T consists of 10 326 072 base pairs with 9153 predicted coding sequences and a G+C content of 47.7 mol%. Clear distinctions between strain I-24T and S. agri KCTC 52727T or S. terrae KCTC 52035T were shown in the pairwise average nucleotide identity results with values of 76.71 and 74.01 %, respectively. Moreover, the digital DNA-DNA relatedness values to these strains were 20.8 and 19.0 %. Based on its phenotypic, genotypic and chemotaxonomic characteristics, strain I-24T represents a novel species of the genus Spirosoma, for which the name Spirosoma endbachense sp. nov. is proposed. The type strain is I-24T (DSM 111055T=KCTC 72613T).


Asunto(s)
Cytophagaceae/clasificación , Pradera , Filogenia , Salinidad , Microbiología del Suelo , Técnicas de Tipificación Bacteriana , Composición de Base , Cytophagaceae/aislamiento & purificación , ADN Bacteriano/genética , Ácidos Grasos/química , Alemania , Hibridación de Ácido Nucleico , Fosfolípidos/química , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Vitamina K 2/análogos & derivados , Vitamina K 2/química
7.
World J Microbiol Biotechnol ; 37(11): 188, 2021 Oct 06.
Artículo en Inglés | MEDLINE | ID: mdl-34611812

RESUMEN

In this study, the taxonomic and functional diversity of methanogenic archaea in two parallel 120 l fermenters operated at different temperatures and fed with maize silage was estimated by mcrA metabarcoding analysis using two typical primer pairs (ML and MLA) amplifying part of the functional methyl coenzyme M reductase (mcrA) gene. The alpha diversity indices showed that the ML primer pair detected a higher Operational Taxonomic Unit (OTU) abundance compared to the MLA primer pair and methanogen diversity was significantly lower in the 60 °C fermenters. The beta diversity analysis showed the methanogenic community clustered together at 50 °C and 40° and was statistically different from the 60 °C community. Similar, to alpha diversity, beta diversity was also significantly different between primer pairs. At all temperatures analysed, the primer pairs showed a different abundance of the different methanogenic OTUs, e.g. more OTUs relative to Methanoculleus sp. with the ML primer pair, and more OTUs corresponding to Methanobacterium sp. with the MLA primer pair. Moreover, OTUs corresponding to Methanosphaera sp. and Methanobrevibacter sp. were found only by using ML primer pair, while the MLA primer pair detected sequences corresponding to Methanothrix sp.


Asunto(s)
Archaea/genética , Archaea/metabolismo , Biocombustibles , Fermentación , Oxidorreductasas/genética , Temperatura , Biodiversidad , Reactores Biológicos , ADN de Archaea/genética , Euryarchaeota , Metano , Filogenia
8.
Can J Microbiol ; 66(8): 491-494, 2020 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-32134703

RESUMEN

RNA-based stable isotope probing (RNA-SIP) is used in molecular microbial ecology to link the identity of microorganisms in a complex community with the assimilation of a distinct substrate. The technique is highly dependent on a reliable separation of isotopic-labeled RNA from unlabeled RNA by isopycnic density gradient ultracentrifugation. Here we show that 13C-labeled and unlabeled Escherichia coli RNA can be sufficiently separated by isopycnic ultracentrifugation even in the absence of formamide. However, a slightly lower starting density is needed to obtain a distribution pattern similar to that obtained when formamide was used. Hence, the commonly used addition of formamide to the centrifugation solution might not be needed to separate 13C-labeled RNA from unlabeled RNA, but this must be verified for more complex environmental mixtures of RNA. Clearly, an omission of formamide would increase the safety of RNA-SIP analyses.


Asunto(s)
Escherichia coli/genética , ARN Bacteriano/genética , ARN Bacteriano/aislamiento & purificación , Isótopos de Carbono/química , Centrifugación por Gradiente de Densidad/métodos , Escherichia coli/química , Formamidas/química , Marcaje Isotópico/métodos , ARN Bacteriano/química , Ultracentrifugación/métodos
9.
Microb Ecol ; 77(3): 689-700, 2019 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-30259168

RESUMEN

Phosphate is a macronutrient and often the limiting growing factor of many ecosystems. The aim of this work was to assess the effect of various phosphate sources on the active bacterial microbiota of barley rhizosphere and endorhiza. Barley was grown on poor soil supplemented with either Ca(H2PO4)2 (CaP), Gafsa rock phosphate (Gafsa), sodium hexaphytate (NaHex), or not amended (P0). RNA was extracted and cDNA synthesized via reverse transcription from both rhizosphere and endorhiza of barley roots; the obtained 16S rRNA cDNA was sequenced by Ion Torrent and analyzed with QIIME and co-occurrence network analysis. Phosphatase activity was measured in the rhizosphere. The phosphate source significantly affected alpha- and beta-diversities of the active microbiota, especially in the rhizosphere. CaP enriched the relative abundance of a broad range of taxa, while NaHex and Gafsa specifically enriched one dominant Massilia-related OTU. Co-occurrence network analysis showed that the most abundant OTUs were affected by phosphate source and, at the same time, were low connected to other OTUs (thus they were relatively "independent" from other bacteria); this indicates a successful adaptation to the specific abiotic conditions. In the rhizosphere, the phosphatase activities were correlated to several OTUs. Moreover, the phosphodiesterase/alk. phosphomonoesterase ratio was highly correlated to the dominance index of the microbiota and to the relative abundance of the dominant Massilia OTU. This study shows the differential response of the rhizosphere- and endorhiza bacterial microbiota of barley to various phosphate sources in soil, thus providing insights onto this largely unknown aspect of the soil microbiome ecology and plant-microbe interactions.


Asunto(s)
Bacterias/aislamiento & purificación , Hordeum/microbiología , Microbiota , Fosfatos/análisis , Bacterias/clasificación , Bacterias/genética , Bacterias/metabolismo , Fosfatos/metabolismo , Filogenia , Rizosfera , Suelo/química , Microbiología del Suelo , Túnez
10.
Methods ; 149: 25-30, 2018 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-29857194

RESUMEN

The RNA-SIP technology, introduced into molecular microbial ecology in 2002, is an elegant technique to link the structure and function of complex microbial communities, i.e. to identify microbial key-players involved in distinct degradation and assimilation processes under in-situ conditions. Due to its dependence of microbial RNA, this technique is particularly suited for environments with high numbers of very active, i.e. significantly RNA-expressing, bacteria. So far, it was mainly used in environmental studies using microbiotas from soil or water habitats. Here we outline and summarize our application of RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in intestinal samples of human and animal origin. Following an isotope label from a prebiotic substrate into the RNA of distinct bacterial taxa will help to better understand the functionality of these medically and economically important nutrients in an intestinal environment.


Asunto(s)
Microbioma Gastrointestinal/fisiología , Interacciones Microbiota-Huesped/fisiología , Marcaje Isotópico/métodos , Microbiota/fisiología , Sondas ARN/metabolismo , Humanos , Marcaje Isotópico/instrumentación , Sondas ARN/análisis , Ultracentrifugación/métodos
11.
J Environ Manage ; 232: 428-437, 2019 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-30500707

RESUMEN

Recycling of process wastes will be in future an essential step to meet the demands for valuable metals of a growing market. Depending on their particle sizes incineration slags are already used to recover metals but particle size fractions below 4 mm are still difficult to recycle. Therefore, different particle size fractions (mesh size 2 and 4 mm, high energy grinded) of dry discharged slags were used for bioleaching with and without the pure cultures Acidithiobacillus ferrooxidans or Leptospirillum ferrooxidans or a mixture of Acidithiobacillus thiooxidans and Acidithiobacillus ferrooxidans in batch cultures. Regarding Al, Cr, Cu, Ni, Mn and the rare earth elements Ce, La and Er, bioleaching was significantly more successful with iron oxidizing bacteria compared to abiotic controls. Metal mobilization for Al, Cu, Mn, Cr and Er with bacteria was between 70 and 100% and for Ce, Ni and La around 50% almost after 7 days, making an industrial application for the high concentrated metals like Al and Cu feasible. In addition to the recovery of valuable metals, a reduction in cost of landfilling was identified. After treatment of the slag with the microorganisms, concentrations of harmful substances in the residues could be reduced and thus a classification in lower safety levels regarding the LAGA or EU regulations was calculated.


Asunto(s)
Acidithiobacillus , Contaminantes Ambientales , Incineración , Metales , Reciclaje
12.
Int J Syst Evol Microbiol ; 68(10): 3248-3254, 2018 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-30132752

RESUMEN

A Gram-negative bacterium, strain HA7T, was isolated from the microhabitat of common hazel (Corylus avellana L.) pollen. HA7T was found to be an aerobic, rod-shaped, catalase-positive, oxidase-negative bacterium with an optimum growth temperature of 25 °C and pH of 7. The nearly complete 16S rRNA gene sequence of HA7T strain showed the closest similarities to Spirosoma linguale DSM 74T (97.4 %) and Spirosoma fluviale DSM 29961T (97.43 %). The major fatty acids (>5 %) were C16 : 1ω5c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were an unidentified aminophospholipid and phosphatidylethanolamine. The major respiratory quinone detected was menaquinone MK-7 (95 %). The draft genome sequence included 8 794 837 bases, which contained 3665 predicted coding sequences and had a G+C content of 47.9 mol%. The genome-based comparison between HA7T and S. linguale DSM 74T and S. fluviale DSM 29961T with pairwise average nucleotide identity indicated a clear distinction, between 76.2-76.3 %. Moreover, the digital DNA-DNA relatedness of HA7T to these strains was 26.5 and 25.1 %. Based on the differential genotypic, phenotypic and chemotaxonomic properties to closely related type strains, strain HA7T ought to be assigned with the status of a new species, for which the name Spirosomapollinicola sp. nov. is proposed. The type strain is HA7T (DSM 105799T=LMG 30282T).


Asunto(s)
Corylus/microbiología , Cytophagaceae/clasificación , Filogenia , Polen/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , Secuencia de Bases , Cytophagaceae/genética , Cytophagaceae/aislamiento & purificación , ADN Bacteriano/genética , Ácidos Grasos/química , Alemania , Fosfatidiletanolaminas/química , Fosfolípidos/química , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Vitamina K 2/análogos & derivados , Vitamina K 2/química
13.
Int J Syst Evol Microbiol ; 67(11): 4500-4506, 2017 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-28945527

RESUMEN

A Gram-negative bacterium, designated E130T, was isolated from rhizospheric soil of Plantago winteri Wirtg. from a natural salt meadow as part of an investigation on rhizospheric bacteria from salt-resistant plant species and evaluation of their plant growth-promoting abilities. Cells were rods, non-motile, aerobic, and oxidase and catalase positive, grew in a temperature range of between 4 and 37 °C, and in the presence of 0.5-5 % NaCl (w/v). Based on 16S rRNA gene sequence analysis, strain E130T is affiliated within the genus Ancylobacter, sharing the highest similarity with Ancylobacter rudongensis DSM 17131T (97.6 %), Ancylobacter defluvii CCUG 63806T (97.5 %) and Ancylobacter dichloromethanicus DSM 21507T (97.4 %). The DNA G+C content of strain E130T was 65.1 mol%. Its respiratory quinones were Q-9 and Q-10 and its major polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and unidentified phospholipid. Major fatty acids of the strains E130T were C12 : 0, C16 : 0, C18 : 1ω7c and C19 : 0cycloω8c. The DNA-DNA relatedness of E130T to A. rudongensis DSM 17131T, A. defluvii CCUG 63806T and A. dichloromethanicus DSM 21507T was 29.2, 21.2 and 32.2 % respectively. On the basis of our polyphasic taxonomic study the new isolate represents a novel species, for which the name Ancylobacter pratisalsi sp. nov. is proposed. The type strain is E130T (LMG 29367T=DSM 102029T).


Asunto(s)
Alphaproteobacteria/clasificación , Filogenia , Plantago/microbiología , Rizosfera , Plantas Tolerantes a la Sal/microbiología , Microbiología del Suelo , Alphaproteobacteria/genética , Alphaproteobacteria/aislamiento & purificación , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Alemania , Fosfolípidos/química , Plantago/crecimiento & desarrollo , ARN Ribosómico 16S/genética , Plantas Tolerantes a la Sal/crecimiento & desarrollo , Análisis de Secuencia de ADN , Vitamina K 2/química
14.
Environ Microbiol ; 18(12): 5161-5174, 2016 12.
Artículo en Inglés | MEDLINE | ID: mdl-27612299

RESUMEN

Diverse microorganisms colonise the different plant-microhabitats, such as rhizosphere and phyllosphere, and play key roles for the host. However, bacteria associated with pollen are poorly investigated, despite its ecological, commercial and medical relevance. Due to structure and nutritive composition, pollen provides a unique microhabitat. Here the bacterial abundance, community structure, diversity and colonization pattern of birch, rye, rapes and autumn crocus pollens were examined, by using cultivation, high-throughput sequencing and microscopy. Cultivated bacteria belonged to Proteobacteria, Actinobacteria and Firmicutes, with remarkable differences at species level between pollen species. High-throughput sequencing of 16S rRNA gene amplicon libraries showed Proteobacteria as the dominant phylum in all pollen species, followed by Actinobacteria, Acidobacteria and Firmicutes. Both plant species and pollination type significant influenced structure and diversity of the pollen microbiota. The insect-pollinated species possessed a more similar microbiota in comparison to the wind-pollinated ones, suggesting a levelling effect by insect vectors. Scanning electron microscopy as well as fluorescent in situ hybridisation coupled with confocal laser scanning microscopy (FISH-CLSM) indicated the tectum surface as the preferred niche of bacterial colonisation. This work is the most comprehensive study of pollen microbiology, and strongly increases our knowledge on one of the less investigated plant-microhabitats.


Asunto(s)
Bacterias/aislamiento & purificación , Insectos/fisiología , Microbiota , Polen/microbiología , Animales , Bacterias/clasificación , Bacterias/genética , Flores/microbiología , Biblioteca de Genes , Polinización , ARN Ribosómico 16S/genética , Rizosfera , Especificidad de la Especie
16.
Int J Syst Evol Microbiol ; 64(Pt 9): 3160-3167, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-24961682

RESUMEN

A phosphate-mobilizing, Gram-negative bacterium was isolated from rhizospheric soil of Plantago winteri from a natural salt meadow as part of an investigation of rhizospheric bacteria from salt-resistant plant species and evaluation of their plant-growth-promoting abilities. Cells were rods, motile, strictly aerobic, oxidase-positive and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E19(T) was distinct from other taxa within the class Alphaproteobacteria. Strain E19(T) showed less than 93.5 % 16S rRNA gene sequence similarity with members of the genera Rhizobium (≤93.5 %), Labrenzia (≤93.1 %), Stappia (≤93.1 %), Aureimonas (≤93.1 %) and Mesorhizobium (≤93.0 %) and was most closely related to Rhizobium rhizoryzae (93.5 % 16S rRNA gene sequence similarity to the type strain). The sole respiratory quinone was Q-10, and the polar lipids comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an aminolipid and an unidentified phospholipid. Major fatty acids were C18 : 1ω7c (71.4 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1; 8.3 %), C20 : 0 (7.9 %) and C16 : 0 (6.1 %). The DNA G+C content of strain E19(T) was 59.9±0.7 mol%. The capacity for nitrogen fixation was confirmed by the presence of the nifH gene and the acetylene reduction assay. On the basis of the results of our polyphasic taxonomic study, the new isolate represents a novel genus and species, for which the name Hartmannibacter diazotrophicus gen. nov., sp. nov. is proposed. The type strain of Hartmannibacter diazotrophicus is E19(T) ( = LMG 27460(T) = KACC 17263(T)).


Asunto(s)
Fijación del Nitrógeno , Filogenia , Plantago/microbiología , Rizosfera , Rhodobacteraceae/clasificación , Plantas Tolerantes a la Sal/microbiología , Técnicas de Tipificación Bacteriana , Composición de Base , ADN Bacteriano/genética , Ácidos Grasos/química , Alemania , Datos de Secuencia Molecular , Fosfatos , Fosfolípidos/química , ARN Ribosómico 16S/genética , Rhodobacteraceae/genética , Rhodobacteraceae/aislamiento & purificación , Análisis de Secuencia de ADN , Ubiquinona/química
17.
Int J Syst Evol Microbiol ; 64(Pt 4): 1202-1209, 2014 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-24408528

RESUMEN

Two motile, Gram-staining-negative, aerobic, rod-shaped bacteria designated strains E48(T) and E49(T) were isolated from the rhizosphere of Hordeum secalinum from a natural salt meadow near Münzenberg, Germany. 16S rRNA gene sequence similarity analysis revealed that strains E48(T) and E49(T) shared similarities of 97.6 % with Rheinheimera pacifica KMM 1406(T) and 98.5 % with Rheinheimera nanhaiensis E407-8(T), respectively. Major fatty acids of strain E48(T) were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C17 : 1ω8c, and of strain E49(T) were C16 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω7c. The DNA G+C contents were 50.5 mol% (E48(T)) and 50.0 mol% (E49(T)). Strains E48(T) and E49(T) grew at 4-37 °C (optimum 28 °C) and with 0-6 % NaCl (optimum 0-3 %) and 0-5 % NaCl (optimum 0-3 %), respectively. The potential for nitrogen fixation by strains E48(T) and E49(T) was evaluated by molecular techniques and the acetylene reduction assay. The DNA-DNA hybridization, physiological and molecular data demonstrated that strains E48(T) and E49(T) represent two novel species of the genus Rheinheimera, and therefore the names Rheinheimera hassiensis sp. nov. (type strain E48(T) = LMG 27268(T) = KACC 17070(T)) and Rheinheimera muenzenbergensis sp. nov. (type strain E49(T) = LMG 27269(T) = KACC 17071(T)) are proposed.


Asunto(s)
Chromatiaceae/clasificación , Hordeum/microbiología , Filogenia , Rizosfera , Técnicas de Tipificación Bacteriana , Composición de Base , Chromatiaceae/genética , Chromatiaceae/aislamiento & purificación , ADN Bacteriano/genética , Ácidos Grasos/química , Alemania , Datos de Secuencia Molecular , Fijación del Nitrógeno , Hibridación de Ácido Nucleico , Oxidorreductasas/genética , ARN Ribosómico 16S/genética , Plantas Tolerantes a la Sal/microbiología , Análisis de Secuencia de ADN
18.
Int J Syst Evol Microbiol ; 64(Pt 2): 481-486, 2014 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-24105943

RESUMEN

Two Gram-reaction-negative, aerobic, nitrogen-fixing, rod-shaped bacteria, designated strains E20 and E50(T), were isolated from the rhizosphere of salt meadow plants Plantago winteri and Hordeum secalinum, respectively, near Münzenberg, Germany. Based on the 16S rRNA gene sequence analysis both strains E20 and E50(T) are affiliated with the genus Cellvibrio, sharing the highest similarity with Cellvibrio gandavensis LMG 18551(T) (96.4%) and (97.1%), respectively. Strains E20 and E50(T) were oxidase and catalase-positive, grew at a temperature range between 16 and 37 °C and in the presence of 0-5% NaCl (w/v). The DNA G+C contents were 52.1 mol% (E20) and 51.6 mol% (E50(T)). Major fatty acids of strains E20 and E50(T) were summed feature 3 (C16 : 1ω7c and/or iso-C(15 : 0) 2-OH), C(16 : 0), C(18 : 1)ω7c, C(12 : 0), C(18 : 0) and C(12 : 0) 3-OH. The DNA-DNA relatedness of the strains to Cellvibrio gandavensis LMG 18551(T) was 39% for strain E20 and 58% for strain E50(T). The nitrogen fixation capability of strains E20 and E50(T) was confirmed by the acetylene reduction assay. On the basis of our polyphasic taxonomic study, strains E20 and E50(T) represent a novel species of the genus Cellvibrio, for which the name Cellvibrio diazotrophicus is proposed. The type strain of Cellvibrio diazotrophicus is E50(T) ( = LMG 27267(T) = KACC 17069(T)). An emended description of the genus Cellvibrio is proposed based on the capability of fixing nitrogen and growth in presence of up to 5% NaCl (w/v).


Asunto(s)
Cellvibrio/clasificación , Fijación del Nitrógeno , Filogenia , Rizosfera , Plantas Tolerantes a la Sal/microbiología , Microbiología del Suelo , Técnicas de Tipificación Bacteriana , Composición de Base , Cellvibrio/genética , Cellvibrio/aislamiento & purificación , Ácidos Grasos/química , Alemania , Hordeum/microbiología , Datos de Secuencia Molecular , Hibridación de Ácido Nucleico , Plantago/microbiología , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN
19.
Microbiol Res ; 281: 127601, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38218094

RESUMEN

Modern crops might have lost some of their functional traits, required for interacting with beneficial microbes, as a result of the genotypic/phenotypic modifications that occurred during domestication. Here, we studied the bacterial and fungal microbiota in the rhizosphere of two cultivated wheat species (Triticum aestivum and T. durum) and their respective ancestors (Aegilops tauschii and T. dicoccoides), in three experimental fields, by using metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. Moreover, the abundance of bacterial genes involved in N- and P-cycles was estimated by quantitative PCR, and urease, alkaline phosphatase and phosphomonoesterase activities were assessed by enzymatic tests. The relationships between microbiota and environmental metadata were tested by correlation analysis. The assemblage of core microbiota was affected by both site and plant species. No significant differences in the abundance of potential fungal pathogens between wild and cultivated wheat species were found; however, co-occurrence analysis showed more bacterial-fungal negative correlations in the wild species. Concerning functions, the nitrogen denitrification nirS gene was consistently more abundant in the rhizosphere of A. tauschii than T. aestivum. Urease activity was higher in the rhizosphere of each wild wheat species in at least two of the research locations. Several microbiota members, including potentially beneficial taxa such as Lysobacter and new taxa such as Blastocatellaceae, were found to be strongly correlated to rhizospheric soil metadata. Our results showed that a functional microbiome shift occurred as a result of wheat domestication. Notably, these changes also included the reduction of the natural biocontrol potential of rhizosphere-associated bacteria against pathogenic fungi, suggesting that domestication disrupted the equilibrium of plant-microbe relationships that had been established during million years of co-evolution.


Asunto(s)
Microbiota , Rizosfera , Domesticación , Triticum/microbiología , ARN Ribosómico 16S/genética , Ureasa , Microbiota/genética , Bacterias/genética , Suelo , Productos Agrícolas/microbiología , Microbiología del Suelo , Raíces de Plantas/microbiología
20.
FEMS Microbiol Ecol ; 100(3)2024 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-38366928

RESUMEN

Monitoring of bioinoculants once released into the field remains largely unexplored; thus, more information is required about their survival and interactions after root colonization. Therefore, specific primers were used to perform a long-term tracking to elucidate the effect of Hartmannibacter diazotrophicus on wheat and barley production at two experimental organic agriculture field stations. Three factors were evaluated: organic fertilizer application (with and without), row spacing (15 and 50 cm), and bacterial inoculation (H. diazotrophicus and control without bacteria). Hartmannibacter diazotrophicus was detected by quantitative polymerase chain reaction on the roots (up to 5 × 105 copies g-1 dry weight) until advanced developmental stages under field conditions during two seasons, and mostly in one farm. Correlation analysis showed a significant effect of H. diazotrophicus copy numbers on the yield parameters straw yield (increase of 453 kg ha-1 in wheat compared to the mean) and crude grain protein concentration (increase of 0.30% in wheat and 0.80% in barley compared to the mean). Our findings showed an apparently constant presence of H. diazotrophicus on both wheat and barley roots until 273 and 119 days after seeding, respectively, and its addition and concentration in the roots are associated with higher yields in one crop.


Asunto(s)
Agricultura , Alphaproteobacteria , Hordeum , Estaciones del Año , Triticum/microbiología , Bacterias
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