Alpha Subclass Of Proteobacteria Research Articles

Nitrogen fixation in grasses - gluconacetobacter activates genes in sugarcane

Nitrogen-fixing bacteria have been isolated from sugarcane (Saccharum spp.) and other grasses in an endophytic and beneficial interaction that promotes plant growth. In this interaction, bacteria colonize the intercellular spaces and vascular tissues of most plant organs without causing disease symptoms. The best characterized sugarcane endophytic diazotrophs are Gluconacetobacter diazotrophicus, clustered in the alpha subclass of Proteobacteria, and Herbaspirillum seropedicae, Herbaspirullum rubrisubalbicans and Burkholderia sp, clustered in the beta subclass of the Proteobacteria (Reis et al. 2000). These particular types of endophytic plant growth promoting bacteria (PGPB) can offer several benefits to host plants such as to provide nitrogen trough Biological Nitrogen Fixation (BNF) and to produce plant growth hormones (eg. auxins and gibberellins), promoting plant development, increase in biomass, defense against pathogens and tolerance to abiotic stresses [1,2]. In Brazil, BNF plays a fundamental role in sugarcane cultivation by reduction of the use of nitrogen fertilizers, making Brazilian sugarcane culture more competitive in global markets. It has been suggested that the relatively low mineral N-inputs used for Brazilian sugarcane production over the last 100 years has historically selected for varieties with a low response to applied mineral N and a high N2-fixing ability [3]. Studies on the quantification of BNF to the Brazilian sugarcane varieties, using 15N isotope dilution and 15N natural abundance, have demonstrated that the amount of fixed N2 can be highly variable. Very large BNF-inputs were observed in several sugarcane varieties, especially the wild noncommercial species Krakatau (Saccharum spontaneum) used in plant breeding in Brazil, as well as the commercial varieties SP 70-1143 and CB 45-3, that exhibit high yields in lowfertility soils. SP70-1143 could obtain 72% of N-requirement from BNF, while Chunee (Saccharum barberi), a wild noncommercial species, obtained only 14% [3,4]. An important biotechnological challenge of this century is to develop tools to apply for a sustainable agriculture, that would increase productivity using less fertilizers, pesticides, water and cultivated area. The associations that occur between sugarcane and other grasses with nitrogenfixing endophytic bacteria have raised a large interest in their use in agriculture, in view of the positive effects on root development, and the increase in biomass and productivity. Experiments carried out at EMBRAPA Agrobiologia have shown significant results in biomass increase and grain yield due the use of diazotrophic endophytic bacteria inoculation in sugarcane, maize and rice inoculants. However, studies have also shown that the plant genotype and the environment where the association is established can influence the degree of beneficial results obtained by the plant caused by the association with endophytic bacteria. This plant / nitrogen-fixing endophytic bacteria interaction represents a novel system of beneficial plantmicroorganism association, which has unique features that remain to be characterized. The studies on BNF quantification have indicated that the selection of the best combination of endophytic diazotroph strains as well as sugarcane varieties needs to be exploited to obtain the maximum benefit from this association in agriculture. The signaling pathways by which sugarcane plants can decipher bacterial signals and respond properly for a successful association, by controlling endophyte recognition, colonization and nitrogen fixation rates, are still not clearly understood. Therefore, the major goal of our research is to develop biotechnological tools to help to obtain novel plant varieties more responsive to bacteria Laboratorio de Biologia Molecular de Plantas, Instituto de Bioquimica Medica, Centro de Ciencias da Saude, Universidade Federal do Rio de Janeiro, 21.941-590, Rio de Janeiro, RJ, Brazil Full list of author information is available at the end of the article Carvalho et al. BMC Proceedings 2014, 8(Suppl 4):O20 http://www.biomedcentral.com/1753-6561/8/S4/O20

Characterization of a homogeneous taxonomic group of marine magnetotactic cocci within a low tide zone in the China Sea

Magnetotactic bacteria are a heterologous group of motile prokaryotes, ubiquitous in aquatic habitats and cosmopolitan in distribution. Here, we studied the diversity of magnetotactic bacteria in a seawater pond within an intertidal zone at Huiquan Bay in the China Sea. The pond is composed of a permanently submerged part and a low tide subregion. The magnetotactic bacteria collected from the permanently submerged part display diversity in morphology and taxonomy. In contrast, we found a virtually homogenous population of ovoid-coccoid magnetotactic bacteria in the low tide subregion of the pond. They were bilophotrichously flagellated and exhibited polar magnetotactic behaviour. Almost all cells contained two chains of magnetosomes composed of magnetite crystals. Intriguingly, the combination of restriction fragment length polymorphism analysis (RFLP) and sequencing of cloned 16S rDNA genes from the low tide subregion samples as well as fluorescence in situ hybridization (FISH) revealed the presence of a homogenous population. Moreover, phylogenetic analysis indicated that the Qingdao Huiquan low tide magnetotactic bacteria belong to a new genus affiliated with the alpha-subclass of Proteobacteria. This finding suggests the adaptation of the magnetotactic bacterial population to the marine tide.

Spatial distribution and species composition of prosthecate bacteria in Lake Baikal

From the water column of Lake Baikal, several strains of prosthecate bacteria belonging to the genera Caulobacter and Brevundimonas were isolated. In this article, the methods applied for their isolation and cell number determination are described; the occurrence frequency and spatial distribution of these microorganisms in the lake are demonstrated. Characterization of the species composition of cultivable and uncultivable prosthecate bacteria was carried out using the methods of traditional and molecular microbiology, respectively. A comparative phylogenetic analysis of the DNA sequences of uncultivable bacteria, which showed homology to the members of the alpha subclass of proteobacteria, was carried out. It was demonstrated that the lake water column is inhabited by uncultivable alpha-proteobacteria of uncertain phylogenetic affinity, in addition to representatives of the species Caulobacter vibrioides and C. leidyi, which were detected by traditional microbiological methods.

Isolation and characterization of Dechlorospirillum anomalous strain JB116 from a sewage treatment plant

The dissimilatory perchlorate reducers mainly belong to two monophyletic groups, viz. Dechloromonas and Azospira in the beta subclass of Proteobacteria. The present study describes isolation and genetic characterization of Dechlorospirillum anomalous strain JB116 that belongs to alpha subclass of Proteobacteria. The strain JB116 was isolated under facultative anaerobic conditions on a growth medium containing sodium perchlorate and sodium acetate as electron (e(-)) acceptor and e(-) donor, respectively. The strain is a spirillum shaped, dissimilatory perchlorate and nitrate reducer that prefers nitrate to perchlorate. It grows heterotrophically with acetate at temperatures between 25-35 degrees C, NaCl concentrations between 0-0.5% and pH of 7-7.8. The strain JB116 is the second only representative strain within D. anomalous that shares 99% 16S rDNA sequence similarity with the type strain D. anomalous strain WD.

Isolation and characterization of bacteria capable of degrading phenol and reducing nitrate under low-oxygen conditions.

Nitrate-reducing bacteria capable of degrading phenol were isolated from natural and contaminated environments under low-oxygen conditions with nitrate-containing media, using phenol as a sole carbon and energy source. A total of 27 bacteria able to degrade phenol and reduce nitrate under low-oxygen conditions were isolated from all of the inoculum samples, regardless of previous phenol contamination. For all of these bacteria, oxygen was an essential requirement for phenol degradation. Nitrate reduction by 19 of the strains was insensitive to 10 mM sodium azide, and these strains were placed into the alpha- and beta-subclasses of Proteobacteria and two were Gram-positive bacteria. To date, the order of Rhizobiales has hardly been reported to have an ability to degrade aromatic compounds. Interestingly, our study showed that all isolates that were placed into the alpha-subclass of Proteobacteria are in the order of Rhizobiales. Furthermore, the genus Agrobacterium was isolated from most inoculum samples and one genus of Gram-positive bacteria, Staphylococcus, was also isolated. In the case of the remaining eight strains, nitrate reduction was inhibited by 10 mM sodium azide. Of these strains, seven were placed into the gamma-subclass of Proteobacteria.

Characterization of three spiral-shaped purple nonsulfur bacteria isolated from coastal lagoon sediments, saline sulfur springs, and microbial mats: emended description of the genus Roseospira and description of Roseospira marina sp. nov., Roseospira navarrensis sp. nov., and Roseospira thiosulfatophila sp. nov.

Three new spirilloid phototrophic purple nonsulfur bacteria were isolated in pure culture from three different environments: strain CE2105 from a brackish lagoon in the Arcachon Bay (Atlantic coast, France), strain SE3104 from a saline sulfur spring in the Pyrenees (Navarra, Spain), and strain AT2115 a microbial mat (Tetiaroa Atoll, Society Islands). Single cells of the three strains were spiral-shaped and highly motile. Their intracellular photosynthetic membranes were of the vesicular type. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were present as photosynthetic pigments. Optimal growth occurred under photoheterotrophic conditions and in the presence of 0.5-4% w/v NaCl. These features are similar to those described for Roseospira mediosalina. Comparative sequence analysis of their 16S rRNA genes placed these strains within the alpha-subclass of Proteobacteria, in a cluster together with Roseospira mediosalina and Rhodospira trueperi. They form a closely related group of slightly to moderately halophilic spiral-shaped purple nonsulfur bacteria.However, the three new isolates exhibited some differences in their physiology and genetic characteristics. Consequently, we propose that they are members of three new species within the genus Roseospira, Roseospira marina sp. nov., Roseospira navarrensis sp. nov., and Roseospira thiosulfatophila sp. nov., with strains CE2105, SE3104, and AT2115 as the type strains, respectively. As a consequence, an emended description of the genus Roseospira is also given.

Identification and characterization of humic substances-degrading bacterial isolates from an estuarine environment.

Bacterial isolates were obtained from enrichment cultures containing humic substances extracted from estuarine water using an XAD-8 resin. Eighteen isolates were chosen for phylogenetic and physiological characterization based on numerical importance in serial dilutions of the enrichment culture and unique colony morphology. Partial sequences of the 16S rRNA genes indicated that six of the isolates were associated with the alpha subclass of Proteobacteria, three with the gamma-Proteobacteria, and nine with the Gram-positive bacteria. Ten isolates degraded at least one (and up to six) selected aromatic single-ring compounds. Six isolates showed ability to degrade [(14)C]humic substances derived from the dominant salt marsh grass in the estuary from which they were isolated (Spartina alterniflora), mineralizing 0.4-1.1% of the humic substances over 4 weeks. A mixture of all 18 isolates did not degrade humic substances significantly faster than any of the individual strains, however, and no isolate degraded humic substances to the same extent as the natural marine bacterial community (3.0%). Similar studies with a radiolabeled synthetic lignin ([beta-(14)C]dehydropolymerisate) showed measurable levels of degradation by all 18 bacteria (3.0-8.8% in 4 weeks), but mineralization levels were again lower than that observed for the natural marine bacterial community (28.2%). Metabolic capabilities of the 18 isolates were highly variable and generally did not map to phylogenetic affiliation.

Phylogenetic affiliation and ultrastructure of uncultured magnetic bacteria with unusually large magnetosomes.

Natural enrichments of magnetic bacteria from the Itaipu lagoon near Rio de Janeiro were dominated by coccoid-to-ovoid morphotypes that produced unusually large magnetosomes. To determine the phylogenetic position of these unusual microorganisms, 16S rRNA genes were retrieved from bacteria magnetically separated from sediment of the Itaipu lagoon by in vitro amplification and cloning of PCR products into a plasmid vector. Partial sequencing of the obtained clones revealed two clusters of closely related sequences affiliated to a distinct lineage consisting exclusively of magnetic bacteria within the alpha-subclass of Proteobacteria. For a detailed phylogenetic analysis, several almost complete sequences of the 16S rRNA genes were determined. One representative clone of each cluster provided a PCR template for the in vitro transcription of group-specific polynucleotide probes complementary to a variable region of the 16S rRNA molecule. At least three different morphotypes of magnetic bacteria were reliably identified by post-embedding hybridization of ultra-thin sections. Electron microscopic analyses of hybridized cells enabled for the first time a detailed description of the morphological variety and ultrastructure of phylogenetically identified, uncultured magnetic bacteria. Two distinct coccoid bacteria were identified by the transcript probe complementary to the 16S rRNA sequence mabrj12, whereas the probe complementary to the sequence mabrj58 allowed the identification of an ovoid morphotype that displayed magnetosomes with the largest volumes observed to date.

Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture.

Culturable bacteria that were numerically important members of a marine enrichment community were identified and characterized phylogenetically. Selective and nonselective isolation methods were used to obtain 133 culturable bacterial isolates from model marine communities enriched with the high-molecular-weight (lignin-rich) fraction of pulp mill effluent. The culture collection was screened against community DNA from the lignin enrichments by whole-genome hybridization methods, and three marine bacterial isolates were identified as being numerically important in the communities. One isolate was in the alpha-subclass of Proteobacteria, and the other two were in the gamma-subclass of Proteobacteria. Isolate-specific 16S rRNA oligonucleotide probes designed to precisely quantify the isolates in the lignin enrichment communities indicated contributions ranging from 2 to 32% of enrichment DNA, values nearly identical to those originally obtained by the simpler whole-genome hybridization method. Two 16S rRNA sequences closely related to that of one of the isolates, although not identical, were amplified via PCR from the seawater sample originally used to inoculate the enrichment medium. Partial sequences of 14 other isolates revealed significant phylogenetic diversity and unusual sequences among the culturable lignin enrichment bacteria, with the Proteobacteria, Cytophaga-Flavobacterium, and gram-positive groups represented.

Phylogeny of the genus Azospirillum based on 16S rDNA sequence.

The 16S rDNA of 17 strains of Azospirillum, 14 assigned to one of the known species A. amazonense, A. brasilense, A. halopraeferens, A. irakense and A. lipoferum, and the other three of uncertain taxonomic position, was sequenced after polymerase chain reaction amplification and analysed in order to investigate the phylogenetic relationships at the intra-generic and super-generic level. The phylogenetic analysis confirms that the genus Azospirillum constitutes a phylogenetically separate entity within the alpha subclass of Proteobacteria and that the five species are well defined. A. brasilense and A. lipoferum are closely related species and form one cluster together with A. halopraeferens; the pair of species A. amazonense and A. irakense forms a second cluster in which Rhodospirillum centenum is also placed.

Zoogloea ramigera: A phylogenetically diverse species

Comparative sequence analysis of in vitro amplified 16S rRNA genes from three strains of Zoogloea ramigera demonstrated that they are phylogenetically quite diverse. Based on the 16S rRNA studies and on chemotaxonomic data from the literature it is now evident that Z. ramigera strain I-16-M (ATCC 19623, WS 1610), the former type strain, belongs to the alpha subclass of Proteobacteria, whereas the two other strains, ATCC 19544T (neotype strain) and ATCC 25935, are members of the beta subclass. Therefore, Z. ramigera strain I-16-M (ATCC 19623) has to be excluded from the genus Zoogloea since it does not belong to the same proteobacterial subclass as the type strain of the species Z. ramigera. Differences in their 16S rRNA sequences, in phenotypic and chemotaxonomic properties indicate that Z. ramigera strains ATCC 19544 and ATCC 25935 should be placed in different species.