Benthic phototrophic community from Kiran soda lake,south-eastern Siberia

Phototrophic bacterial mats from Kiran soda lake (south-eastern Siberia) were studied using integrated approach including analysis of the ion composition of water, pigments composition, bacterial diversity and the vertical distribution of phototrophic microorganisms in the mats. Bacterial diversity was investigated using microscopic examination, 16S rRNA gene Illumina sequencing and culturing methods. The mats were formed as a result of decomposition of sedimented planktonic microorganisms, among which cyanobacteria of the genus Arthrospira predominated. Cyanobacteria were the largest part of phototrophs in the mats, but anoxygenic phototrophs were significant fraction. The prevailing species of the anoxygenic phototrophic bacteria are typical for soda lakes. The mats harbored aerobic anoxygenic phototrophic bacteria, purple sulfur and non-sulfur bacteria, as well as new filamentous phototrophic Chloroflexi. New strains of Thiocapsa sp. Kir-1, Ectothiorhodospira sp. Kir-2 and Kir-4, Thiorhodospira sp. Kir-3 and novel phototrophic Chloroflexi bacterium Kir15-3F were isolated and identified.

     

Coexisting <Emphasis Type="Italic">Curtobacterium</Emphasis> Bacterium Promotes Growth of White-Rot Fungus <Emphasis Type="Italic">Stereum</Emphasis> sp.

White-rot basidiomycetes are the main decomposers of woody biomass in forest ecosystems. Little is known, however, about the interactions between white-rot fungi and other microorganisms in decayed wood. A wood-rotting fungus, Stereum sp. strain TN4F, was isolated from a fruit body, and its coexisting cultivable bacteria were isolated from its substrate; natural white-rot decayed wood. The effects of bacteria on fungal growth were examined by confrontational assay in vitro. A growth-promoting bacterium for this Stereum strain was identified as Curtobacterium sp. TN4W-19, using 16SrRNA sequencing. A confrontational assay revealed that Curtobacterium sp. TN4W-19 significantly promoted the mycelial growth of Stereum sp. TN4F in the direction of the bacterial colony, without direct contact between the mycelium and bacterial cells. This is the first report of a positive interaction between a white-rot fungus and a coexisting bacterial strain in vitro.     

Degradation of O,O-Dimethyl Phosphorodithioate by Thiobacillus thioparus TK-1 and Pseudomonas AK-2

O,O-Dimethyl phosphorodithioate (DMDTP) is an initial breakdown product of organophosphorus pesticides in fields. DMDTP is also released to natural environments by pesticide manufacturers. DMDTP-degrading microorganisms were not known. We isolated two bacteria from activated sludge. One of them, strain TK-1 identified as Thiobacillus thioparus, utilized DMDTP as a sole energy source and produced dimethyl phosphate (DMP) and sulfate. The other, strain AK-2 identified as Pseudomonas sp., utilized DMP as a sole energy and carbon source and degraded DMP to inorganic orthophosphate (P_i). DMDTP was degraded to P_i by the coaction of the two bacteria.     

Polynucleotide Phosphorylase from Acromobacter sp. KR 170-4

Eighty-five strains of bacteria were screened for selection of microorganisms suitable for industrial production of polynucleotides. Among these bacteria, Achromobacter sp. KR 170-4 (ATCC 21942) was found to be rich in polynucleotide Phosphorylase (PNPase) in its “salt-shockate” as compared with the other strains tested. PNPase was purified about 50-fold from the “salt-shockate” of Achromobacter sp. KR 170-4, and properties of the enzyme were elucidated. Optimal pH for reaction was 10.1. Stable pH range at 37°C was between pH 6.5 and 10.5. Optimal temperatures were 46°C for polymerization of ADP or IDP, and 43°C for CDP or UDP. The enzyme was stable below 55°C at pH 9.2. The enzyme required Mn²⁺ rather than Mg²⁺ unlike the other PNPases reported. Optimal concentration of Mn²⁺ was 6 mM.     

The Production of α-Ketoglutaric Acid from Salicylic Acid by Pseudomonas sp.†

Metabolites from salicylic acid by microorganisms were investigated. About eighty strains of bacteria which were able to utilize salicylic acid as a sole source of carbon were isolated from soil and other natural sources.

Among these bacteria, several strains produced a large amount of keto acids in the culture fluid during the cultivation. The acid was isolated from the culture fluid of strain K 102 in crystalline form. The crystal was identified as α-ketoglutaric acid by physicochemical methods. From the taxonomical studies, the isolated bacterial strains K 102 and K 362 were assumed to be Pseudomonas sp.     

Synthetic extreme environments: overlooked sources of potential biotechnologically relevant microorganisms

Synthetic extreme environments like carwash effluent tanks and drains are potential sources of biotechnologically important microorganisms and molecules which have, however, remained unexplored. Using culture‐ and molecular‐based methods, a total of 17 bacterial isolates belonging to the genera Shewanella, Proteus, Paenibacillus, Enterobacter and Citrobacter, Aeromonas, Pseudomonas and Pantoea were identified. Hydrocarbon utilization and enzyme production screening assays showed that Aeromonas sp. CAC11, Paenibacillus sp. CAC12 and Paenibacillus sp. CAC13 and Citrobacter sp. PCW7 were able to degrade benzanthracene, naphthalene and diesel oil, Paenibacillus sp. CAC12 and Paenibacillus sp. CAC13 could produce cellulase enzyme, while Proteus sp. BPS2, Pseudomonas sp. SAS8 and Proteus sp. CAL3 could produce lipase. GC‐MS analysis of bacterial secondary metabolites resulted in identification of 107 different compounds produced by Proteus sp. BPS2, Paenibacillus sp. CAC12, Pseudomonas sp. SAS8, Proteus sp. CAL3 and Paenibacillus sp. CAC13. Most of the compounds identified by both GC‐MS and LC‐MS have previously been determined to have antibacterial, antifungal and/or anticancer properties. Further, microbial metabolites which have previously been known to be produced only by plants or microorganisms found in natural extreme environments were also identified in this study. This research has revealed the immense bioresource potential of microorganisms inhabiting synthetic extreme environments.     

Quantitative Assessment of the Biocidal Activity of Chemicals Using Soil Microbial Associations

Quantitative assessment, using three Pseudomonas sp. strains, of the activity of the microbial biocide Soncid 8101 demonstrated that the values of effective sublethal concentrations (L₅₀) differed by 500% (because of individual variations in the sensitivity of the test strains). The spread of parameters of biocidal activity could be narrowed by using a mixture of microorganisms with high, medium, and weak resistance. A method for quantitative assessment of the activity of microbial biocides was proposed based on the use of natural associations of soil bacteria.     

Atrazine degradation by aerobic microorganisms isolated from the rhizosphere of sweet flag (Acorus calamus L.)

In presented study the capability of microorganisms isolated from the rhizosphere of sweet flag (Acorus calamus) to the atrazine degradation was assessed. Following isolation of the microorganisms counts of psychrophilic bacteria, mesophilic bacteria and fungi were determined. Isolated microorganisms were screened in terms of their ability to decompose a triazine herbicide, atrazine. Our results demonstrate that within the rhizosphere of sweet flag there were 3.8 × 10⁷ cfu of psychrophilic bacteria, 1.8 × 10⁷ cfu of mesophilic bacteria, and 6 × 10⁵ cfu of fungi per 1 g of dry root mass. These microorganisms were represented by more than 20 different strains, and at the first step these strains were grown for 5 days in the presence of atrazine at a concentration of 5 mg/l. In terms of the effect of this trial culture, the bacteria reduced the level of atrazine by an average of about 2–20%, but the average level of reduction by fungi was in the range 18–60%. The most active strains involved in atrazine reduction were then selected and identified. These strains were classified as Stenotrophomonas maltophilia, Bacillus licheniformis, Bacillus megaterium, Rahnella aquatilis (three strains), Umbelopsis isabellina, Volutella ciliata and Botrytis cinerea. Culturing of the microorganisms for a longer time resulted in high atrazine degradation level. The highest degradation level was observed at atrazine concentrations of 5 mg/l for S. maltophilia (83.5% after 15 days of culture) and for Botrytis sp. (82% after 21 days of culture). Our results indicate that microorganisms of the sweet flag rhizosphere can play an important role in the bioremediation of atrazine-contaminated sites.     

Grape marc compost: microbial studies and suppression of soil-borne mycosis in vegetable seedlings

Compost suppression of soil-borne diseases in horticultural crops has been attributed to the activities of antagonistic microorganisms. A great diversity of microorganisms, capable of suppressing pathogens naturally colonize compost. A large number of microbes appeared in microbiological analyses of grape marc compost. Most microorganisms were bacteria. Average percentages were 31% mesophilic and 28% thermophylic bacteria, 16% mesophilic actinomycetes and 20% thermophylic actinomycetes. Only a few mould and yeast morphologies were obtained, 4% and 1% respectively. Antagonist in vitro assays were performed with 432 microbial morphologies isolated from grape marc compost. The microbes isolated were extremely effective antagonists in in vitro assays against all the fungal pathogens tested. Seven microorganisms were selected for further bioassay with Rhizoctonia solani in radish, Fusarium oxysporum f. sp. radicis-cucumerinum in melon, and Phytophthora parasitica in tomato and two microorganisms with Pythium aphanidermatum in cucumber. Those experiments indicate that grape marc compost reduces the severity of Pythium damping-off in cucumber, but does not reduce the severity of Phytophthora root rot in tomato, Fusarium oxysporum f. sp. radicis-cucumerinum in melon and Rhizoctonia solani in radish. Better suppressive effects were not demonstrated by either compost or vermiculite amended with microbes selected from grape marc compost.     

Variation in sessile microflora during biofilm formation on AISI-304 stainless steel coupons

Coupons of stainless steel type AISI-304 were exposed to the industrial cooling system of a petrochemical plant fed by seawater from the Guanabara Bay, Rio de Janeiro, Brazil, in order to study thein situ formation of biofilms. Bacteria, microalgae and fungi were detected on the coupons as soon as 48 h after exposure. Their respective numbers were determined at times 48, 96 and 192 h and over the following 8 weeks. Aerobic, anaerobic and sulfate-reducing bacteria were quantified according to the technique of the most probable number, and fungi by the pour plate technique. The number of microorganisms present in the forming biofilm varied over the experimental period, reaching maximal levels of 14×10¹¹ cells cm^–2, 30×10¹³ cells cm^–2, 38×10¹¹ cells cm^–2 and 63×10⁵ cells cm^–2, respectively, for aerobic bacteria, anaerobic bacteria, sulfate-reducing bacteria and fungi, and the dynamics of this variation depended on the group of microorganisms.Bacillus sp,Escherichia coli, Serratia sp andPseudomonas putrefaciens were identified among the aerobic bacteria isolated. Additionally, microalgae and bacteria of the genusGallionella were also detected. Nonetheless, no evidence of corrosion was found on the stainless steel type AISI-304 coupons over the experimental period.     

Microbial transformations of inorganic sulphur compounds in soil under conditions of heterocontinuous cultivation

Development and activity of the association of the sulphur cycle bacteria, represented byThiobacillus thioparus andDesulfovibrio sp., were followed in chernozem soil continuously supplemented with sodium thiosulphate. The technique of heterocontinuous cultivation made it possible (i) to determine changes in the individual components of microflora involved in successive metabolic steps, their time and space sequence, (ii) to follow changes in the transformations of substrate and formation of metabolic products, and (iii) to reach a steady state in the system. A possible use of this approach for the evaluation of the effect of ecological factors, for modelling microbiological processes of the sulphur cycle, for the investigation of trophic relationships among microorganisms in natural and artificial association and for the evaluation of the geochemical activity of sulphur bacteria is discussed.     

Different co-occurring bacteria enhance or decrease the growth of the microalga Nannochloropsis sp. CCAP211/78

Marine photosynthetic microalgae are ubiquitously associated with bacteria in nature. However, the influence of these bacteria on algal cultures in bioreactors is still largely unknown. In this study, eighteen different bacterial strains were isolated from cultures of Nannochloropsis sp. CCAP211/78 in two outdoor pilot-scale tubular photobioreactors. The majority of isolates was affiliated with the classes Alphaproteobacteria and Flavobacteriia. To assess the impact of the eighteen strains on the growth of Nannochloropsis sp. CCAP211/78, 24-well plates coupled with custom-made LED boxes were used to simultaneously compare replicate axenic microalgal cultures with addition of individual bacterial isolates. Co-culturing of Nannochloropsis sp. CCAP211/78 with these strains demonstrated distinct responses, which shows that the technique we developed is an efficient method for screening the influence of harmful/beneficial bacteria. Two of the tested strains, namely a strain of Maritalea porphyrae (DMSP31) and a Labrenzia aggregata strain (YP26), significantly enhanced microalgal growth with a 14% and 12% increase of the chlorophyll concentration, respectively, whereas flavobacterial strain YP206 greatly inhibited the growth of the microalga with 28% reduction of the chlorophyll concentration. Our study suggests that algal production systems represent a ‘natural’ source to isolate and study microorganisms that can either benefit or harm algal cultures.     

Formation of cadmium sulfide nanoparticles mediates cadmium resistance and light utilization of the deep-sea bacterium Idiomarina sp. OT37-5b

Heavy metal is one of the major factors threatening the survival of microorganisms. Here, a deep-sea bacterium designated Idiomarina sp. OT37-5b possessing strong cadmium (Cd) tolerance was isolated from a typical hydrothermal vent. Both the Cd-resistance and removal efficiency of Idiomarina sp. OT37-5b were significantly promoted by the supplement of cysteine and meanwhile large amount of CdS nanoparticles were observed. Production of H₂S from cysteine catalysed by methionine gamma-lyase was further demonstrated to contribute to the formation of CdS nanoparticles. Proteomic results showed the addition of cysteine effectively enhanced the efflux of Cd, improved the activities of reactive oxygen species scavenging enzymes, and thereby boosted the nitrogen reduction and energy production of Idiomarina sp. OT37-5b. Notably, the existence of CdS nanoparticles obviously promoted the growth of Idiomarina sp. OT37-5b when exposed to light, indicating this bacterium might grab light energy through CdS nanoparticles. Proteomic analysis revealed the expression levels of essential components for light utilization including electron transport, cytochrome complex and F-type ATPase were significantly up-regulated, which strongly suggested the formation of CdS nanoparticles promoted light utilization and energy production. Our results provide a good model to investigate the uncovered mechanisms of self-photosensitization of nonphotosynthetic bacteria for light-to-chemical production in the deep biosphere.     

Cell-to-cell non-conjugative plasmid transfer between Bacillus subtilis and lactic acid bacteria

Bacillus subtilis is a soil-dwelling bacterium that can interact with a plethora of other microorganisms in its natural habitat. Due to the versatile interactions and its ability to form nanotubes, i.e., recently described membrane structures that trade cytoplasmic content between neighbouring cells, we investigated the potential of HGT from B. subtilis to industrially-relevant members of lactic acid bacteria (LAB). To explore the interspecies HGT events, we developed a co-culturing protocol and provided proof of transfer of a small high copy non-conjugative plasmid from B. subtilis to LABs. Interestingly, the plasmid transfer did not involve conjugation nor activation of the competent state by B. subtilis. Moreover, our study shows for the first time non-conjugative cell-to-cell intraspecies plasmid transfer for non-competent Lactococcus lactis sp. cremoris strains. Our study indicates that cell-to-cell transformation is a ubiquitous form of HGT and can be potentially utilized as an alternative tool for natural (non-GMO) strain improvement.     

Fatty Acid Metabolism in Microorganisms

The production of pimelic acid from azelaic acid by microorganisms was studied. About 100 strains of bacteria which were able to utilize azelaic acid as a sole carbon source were isolated from soil and other natural materials. Among these bacteria, several strains produced a large quantity of an organic acid (pimelic acid) from azelaic acid in their culture fluids during the cultivation. The acid was isolated from the culture fluid of strain A133 in crystalline form. The crystal was identified as pimelic acid by physicochemical and biological methods.

From the results of investigations on the morphological and physiological characters, the bacterial strain A133 was assumed to be Micrococcus sp.     

Potential use of endophytic root bacteria and host plants to degrade hydrocarbons

Abstract

Microbe-assisted phytoremediation depends on competent root-associated microorganisms that enhance remediation efficiency of organic compounds. Endophytic bacteria are a key element of the root microbiome and may assist plant degradation of contaminants. The aim of this study was to investigate the application of four hydrocarbon-degrading endophytic strains previously isolated from an oil sands reclamation area. Strains EA1-17 (Stenotrophomonas sp.), EA2-30 (Flavobacterium sp.), EA4-40 (Pantoea sp.), and EA6-5 (Pseudomonas sp.) were inoculated in white sweet clover growing on soils amended with diesel at 5,000, 10,000, and 20,000?mg·kg^?1. Our results indicate that plant growth inhibition caused by diesel fuel toxicity was overcome in inoculated plants, which showed significantly higher plant biomass. Analysis of soil F2 and F3 hydrocarbon fractions also revealed that these soils were remediated by inoculated plants when diesel was applied at 10,000?mg·kg^?1 and 20,000?mg·kg^?1. In addition, quantification of hydrocarbon-degrading genes suggests that all bacterial strains successfully colonized sweet clover plants. Overall, the endophytic strain EA6-5 (Pseudomonas sp.), which harbored hydrocarbon-degrading genes, was the most effective candidate in phytoremediation experiments and could be a strategy to increase plant tolerance and hydrocarbon degradation in contaminated (e.g., diesel fuel) soils.     

Isolation of High Molecular Weight DNA from Marine Sponge Bacteria for BAC Library Construction

Metagenomics is a powerful tool for mining the genetic repositories from environmental microorganisms. Bacteria associated with marine sponges (phylum Porifera) are rich sources of biologically active natural products. However, to date, few compounds are discovered from the sponge metagenomic libraries, and the main reason might be the difficulties in recovery of high molecular weight (HMW) DNA from sponge symbionts to construct large insert libraries. Here, we describe a method to recover HMW bacterial DNA from diverse sponges with high quality for bacterial artificial chromosome (BAC) library construction. Microorganisms concentrated from sponges by differential centrifugation were embedded in agarose plugs to lyse out the HMW DNA for recovery. DNA fragments over 436 kb size were recovered from three different types of sponges, Halichondria sp., Haliclona sp., and Xestospongia sp. To evaluate the recovered DNA quality, the diversity of bacterial DNA comprised in the HMW DNA derived from sponge Halichondria sp. was analyzed, and this HMW DNA sample was also cloned into a shuttle BAC vector between Escherichia coli and Streptomyces sp. The results showed that more than five types of bacterial DNA, i.e., Proteobacteria, Nitrospirae, Cyanobacteria, Planctomycetes, and unidentified bacteria, had been recovered by this method, and an average 100 kb size insert DNA in a constructed BAC library demonstrated that the recovered HMW DNA is suitable for metagenomic library construction.     

芽孢杆菌T3菌株对镉胁迫下蒌蒿生理特性和根际微生物的影响

为探讨镉(Cd)胁迫条件下蒌蒿对促生细菌(PGPB)的响应机制,以芽孢杆菌T3(Bacillus sp.)菌株为对象,通过盆栽试验,研究不同Cd处理水平下芽孢杆菌T3菌株对蒌蒿生长、生理、Cd富集转运以及根际微生物的影响。结果表明:(1)在Cd胁迫条件下,芽孢杆菌T3菌株可显著促进蒌蒿地上部、地下部及总干物质的积累,但对株高和根冠比的影响不明显。(2)芽孢杆菌T3菌株能显著促进Cd胁迫条件下蒌蒿对Cd的富集与转运,相比单一Cd胁迫,蒌蒿地上部生物富集系数(BCF)增加了8.3%~29.3%,地下部BCF减少了6.6%~11.1%,同时转运系数(TF)增加了20.8%~38.3%。(3)在Cd胁迫和芽孢杆菌T3菌株的共同作用下,蒌蒿叶绿素a、叶绿素b和总叶绿素含量明显增加。(4)芽孢杆菌T3菌株使Cd胁迫条件下蒌蒿体内丙二醛(MDA)含量显著减少,超氧化物歧化酶(SOD)、过氧化物酶(POD)和过氧化氢酶(CAT)活性明显增加,可有效抵御由Cd胁迫所产生的氧化伤害。(5)芽孢杆菌T3菌株能显著增加Cd胁迫条件下蒌蒿根际土壤细菌、放线菌数量及微生物总量,可减少蒌蒿根际土壤真菌的数量,但与对照差异不显著。研究表明,在Cd胁迫条件下芽孢杆菌T3菌株对蒌蒿生长、生理和根际土壤微生物环境可产生积极影响,可增强蒌蒿植物对Cd胁迫环境的适应性,从而提高其对Cd的耐受能力。     

Mixed culture hydrogenotrophic nitrate reduction in drinking water

Isolation and identification of the bacteria from a hydrogenotrophic reactor for the denitrification of drinking water revealed that several microorganisms are involved. Acinetobacter sp., Aeromonas sp., Pseudomonas sp. and Shewanella putrefaciens were repeatedly isolated from the hydrogenotrophic sludge and postulated to be of primary importance in the process. Nitrate reduction to nitrite appears to be a property of a diverse group of organisms. Nitrite reduction was found to be stimulated by the presence of organic growth factors. Thus, in a mixed culture, hydrogenotrophic denitrification reactor, NO _inf2 ^sup– formed by NO _inf3 ^sup– -reducers can be converted by true denitrifiers thriving on organic growth factors either present in the raw water, or excreted by the microbial community. Mixotrophic growth also contributes to NO _inf2 ^sup– reduction. Finally, chemolithotrophic bacteria participate in the nitrite to nitrogen gas conversion.Offprint requests to: W. Verstraete.     

Studies on Substances Active on the Behavior of Planarian

Substances which acted on the behavior of planarian were searched for, and two active components were isolated from culture broth of Streptomyces sp. 340. They were identified as trans-3-methylthioacrylic acid (MTAA) and 3-methylthiopropionic acid (MTPA).

It was found that many Streptomyces and some fungi accumulated MTAA, and many Streptomyces, fungi, bacteria and yeasts accumulated MTPA when the microorganisms were grown in the medium containing methionine.