Genus Rubrobacter Research Articles

Impact of ryegrass cover crop inclusion on soil phosphorus and pqqC- and phoD-harboring bacterial communities

Italian ryegrass (Lolium multiflorum L.) is widely used as a cover crop with rice to promote soil fertility and reduce nutrient loss, although the specific impacts on phosphorus (P) dynamics and bioavailability are not clear. Soil samples were taken from a 4-year field experiment that included fertilized fallow-rice and ryegrass cover crop-rice rotations, together with an unfertilized fallow-rice control. Soil analyses included pH, total carbon (C) and nitrogen (N), together with soil P fractionations, acid and alkaline phosphatase enzyme activities, and assessment of the diversity and community of bacterial genes associated with inorganic P solubilization (pqqC) and organic P mineralization (phoD). Results showed that inclusion of the ryegrass cover crop enhanced biological P cycling in soil by significant increases in soil organic P and phosphatase enzyme activities compared with the fertilized fallow. The ryegrass cover crop was shown to reinforce the connection between soil P fractions and pqqC- and phoD-harboring bacterial communities, especially for the genus Rubrobacter. Cover crop inclusion also affected pqqC-harboring bacterial community composition by increasing the relative abundance of Actinobacteria, which reflected changes in the ratios of total P to total carbon and nitrogen in soil. In addition, the pqqC-harboring bacterial community was more affected by the ryegrass cover crop than the corresponding phoD-harboring community. The findings of this study demonstrated that the inclusion of ryegrass as a cover crop with rice significantly impacted biological P cycling in soil which may contribute to improved long-term P use efficiency.

The First Insight into Polyhydroxyalkanoates Accumulation in Multi-Extremophilic Rubrobacter xylanophilus and Rubrobacter spartanus.

Actinobacteria belonging to the genus Rubrobacter are known for their multi-extremophilic growth conditions—they are highly radiation-resistant, halotolerant, thermotolerant or even thermophilic. This work demonstrates that the members of the genus are capable of accumulating polyhydroxyalkanoates (PHA) since PHA-related genes are widely distributed among Rubrobacter spp. whose complete genome sequences are available in public databases. Interestingly, all Rubrobacter strains possess both class I and class III synthases (PhaC). We have experimentally investigated the PHA accumulation in two thermophilic species, R. xylanophilus and R. spartanus. The PHA content in both strains reached up to 50% of the cell dry mass, both bacteria were able to accumulate PHA consisting of 3-hydroxybutyrate and 3-hydroxyvalerate monomeric units, none other monomers were incorporated into the polymer chain. The capability of PHA accumulation likely contributes to the multi-extremophilic characteristics since it is known that PHA substantially enhances the stress robustness of bacteria. Hence, PHA can be considered as extremolytes enabling adaptation to extreme conditions. Furthermore, due to the high PHA content in biomass, a wide range of utilizable substrates, Gram-stain positivity, and thermophilic features, the Rubrobacter species, in particular Rubrobacter xylanophilus, could be also interesting candidates for industrial production of PHA within the concept of Next-Generation Industrial Biotechnology.

Composition and Diversity of Soil Bacterial Communities along an Environmental Gradient in the Sudano-Sahelian Region of Senegal

The soils of the semi-arid Sudano-Sahelian region of West Africa have been identified as being highly vulnerable to soil degradation with impacts on their capacity to provide goods and services in which soil microorganisms participate. Unfortunately, soil microbial diversity from this semi-arid region with high rainfall variability remains largely unexplored. The aim of the present study was to characterize the diversity and composition of the soil bacterial communities and to identify factors involved in their spatial distribution along an environmental gradient in Senegal. Samples were collected from non-anthropogenic sites across four pedoclimatic zones. Bacterial communities were characterized using next-generation sequencing and soil physico-chemical parameters were determined. Our results showed that Firmicutes, Actinobacteria, Proteobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria, and Verrucomicrobia phyla were predominant in the soils of the region. Bacterial α-diversity was stable along the environmental gradient whereas β-diversity highlighted significant changes in the composition of the soil bacterial community. Changes were driven by shifts in the relative abundance of OTUs belonging mainly to the genus Bacillus, Conexibacter, Kaistobacter, Solirubrobacter, Ktedonobacter, Sphingomonas, Microvirga, Rubrobacter and Pelobacter. Soil properties like pH, soil moisture and clay content were the environmental parameters identified as drivers of the composition of the bacterial communities in the semi-arid Sudano-Sahelian region of Senegal (West Africa).

Microbial communities of the Mediterranean rocky shore: ecology and biotechnological potential of the sea-land transition.

SummaryMicrobial communities from harsh environments hold great promise as sources of biotechnologically relevant strains and compounds. In the present work, we have characterized the microorganisms from the supralittoral and splash zone in three different rocky locations of the Western Mediterranean coast, a tough environment characterized by high levels of irradiation and large temperature and salinity fluctuations. We have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. All three locations displayed very similar taxonomic profiles, with the genus Rubrobacter and the families Xenococcaceae, Flammeovirgaceae, Phyllobacteriaceae, Rhodobacteraceae and Trueperaceae being the most abundant taxa; and Ascomycota and halotolerant archaea as members of the eukaryotic and archaeal community respectively. In parallel, the culture‐dependent approach yielded a 100‐isolates collection, out of which 12 displayed high antioxidant activities, as evidenced by two in vitro (hydrogen peroxide and DPPH) and confirmed in vivo with Caenorhabditis elegans assays, in which two isolates, CR22 and CR24, resulted in extended survival rates of the nematodes. This work is the first complete characterization of the Mediterranean splash‐zone coastal microbiome, and our results indicate that this microbial niche is home of an extremophilic community that holds biotechnological potential.

New genus-specific primers for PCR identification of Rubrobacter strains

A set of oligonucleotide primers, Rubro223f and Rubro454r, were found to amplify a 267 nucleotide sequence of 16S rRNA genes of Rubrobacter type strains. The primers distinguished members of this genus from other deeply-rooted actinobacterial lineages corresponding to the genera Conexibacter, Gaiella, Parviterribacter, Patulibacter, Solirubrobacter and Thermoleophilum of the class Thermoleophilia. Amplification of DNA bands of about 267 nucleotides were generated from environmental DNA extracted from soil samples taken from two locations in the Atacama Desert. Sequencing of a DNA library prepared from the bands showed that all of the clones fell within the evolutionary radiation occupied by the genus Rubrobacter. Most of the clones were assigned to two lineages that were well separated from phyletic lines composed of Rubrobacter type strains. It can be concluded that primers Rubro223f and Rubro454r are specific for the genus Rubrobacter and can be used to detect the presence and abundance of members of this genus in the Atacama Desert and other biomes.

Rubrobacter indicoceani sp. nov., a new marine actinobacterium isolated from Indian Ocean sediment.

A novel mesophilic marine actinobacterial strain, designated as SCSIO 08198T, was isolated from a deep-sea sediment sample collected from the Indian Ocean. The strain was Gram-stain-positive, rod-shaped and salmon pink in colour. Good growth occurred on marine agar with 1-5 % (w/v) NaCl and incubation at 28 °C for more than a fortnight. Sensitive to short ultraviolet radiation. Analysis of 16S rRNA gene sequences revealed that strain SCSIO 08198T had the highest similarity of 97.2 % to Rubrobacter radiotolerans DSM 5868T, and loosely related (<94.2 %) to all other species in the genus Rubrobacter. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that the novel isolate shared a lineage with members of the genus Rubrobacter. The total cellular fatty acid profile was dominated by C16 : 0 12-methyl. MK-8 was the main menaquinone. The peptidoglycan type was A3α (l-Lys-l-Ala). The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol and unidentified phospholipids. Based on the whole genome sequence analysis, the genome size is 3 078 689 bp with DNA G+C value of 63.8 mol%, including one circular chromosome and two plasmids. Based on these polyphasic data, a new species, Rubrobacterindicoceani sp. nov., is proposed, with the type strain SCSIO 08198T (=DSM 105148T=CGMCC 1.16398T).

Rubrobacter spartanus sp. nov., a moderately thermophilic oligotrophic bacterium isolated from volcanic soil.

Bacterial strain HPK2-2T was isolated from soil adjacent to the caldera of Kilauea Volcano in Hawaii Volcanoes National Park. HPK2-2T is a chemoorganoheterotroph that shows optimal growth at 50 °C (range 45-55 °C) and pH 8.0 (range 5.0-10.0). Sequence analysis of the 16S subunit of the rRNA gene showed that HPK2-2T is most closely related to the type strain of Rubrobactertaiwanensis (ATCC BAA-406T), with which it shared 94.5 % sequence identity. The major fatty acids detected in HPK2-2T were C18 : 0 14-methyl and C16 : 0 12-methyl; internally branched fatty acids such as these are characteristic of the genus Rubrobacter. The only respiratory quinone detected was MK-8, which is the major respiratory quinone for all members of the family Rubrobacteraceae examined thus far. We propose that HPK2-2T represents a novel species of the genus Rubrobacter, for which we propose the name Rubrobacterspartanus (type strain HPK2-2T; DSM 102139T; LMG 29988T).

Development and characterization of a thermophilic, lignin degrading microbiota

Microbial communities and associated enzymes that hydrolyze lignocellulose in the presence of lignin decomposition products are important for industrial and environmental bioconversion processes. The aims of this study were to identify microorganisms capable of decomposing lignocellulose and tolerating lignin decomposition products under high-solids and thermophilic conditions, and to elucidate potential mechanisms of tolerance. High-solids incubations were conducted to enrich for thermophilic communities that decompose Douglas fir. Bacterial and fungal communities were determined using 16S rRNA and ITS region gene sequencing, and PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was applied to predict genes involved in lignocellulose degradation and tolerance to lignin decomposition products. Lignin decomposition increased with enrichment of specific microorganisms. The dominant bacterium identified with enrichment was from the genus Rubrobacter while the dominant fungus was from the genus Talaromyces. Bacteria containing predicted genes associated with lignin degradation and tolerance to breakdown products were identified. These included organisms from the genus Rubrobacter, and families Beijerinckiaceae and Xanthomonadaceae. The dominant bacteria and fungi identified may be promising sources of enzymes that degrade lignocellulose and genes that confer tolerance to lignin decomposition products.

Evidence for the presence of key chlorophyll-biosynthesis-related proteins in the genus Rubrobacter (Phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis.

Homologs showing high degree of sequence similarity to the three subunits of the protochlorophyllide oxidoreductase enzyme complex (viz. BchL, BchN, and BchB), which carries out a central role in chlorophyll-bacteriochlorophyll (Bchl) biosynthesis, are uniquely found in photosynthetic organisms. The results of BLAST searches and homology modeling presented here show that proteins exhibiting a high degree of sequence and structural similarity to the BchB and BchN proteins are also present in organisms from the high G+C Gram-positive phylum of Actinobacteria, specifically in members of the genus Rubrobacter (R. x ylanophilus and R. r adiotolerans). The results presented exclude the possibility that the observed BLAST hits are for subunits of the nitrogenase complex or the chlorin reductase complex. The branching in phylogenetic trees and the sequence characteristics of the Rubrobacter BchB/BchN homologs indicate that these homologs are distinct from those found in other photosynthetic bacteria and that they may represent ancestral forms of the BchB/BchN proteins. Although a homolog showing high degree of sequence similarity to the BchL protein was not detected in Rubrobacter, another protein, belonging to the ParA/Soj/MinD family, present in these bacteria, exhibits high degree of structural similarity to the BchL. In addition to the BchB/BchN homologs, Rubrobacter species also contain homologs showing high degree of sequence similarity to different subunits of magnesium chelatase (BchD, BchH, and BchI) as well as proteins showing significant similarity to the BchP and BchG proteins. Interestingly, no homologs corresponding to the BchX, BchY, and BchZ proteins were detected in the Rubrobacter species. These results provide the first suggestive evidence that some form of photosynthesis either exists or was anciently present within the phylum Actinobacteria (high G+C Gram-positive) in members of the genus Rubrobacter. The significance of these results concerning the origin of the Bchl-based photosynthesis is also discussed.

Halophilic microorganisms are responsible for the rosy discolouration of saline environments in three historical buildings with mural paintings.

A number of mural paintings and building materials from monuments located in central and south Europe are characterized by the presence of an intriguing rosy discolouration phenomenon. Although some similarities were observed among the bacterial and archaeal microbiota detected in these monuments, their origin and nature is still unknown. In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques. The bacterial communities were dominated by halophilic members of Actinobacteria, mainly of the genus Rubrobacter. Representatives of the Archaea were also detected with the predominating genera Halobacterium, Halococcus and Halalkalicoccus. Furthermore, halophilic bacterial strains, mainly of the phylum Firmicutes, could be retrieved from two monuments using special culture media. Inoculation of building materials (limestone and gypsum plaster) with selected isolates reproduced the unaesthetic rosy effect and biodeterioration in the laboratory.

Description of two new thermophilic species of the genus Rubrobacter, Rubrobacter calidifluminis sp. nov. and Rubrobacter naiadicus sp. nov., and emended description of the genus Rubrobacter and the species Rubrobacter bracarensis

Four isolates, designated, RG-1T, RG-3T, RG-6 and RG-8 with optimum growth temperatures around 60°C were recovered from a hot stream near Ribeira Grande on the Island of São Miguel in the Azores. These strains were strictly aerobic, catalase and oxidase positive. The organisms could be divided into two groups; one comprising strains RG-1T and RG-6, the other formed by strains RG-3T and RG-8, with distinctive phenotypic and chemotaxonomic characteristics. Major fatty acids varied between the groups, but all contained iso-branched components such as iso-C16:0 10-methyl and iso-C17:0 10-methyl. Analysis of the 16S rRNA gene shows the strains to cluster with species of the genus Rubrobacter, specifically with Rubrobacter xylanophilus to which they have pairwise sequence similarity in the range of 98.4–98.6%. The DNA–DNA hybridization result show that strains RG-1T and RG-3T share 72% reassociation. Strains RG-1T and RG-3T displayed extreme tolerance to desiccation when compared to other species of the genus. Based on genotypic, physiological and biochemical characteristics we describe two new species: Rubrobacter calidifluminis sp. nov., represented by strain RG-1T (=CECT 8308T =JCM 19154T) and Rubrobacter naiadicus sp. nov. represented by strain RG-3T (=CECT 8310T=JCM 19155T). The description of the species Rubrobacter bracarensis[16] is emended to correct the fatty acid composition of these organisms. The discovery of new fatty acids in these species requires emendation of the description of the genus Rubrobacter.

Rubrobacter bracarensis sp. nov., a novel member of the genus Rubrobacter isolated from a biodeteriorated monument

Three actinobacteria strains isolated from a green biofilm covering the biodeteriorated interior walls of Vilar de Frades Church (Portugal) were studied using a polyphasic approach. The three strains were aerobic, non-spore forming and Gram-positive. Phylogenetically, the most closely related described species was Rubrobacter radiotolerans (94.2–94.3% and 81.9–82.5% similarities for the 16S rRNA and rpoB gene sequences, respectively). The fatty acid profile was dominated by anteiso-C17:1 ω9c, and MK-8 was the only menaquinone present. These data clearly showed that the three strains could represent a new species, for which we propose the name Rubrobacter bracarensis sp. nov., with strain VF70612_S1T (=CECT 7924=DSMZ 24908) as the type strain.

Isolation of five Rubrobacter strains from biodeteriorated monuments

In the last few years, the microbial colonisation of mural paintings in ancient monuments has been attracting the attention of microbiologists and conservators. The genus Rubrobacter is commonly found in biodeteriorated monuments, where it has been reported to cause rosy discolouration. However, to date, only three species of this genus have been isolated, all from thermophilic environments. In this paper, we studied three monuments: the Servilia and Postumio tombs in the Roman Necropolis of Carmona (Spain), and Vilar de Frades church (Portugal), in search of Rubrobacter strains. In all cases, biodeterioration and the formation of efflorescences were observed, and five Rubrobacter strains were isolated. These isolates showed different physiology and migration in denaturing gradient gel electrophoresis, suggesting they might represent new species within this genus. The isolates reproduced some biodeterioration processes in the laboratory and revealed their biomediation in crystal formation.

Rubrobacter taiwanensis sp. nov., a novel thermophilic, radiation-resistant species isolated from hot springs.

Two novel bacteria, with an optimum growth temperature of approximately 60 degrees C, were isolated from Lu-shan hot springs in the central region of Taiwan. These isolates were aerobic, thermophilic, halotolerant, pink-pigmented, heterotrophic and resistant to gamma-radiation. Both pleomorphic, short, rod-shaped cells and coccoid cells were observed. Strains LS-286 (= ATCC BAA-452 = BCRC 17198) and LS-293T (= ATCC BAA-406T = BCRC 17173T) represented a novel species of the genus Rubrobacter, according to a phylogenetic analysis of the 16S rRNA gene, DNA-DNA hybridization, biochemical features and fatty acid composition. The name Rubrobacter taiwanensis sp. nov. is proposed for this novel species, with LS-293T as the type strain.

Rubrobacter-related bacteria associated with rosy discolouration of masonry and lime wall paintings.

A molecular approach was chosen to analyse the correlation between bacterial colonisation and rosy discolouration of masonry and lime wall paintings of two historically important buildings in Austria and Germany. The applied molecular method included PCR amplification of genes encoding the small subunit rRNA of bacteria (16S rDNA), genetic fingerprinting by denaturing gradient gel electrophoresis (DGGE), construction of 16S rDNA clone libraries, and comparative phylogenetic sequence analyses. The bacterial community of one red-pigmented biofilm sampled in Herberstein (Austria) contained bacteria phylogenetically related to the genera Saccharopolyspora, Nocardioides, Pseudonocardia, Rubrobacter, and to a Kineococcus-like bacterium. The bacterial community of the second red-pigmented biofilm sampled in Herberstein contained bacteria related to Arthrobacter, Comamonas, and to Rubrobacter. Rubrobacter-related 16S rDNA sequences were the most abundant. In the red-pigmented biofilm sampled in Burggen (Germany), only Rubrobacter-related bacteria were identified. No Rubrobacter-related bacteria were detected in non-rosy biofilms. The majority of sequences (70%) obtained from the bacterial communities of the three investigated rosy biofilms were related to sequences of the genus Rubrobacter (red-pigmented bacteria), demonstrating a correlation between Rubrobacter-related bacteria and the phenomenon of rosy discolouration of masonry and lime wall paintings.

Chemotaxonomic characterization of a radiotolerant bacterium,Arthrobacter radiotolerans: Description ofRubrobacter radiotoleransgen. nov., comb. nov.

The chemotaxonomic characteristics of Arthrobacter radiotolerans were investigated. The species possesses a peptidoglycan based on l-lysine (variation A3α) and a DNA base composition of 67.9 mol% G + C. The cellular fatty acids were primarily of the methyl branched types with 12-methyl-hexadecanoic acid as the predominant component. The major isoprenoid quinone was menaquinone with eight isoprene units and the polar lipids consisted of four phospholipids, one phosphoglycolipid and one glycolipid. On the basis of chemical characteristics it is suggested that Arthrobacter radiotolerans be reclassified in a new genus Rubrobacter, as Rubrobacter radiotolerans comb. nov.