Physiology of nitrogen fixation by Bacillus polymyxa

Mechanisms for Generating Low Potential Electrons across the Metabolic Diversity of Nitrogen-Fixing Bacteria

The availability of fixed nitrogen is a limiting factor in the net primary production of all ecosystems. Diazotrophs overcome this limit through the conversion of atmospheric dinitrogen to ammonia. Diazotrophs are phylogenetically diverse bacteria and archaea that exhibit a wide range of lifestyles and metabolisms, including obligate anaerobes and aerobes that generate energy through heterotrophic or autotrophic metabolisms. Despite the diversity of metabolisms, all diazotrophs use the same enzyme, nitrogenase, to reduce N2. Nitrogenase is an O2-sensitive enzyme that requires a high amount of energy in the form of ATP and low potential electrons carried by ferredoxin (Fd) or flavodoxin (Fld). This review summarizes how the diverse metabolisms of diazotrophs utilize different enzymes to generate low potential reducing equivalents for nitrogenase catalysis. These enzymes include substrate-level Fd oxidoreductases, hydrogenases, photosystem I or other light-driven reaction centers, electron bifurcating Fix complexes, proton motive force-driven Rnf complexes, and Fd:NAD(P)H oxidoreductases. Each of these enzymes is critical for generating low potential electrons while simultaneously integrating the native metabolism to balance nitrogenase's overall energy needs. Understanding the diversity of electron transport systems to nitrogenase in various diazotrophs will be essential to guide future engineering strategies aimed at expanding the contributions of biological nitrogen fixation in agriculture.

Paenibacillus turpanensis sp. nov., isolated from a salt lake of Turpan city in Xinjiang province, north-west China

Strain YIM B00363^T, a Gram-positive, aerobic, non-motile, rod-shaped, spore-forming bacterium, was isolated from saline soil samples collected from a salt lake in Xinjiang province, north-west China, and was characterized using a polyphasic approach. The optimum growth temperature was 37 °C and the optimum pH was 7.5-8.0. The major menaquinone was MK-7; anteiso-C_15:0 (53.52%), iso-C_15:0 (15.04%) and C_16:0 (12.76%) were the predominant cellular fatty acids. The diagnostic diamino acid of the cell wall peptidoglycan was meso-diaminopimelic acid. The phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, unidentified glycolipids and unknown lipids. The DNA G + C content of the type strain was 50.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain YIM B00363^T belonged to a cluster comprising species of the genus Paenibacillus. The nearest relatives were P. residui MC-246^T and P. senegalensis JC66^T, with 93.2% and 92.8% gene sequence similarities, respectively. On the basis of its phenotypic characteristics and phylogenetic distinctivenes, strain YIM B00363^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus turpanensis sp. nov. is proposed. The type strain is YIM B00363^T (= CGMCC 1.17507^T = KCTC 43184^T).

Genome-based reclassification of Paenibacillus jamilae Aguilera et al. 2001 as a later heterotypic synonym of Paenibacillus polymyxa (Prazmowski 1880) Ash et al. 1994

Paenibacillus is one of the genera that has high species diversity and Paenibacillus polymyxa, the type species of the genus, is mainly isolated from plant-associated environments. Among the plant-associated species, Paenibacillus jamilae B.3^T (=CECT 5266^T=DSM 13815^T=KACC 10925^T=KCTC 13919^T) was proposed to be a novel species according to 16S rRNA gene similarity and DNA-DNA relatedness with related species, including Paenibacillus polymyxa. Nevertheless, in the description of Paenibacillus jamilae the used strain of Paenibacillus polymyxa was not the type strain of this species. In this work we found that the type strains of both species showed 16S rRNA gene similarity of 99.6 %. Therefore, in this study, we sequenced the genome of Paenibacillus jamilae KACC 10925^T and compared it with those of the type strain of Paenibacillus polymyxa ATCC 842^T and other phylogenetically related species. Genome relatedness value calculated by DNA-DNA hybridization between type strains of Paenibacillus polymyxa and Paenibacillus jamilae was 73.5 %, which is higher than the threshold value (70 %). For more objective and repeatable results of genome relatedness, we analysed an average nucleotide identity (ANI) between two strains. Our results showed that ANI value between the type strains of Paenibacillus jamilae and Paenibacillus polymyxa is 98.5 %, a phylogenetic distance also higher than the threshold values (95~96 %). These values were proposed by Yoon et al. (2017). In addition, their phylogenetic distance based on 92 bacterial core genes is highly close compared to other species. These mean that Paenibacillus jamilae and Paenibacillus polymyxa should be reclassified as a single species. Based on the results from genomic level comparison as well as reexamination results of physiological and chemotaxonomic features, we propose reclassification of Paenibacillus jamilae as a later heterotypic synonym of Paenibacillus polymyxa.

Paenibacillus strains with nitrogen fixation and multiple beneficial properties for promoting plant growth

Paenibacillus is a large genus of Gram-positive, facultative anaerobic, endospore-forming bacteria. The genus Paenibacillus currently comprises more than 150 named species, approximately 20 of which have nitrogen-fixation ability. The N₂-fixing Paenibacillus strains have potential uses as a bacterial fertilizer in agriculture. In this study, 179 bacterial strains were isolated by using nitrogen-free medium after heating at 85 °C for 10 min from 69 soil samples collected from different plant rhizospheres in different areas. Of the 179 bacterial strains, 25 Paenibacillus strains had nifH gene encoding Fe protein of nitrogenase and showed nitrogenase activities. Of the 25 N₂-fixing Paenibacillus strains, 22 strains produced indole-3-acetic acid (IAA). 21 strains out of the 25 N₂-fixing Paenibacillus strains inhibited at least one of the 6 plant pathogens Rhizoctonia cerealis, Fusarium graminearum, Gibberella zeae, Fusarium solani, Colletotrichum gossypii and Alternaria longipes. 18 strains inhibited 5 plant pathogens and Paenibacillus sp. SZ-13b could inhibit the growth of all of the 6 plant pathogens. According to the nitrogenase activities, antibacterial capacities and IAA production, we chose eight strains to inoculate wheat, cucumber and tomato. Our results showed that the 5 strains Paenibacillus sp. JS-4, Paenibacillus sp. SZ-10, Paenibacillus sp. SZ-14, Paenibacillus sp. BJ-4 and Paenibacillus sp. SZ-15 significantly promoted plant growth and enhanced the dry weight of plants. Hence, the five strains have the greater potential to be used as good candidates for biofertilizer to facilitate sustainable development of agriculture.

Complex Multimeric [FeFe] Hydrogenases: Biochemistry, Physiology and New Opportunities for the Hydrogen Economy

Hydrogenases are key enzymes of the energy metabolism of many microorganisms. Especially in anoxic habitats where molecular hydrogen (H₂) is an important intermediate, these enzymes are used to expel excess reducing power by reducing protons or they are used for the oxidation of H₂ as energy and electron source. Despite the fact that hydrogenases catalyze the simplest chemical reaction of reducing two protons with two electrons it turned out that they are often parts of multimeric enzyme complexes catalyzing complex chemical reactions with a multitude of functions in the metabolism. Recent findings revealed multimeric hydrogenases with so far unknown functions particularly in bacteria from the class Clostridia. The discovery of [FeFe] hydrogenases coupled to electron bifurcating subunits solved the enigma of how the otherwise highly endergonic reduction of the electron carrier ferredoxin can be carried out and how H₂ production from NADH is possible. Complexes of [FeFe] hydrogenases with formate dehydrogenases revealed a novel enzymatic coupling of the two electron carriers H₂ and formate. These novel hydrogenase enzyme complex could also contribute to biotechnological H₂ production and H₂ storage, both processes essential for an envisaged economy based on H₂ as energy carrier.

Complete genome sequence of Paenibacillus beijingensis 7188(T) (=DSM 24997(T)), a novel rhizobacterium from jujube garden soil

We present here the complete genome sequence of a novel species Paenibacillus beijingensis 7188(T) (=DSM 24997(T)) from jujube rhizosphere soil that consists of one circular chromosome of 5,749,967 bp with a GC content of 52.5%. On the significance of first genome information in this species, the genome sequence of strain 7188(T) will provide a better comprehension of Paenibacillus species for the practical uses as a biofertilizer in agriculture.

Paenibacillus beijingensis sp. nov., a nitrogen-fixing species isolated from wheat rhizosphere soil

A novel nitrogen-fixing bacterium, BJ-18(T), was isolated from wheat rhizosphere soil. Strain BJ-18(T) was observed to be Gram-positive, facultatively anaerobic, motile and rod-shaped (0.4-0.9 μm × 2.0-2.9 μm). Phylogenetic analysis based on a partial nifH gene sequence and an assay for nitrogenase activity showed its nitrogen-fixing capacity. Phylogenetic analysis based on full 16S rRNA gene sequences suggested that strain BJ-18(T) is a member of the genus Paenibacillus. High similarity of 16S rRNA gene sequence was found between BJ-18(T) and Paenibacillus peoriae DSM 8320(T) (99.05 %), Paenibacillus jamilae DSM 13815(T) (98.86 %), Paenibacillus brasiliensis DSM 13188(T) (98.55 %), Paenibacillus polymyxa DSM 36(T) (98.74 %), Paenibacillus terrae DSM 15891(T) (97.99 %) and Paenibacillus kribbensis JCM 11465(T) (97.92 %), whereas the similarity was below 96.0 % between BJ-18(T) and the other Paenibacillus species. DNA-DNA relatedness between strain BJ-18(T) and P. peoriae DSM 8320(T), P. jamilae DSM 13815(T), P. brasiliensis DSM 13188(T), P. polymyxa DSM 36(T), P. kribbensis JCM 11465(T) and P. terrae DSM 15891(T) was determined to be 43.6 ± 2.7, 34.2 ± 5.3, 47.9 ± 6.6, 36.8 ± 3.5, 27.4 ± 4.3 and 23.6 ± 4.1 % respectively. The DNA G+C content of BJ-18(T) was determined to be 45.8 mol %. The major fatty acid was identified as anteiso-C15:0 (67.1 %). The polar lipids present in strain BJ-18(T) were identified as diphosphatidylglycerol, phosphatidyl methylethanolamine, phosphatidylethanolamine and phosphatidylglycerol. The phenotypic and genotypic characteristics, and DNA-DNA relatedness data, suggest that BJ-18(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus beijingensis sp. nov. (Type strain BJ-18(T)=DSM25425(T)=CGMCC 1.12045(T)) is proposed.

Resistance phenotypes mediated by aminoacyl-phosphatidylglycerol synthases

The specific aminoacylation of the phospholipid phosphatidylglycerol (PG) with alanine or with lysine catalyzed by aminoacyl-phosphatidylglycerol synthases (aaPGS) was shown to render various organisms less susceptible to antibacterial agents. This study makes use of Pseudomonas aeruginosa chimeric mutant strains producing lysyl-phosphatidylglycerol (L-PG) instead of the naturally occurring alanyl-phosphatidylglycerol (A-PG) to study the resulting impact on bacterial resistance. Consequences of such artificial phospholipid composition were studied in the presence of an overall of seven antimicrobials (β-lactams, a lipopeptide antibiotic, cationic antimicrobial peptides [CAMPs]) to quantitatively assess the effect of A-PG substitution (with L-PG, L-PG and A-PG, increased A-PG levels). For the employed Gram-negative P. aeruginosa model system, an exclusive charge repulsion mechanism does not explain the attenuated antimicrobial susceptibility due to PG modification. Additionally, the specificity of nine orthologous aaPGS enzymes was experimentally determined. The newly characterized protein sequences allowed for the establishment of a significant group of A-PG synthase sequences which were bioinformatically compared to the related group of L-PG synthesizing enzymes. The analysis revealed a diverse origin for the evolution of A-PG and L-PG synthases, as the specificity of an individual enzyme is not reflected in terms of a characteristic sequence motif. This finding is relevant for future development of potential aaPGS inhibitors.

Genome sequence of the diazotrophic Gram-positive rhizobacterium Paenibacillus riograndensis SBR5(T)

Paenibacillus riograndensis SBR5(T), a nitrogen-fixing Gram-positive rhizobacterium isolated from a wheat field in the south of Brazil, has a great potential for agricultural applications due to its plant growth promotion effects. Here we present the draft genome sequence of P. riograndensis SBR5(T). Its 7.37-Mb genome encodes determinants of the diazotrophic lifestyle and plant growth promotion, such as nitrogen fixation, antibiotic resistance, nitrate utilization, and iron uptake.

Isolation and characterization of bacteriophage PhiBP from Paenibacillus polymyxa CCM 7400

A bacteriophage PhiBP infecting Paenibacillus polymyxa CCM 7400 was isolated from culture lysate. Electron microscopy of lysate samples revealed the presence of bacteriophage particles with polyhedral heads 56 nm in diameter and flexible noncontractile tails 144 nm in length. The profile of PhiBP structural proteins resembles that of other bacteriophages. The PhiBP genome consists of double-stranded DNA of 43-kbp size. Homology search of sequenced DNA fragments from EcoRI digest revealed regions with significant similarity to other known bacteriophage genes. Regions similar to phage terminase genes were identified within the 1.2-kbp fragment. Three lytic genes, two holin genes and one endolysin gene were identified within the 2.5-kbp fragment. We tested the isolates of P. polymyxa CCM 7400 for the presence of phage DNA on bacterial chromosome using PCR amplification with primers derived from proposed terminase and holin gene sequences. We confirmed the presence of PhiBP DNA on P. polymyxa chromosome by Southern hybridization. The bacteriophage PhiBP was capable of causing lysis of a P. polymyxaPhiBP lysogen despite the presence of the phage DNA on bacterial chromosome. Therefore, we concluded that PhiBP was a virulent mutant phage.

Paenibacillus riograndensis sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Triticum aestivum

A bacterial strain designated SBR5T was isolated from the rhizosphere of Triticum aestivum. A phylogenetic analysis based on the 16S rRNA gene sequence placed the isolate within the genus Paenibacillus, being most closely related to Paenibacillus graminis RSA19T (98.1 % similarity). The isolate was a Gram-reaction-variable, motile, facultatively anaerobic bacterium, with spores in a terminal position in cells. Starch was utilized and dihydroxyacetone and catalase were produced. Strain SBR5T displayed plant-growth-promoting rhizobacteria characteristics: the ability to fix nitrogen and to produce siderophores and indole-3-acetic acid. The DNA G+C content was 55.1 mol%. Chemotaxonomic analysis of the isolated strain revealed that MK-7 was the predominant menaquinone, while the major fatty acid was anteiso-C15 : 0. DNA–DNA hybridization values between strain SBR5T and P. graminis RSA19T, Paenibacillus odorifer TOD45T and Paenibacillus borealis KK19T were 43, 35 and 28 %, respectively. These DNA relatedness data and the results of phylogenetic and phenotypic analyses showed that strain SBR5T should be considered as the nitrogen-fixing type strain of a novel species of the genus Paenibacillus, for which the name Paenibacillus riograndensis sp. nov. is proposed. The type strain is SBR5T (=CCGB 1313T =CECT 7330T).

Citrinin, a mycotoxin from Penicillium citrinum, plays a role in inducing motility of Paenibacillus polymyxa

Paenibacillus polymyxa, a Gram-positive low-G+C spore-forming soil bacterium, belongs to the plant growth-promoting rhizobacteria. The swarming motility of P. polymyxa strain E681 was greatly induced by a secondary metabolite, citrinin, produced by Penicillium citrinum KCTC6549 in a dose-dependent manner at concentrations of 2.5-15.0 microg mL(-1) on tryptic soy agar plates containing 1.0% (w/v) agar. Flagellum staining showed that citrinin activated the production of flagella by P. polymyxa. This result was supported by reverse transcriptase-PCR analysis of gene expression, which showed increased transcriptional levels of sigD and hag homologues of P. polymyxa E681 in the presence of citrinin. The results presented here show that a mycotoxin, citrinin, has a newly identified function of inducing bacterial motility by transcriptional activation of related genes. This finding contributes to our understanding of the interactions between bacteria and fungal strains in nature.

Paenibacillus zanthoxyli sp. nov., a novel nitrogen-fixing species isolated from the rhizosphere of Zanthoxylum simulans

Five endospore-forming, nitrogen-fixing strains were isolated from rhizosphere soils of Zanthoxylum simulans planted in Beijing, China. Phylogenetic analysis based on full-length 16S rRNA gene sequences revealed that the five strains formed a distinct cluster within the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between these novel strains and Paenibacillus azotofixans ATCC 35681(T) (97.8-98.5 % similarity) and Paenibacillus stellifer DSM 14472(T) (95.4-96.3 %). Levels of 16S rRNA gene sequence similarity between the novel isolates and other species of the genus Paenibacillus were less than 95.0 %. Levels of 16S rRNA gene sequence similarity among the isolates were more than 98.0 %. DNA-DNA relatedness between the five novel isolates and P. azotofixans ATCC 35681(T) was 45.50-47.45 % and relatedness among the five novel strains was 95.8-99.6 %. A significant feature of the novel strains that differentiated them from P. azotofixans and other Paenibacillus species was that none of the novel strains could produce acid or gas from the following various carbohydrates: glucose, sucrose, lactose, fructose, glycerol, xylose, maltose, d-sorbitol, sodium succinate, sodium citrate, glycine or l-aspartate. Anteiso-branched C(15 : 0) was the major fatty acid component (36.59 %) of novel strain JH29(T). On the basis of phenotypic properties, 16S rRNA gene sequences, DNA G+C content, DNA-DNA hybridization, chemotaxonomic properties and the nifH gene sequence, the five novel strains form a very homogeneous group which is different from other related species within the genus Paenibacillus. Therefore, the five novel strains are considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus zanthoxyli sp. nov. is proposed. The type strain is JH29(T) (=CCBAU 10243(T)=DSM 18202(T)).

Paenibacillus sabinae sp. nov., a nitrogen-fixing species isolated from the rhizosphere soils of shrubs

Five novel endospore-forming, nitrogen-fixing bacterial strains were isolated from the rhizosphere soils of plants of the species Sabina squamata, Weigela florida and Zanthoxylum simulans. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the five strains formed a distinct cluster within the genus Paenibacillus. These novel strains showed the highest levels (96.2-98.2 %) of 16S rRNA gene sequence similarity with Paenibacillus azotofixans. However, the DNA-DNA relatedness between these novel strains and P. azotofixans was 12.9-29.5 %. The DNA G+C contents of the five strains were found to be 51.9-52.9 mol%. Phenotypic analyses showed that a significant feature of the novel strains (differentiating them from P. azotofixans and other Paenibacillus species) is that all of them were unable to produce acid and gas from various carbohydrates such as glucose, sucrose, lactose and fructose. Anteiso-branched C(15 : 0) was the major fatty acid present in the novel type strain. On the basis of these data, the five novel strains represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sabinae sp. nov. is proposed. The type strain is T27(T) (=CCBAU 10202(T)=DSM 17841(T)).

Isolation and identification of nitrogen-fixing bacilli from plant rhizospheres in Beijing region

AIMS

To isolate and identify nitrogen-fixing bacilli from the plant rhizospheres in Beijing region of China.

METHODS AND RESULTS

A total of 29 isolates were selectively obtained from the rhizospheres of wheat, maize, ryegrass and willow based on their growth on nitrogen-free medium and their resistance to 100 degrees C for 10 min. Of the 29 isolates, seven had nifH gene determined by PCR amplification. The seven isolates were found to belong to the genera Bacillus and Paenibacillus based on phenotypic characterization, 16S rDNA sequence, G+C content and DNA-DNA hybridization. Isolates T1 and W5 were identified as Bacillus cereus and Bacillus marisflavi respectively. Isolates G1, C4 and C5 were identified as Bacillus megaterium. Isolate G2 was identified as Paenibacillus polymyxa and isolate T7 as Paenibacillus massiliensis.

CONCLUSIONS

This study suggests that nifH gene could be detected in the both genera Bacillus and Paenibacillus. These degenerate primers for nifH gene fragment used in this study were shown to be useful for identifying nitrogen-fixing bacilli.

SIGNIFICANCE AND IMPACT OF THE STUDY

It is the first demonstration that nitrogen fixation exists in B. marisflavi and P. massiliensis and the first report of the sequences of the nifH gene from B. megaterium and B. cereus. The nitrogen-fixing bacilli obtained in this study will be used in our future research for investigating the mechanisms of nitrogen fixation in bacilli.

Paenibacillus lactis sp. nov., isolated from raw and heat-treated milk

Endospore-forming bacteria were recovered from individual packages from different processing lines in a dairy plant during a tenacious periodical contamination of their UHT-milk production. Two colony types were seen, one of which was identified as Bacillus sporothermodurans. Analysis of the 16S rRNA gene of the second colony type placed these isolates within the genus Paenibacillus, with Paenibacillus lautus as the closest known relative. Moreover, over 99 % similarity was observed to the 16S rDNA sequence of MB 2035, a strain isolated previously from raw milk during a survey at dairy farms for very heat-resistant spore-forming bacteria. Nine other potentially closely related strains among the dairy farm isolates were found using rep-PCR typing. The taxonomic positions of these 19 isolates were further investigated using 16S rRNA gene sequencing and DNA-DNA hybridizations of representative strains. All 19 isolates shared a high degree of phenotypic similarity and were easily distinguished from closely related members of the genus. Anteiso-C(15 : 0), C(16 : 0) and iso-C(15 : 0) were among the major fatty acids and the genomic DNA G+C content was 51.6-51.7 mol%. Therefore, based on their phenotypic, phylogenetic and genomic distinctiveness, these 19 strains, isolated from both raw and heat-treated milk, are placed in the genus Paenibacillus as Paenibacillus lactis sp. nov. The type strain is MB 1871(T) (=LMG 21940(T)=DSM 15596(T)).

Use of rpoB gene analysis for identification of nitrogen-fixing Paenibacillus species as an alternative to the 16S rRNA gene

AIM

To avoid the limitations of 16S rRNA-based phylogenetic analysis for Paenibacillus species, the usefulness of the RNA polymerase beta-subunit encoding gene (rpoB) was investigated as an alternative to the 16S rRNA gene for taxonomic studies.

METHODS AND RESULTS

Partial rpoB sequences were generated for the type strains of eight nitrogen-fixing Paenibacillus species. The presence of only one copy of rpoB in the genome of P. graminis strain RSA19(T) was demonstrated by denaturing gradient gel electrophoresis and hybridization assays. A comparative analysis of the sequences of the 16S rRNA and rpoB genes was performed and the eight species showed between 91.6-99.1% (16S rRNA) and 77.9-97.3% (rpoB) similarity, allowing a more accurate discrimination between the different species using the rpoB gene. Finally, 24 isolates from the rhizosphere of different cultivars of maize previously identified as Paenibacillus spp. were assigned correctly to one of the nitrogen-fixing species.

CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY

The data obtained in this study indicate that rpoB is a powerful identification tool, which can be used for the correct discrimination of the nitrogen-fixing species of agricultural and industrial importance within the genus Paenibacillus.

Application of a novel Paenibacillus-specific PCR-DGGE method and sequence analysis to assess the diversity of Paenibacillus spp. in the maize rhizosphere

In this study, a Paenibacillus-specific PCR system, based on the specific primer PAEN515F in combination with bacterial primer R1401, was tested and used to amplify specific fragments of the 16S rRNA gene from rhizosphere DNA. The amplicons were used in a second (semi-nested) PCR for DGGE, in which bacterial primers F968GC and R1401 were used. The resulting products were separated into community fingerprints by DGGE. To assess the reliability of the method, the diversity of Paenibacillus species was evaluated on the basis of DNA extracted directly from the rhizospheres of four different cultivars of maize (Zea mays), i.e. CMS04, CMS11, CMS22 and CMS36, sown in two Brazilian field soils (Cerrado and Várzea). In addition, a clone library was generated from the PCR-generated 16S rDNA fragments, and selected clones were sequenced. The results of the bacterial community analyses showed, at the level of clone libraries, that considerable diversity among Paenibacillus spp. was present. The most dominantly found sequences clustered into 12 groups, each one potentially representing a species complex. Sequences closely affiliated with the P. macerans and P. azotofixans complexes were found in all samples, whereas other sequences were scarcer. Clones affiliated with the latter species complex were most abundant, representing 19% of all clones analysed. The Paenibacillus fingerprints generated via semi-nested PCR followed by DGGE showed a clear distinction between the maize plants grown in Cerrado versus Várzea soils. Thus, soil type, instead of maize cultivar type, was the overriding determinative factor that influenced the community structures of the Paenibacillus communities in the rhizospheres investigated. At a lower level (subcluster), there was a trend for maize cultivars CMS11 and CMS22 on the one hand, and CMS36 and CMS04 on the other hand, to cluster together, indicating that these respective pair of cultivars were similar in their Paenibacillus species composition. This trend was tentatively linked to the growth characteristics of these maize cultivars. These results clearly demonstrated the efficacy of the Paenibacillus-specific PCR-DGGE method in describing Paenibacillus species diversity in rhizosphere soils.

Characterization of nitrogen-fixing Paenibacillus species by polymerase chain reaction-restriction fragment length polymorphism analysis of part of genes encoding 16S rRNA and 23S rRNA and by multilocus enzyme electrophoresis

Forty-two strains representing the eight recognized nitrogen-fixing Paenibacillus species and 12 non-identified strains were examined by restriction fragment length polymorphism (RFLP) analysis of part of 16S and 23S rRNA genes amplified by polymerase chain reaction (PCR). Eleven different 16S rDNA genotypes were obtained from the combined data of RFLP analysis with four endonucleases and they were in agreement with the established taxonomic classification. Only one group of unclassified strains (Group I) was assigned in a separate genotype, suggesting they belong to a new species. Using the 23S PCR-RFLP method only six genotypes were detected, showing that this method is less discriminative than the 16S PCR-RFLP. Using the multilocus enzyme electrophoresis (MLEE) assay, the 48 strains tested could be classified into 35 zymovars. The seven enzymatic loci tested were polymorphic and the different profiles obtained among strains allowed the grouping of strains into 10 clusters. The PCR-RFLP methods together with the MLEE assay provide a rapid tool for the characterization and the establishment of the taxonomic position of isolates belonging to this nitrogen-fixing group, which shows a great potentiality in promoting plant growth.

Diversity of Paenibacillus polymyxa strains isolated from the rhizosphere of maize planted in Cerrado soil

Paenibacillus polymyxa populations present in the rhizosphere of maize (cultivar BR-201) planted in Cerrado soil were investigated in order to assess their diversity at four stages of plant growth. A total of 67 strains were isolated and all strains were identified as P. polymyxa by classical biochemical tests, API 50CH tests and a set of species-specific primers based on the 23S rDNA sequence. To compare the isolated strains, phenotypic characteristics (utilization of different carbohydrates, resistance to antibiotics and production of antimicrobial substances) and genetic approaches (hybridization with a Klebsiella pneumoniae nifKDH probe and BOX-PCR) were used. Fermentation of glycerol, arabinose, xylose and rhamnose varied among the isolates and these data divided the strains into five groups. Fifty strains (75%) showed homology to plasmid pSA30 (containing the nifKDH genes) resulting in five different hybridization patterns. Using BOX-PCR, 18 groups were observed. Phenetic analyses were applied based on the unweighted pair group method with arithmetic means using the phenotypic and genetic data, separately. All P. polymyxa isolates could be divided into two main clusters at approximately 52% and into 18 groups at approximately 89% of similarity, when phenotypic data were used. Also, two main clusters were formed at 65% of similarity when genetic data were used. In this dendrogram, clusters were further split into 10 and 22 groups, at about 88 and 97% of similarity, respectively. Finally, all phenotypic and genetic data, or just the genetic data, were used in a multivariate analysis of variance (MANOVA) in order to address the heterogeneity among P. polymyxa populations during the different stages of maize growth. The resulting data showed that strains isolated 10, 30, 60 and 90 days after maize sowing were statistically different.

Hydrogenase and nitrogenase in cell-free extracts of Bacillus polymyxa

Grau, F. H. (University of Wisconsin, Madison), and P. W. Wilson. Hydrogenase and nitrogenase in cell-free extracts of Bacillus polymyxa. J. Bacteriol. 85:446-450. 1963.-Washed cells of Bacillus polymyxa strain Hino, treated with lysozyme, yield cell-free extracts that rapidly evolve hydrogen from reduced methyl viologen, formate, and pyruvate. Hydrogenase is particulate, 86% being sedimented at 105,000 x g for 60 min. About 65% of the pyruvate metabolized is oxidized to acetyl phosphate, hydrogen, and carbon dioxide; the rest is converted to acetoin. These extracts fix considerable amounts of N(2) (15) when pyruvate is supplied as substrate, but will not fix with formate or mannitol. Centrifugation studies, and the absence of fixation with mannitol, show that this fixation is not caused by residual whole cells or spheroplasts. Cell-free fixation by B. polymyxa is similar to that by Clostridium pasteurianum. A short time lag in fixation occurs, and an optimal concentration of pyruvate is needed for maximal fixation. Arsenate causes a strong inhibition of fixation, presumably because arsenolysis of acetyl phosphate makes high-energy phosphate unavailable for the fixation process.

BIOLOGICAL FORMATION OF MOLECULAR HYDROGEN

From a general standpoint, the formation of molecular hydrogen can be considered a device for disposal of electrons released in metabolic oxidations. We presume that this means of performing anaerobic oxidations is of ancient origin and that the hydrogen-evolving system of strict anaerobes represents a primitive form of cytochrome oxidase, which in aerobes effects the terminal step of respiration, namely the disposal of electrons by combination with molecular oxygen. We further assume that the original pattern of reactions leading to H(2) production has become modified in various ways (with respect to both mechanisms and functions) during the course of biochemical evolution, and we believe that this point of view suggests profitable approaches for clarifying a number of problems in the intermediary metabolism of microorganisms which produce or utilize H(2). Of special general importance in this connection is the basic problem of defining more precisely the fundamental elements in the regulatory control of anaerobic energy metabolism. Among the more specific aspects awaiting further elucidation are: the relations between formation of H(2) and use of H(2) as a primary reductant for biosynthetic purposes; the various forms of direct and indirect interactions between hydrogenase and N(2) reduction systems; and the transitional stages between anaerobic and aerobic energy-metabolism patterns of facultative organisms.

Cellulose Decomposition and Associated Nitrogen Fixation by Mixed Cultures of Cellulomonas gelida and Azospirillum Species or Bacillus macerans

Mixed cultures of Cellulomonas gelida plus Azospirillum lipoferum or Azospirillum brasilense and C. gelida plus Bacillus macerans were shown to degrade cellulose and straw and to utilize the energy-yielding products to fix atmospheric nitrogen. This cooperative process was followed over 30 days in sand-based cultures in which the breakdown of 20% of the cellulose and 28 to 30% of the straw resulted in the fixation of 12 to 14.6 mg of N per g of cellulose and 17 to 19 mg of N per g of g straw consumed. Cellulomonas species have certain advantages over aerobic cellulose-degrading fungi in being able to degrade cellulose at oxygen concentrations as low as 1% O 2 (vol/vol) which would allow a close association between cellulose-degrading and microaerobic diazotrophic microorganisms. Cultures inoculated with initially different proportions of A. brasilense and C. gelida all reached a stable ratio of approximately 1 Azospirillum /3 Cellulomonas cells.

Studies on the aerobic non-symbiotic nitrogen-fixing bacteria, other than Azotobacter, in Egyptian soils

Twenty isolates of micro-organisms capable of growing on nitrogen-deficient medium and found as contaminants in Azotobacter cultures were isolated from Egyptian soils and studied for their morphological, cultural, and physiological properties. These micro-organisms s are members of Rhizobiaceae, Pseudomonadaceae, Achromobacteriaceae, Enterobacteriaceae, Micrococcaceae, Bacillaceae, and Streptomycetaceae as well as some yeasts. In nitrogen-free medium the micro-organism fixed only small amounts of atmospheric nitrogen, hardly exceeding 3 ppm and because of their low sugar consumption rates, efficiences of N2-fixation sometimes reaching 18 mg nitrogen fixed/g carbon oxidized were recorded. Addition of 15 ppm combined nitrogen to the medium increased the amounts of nitrogen fixed to 3--9 ppm.

Nitrogenase from Bacillus polymyxa. Purification and properties of the component proteins

A purification procedure is described for the components of Bacillus polymyxa nitrogenase. The procedure requires the removal of interfering mucopolysaccharides before the two nitrogenase proteins can be purified by the methods used with other nitrogenase components. The highest specific activities obtained were 2750 nmol C2H4 formed . min-1 . mg-1 MoFe protein and 2521 nmol C2H4 formed . min-1 . mg-1 Fe protein. The MoFe protein has a molecular weight of 215 000 and contains 2 molybdenum atoms, 33 iron atoms and 21 atoms of acid-labile sulfur per protein molecule. The Fe protein contains 3.2 iron atoms and 3.6 acid-labile sulfur atoms per molecule of 55 500 molecular weight. Each Fe protein binds two ATP molecules. The EPR spectra are similar to those of other nitrogenase proteins. MgATP changes the EPR of the Fe protein from a rhombic to an axial-type signal.

Purification and characterization of ferredoxin-nicotinamide adenine dinucleotide phosphate reductase from a nitrogen-fixing bacterium

Evidence suggesting that Bacillus polymyxa has an active ferredoxin-NADP(+) reductase (EC 1.6.99.4) was obtained when NADPH was found to provide reducing power for the nitrogenase of this organism; direct evidence was provided when it was shown that B. polymyxa extracts could substitute for the native ferredoxin-NADP(+) reductase in the photochemical reduction of NADP(+) by blue-green algal particles. The ferredoxin-NADP(+) reductase was purified about 80-fold by a combination of high-speed centrifugation, ammonium sulfate fractionation, and chromatography on Sephadex G-100 and diethylaminoethyl-cellulose. The molecular weight was estimated by gel filtration to be 60,000. A small amount of the enzyme was further purified by polyacrylamide gel electrophoresis and shown to be a flavoprotein. The reductase was specific for NADPH in the ferredoxin-dependent reduction of cytochrome c and methyl viologen diaphorase reactions; furthermore, NADP(+) was the acceptor of preference when the electron donor was photoreduced ferredoxin. The reductase also has an irreversible NADPH-NAD(+) transhydrogenase (reduced-NADP:NAD oxidoreductase, EC 1.6.1.1) activity, the rate of which was proportional to the concentration of NAD (K(m) = 5.0 x 10(-3)M). The reductase catalyzed electron transfer from NADPH not only to B. polymyxa ferredoxin but also to the ferredoxins of Clostridium pasteurianum, Azotobacter vinelandii, and spinach chloroplasts, although less effectively. Rubredoxin from Clostridium acidi-urici and azotoflavin from A. vinelandii also accept electrons from the B. polymyxa reductase. The pH optima for the various reactions catalyzed by the B. polymyxa ferredoxin-NADP reductase are similar to those of the chloroplast reductase. NAD and acetyl-coenzyme A, which obligatorily activate NADPH- and NADH-ferredoxin reductases, respectively, in Clostridium kluyveri, have no effect on B. polymyxa reductase.

Four-iron (sulfide) ferredoxin from Bacillus polymyxa

Ferredoxin from Bacillus polymyxa contains (per mole) four non-heme iron residues, four acid-labile sulfide residues, and four cysteine residues. Its molecular weight is approximately 8,800, and it has an oxidation-reduction potential (E(m)) of -390 mv. It is active as an electron carrier in several ferredoxin-linked enzyme systems.

Pyruvate metabolism by a nitrogen-fixing bacterium

1. The major products of pyruvate dissimilation by washed intact cells of Achromobacter N4-B under nitrogen-fixing conditions are acetate and formate. The formation of succinate and isocitrate and the assimilated amino acids requires carbon dioxide fixation. 2. The products formed by cells incubated with pyruvate in an atmosphere of nitrogen were compared with those formed by cells incubated in an atmosphere of helium. Production of hydrogen and the formation of succinate were greater under helium than under nitrogen. Production of acetate and formate and the utilization of pyruvate were the same in both atmospheres. 3. Cell-free preparations, unlike intact cells of Achromobacter N4-B, do not evolve hydrogen, but do produce lactate. 4. It is suggested that, in cell-free preparations incapable of fixing nitrogen, electrons are accepted from pyruvate to form lactate rather than being used for the reductive formation of ammonia and hydrogen.