Large scale MALDI-TOF MS based taxa identification to identify novel pigment producers in a marine bacterial culture collection

A challenge in the rational exploitation of microbial culture collections is to avoid superfluous testing of replicas. MALDI-TOF MS has been shown to be an efficient dereplication tool as it can be used to discriminate between bacterial isolates at the species level. A bacterial culture collection of more than 10,000 heterotrophic marine bacterial isolates from sea-water surface layers of the Norwegian Trondheimsfjord and neighbouring coastal areas has been established. A sub-collection of pigmented isolates was earlier screened for novel carotenoids with UVA-Blue light absorbing properties. This was a comprehensive analytical task and it was observed that a significant number of extracts with identical pigment profile were recovered. Hence, this study was undertaken to explore the use of MALDI-TOF MS as a dereplication tool to quickly characterize the bacterial collection. Furthermore, LC-DAD-MS analysis of pigment profiles was performed to check if pigment profile diversity was maintained among isolates kept after the potential MALDI-TOF MS selection step. Four hundred isolates comprising both pigmented and non-pigmented isolates were used for this study. The resulting MALDI-TOF MS dendrogram clearly identified a diversity of different taxa and these were supported by the pigment profile clustering, thus linking the pigment production as species-specific properties. Although one exception was found, it can be concluded that MALDI-TOF MS dereplication is a promising pre-screening tool for more efficient screening of microbial culture collection containing pigments with potential novel properties.     

Differences in carotenoid composition among hymenobacter and related strains support a tree-like model of carotenoid evolution

Carotenoids are structurally diverse pigments of biotechnological interest as natural colorants and in the prevention of human disease. The carotenoids present in 19 strains taxonomically related to the poorly described, nonphotosynthetic bacterial genus Hymenobacter, including 10 novel isolates cultivated from Victoria Upper Glacier, Antarctica, were characterized using high-performance liquid chromatography (HPLC). Nine chemically distinct carotenoids, present in various combinations irresolvable by conventional crude spectrophotometric analyses, were purified by preparative HPLC and characterized using UV-visible light absorption spectroscopy and high-resolution mass spectrometry. All major Hymenobacter carotenoids appear to be derived from a common backbone of 2'-hydroxyflexixanthin and include previously unreported presumptive hexosyl, pentosyl, and methyl derivatives. Their distribution does not, however, correlate perfectly with 16S rRNA gene phylogeny. Carotenoid composition, therefore, may be strain specific and does not follow a strictly homogeneous pattern of vertical evolutionary descent.     

Pigments of Rubrobacter radiotolerans

The highly radioresistant Rubrobacter radiotolerans, contains red pigments. Since the pigments could not be extracted by usual methods, a new method was developed in which the pigments were extracted with organic solvents after addition of 10 N KOH to the intact cells, followed by neutralization. These pigments were also extracted after treatment with achromopeptidase, but not with lysozyme. The extracted pigments separated into two main spots by TLC (48.6% and 22.6%), and were confirmed to be carotenoids by chemical tests. The two major pigments had 13 conjugated double bonds as determined from the main maximum wavelength of the light absorption spectra. Their molecular weights were determined to be 740 and 722 by mass spectrometry. The mass spectra of their TMS-derivatives revealed that they contained four and three tertiary OH groups, respectively. Confirming their identical light and IR spectra, these pigments were determined to be bacterioruberin and monoanhydrobacterioruberin, respectively, the characteristic carotenoids of halophilic bacteria. The existence of these pigments in bacteria other than halobacteria provides interesting new evidence on the distribution of these compounds.     

Improvement of carotenoid-synthesizing yeast Rhodotorula rubra by chemical mutagenesis

A mutant Rhodotorula rubra with enhanced carotenoid-synthesizing activity for synthesizing total carotenoids and beta-carotene was obtained by N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis. When co-cultivated with yogurt starter bacteria (Lactobacillus bulgaricus + Streptococcus thermophilus) in whey ultrafiltrate it produced 15.7 mg total carotenoids l(-1) culture fluid or 946 microg total carotenoids g(-1) dry cells of which 71% was beta-carotene. Grown as a monoculture in glucose substrate, the mutant shown 1.4 times lower carotenoid-synthesizing activity, and the relative share of beta-carotene in the total carotenoids was lower (63%). The individual pigments torulene and torularhodin were identified, whose mass fractions were (29% and 7%) and (24% and 4%), respectively, for the mutant grown as a monoculture and as a mixed culture with the yogurt bacteria.     

不产氧光合细菌光合色素的光氧调控机制

[目的]为不产氧光合细菌光合色素研究提供可行的较系统规范的研究方法和数据,揭示固氮红细菌(Rhodobacter azotoformans 134K20)光合色素光氧适应性机制.[方法]采用光谱法和色谱法对光和氧调控下的类胡萝卜素和细菌叶绿素合成代谢进行了研究.[结果]134K20菌株光照好氧时细胞得率最高.光照厌氧时主要合成3黄、1红、1紫、2绿、2蓝9种色素,黄色素大量表达.有氧时红色素大量表达,且启动2种新的红色素和1种新的紫色素表达,而黄色和蓝绿色素则受氧抑制.黑暗好氧主要合成2黄、3红、2紫、1绿、1蓝9种色素,但不同于光照厌氧.光照好氧时黄色素减少到1种,紫色素含量增加,其余同黑暗好氧.[结论]固氮红细菌(Rhodobacter azotoformans 134K20)是通过PpsR调节途径来调节光合基因表达的.黄色和红色素属于类胡萝卜素.黄色素1属于球形烯系列,其余两种黄色素是新的类胡萝卜素组分.红色素为新的球形烯酮组分,3种红色素极性、峰形和峰位差别显著,正己烷能显示其精细结构.紫色为极性较大的细菌脱镁叶绿素,绿色和蓝色为4种极性不同的细菌叶绿素a中间产物.乙醚甲醇法适合类胡萝卜素的提取,丙酮甲醇冰冻研磨法能快速有效完全提取光合色素.溶剂效应可有效鉴别细菌叶绿素a中间产物.     

Phylogenetic Analysis of Microbial Diversity in the Rhizoplane of Oilseed Rape (Brassica napus cv. Westar) Employing Cultivation-Dependent and Cultivation-Independent Approaches

The structure of the microbial rhizoplane community of the important crop plant oilseed rape was studied by using a culture-dependent as well as a culture-independent approach based on 16S rDNA amplification. After isolation of the microbial community from the rhizoplane of oilseed rape (Brassica napus cv. Westar), the collected suspension was divided into two parts. One part was used for cultivation of bacteria onto three different growth media to establish a culture collection. From the other part of the rhizoplane suspension, genomic DNA was isolated and purified. Thereafter, 16S rDNA was amplified by PCR and cloned to obtain a library of 16S rDNA genes representative for the bacterial communities of this habitat. Phylogenetic 16S rDNA sequence analysis of 103 clones of this library revealed considerable differences from the corresponding nucleotide sequences of 111 cultured bacteria. Whereas the 16S rDNA clone library was dominated by a-Proteobacteria and bacteria of the Cytophaga-Flavobacterium-Bacteroides (CFB) phylum (51% and 30%, respectively), less than 17% of the cultured bacteria belonged to these two groups. More than 64% of the cultivated isolates were allocated to the b- and g-subclasses of the Proteobacteria, which were present in the clone library at about 14%. Most of the clones of the a-Proteobacteria of the library showed highest similarity to Bradyrhizobium sp. No such bacteria were found in the culture collection. Similarly, the second dominant group of the clone library comprising members of the CFB phylum was represented in the culture collection by a single isolate. The phylogenetic analysis of isolates of the culture collection clearly emphasized the need to use different growth media for recovery of rhizoplane bacteria. Whereas most of the a-Proteobacteria were recovered on complex medium, most of the b-Proteobacteria were isolated onto minimal media. Our results demonstrate that the combined approach pursued in this paper is necessary to explore the biodiversity of bacterial rhizoplane communities.     

Phototrophic purple sulfur bacteria as heat engines in the South Andros Black Hole

Photosynthetic organisms normally endeavor to optimize the efficiency of their light-harvesting apparatus. However, here we describe two bacterial isolates belonging to the genera Allochromatium and Thiocapsa that demonstrate a novel adaptation by optimizing their external growth conditions at the expense of photosynthetic efficiency. In the South Andros Black Hole, Bahamas, a dense l-m thick layer of these anoxygenic purple sulfur bacteria is present at a depth of 17.8 m. In this layer the water temperature increases sharply to 36°C as a consequence of the low-energy transfer efficiency of their carotenoids (ca. 30%). These include spirilloxanthin, and related polyene molecules and a novel chiral carotenoid identified as spirilloxanthin-2-ol, not previously reported in purple bacteria. To our knowledge, this study presents the first evidence of such a bacterial mass significantly increasing the ambient water temperature. The transduction of light to heat energy to excess heat may provide these anoxygenic phototropic bacteria with a competitive advantage over non-thermotolerant species, which would account for their predominance within the microbial layer. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Absence of carotenes and presence of a tertiary methoxy group in a carotenoid from a thermophilic filamentous photosynthetic bacterium Roseiflexus castenholzii.

We identified pigments in a thermophilic filamentous photosynthetic bacterium Roseiflexus castenholzii strain HL08. We detected neither bacteriochlorophyll (BChl) c nor carotenes in this bacterium cultured under the aerobic dark and the anaerobic light conditions, which may correspond to its lack of chlorosomes. In the cells cultured under the aerobic dark conditions, the carotenoids were derivatives of keto-gamma-carotene, and the major ones were methoxy-keto-myxocoxanthin and keto-myxocoxanthin glucoside fatty acid ester. Although the tertiary methoxy group at C-1' and the double bond at C-3',4' in the psi end group of carotenoid, such as spirilloxanthin, have only been found in purple bacteria, this was the first such report in other bacterial groups. The fatty acid moiety was composed of iso fatty acids, which were rare in the cellular lipids. In the cells cultured under the anaerobic light conditions, in addition to these keto-carotenoids, we also found non-oxidized carotenoids (derivatives of gamma-carotene). Concerning the esterifying alcohol of BChl a, we found a substantial amount of geranylgeraniol, although the major component was phytol. The existence of these pigments makes this bacterium unique among the known species in CHLOROFLEXACEAE.     

New evidence for bacterial diversity in the ascoma of the ectomycorrhizal fungus Tuber borchii Vittad

The microbial community associated with ascocarps of the ectomycorrhizal fungus Tuber borchii Vittad. was studied by both cultivation and direct extraction of bacterial 16S rRNA gene (rDNA) sequence approaches. The inner part of six T. borchii ascoma collected in North-Central Italy was used to establish a bacterial culture collection and to extract the total genomic DNA to obtain a library of 16S rDNAs representative of the truffle bacterial community. Most of the isolates were affiliated to the gamma-Proteobacteria, mainly Fluorescent pseudomonads; some isolates were members of the Bacteroidetes group and Gram-positive bacteria, mostly Bacillaceae. The majority of the clones from the library were alpha-Proteobacteria showing significant similarity values, of greater than 97%, with members of the Sinorhizobium/Ensifer Group, Rhizobium and Bradyrhizobium spp. not previously identified as Tuber-associated bacteria. Only a few bacterial strains belonging to this bacterial subclass were found in the culture collection and isolated on a medium specific for Rhizobium-like organisms. A few clones were members of the beta- and gamma-Proteobacteria; as well as low and high G+C Gram-positive bacteria. Our findings clearly indicate that a dual approach increases the information obtained on the structural composition of a truffle bacterial community as compared to that derived via cultivation or direct recovery of 16S rDNA sequences alone.     

一株红假单胞菌的分离及生理特性研究

光合细菌在水处理和水生态修复领域应用前景广阔, 对其生理特性研究具有重要价值。从武汉东湖分离得到一株不产氧光合细菌PUF1, 通过对菌落形态、细胞超微结构、特征吸收光谱以及系统发育等分析, 初步确定为红假单胞菌属(Rhodopseudomonas sp.)紫色非硫光合细菌。PUF1细胞呈直的或稍弯曲的杆状, 长3.05—10.06 μm, 直径0.32—0.68 μm, 具有片层膜结构。PUF1培养物呈深紫红色, 主要色素为细菌叶绿素a (Bchl. a)和类胡萝卜素。初始pH 6.0—8.0, 光照强度500—3000 lx, 稳定期细菌生物量无显著差异, 但培养液pH>8.0会显著抑制PUF1最大光量子产量(F_v/F_m)。试验进一步研究了细菌不同生长阶段粗蛋白含量、ATP酶(ATPase)活性及F_v/F_m的变化规律。结果表明, PUF1不同生长阶段其蛋白含量有所差异, 以稳定期为最高(>60%), 而ATPase活性随培养时间的延长而逐渐降低。此外, PUF1光合作用与其生长状态也有一定的关系, 具体表现为细菌生长周期内F_v/F_m变化规律适用单峰高斯模型, 且以对数期F_v/F_m为最高。研究结果可为光合细菌生理生化特性研究提供重要的参考依据。     

Carotenoid Formation by Staphylococcus aureus

The carotenoid pigments of Staphylococcus aureus U-71 were identified as phytoene; zeta-carotene; delta-carotene; phytofluenol; a phytofluenol-like carotenoid, rubixanthin; and three rubixanthin-like carotenoids after extraction, saponification, chromatographic separation, and determination of their absorption spectra. There was no evidence of carotenoid esters or glycoside ethers in the extract before saponification. During the aerobic growth cycle the total carotenoids increased from 45 to 1,000 nmoles per g (dry weight), with the greatest increases in the polar, hydroxylated carotenoids. During the anaerobic growth cycle, the total carotenoids increased from 20 nmoles per g (dry weight) to 80 nmoles per g (dry weight), and only traces of the polar carotenoids were formed. Light had no effect on carotenoid synthesis. About 0.14% of the mevalonate-2-(14)C added to the culture was incorporated into the carotenoids during each bacterial doubling. The total carotenoids did not lose radioactivity when grown in the absence of (14)C for 2.5 bacterial doublings. The total carotenoids did not lose radioactivity when grown in the absence of (14)C for 2.5 bacterial doublings. The incorporation and turnover of (14)C indicated the carotenes were sequentially desaturated and hydroxylated to form the polar carotenoids.     

Carotenoids of an Antarctic psychrotolerant bacterium, Sphingobacterium antarcticus, and a mesophilic bacterium, Sphingobacterium multivorum

The major carotenoid pigments of an Antarctic psychrotolerant bacterium, Sphingobacterium antarcticus, and a mesophilic bacterium, Sphingobacterium multivorum, were identified as zeaxanthin, beta-cryptoxanthin, and beta-carotene. Analysis was based on ultraviolet-visible spectroscopy, mass spectroscopy, and reversed-phase HPLC. Photoacoustic spectroscopy of intact bacterial cells revealed that the bulk of the pigments in S. antarcticus and S. multivorum was associated with the cell membrane. In vitro studies with synthetic membranes of phosphatidylcholine demonstrated that the major pigment was bound to the membranes and decreased their fluidity. The relative amounts of polar pigments were higher in cells grown at 5 degrees C than in cells grown at 25 degrees C. In the mesophilic strain, the synthesis of polar carotenoids was quantitatively less than that of the psychrotolerant strain.     

Chromatic adaptation in lichen phyco- and photobionts

The effect of light quality on the photosynthetic pigments as chromatic adaptation in 8 species of lichens were examined. The chlorophylls, carotenoids in 5 species with green algae as phycobionts (Cladonia mitis, Hypogymnia physodes, H. tubulosa var. tubulosa and subtilis, Flavoparmelia caperata, Xanthoria parietina) and the chlorophyll a, carotenoids and phycobiliprotein pigments in 3 species with cyanobacteria as photobionts (Peltigera canina, P. polydactyla, P. rufescens) were determined. The total content of photosynthetic pigments was calculated according to the formule and particular pigments were determined by means CC, TLC, HPLC and IEC chromatography. The total content of the photosynthetic pigments (chlorophylls, carotenoids) in the thalli was highest in red light (genus Peltigera), yellow light (Xanthoria parietina), green light (Cladonia mitis) and at blue light (Flavoparmelia caperata and both species of Hypogymnia). The biggest content of the biliprotein pigments at red and blue lights was observed. The concentration of C-phycocyanin increased at red light, whereas C-phycoerythrin at green light.     

Carotenoids present in halotolerant Bacillus spore formers

Six isolates of pigmented spore-forming bacteria were recovered from human faeces from subjects in Vietnam. 16S rRNA analysis demonstrated close association with known pigmented Bacillus species. All isolates were able to tolerate growth on 8% NaCl and were resistant to arsenate, characteristics that make them most related to Bacillus indicus. Two visible pigments were apparent, a yellow pigment found in vegetative cells and an orange pigment found only in spores. We used high-performance liquid chromatography to characterize and quantify these pigments and found them to be carotenoids. The biosynthetic pathway that generates them branches with one that could lead to the spore-associated orange pigmentation. Although these bacteria were found in faeces, the seafood-rich diet of Vietnam and the recovery of other pigmented Bacillus species from seafood and marine environments makes it highly probable that the true origin of these bacteria is from ingested seafood.     

Separation and quantification of pigments from natural phototrophic microbial populations

Abstract A simple high-performance liquid chromatography (HPLC) method is described for the rapid (approx. 20 min) simultaneous separation and identification of the major chlorophylls and carotenoids from phytoplankton cells and phototrophic sulfur bacteria. Lyophilized samples were extracted with acetone in the dark at room temperature. Pigments were eluted from a silica column with a hexane-acetone mixture (80: 20, v/v). About 20 algal and bacterial chlorophyll and carotenoid pigments could be separated in one run. The method allowed for the detection of trace amounts of major carotenoids (> approx. 6 ng · 1⁻¹) and of chlorophylls and pheophytins (> approx. 200 ng · 1⁻¹) in natural samples. The method has been applied to samples from the metalimnion of Lake Vechten (The Netherlands) and has proved very useful in estimating algal and bacterial pigments simultaneously with respect to depth distribution and biomass changes of the microbial populations.     

Production,characterization and antimicrobial activities of bio-pigments by Aquisalibacillus elongatus MB592, Salinicoccus sesuvii MB597, and Halomonas aquamarina MB598 isolated from Khewra Salt Range,Pakistan

Hypersaline ecosystems offer unique habitats to microbial populations capable of withstanding extreme stress conditions and producing novel metabolites of commercial importance. Herein, we have characterized for the first time the production of bioactive pigments from newly isolated halophilic bacterial species. Halophilic bacteria were isolated from Khewra Salt Range of Pakistan. Three distinctly colored isolates were selected for pigment production. Selected colonies were identified as Aquisalibacillus elongatus MB592, Salinicoccus sesuvii MB597, and Halomonas aquamarina MB598 based on morphological, biochemical, and physiological evidences as well as 16S rRNA analysis. The optimum pigment production observed at mesophilic condition, nearly neutral pH, and moderate salinity was validated using response surface methodology. Different analytical techniques (UV spectroscopy, infrared spectroscopy, and HPLC) characterized these purified pigments as derivatives of bacterioruberin carotenoids. Antioxidant activity of pigments revealed up to 85% free-radical scavenging activity at the concentration of 30 µg ml⁻¹. Pigments also showed significant antimicrobial activity against Bacillus subtilis, Bacillus pumilus, Enterococcus faecalis, Bacillus cereus, Klebsiella pneumoniae, Alcaligenes faecalis, Pseudomonas geniculata, Enterococcus faecium, Aspergillus fumigatus, Aspergillus flavus, Fusarium solani, and Mucor spp., suggesting potential biomedical applications.

     

Profiling and Quantitation of Bacterial Carotenoids by Liquid Chromatography and Photodiode Array Detection

An analytical method for the profiling and quantitative determination of carotenoids in bacteria is described. Exhaustive extraction of the pigments from four selected bacterial strains required treatment of the cells with potassium hydroxide or liquefied phenol or both before the addition of the extracting solvent (methanol or diethyl ether). The carotenoids in the extracts were separated by nonaqueous reversed-phase liquid chromatography in conjunction with photodiode array absorption detection. The identity of a peak was considered definitive only when both its retention time and absorption spectrum, before and after chemical reactions, matched those of a reference component. In the absence of the latter, most peaks could be tentatively identified. Two examples illustrate how in the analysis of pigmented bacteria errors may result from using nonchromatographic procedures or liquid chromatographic methods lacking sufficient criteria for peak identification. Carotenoids of interest were determined quantitatively when the authentic reference substance was available or, alternatively, were determined semiquantitatively.     

产生辅酶Q10的光合细菌菌株的分离及鉴定

对水塘污泥中富集分离的13株光合细菌产生的CoQ10进行定性定量分析,筛出CoQ10含量较高的菌株2c并对其进行系统鉴定。菌株2c为革兰氏阴性菌,细胞杆状,菌体大小0.6μm～0.9μm×1.2μm～2.0μm,单极生鞭毛,片层状光合内膜,位于细胞质膜下并与之平行。光照厌氧或黑暗好氧条件下均可生长,光照下菌体产生红色素,菌体含有细菌叶绿素a和类胡萝卜素。最适生长温度30～35℃,pH7.0～8.0。多种有机化合物均可作为光合作用的电子供体和碳源,蛋白胨和硫酸铵是其生长的较好氮源,酵母膏对其生长有明显刺激作用。16S rDNA序列系统发育分析表明,菌株2c在系统进化树上与GenBank中序列号为AY751758、DQ001155、DQ001158的沼泽红假单胞菌聚为一族。菌株2c至少能稳定传代15次。初步确定菌株2c为沼泽红假单胞菌。     

The distribution and drivers of microbial pigments in the cryoconite of four Tibetan glaciers

Microbial pigments play a significant role in glacier albedo reduction, thereby contributing to accelerated glacier retreat. The Tibetan Plateau has experienced rapid glacier retreat in recent decades due to global warming, yet there is limited understanding of microbial pigment distribution in the region. Here, we investigated the pigment concentration and composition in cryoconite from four glaciers. Our results showed that chlorophylls were the dominant pigments in Palong No. 4 (PL) and Jiemayangzong (JMYZ) glaciers located in the south of the Tibetan Plateau, while carotenoids were dominant in Qiangyong (QY) and Tanggula (TGL) glaciers located in the central region. Additionally, the chlorophyll b to chlorophyll a ratio, which is an indicator of the algae-to-cyanobacteria ratio, was higher in PL and JMYZ compared to QY and TGL. By using Random Forest Regression and Structural Equation Modelling, we determined that the concentrations of chlorophyll a, chlorophyll b, and carotenoids were associated with autotrophic bacteria relative abundance, climatic factors, and a combination of bacterial and climatic factors, respectively. This study is the first to describe the distribution of microbial pigments in cryoconite from Tibetan glaciers, providing additional support on the influence of algal pigment on glacier retreat.