Hydrogen and polyhydroxybutyrate producing abilities of microbes from diverse habitats by dark fermentative process

Thirty five bacterial isolates from diverse environmental sources such as contaminated food, nitrogen rich soil, activated sludges from pesticide and oil refineries effluent treatment plants were found to belong to Bacillus, Bordetella, Enterobacter, Proteus, and Pseudomonas sp. on the basis of 16S rRNA gene sequence analysis. Under dark fermentative conditions, maximum hydrogen (H₂) yields (mol/mol of glucose added) were recorded to be 0.68 with Enterobacter aerogenes EGU16 followed by 0.63 with Bacillus cereus EGU43 and Bacillus thuringiensis EGU45. H₂ constituted 63–69% of the total biogas evolved. Out of these 35 microbes, 18 isolates had the ability to produce polyhydroxybutyrate (PHB), which varied up to 500 mg/l of medium, equivalent to a yield of 66.6%. The highest PHB yield was recorded with B. cereus strain EGU3. Nine strains had high hydrolytic activities (zone of hydrolysis): lipase (34–38 mm) – Bacillus sphaericus strains EGU385, EGU399 and EGU542; protease (56–62 mm) – Bacillus sp. strains EGU444, EGU447 and EGU445; amylase (23 mm) – B. thuringiensis EGU378, marine bacterium strain EGU409 and Pseudomonas sp. strain EGU448. These strains with high hydrolytic activities had relatively low H₂ producing abilities in the range of 0.26–0.42 mol/mol of glucose added and only B. thuringiensis strain EGU378 had the ability to produce PHB. This is the first report among the non-photosynthetic microbes, where the same organism(s) – B. cereus strain EGU43 and B. thuringiensis strain EGU45, have been shown to produce H₂ – 0.63 mol/mol of glucose added and PHB – 420–435 mg/l medium.     

yhcZ基因在苏云金芽胞杆菌生长中的功能研究

在枯草芽胞杆菌和蜡样芽胞杆菌中,yhcZ基因和yhcY基因组成双组分系统调控细菌生长,但yhcZ基因在苏云金芽胞杆菌中发挥的生物学功能尚未明确。本研究通过基因功能注释、上下游基因排列分析和氨基酸序列比对,证实苏云金芽胞杆菌库斯塔克亚种HD73中HD73_5824基因为yhcZ基因,推测其与HD73_5825基因(yhcY基因)共同组成双组份系统调控细菌生长。利用同源重组技术敲除HD73菌株中的yhcZ基因获得缺失突变体HD (ΔyhcZ),其在LB和SSM培养基中生长均慢于野生型HD73,而互补菌株HD(ΔyhcZ::yhcZ)菌株则能够部分恢复生长,表明yhcZ基因的缺失影响了该菌株细胞的生长。在以0.4%葡萄糖为唯一碳源的M9培养基中,HD (ΔyhcZ)生长速度快于HD73,表明yhcZ基因在该菌株吸收利用葡萄糖的过程中发挥重要作用。Biolog实验显示HD (ΔyhcZ)的单孔颜色变化率低于HD73,且对D/L-丝氨酸、甲酸、D-葡糖酸、L-组胺,D-乳酸甲酯以及柠檬酸等的吸收利用能力低于HD73,表明yhcZ基因能显著影响HD73菌株对碳源的利用。同时,HD(ΔyhcZ)对8% NaCl的耐受能力弱于HD73,表明该基因可能参与细菌细胞应力响应相关基因的表达与调控。以上结果表明yhcZ基因在HD73菌株生长过程中对葡萄糖及其他碳源的利用具有重要的促进作用。本研究结果为解析yhcZ基因调控葡萄糖及碳源利用的分子机制奠定基础,且为进一步研究细菌生长及发酵提供参考。     

Enhanced stability of the cloned Bacillus subtilis alkaline protease gene in alginate-immobilized B. subtilis cells

Expression and stability of the cloned Bacillus subtilis alkaline protease (aprE)gene was monitored throughout the growth of free and alginate-immobilized B. subtilis cells. The time as well as the level of expression of the aprE gene in alginate-immobilized cells was found to be close to that of free cells. The multicopy plasmid that carries the aprE gene was stably maintained in alginate-immobilized cells. Plasmid stability was greatly enhanced, it reached 83% and 8% after ten growth cycles for alginate-immobilized and free cells in the absence of stress, respectively. Data presented demonstrate that immobilization of B. subtilis recombinant cells would partially solve the problem of plasmid instability in B. subtilis.     

Natural occurrence of Bacillus thuringiensis and Bacillus cereus in eukaryotic organisms: a case for symbiosis

Bacillus thuringiensis and Bacillus cereus, two members of the Bacillus cereus sensu lato group, are most noted for their virulence in, respectively, arthropods and mammals including humans. Because of their pathogenicity to insects in particular, and their narrow host range, strains of B. thuringiensis have been utilised successfully as biocontrol agents of insect pests. Whereas B. cereus is not an established entomopathogen, certain strains of this species are well known to be etiological agents of gastrointestinal and emetic syndromes in humans. While much is known about the taxonomic properties and molecular basis for virulence of B. thuringiensis and B. cereus, comparatively less is known about their ecology in natural environments. Thus, there are limited data regarding their resilience, i.e. recycling of vegetative and sporulated phases of growth in soil, ecolgical niches including symbiotic interactions with other organisms, and the impact on ecosystems in which they proliferate. Nevertheless, based on recent data, a picture is beginning to emerge that B. thuringiensis and B. cereus are capable of establishing mutual and commensal relationships with both animals and plants. In this regard, these bacilli can proliferate in the digestive tracts of animals, where upon defecation they form dormant spores in the soil, and to a lesser extent on the phylloplane and rhizospheres of plants. Altogether, current evidence strongly suggests that B. thuringiensis and B. cereus are capable of completing their life cycles and recycling through various reservoirs, including animals, plants, and soil. This review focuses on the current knowledge pertaining to the ecologic interactions between B. thuringiensis and B. cereus and eukaryotic hosts, with special emphasis on symbiosis.     

Isolation of the epidermal growth factor from the shrew submaxillary gland

Entomocidal crystals produced by Bacillus thuringiensis ssp. israelensis are formed by two proteins with molecular masses of 130 and 28 kDa, whereas the protein with a molecular mass of 70 kDa appears as a result of 130 kDa protein limited proteolysis by admixtures of bacterial proteinases in the course of its dissolution. The comparison of the N-terminal sequences of the protein with molecular mass of 70 kDa (Met-Glu-Asn-Xaa-Pro-Leu-Asp-Thr-Leu-Ser-Ile-Val-Asn-Glu-Thr-Asp) and that of 28 kDa (Met-Glu-Asn-Leu-Asn-[Phe]-[Trp]-Pro-Leu-Gln-Asp-Ile-Lys-Val-Asn-Pro) reveals only marginal similarity between them (only 4 identical residues among 16 aligned). Both B. thuringiensis israelensis crystal-forming proteins appear hardly related to those contained in the crystal produced by other B. thuringiensis subspecies, e.g. kurstaki. It might be concluded that at least some of the entomocidal proteins found in the crystalline inclusion bodies of various B. thuringiensis subspecies revealed rather strong variations in their primary structures that facilitate their adaptation to different hosts.

Bacillus thuringiensis ssp. israelensis δ-Endotoxin Entomocidal crystal Insecticide Mosquito     

Expression of human dihydrofolate reductase cDNA and its induction by chloramphenicol in Bacillus subtilis

A bifunctional plasmid (pMP358) able to replicate and to express cloned human dihydrofolate reductase cDNA (cDHFR) in both Escherichia coli and Bacillus subtilis was constructed. The expression of cDHFR in B. subtilis was the result of a deletion that placed the cDNA fragment under the control of the chloramphenicol acetyltransferase (CAT) gene promoter of Staphylococcus aureus plasmid pC194. By sequence analysis of plasmid pMP358, we observed a gene fusion occurring between the cDHFR and the 32nd codon of the CAT gene. We report that such a “hybrid” gene is able to direct the synthesis of a 25-kDal “hybrid” protein, which was found to be inducible by supplementing B. subtilis cells with sublethal doses of chloramphenicol.     

武夷山自然保护区土壤可培养芽胞杆菌 的物种多样性及分布

为了解武夷山自然保护区土壤中可培养芽胞杆菌的分布状况, 2012年6月从该保护区的黄岗山顶部、中部、底部和桐木关、挂墩、大竹岚等6个地点采集土样75份。用80℃水浴加热、稀释平板法进行芽胞杆菌的分离, 并根据16S rRNA基因序列分析对菌株进行初步鉴定。从土样中分离出芽胞杆菌418株, 鉴定为8个属42个种, 其中Bacillus属的种数最多, 有20种, Paenibacillus属和Lysinibacillus属分别有8种和7种。不同地点分离到的芽胞杆菌在种类、数量上存在差异: 从大竹岚土壤中分离到的芽胞杆菌种类最多, 从黄岗山中部和底部分离到的种类数则较少; 挂墩、大竹岚土壤中芽胞杆菌的数量较大, 达3.6×10⁶ cfu/g以上, 而黄岗山顶部和中部土壤中的数量则少于4.9×10⁵ cfu/g。Bacillus cereus、B. mycoides、B. thuringiensis和Lysinibacillus xylanilyticus等4个种在6个地点的土样中均有分离到, 其中B. thuringiensis、L. xylanilyticus是该保护区土壤中的优势种。桐木关土壤中芽胞杆菌的种类多样性和均匀度指数都比其他5个地点的高, 而挂墩土壤中芽胞杆菌的Shannon-Wiener多样性、均匀度和优势度指数都最低。B. mycoides和B. thuringiensis的数量与海拔显著相关, 相关系数分别为0.852和-0.834, B. cereus、B. mycoides、B. thuringiensis的分离频度与海拔的相关性极显著, 相关系数分别为0.960、0.952和-0.931。研究结果表明, 武夷山自然保护区土壤中可培养芽胞杆菌的种类丰富、数量较大, 具有较高的多样性。     

Cloning, sequencing, and expression of the meso-diaminopimelate dehydrogenase gene from Bacillus sphaericus

The gene encoding the meso-diaminopimelate dehydrogenase of Bacillus sphaericus was cloned into E. coli cells and its complete DNA sequence was determined. The meso-diaminopimelate dehydrogenase gene consisted of 978 nucleotides and encoded 326 amino acid residues corresponding to the subunit of the dimeric enzyme. The amino acid sequence deduced from the nucleotide sequence of the enzyme gene of B. sphaericus showed 50% identity with those of the enzymes from Corynebacterium glutamicum and Brevibacterium flavum. The enzyme gene from B. sphaericus was highly expressed in E. coli cells. We purified the enzyme to homogeneity from a transformant with 76% recovery. The N-terminal amino acid of both the enzyme from B. sphaericus and the transformant were serine, indicating that the N-terminal methionine is removed by post-translational modification in B. sphaericus and E. coli cells.     

Bacillussubtilis holo-cytochrome c-550 can be synthesised in aerobic Escherichia coli

Bacillus subtilis membrane-bound holo-cytochrome c-550 was found to be expressed from the structural gene cloned on a plasmid vector in aerobically grown Escherichia coli and exhibited normal biochemical properties. This occurs despite the lack of endogenous eytochrome c and suggests that eytochrome c-heme lyase activity is also present in aerobic E. coli. The membrane topology of B. subtilis eytochrome c-550 was studied using fusions to alkaline phosphatase (PhoA). The results show that the heme domain (at least when fused to PhoA) can be translocated as apo-cytochrome and confirm that the N-terminal part of the cytochrome functions as both export signal and membrane anchor for the C-tenninal heme domain. A model for the organisation of B. subtilis cytochrome c-550 in the cytoplasmic membrane is presented.     

台湾地区芽胞杆菌物种多样性

了解芽胞杆菌资源多样性, 可为芽胞杆菌功能资源挖掘和菌剂开发提供基础。从台湾地区8个市(县)采集土壤样本, 从20份土壤样品中分离获得了136株芽胞杆菌, 采用16S rRNA基因同源性将其鉴定为芽胞杆菌科的2个属、20个种。分别属于芽胞杆菌属(Bacillus)的16个种和赖氨酸芽胞杆菌属(Lysinibacillus)的4个种。根据分离频度分析得知, 台湾地区土壤中的芽胞杆菌优势菌群为阿氏芽胞杆菌(Bacillus aryabhattai)、苏云金芽胞杆菌(B. thuringiensis)和蜡样芽胞杆菌(B. cereus), 其他种类分布极其不均匀。芽胞杆菌Shannon多样性指数为1.2925-2.5850, 最高的为台中市和嘉义市(2.5850), 最低的为桃园县(1.2925)。根据分离频度对芽胞杆菌种类的聚类分析显示, 当欧式距离λ = 20时, 芽胞杆菌种类可分为高频度分布类型如阿氏芽胞杆菌(B. aryabhattai), 低频度分布类型如简单芽胞杆菌(B. simplex)。依据分离频度对8个采样点间的聚类分析未发现采样点间的芽胞杆菌种类分布的相关性。本研究认为台湾地区土壤中蕴藏着丰富芽胞杆菌种类多样性高, 具有很大的开发潜力。     

Enantiomeric oxidation of organic sulfides by the filamentous fungi Botrytis cinerea, Eutypa lata and Trichoderma viride

The biotransformations of a series of substituted sulfides were carried out with the filamentous fungi Botrytis cinerea, Eutypa lata and Trichoderma viride. Several products underwent microbial oxidation of sulfide to sulfoxide with medium to high enantiomeric purity. With regard to sulfoxide enantioselectivity, the (R)-enantiomer was favoured in biotransformations by T. viride and E. lata while the (S)-enantiomer was favoured in those by B. cinerea. A minor amount of sulfone product was also obtained.     

Serological diagnostic potential of recombinant outer membrane protein (Omp31) from Brucella melitensis in goat and sheep brucellosis

Outer membrane proteins of Brucella have been classified as group 1 (94 or 88 kDa), group 2 (36–38 kDa), and group 3 (31–34 and 25–27 kDa). Two proteins of 25 and 31 kDa with only 34% of identity are included in group 3 and they are coded for by the omp25 and omp31 genes. Proposed study planned to detect antibodies to Brucella melitensis Omp31 in farm goats having history of B. melitensis induced abortions, in B. melitensis-infected goats and sheep. By enzyme-linked immunosorbent assay (ELISA), using recombinant Omp31 as antigen, of 872 farm goats antibodies to Omp31 were detected in 112 (12.8%) cases. Out of 14 naturally infected goats infected with B. melitensis 12 (85.7%) showed anti Omp31 antibodies. Out of 10 naturally infected sheep with Brucella ovis, antibodies to Omp31 were detected only in 6 (60%) cases and in 18 (81.8%) out of 22 cases infected with B. melitensis. Obtained results were also compared with the rose Bengal plate test (RBPT). In controlled experiments, sensitivity and specificity of recombinant Omp31 (rOmp31) ELISA and RBPT were also evaluated and it was found that former test is 100% specific though RBPT has slightly higher sensitivity. In this study, we found a significant difference between the two groups (B. melitensis and B. ovis infected) in terms of the percentage of positive reactions or signal level by an ELISA. The reactivity of the positive sera against the purified rOmp31 was also tested by Western blotting. Sera from B. melitensis-infected animals showed a strong reactivity in comparison to sera from B. ovis-infected animals. The potential diagnostic usefulness of this antigen in combination with other recombinant proteins from B. melitensis would be of great importance in future in eradication of brucellosis.     

Overexpression of serine alkaline protease encoding gene in Bacillus species: performance analyses

Bacillus species carrying subC gene encoding serine alkaline protease (SAP) enzyme were developed in order to increase the yield and selectivity in the bioprocess for SAP production. For this aim, subC gene was cloned into pHV1431 Escherichia coli–Bacillus shuttle vector, and transferred into nine host Bacillus species, i.e. B. alvei, B. amyloliquefaciens, B. badius, B. cereus, B. coagulans, B. firmus, B. licheniformis, B. sphaericus and B. subtilis. The influence of the host Bacillus species on SAP production on a defined medium with glucose was investigated in bioreactor systems. For each of the recombinant (r-) Bacillus species, effects of initial glucose concentration on cell growth and SAP production were investigated; and, physiological differences and similarities between the wild-type and r-Bacillus species are discussed. The highest biomass concentration was obtained with r-B. coagulans as 3.8 kg m⁻³ at the initial glucose concentration of C_Go=20 kg m⁻³ and the highest volumetric SAP activity was obtained with r-B. amyloliquefaciens as 1650 U cm⁻³ at C_Go=20 kg m⁻³. Overall SAP activity per amount of substrate consumed was the highest for r-B. sphaericus (137 U g⁻¹ cm⁻³) and r-B. licheniformis (130 U g⁻¹ cm⁻³). Among the r-Bacillus species the highest activity increase compared to the wild types was obtained with r-B. sphaericus while the lowest increase was obtained with r-B. amyloliquefaciens and r-B. licheniformis due to high SAP production potential of the wild-type strains. During storage of the host microorganisms, r-B. alvei and r-B. amyloliquefaciens were not able to bear the recombinant plasmid, probably, due to the restriction enzymes synthesized. Due to the highest stable volumetric activities r-B. licheniformis (950 U cm⁻³) and r-B. sphaericus (820 U cm⁻³) appear to be the favorable hosts for the production of SAP. All the r-Bacillus species excreted organic acids oxaloacetic and succinic acids, but, none excreted the amino acid valine. The variations in by-product distributions with each recombinant organism were also discussed.     

Responses of four Brassica species to sodium chloride

Responses in sand culture of four Brassica species, B. campestris, B. carinata, B. juncea and B. napus to NaCl were assessed for growth and yield. B. napus produced significantly greater fresh and dry biomass than the other three species in NaCl treatments and also a higher seed yield in both absolute and relative terms when grown at 125 mol/m³ NaCl. In contrast, B. campestris had the lowest biomass production, seed yield and oil content. B. campestris did not differ significantly from B. juncea and B. carinata in biomass production for growth, but B. carinata had a significantly higher seed yield (1.60 g/plant) than that of B. juncea and B. campestris (0.69 and 0.61 g/plant, respectively). The higher seed yielding species, B. napus (1.74 g/plant) and B. carinata (1.60 g/plant) accumulated lower amounts of Na⁺ and Cl⁻ in their tissues and had significantly higher K selectivity (S_K,Na) in their shoots than did those of B. campestris and B. juncea, B. napus and B. carinata also had higher leaf succulence than that of B. campestris. In view of the results presented here it can be concluded that B. napus and B. carinata are relatively tolerant to NaCl whereas B. campestris and B. juncea are relatively sensitive to NaCl.     

Expression of the tyrosinase-encoding gene in a colorless melanophore mutant of the medaka fish, Oryzias latipes

In the medaka fish Oryzias latipes many mutants for body colors have been isolated. Among them, a colorless melanophore mutant b, carrying b alleles homozygously, has pigmented black eyes but orange-colored skin with amelanotic melanophores, suggesting the presence of a tissue-specific mechanism of melanin formation. To cast light on the molecular basis of the mechanism, we have cloned cDNAs for tyrosinase (Tyr), a key enzyme in melanin biosynthesis, from the wild-type (wt) fish. DNA sequence analysis revealed that all clones encode a protein of 540 amino acids, having five potential glycosylation sites and two copper-binding sites that are characteristic features of Tyr. Genomic DNA blot analysis disclosed that the Tyr gene is present as a single copy in the fish genome. Using a cDNA clone as a probe, RNA blot analysis was carried out. In the wt, the 2.2-kb Tyr mRNA was expressed in eyes and skin but not in liver, corresponding to tissue-specific melanin formation. In the b mutant, contrary to expectation, the mRNA was detected not only in eyes but also in amelanotic skin. Therefore, pigmentation of the skin controlled by b is not directly related to expression of the Tyr gene.     

Sustained expression of keratinase gene under PxylA and PamyL promoters in the recombinant Bacillus megaterium MS941

The ker gene encoding pre-pro keratinase of Bacillus licheniformis MKU3 was cloned with xylose inducible promoter (PxylA) or -amylase promoter (PamyL) or both in Escherichia coli–Bacillus shuttle vector, pWH1520 generating recombinant plasmids pWHK3, pWAK3 and pWXAK3 respectively. Compared with Bacillius megaterium MS941 (pWXAK3) expressing ker gene with PxylA–PamyL promoters, B. megaterium MS941 (pWAK3) with PamyL displayed higher keratinase yield (168.6 U/ml) and specific activity (14.59 U/mg) after 36 h of growth in LB medium, however the keratinase yield decreased in the culture grown in LB medium supplemented with starch or xylose or both. A maximum yield of 186.3 U/ml with specific activity of 17.25 U/mg was obtained from xylose induced keratinase expression in B. megaterium MS941 (pWHK3) grown for 24 h. The recombinant plasmids were stably maintained with sustained expression of keratinase for about 60 generations in B. megaterium MS941 rather than in B. megaterium 14945.     

太白山巴山冷杉林主要树种与开花秦岭箭竹的空间点格局分析

采用单变量和双变量O-ring函数对太白山大熊猫栖息地巴山冷杉林主要树种的空间分布格局、种间关联性及其与林下开花箭竹的空间关联性进行了多尺度分析.结果表明: 巴山冷杉林中,巴山冷杉数量最多,但种群结构衰退,白桦种群相对年轻,种群结构稳定,红桦种群也呈衰退趋势;3个主要树种在小尺度上呈聚集分布,随尺度增加,逐渐表现为随机分布.3个树种的空间关联性主要表现在小尺度范围内,随尺度增加,空间分布格局逐渐表现为不关联;巴山冷杉和白桦与开花秦岭箭竹在大、中尺度内呈现正相关,而红桦与开花秦岭箭竹在大、中尺度上表现出负相关.大熊猫栖息地内乔木和林下秦岭箭竹共同推动森林的动态演替和发展,进而影响秦岭大熊猫栖息地的环境变化.     

Swarming of Pseudomonas aeruginosa is a complex adaptation leading to increased production of virulence factors and antibiotic resistance

In addition to exhibiting swimming and twitching motility, Pseudomonas aeruginosa is able to swarm on semisolid (viscous) surfaces. Recent studies have indicated that swarming is a more complex type of motility influenced by a large number of different genes. To investigate the adaptation process involved in swarming motility, gene expression profiles were analyzed by performing microarrays on bacteria from the leading edge of a swarm zone compared to bacteria growing in identical medium under swimming conditions. Major shifts in gene expression patterns were observed under swarming conditions, including, among others, the overexpression of a large number of virulence-related genes such as those encoding the type III secretion system and its effectors, those encoding extracellular proteases, and those associated with iron transport. In addition, swarming cells exhibited adaptive antibiotic resistance against polymyxin B, gentamicin, and ciprofloxacin compared to what was seen for their planktonic (swimming) counterparts. By analyzing a large subset of up-regulated genes, we were able to show that two virulence genes, lasB and pvdQ, were required for swarming motility. These results clearly favored the conclusion that swarming of P. aeruginosa is a complex adaptation process in response to a viscous environment resulting in a substantial change in virulence gene expression and antibiotic resistance.