Plant Growth Promoting Bacteria from Cow Dung Based Biodynamic Preparations

Indigenous formulations based on cow dung fermentation are commonly used in organic farming. Three biodynamic preparations viz., Panchagavya (PG), BD500 and ‘Cow pat pit’ (CPP) showed high counts of lactobacilli (10⁹ ml⁻¹) and yeasts (10⁴ ml⁻¹). Actinomycetes were present only in CPP (10⁴ ml⁻¹) and absent in the other two. Seven bacterial isolates from these ferments were identified by a polyphasic approach: Bacillus safensis (PG1), Bacillus cereus (PG2, PG4 PG5), Bacillus subtilis (BD2) Lysinibacillus xylanilyticus (BD3) and Bacillus licheniformis (CPP1). This is the first report of L. xylanilyticus and B. licheniformis in biodynamic preparations. Only three carbon sources—dextrose, sucrose and trehalose out of 21 tested were utilized by all the bacteria. None could utilize arabinose, dulcitol, galactose, inositol, inulin, melibiose, raffinose, rhamnose and sorbitol. All the strains produced indole acetic acid (1.8–3.7 μg ml⁻¹ culture filtrate) and ammonia. None could fix nitrogen; but all except B. safensis and B. licheniformis could solubilize phosphorous from insoluble tri-calcium phosphate. All the strains except L. xylaniliticus exhibited antagonism to the plant pathogen Rhizoctonia bataticola whereas none could inhibit Sclerotium rolfsi. In green house experiment in soil microcosms, bacterial inoculation significantly promoted growth of maize; plant dry weight increased by ~21 % due to inoculation with B. cereus (PG2). Results provide a basis for understanding the beneficial effects of biodynamic preparations and industrial deployment of the strains.

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The online version of this article (doi:10.1007/s12088-014-0468-6) contains supplementary material, which is available to authorized users.     

Culturable Airborne Bacteria in Outdoor Environments in Beijing,China

Airborne bacteria are important biological components of bioaerosol and play an important role in ecosystem. Bacteria at a high concentration in the atmosphere can result in biological air pollution and all kinds of diseases. In this study, a systematical survey on the culturable airborne bacteria was carried out for 1 year at three sites in Beijing urban area. Results showed that concentrations of culturable bacteria ranged from 71 colony forming units (CFU)/m³ to 22,100 CFU/m³, and the mean was 2,217 CFU/m³. Bacterial concentrations at the human activity-enriched site (RCEES) and the highly trafficked site (XZM) were virtually the same point. They were significantly higher than those at the greener site (BBG). Significant variation in bacterial concentrations in different seasons was observed at RCEES and XZM with higher concentrations in summer and autumn. In a single day, significantly lower concentrations were detected at 13:00 hours through all sampling sites. In this study, 165 species in 47 genera of culturable bacteria were identified. Micrococcus was one of the most dominant bacterial groups and contributed to approximately 20∼30% of the total bacterial concentration, followed by Staphylococcus, Bacillus, Corynebacterium, and Pseudomonas. The bacterial species with a high concentration percentage included Micrococcus luteus and Micrococcus roseus.     

Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo,Tibet Autonomous Region

The soil bacterial communities have been widely investigated. However, there has been little study of the bacteria in Qinghai-Tibet Plateau, especially about the culturable bacteria in highland barley cultivation soil. Here, a total of 830 individual strains were obtained at 4°C and 25°C from a highland barley cultivation soil in Qamdo, Tibet Autonomous Region, using fifteen kinds of media. Seventy-seven species were obtained, which belonged to 42 genera and four phyla; the predominant phylum was Actinobacteria (68.82%), followed by Proteobacteria (15.59%), Firmicutes (14.29%), and Bacteroidetes (1.30%). The predominant genus was Streptomyces (22.08%, 17 species), followed by Bacillus (6.49%, five species), Micromonospora (5.19%, four species), Microbacterium (5.19%, four species), and Kribbella (3.90%, three species). The most diverse isolates belonged to a high G+C Gram-positive group; in particular, the Streptomyces genus is a dominant genus in the high G+C Gram-positive group. There were 62 species and 33 genera bacteria isolated at 25°C (80.52%), 23 species, and 18 genera bacteria isolated at 4°C (29.87%). Meanwhile, only eight species and six genera bacteria could be isolated at 25°C and 4°C. Of the 77 species, six isolates related to six genera might be novel taxa. The results showed abundant bacterial species diversity in the soil sample from the Qamdo, Tibet Autonomous Region.     

Isolation and Molecular Characterization of Heavy Metal-Resistant Azotobacter chroococcum from Agricultural Soil and Their Potential Application in Bioremediation

Pollution of soil with heavy metals, herbicides, antibiotics and other chemicals is known to have a negative effect on microbial activities. Therefore, the aim of this study was to isolate cultures of Azotobacter sp. from polluted and unpolluted soils and to study the effect of these pollutants on their growth. A total of 120 Azotobacter sp. were isolated from soils irrigated with wastewater (contaminated soils) and groundwater (uncontaminated soils). These isolates were screened for resistance to heavy metals, herbicide and antibiotics. Also, the soils from which the cultures were isolated were analyzed for the concentrations of Zn²⁺, Cd²⁺, Cu²⁺, Pb²⁺ and Mn²⁺ they contained. Contaminated soil showed high levels of heavy metals as compared to uncontaminated soil. The size of the Azotobacter population in contaminated soil was lower than that in uncontaminated soil. Of the Azotobacter isolates, 64 that were recovered from contaminated soil exhibited high resistance to heavy metals (Hg²⁺, Cd²⁺, Cu²⁺, Cr³⁺, Co²⁺, Ni²⁺, Zn²⁺ and Pb²⁺) and herbicide 2,4-D compared to 56 isolates from uncontaminated soil. Also, isolates from contaminated soil showed high resistance to chloramphenicol, nitrofurantoin and co-trimoxazole compared to those isolated from uncontaminated soil. The majority of Azotobacter isolates from contaminated soil showed multiple-resistance to different metal ions and antibiotics. All isolates failed to grow at pH less than 6. Salt concentration (5%) was found to be inhibitory to all isolates. The most potent isolates from contaminated soil that showed multiresistance to all substances tested were identified on the basis of morphological and biochemical characteristics, and 16S rRNA as A. chroococcum. These resistant isolates could be employed in contaminated soils and/or bioremediation.     

玉米根际高效溶磷菌的筛选、鉴定及促生效应研究

为获得玉米根际高效溶磷促生菌(Plant growth-promoting rhizobacteria,PGPR)并明确其促生特性,采用选择培养方法从玉米根际土壤筛选出优良PGPR 菌株,测定其溶磷及分泌吲哚乙酸(IAA)的能力,并对优良菌株进行鉴定;采用盆栽试验研究菌株的促生作用。结果分离到2 株优良PGPR 菌株CH07和FD11,其溶磷量分别为368.5 mg/L和321.5 mg/L,产IAA量分别为30.93 mg/L和15.93 mg/L。形态学特征、生理生化特征和16S rDNA 序列分析结果表明,CH07为芽孢杆菌属(Bacillus aryabhattai),FD11为链霉菌属(Streptomyces maritimus)。最后通过盆栽试验对这2株细菌分离物的促生效果进行比较,结果发现,CH07、FD11,尤其是CH07与FD11的复合物,对苋菜的株高及地上部鲜重有积极作用,可作为研制生物肥料的优良菌株资源。     

大莲湖池杉林湿地土壤可培养细菌的分离与鉴定

采用牛肉膏蛋白胨培养基培养,从大莲湖池杉林土壤中共分离得到20个菌落形态不同的菌株。通过对这些菌株的形态、培养特征、生理生化特征的研究以及16S rDNA序列分析,初步确定这些菌株分别属于假单胞菌属(Pseudomonas)、芽胞杆菌属(Bacillus)、红球菌属(Rhodococcus)、北里孢菌属(Kitasatosporia)、金黄杆菌属(Chryseobacterium)、不动杆菌属(Acinetobacter)、黄杆菌属(Flavobacterium)、鞘氨醇杆菌属(Sphingobacte-rium)和丛毛单胞菌属(Comamonas)等9个属细菌。其中芽胞杆菌属和不动杆菌属细菌是优势菌,分离到的红球菌属、北里孢菌属、鞘氨醇杆菌属和丛毛单胞菌属细菌在国内湿地土壤中报道较少。     

Whole Genome Sequencing and Analysis of Plant Growth Promoting Bacteria Isolated from the Rhizosphere of Plantation Crops Coconut,Cocoa and Arecanut

Coconut, cocoa and arecanut are commercial plantation crops that play a vital role in the Indian economy while sustaining the livelihood of more than 10 million Indians. According to 2012 Food and Agricultural organization''s report, India is the third largest producer of coconut and it dominates the production of arecanut worldwide. In this study, three Plant Growth Promoting Rhizobacteria (PGPR) from coconut (CPCRI-1), cocoa (CPCRI-2) and arecanut (CPCRI-3) characterized for the PGP activities have been sequenced. The draft genome sizes were 4.7 Mb (56% GC), 5.9 Mb (63.6% GC) and 5.1 Mb (54.8% GB) for CPCRI-1, CPCRI-2, CPCRI-3, respectively. These genomes encoded 4056 (CPCRI-1), 4637 (CPCRI-2) and 4286 (CPCRI-3) protein-coding genes. Phylogenetic analysis revealed that both CPCRI-1 and CPCRI-3 belonged to Enterobacteriaceae family, while, CPCRI-2 was a Pseudomonadaceae family member. Functional annotation of the genes predicted that all three bacteria encoded genes needed for mineral phosphate solubilization, siderophores, acetoin, butanediol, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinase, phenazine, 4-hydroxybenzoate, trehalose and quorum sensing molecules supportive of the plant growth promoting traits observed in the course of their isolation and characterization. Additionally, in all the three CPCRI PGPRs, we identified genes involved in synthesis of hydrogen sulfide (H₂S), which recently has been proposed to aid plant growth. The PGPRs also carried genes for central carbohydrate metabolism indicating that the bacteria can efficiently utilize the root exudates and other organic materials as energy source. Genes for production of peroxidases, catalases and superoxide dismutases that confer resistance to oxidative stresses in plants were identified. Besides these, genes for heat shock tolerance, cold shock tolerance and glycine-betaine production that enable bacteria to survive abiotic stress were also identified.     

具有ACC脱氨酶活性的绞股蓝内生细菌的分离鉴定及其抑菌促生作用

采用富集筛选法从绞股蓝根中筛选得到6株具有ACC脱氨活性的细菌,其中菌株JDG-6、JDG-7、JDG-14、JDG-16、JDG-23均具有较强的分泌铁载体能力,但菌株JDG-32没有产铁载体能力。抑菌试验结果显示,菌株JDG-6、JDG-7、JDG-14和JDG16对一种或多种供试菌有抑菌作用,其中菌株JDG-14能抑制大肠埃希菌、藤黄八叠球菌和白色念球菌的生长。促生试验表明,菌株JDG-6、JDG-7和JDG-14均能促进水稻幼苗根的伸长,其中菌株JDG-14的促生作用最为明显,与对照组相比水稻幼苗的根长和根鲜重分别增长了26%和21%。通过形态特征观察、生理生化试验以及16S rDNA序列分析,菌株JDG-6、JDG-7、JDG-16和JDG-23属于假单胞杆菌属（Pseudomonas）,菌株JDG-14为木糖葡萄球菌（Staphylococcus xylosus）,而菌株JDG-32为枯草芽胞杆菌（Bacillus subtilis）。菌株JDG-6、JDG-7和JDG-14均具有ACC脱氨酶活性和抑菌活性的促生菌,具有农业应用潜力。     

Genetic Diversity of Plant Growth Promoting Rhizobacteria Isolated from Rhizospheric Soil of Wheat Under Saline Condition

In this study, a total of 130 rhizobacteria was isolated from a saline infested zone of wheat rhizosphere, and screened for plant growth promoting (PGP) traits at higher salt (NaCl) concentrations (2, 4, 6, and 8%). The results revealed that 24 rhizobacterial isolates were tolerant at 8% NaCl. Although all the 24 salt tolerable isolates produced indole-3-acetic acid (IAA), while 10 isolates solubilized phosphorus, eight produced siderophore, and six produced gibberellin. However, only three isolates showed the production of 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Diversity was analyzed through 16S rDNA-RFLP, and of these isolates with three tetra cutter restriction enzymes (HaeIII, AluI, and MspI), the representative cluster groups were identified by 16S rDNA sequencing. Bacillus and Bacillus-derived genera were dominant which showed PGP attributes at 8% NaCl concentration. Out of 24 isolates, nitrogen fixing ability (nif H gene) was detected in the two isolates, SU18 (Arthrobacter sp.) and SU48.     

Culturable Bacteria in Subglacial Sediments and Ice from Two Southern Hemisphere Glaciers

Viable prokaryotes have been detected in basal sediments beneath the few Northern Hemisphere glaciers that have been sampled for microbial communities. However, parallel studies have not previously been conducted in the Southern Hemisphere, and subglacial environments in general are a new and underexplored niche for microbes. Unfrozen subglacial sediments and overlying glacier ice samples collected aseptically from the Fox Glacier and Franz Josef Glacier in the Southern Alps of New Zealand now have been shown to harbor viable microbial populations. Total direct counts of 2–7 × 10⁶ cells g^–1 dry weight sediment were observed, whereas culturable aerobic heterotrophs ranged from 6–9 × 10⁵ colony-forming units g^–1 dry weight. Viable counts in the glacier ice typically were 3–4 orders of magnitude smaller than in sediment. Nitrate-reducing and ferric iron–reducing bacteria were detected in sediment samples from both glaciers, but were few or below detection limits in the ice samples. Nitrogen-fixing bacteria were detected only in the Fox Glacier sediment. Restriction fragment analysis of 16S rDNA amplified from 37 pure cultures of aerobic heterotrophs capable of growth at 4°C yielded 23 distinct groups, of which 11 were identified as -Proteobacteria. 16S rDNA sequences from representatives of these 11 groups were analyzed phylogenetically and shown to cluster with bacteria such as Polaromonas vacuolata and Rhodoferax antarcticus, or with clones obtained from permanently cold environments. Chemical analysis of sediment and ice samples revealed a dilute environment for microbial life. Nevertheless, both the sediment samples and one ice sample demonstrated substantial aerobic mineralization of ¹⁴C-acetate at 8°C, indicating that sufficient nutrients and viable psychrotolerant microbes were present to support metabolism. Unfrozen subglacial sediments may represent a significant global reservoir of biological activity with the potential to influence glacier meltwater chemistry.     

Changes in the Weathering Activity and Populations of Culturable Rock-Weathering Bacteria from the Altered Purple Siltstone and the Adjacent Soil

A total of 150 bacteria were isolated from the less and more altered (weathered) purple siltstones and the adjacent soils to compare the changes in the rock weathering patterns and populations of rock-weathering bacteria. The proportions of the highly effective Fe and Si solubilizers were significantly different among the altered rocks and soils. Maximum proportions of the highly effective Fe, Si, and Al solubilizers were observed in the soils, while significantly higher proportion of the highly effective K solubilizers was observed in the more altered rocks and the soils. The rock-weathering bacteria belonged to 37 bacterial species, among which 36, 64, and 56% of the species were specific to the less and more altered rocks and the soils, respectively. In the rock-weathering process, strains M78 and L38 mainly produced acetic acid, while strain H28 mainly produced gluconic acid. Furthermore, dominant rock-weathering members of Ensifer genus had the higher ability to release Fe and Si, while dominant rock-weathering members of Bacillus had the higher ability to release K. The results suggest the changes in the element mobilization patterns and populations of the rock-weathering bacteria and highlight the possible role of these bacteria in the rock weathering and soil formation.     

Inoculation of Cucumber (Cucumis sativus L.) Seedlings with Salt-Tolerant Plant Growth Promoting Bacteria Improves Nutrient Uptake,Plant Attributes and Physiological Profiles

Journal of Plant Growth Regulation - Salinity is one of the major abiotic stresses that cause retarded plant growth and crop production. It has been reported that harmful effects of salinity could...     

Survey of Plant Drought-Resistance Promoting Bacteria from Populus euphratica Tree Living in Arid Area

Two hundred and thirty-two bacterial strains were isolated from the rhizospheric soil of Populus euphratica which is the dominant tree living in extreme arid regions in northwest China. Some strains with plant growth-promoting bacteria related metabolic characteristics were able to promote drought resistance in plants after inoculation. Ten strains with the greatest effects increased the dry weight of wheat shoots from 0.5 to 34.4 %, and the surface area of the root systems from 12.56 to 212.17 % compared to the control after drought treatment whereas no obvious promoting effect was observed in normal water conditions. These 10 strains were identified to be of the genera Pseudomonas, Bacillus, Stenotrophomonas and Serratia by 16S rRNA (rrs) gene sequence alignment. Among these strains, Serratia sp. 1-9 and Pseudomonas sp. 5-23 were the two most effective strains. Both of them produced auxin and the production increased significantly when cultured under simulated drought conditions which are inferred to be the most plausible mechanism for their plant growth-promoting effect under drought stress.

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The online version of this article (doi:10.1007/s12088-014-0479-3) contains supplementary material, which is available to authorized users.     

Novel Hyper Antimony-Oxidizing Bacteria Isolated from Contaminated Mine Soils in China

Antimony (Sb)-oxidizing bacteria play an important role in environmental Sb bioremediation because of their ability to convert the more toxic Sb(III) to the less toxic Sb(V). So far, the information about the Sb(III)-oxidizing bacteria species is still limited. In this study, three highly Sb(III)-resistant bacterial strains were isolated from contaminated mine soils after aerobic enrichment culturing with Sb(III) (1 mM). The morphological, biochemical, and 16S rRNA gene sequencing analysis suggested that the three novel bacterial isolates fell within Cupriavidus, Moraxella, and Bacillus, respectively. Among the strains, Moraxella sp. S2 isolated from soils with the highest Sb content exhibited the highest minimum inhibitory concentration for Sb(III) but the lowest Sb(III) oxidation efficiency, which could not completely oxidize 50 μM Sb(III) in 15 days. Cupriavidus sp. S1 was able to oxidize 50 μM Sb(III) completely in 12 days, but could not oxidize 100 μM Sb(III) even with extended time of incubation, while Bacillus sp. S3 with the lowest resistance to Sb(III) could aerobically oxidize 100 µM Sb(III) within 2 days, showing high Sb(III) oxidation efficiency. Our research demonstrated that indigenous microorganisms associated with Sb mine soils were capable of Sb oxidation, and the novel bacteria isolated could represent good candidates for Sb remediation in heavily polluted sites.     

Real-Time PCR Quantification of the Plant Growth Promoting Bacteria Herbaspirillum seropedicae Strain SmR1 in Maize Roots

The plant growth promoting bacteria Herbaspirillum seropedicae SmR1 is an endophytic diazotroph found in several economically important crops. Considering that methods to monitor the plant–bacteria interaction are required, our objective was to develop a real-time PCR method for quantification of PGPB H. seropedicae in the rhizosphere of maize seedlings. Primer pairs were designed, and their specificity was verified using DNA from 12 different bacterial species. Ten standard curves of qPCR assay using HERBAS1 primers and tenfold serial dilutions of H. seropedicae SmR1 DNA were performed, and PCR efficiency of 91 % and correlation coefficient of 0.99 were obtained. H. seropedicae SmR1 limit of detection was 10¹ copies (corresponding to 60.3 fg of bacterial DNA). qPCR assay using HERBAS1 was used to detect and quantify H. seropedicae strain SmR1 in inoculated maize roots, cultivated in vitro and in pots, harvested 1, 4, 7, and 10 days after inoculation. The estimated bacterial DNA copy number per gram of root was in the range 10⁷–10⁹ for plants grown in vitro and it was around 10⁶ for plants grown in pots. Primer pair HERBAS1 was able to quantify H. seropedicae SmR1, and this assay can be useful for monitoring plant–bacteria interaction.     

Plant Growth Promoting Characterization of Indigenous Azotobacteria Isolated from Soils in Iran

It has been well known that the bacteria of the genus Azotobacter, in addition to the beneficial N₂-fixing activity, are able to improve plant growth by a number of direct and indirect mechanisms. To identify this potential in indigenous azotobacteria, the efficiency of 17 isolates of Azotobacter from the rhizosphere of wheat and barley plants cultivated in salt- and/or drought-affected soils in Iran were evaluated for their ability to dissolve inorganic and organic phosphates, siderophore secretion, indole acetic acid (IAA) production; and protease, chitinase, and ACC deaminase (ACCD) activities. First, they were biochemically characterized and one isolate (strain) was identified by 16S rDNA sequencing. Eight isolates were designated as Azotobacter vinelandii and the remaining isolates were identified as A. chroococcum. All isolates hydrolyzed the organic and inorganic phosphate compounds and effectively produced IAA. Fifteen isolates produced siderophore, but only one isolate showed protease activity which is being reported for the first time in relation to Azotobacter. None of the 17 isolates was capable of producing ACCD or chitinase. However, polymerase chain reaction amplification of the ACCD coding genes, by the use of the gene-specific primers, indicated that not all contain the ACCD gene. The standard screening methods with slight modifications, especially in the case of ACCD assay, were applied. The results showed that the use of specific screening methods, modified according to bacterial nutritional requirements, are the efficient methods for precise evaluation of the plant growth promoting rhizobacteria activity.     

阿尔山不同时期落叶松根际土壤固氮菌的多样性研究

利用传统的细菌分离培养,结合16S rDNA序列分析等方法,对阿尔山地区不同时期落叶松根际可培养固氮菌群落的多样性进行分析,以揭示落叶松根际固氮菌的多样性及群落结构的季节变化规律,为森林生态系统的可持续发展提供理论依据。结果显示:(1)从阿尔山落叶松根际土壤中共计分离纯化细菌菌株112株,分属于14属41种,包括假单胞菌属、伯克氏菌属、根瘤菌属、叶杆菌属、节杆菌属、类芽孢杆菌属、沙雷菌属、欧文菌属、短小杆菌属、芽孢杆菌属、肠杆菌属、不动杆菌属、柄杆菌属、红球菌属;其中优势菌群为假单胞菌属,次优势菌群为叶杆菌属、伯克氏菌属和节杆菌属。(2)季节变化对落叶松固氮菌群的变化有显著影响,表现为4月份和10月份最优势类群为γ-变形菌纲(γ-proteobacteria)中的假单胞菌属,6月份和8月份的最优势类群相同,但组成有所差别,其中6月份优势菌群包括假单胞菌属、短小杆菌属、红球菌属、节杆菌属,8月份的优势菌群为假单胞菌属、不动杆菌属、肠杆菌属、短小杆菌属、红球菌属和节杆菌属。(3)不同时期的物种均匀度指数(McIntosh index)差异显著,8月份最大,4月份最小,变化范围在0.83～1.164之间;物种丰富度指数(Shannon-Wiener index) 6月份和8月份显著高于4月份和10月份;优势度指数(Simpson index) 4月份和10月份显著高于6月份和8月份。研究表明,阿尔山地区落叶松根际微生物的多样性较高,群落相对复杂,分离的14个菌属多为根际促生菌,且不同时期固氮菌的群落组成受季节的影响明显。     

Extraction of Arsenic and Heavy Metals from Contaminated Mine Tailings by Soil Washing

In this study, the soil washing technique has been used to treat mine tailings contaminated heavily with arsenic and heavy metals at Jingok mine, which is one of the abandoned mines in Korea. The results showed that phosphoric acid, citric acid, oxalic acid, and sodium metabisulfite were highly effective in extracting arsenic and heavy metals. Among them, oxalic acid was the most effective (especially for Pb, Cu, and Zn), as even a residual fraction of arsenic was partly extracted. The optimum concentration of washing reagent and the ratio between the mine tailings and washing reagent were found to be 0.5 M and 1:20, respectively. In addition, the extraction kinetics of arsenic and heavy metals was fast, in which the reaction time of 30 minutes was deemed to be a sufficient contact time. From the results, it may be concluded that the low pH of washing solution and the amount of dissolved Fe may be considered as the most important factors in the extraction of arsenic and heavy metals.