A rapid method for the extraction and analysis of carotenoids and other hydrophobic substances suitable for systems biology studies with photosynthetic bacteria

Wild edible yams from Madagascar: New insights into nutritional composition support their use for food security and conservation

Yams (Dioscorea species) are an important food resource in Madagascar, where both cultivated winged yam (D. alata) and wild edible yams are consumed. However, there is limited knowledge on the nutrient composition of wild edible yams in Madagascar, and on how they compare with the cultivated winged yam. Therefore, in this study, nine wild edible yam species, one with two subspecies from Madagascar (D. bako, D. buckleyana, D. irodensis, D. maciba, D. orangeana, D. pteropoda, D. sambiranensis subsp. bardotiae and subsp. sambiranensis, D. seriflora, and Dioscorea species Ovy valiha), were analyzed for their nutrient composition, compared with cultivated D. alata. They include 6/6 of the most favored wild edible yam species in Madagascar. New nutrient composition data (protein, carbohydrate/starch, energy, lipid, β-carotene, and minerals) are presented for these nine wild edible yam species. The results show that they contain comparable levels of lipids and starch to D. alata, but none are better sources of protein than D. alata. The results show that D. irodensis contains a significantly higher β-carotene content when compared to all other edible yams analyzed, and that D. buckleyana, D. irodensis, and D. sambiranensis subsp. bardotiae have a higher calcium content than cultivated D. alata, while all nine wild edible yam species analyzed contain a higher iron content, compared to cultivated D. alata. The nutrient composition data presented could provide new incentives to conserve wild edible yams and inform on strategies to select Dioscorea species for sustainable cultivation and use, providing opportunities to enhance future food security in Madagascar.

Light intensity defines growth and photopigment content of a mixed culture of purple phototrophic bacteria

Purple bacteria (PPB), anoxygenic photoorganoheterotrophic organisms with a hyper-versatile metabolism and high biomass yields over substrate, are promising candidates for the recovery of nutrient resources from wastewater. Infrared light is a pivotal parameter to control and design PPB-based resource recovery. However, the effects of light intensities on the physiology and selection of PPB in mixed cultures have not been studied to date. Here, we examined the effect of infrared irradiance on PPB physiology, enrichment, and growth over a large range of irradiance (0 to 350 W m−2) in an anaerobic mixed-culture sequencing batch photobioreactor. We developed an empirical mathematical model that suggests higher PPB growth rates as response to higher irradiance. Moreover, PPB adapted to light intensity by modulating the abundances of their phototrophic complexes. The obtained results provide an in-depth phylogenetic and metabolic insight the impact of irradiance on PPB. Our findings deliver the fundamental information for guiding the design of light-driven, anaerobic mixed-culture PPB processes for wastewater treatment and bioproduct valorization.

Qipengyuania pacifica sp. nov., a Novel Carotenoid-Producing Marine Bacterium of the Family Erythrobacteraceae, Isolated from Sponge (Demospongiae), and Antimicrobial Potential of Its Crude Extract

A marine Alphaproteobacterium designated as strain NZ-96T was isolated in February 2021, from a sponge species (Demospongiae) collected in muddy sediments with boulders and old chimneys in Otago/Canterbury Slope, Pacific Ocean, New Zealand. The isolate was found to be Gram-negative, rod-shaped, aerobic, motile, and produced yellow-colored colonies. The isolate was positive for alkaline phosphatase, leucine arylamidase, trypsin, catalase, and oxidase and negative for α-galactosidase and urease. It was resistant to many antibiotics including hygromycin, trimethoprim, spectinomycin, ampicillin, oxytetracycline, cephalosporin, bacitracin, and polymyxin. The 16S rRNA gene-based phylogenetic analyses exhibited that strain NZ-96T belonged to the genus Qipengyuania and showed 98.3–98.8% 16S rRNA gene sequence similarity to its closest relatives. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipid profile consisted of phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, one unknown polar lipid, and three unknown glycolipids. The major fatty acids were C18:1ω12t, C16:0, C16:1ω7c, C17:1ω6c, C16:02-OH, and C14:0 2-OH. Carotenoid were produced. The crude extract showed pronounced activity against Staphylococcus aureus Newman and Bacillus subtilis DSM 10. Pairwise ANI and dDDH values of strain NZ-96T and closely related phylogenetic hits were below the threshold values of 95% and 70%, respectively. Genes for trehalose biosynthesis, aspartate-semialdehyde dehydrogenase, flagellar biosynthesis, fatty acid biosynthesis, and antibiotics resistance were present, which aids in isolate survival in a sea or ocean environment. The DNA G+C content was 60.8% (by genome). Based on data obtained by the polyphasic approach, strain NZ-96T (= DSM 112811T = NCCB 100842T) represents a novel species of the genus Qipengyuania, for which the name Qipengyuania pacifica sp. nov. is proposed.

Alteriqipengyuania abyssalis sp. nov., a Novel Member of the Class Alphaproteobacteria Isolated from Sponge, and Emended Description of the Genus Alteriqipengyuania

A novel Gram-negative, aerobic, motile, lemon-yellow-colored, and non-spore-forming rod-shaped bacterium designated strain NZ-12BT was isolated in February 2021 from a sponge species (Crateromorpha) collected at the southern Kermadec Ridge, Pacific Ocean, New Zealand. Comparative 16S rRNA gene-based analyses indicated that strain NZ-12BT shared 98.58%, 96.44%, 96.23%, and 94.78% 16S rRNA sequence similarity to Alteriqipengyuania lutimaris S-5T, Qipengyuania pelagi UST081027-248T, Qipengyuania citreus RE35F/1T, and Alteriqipengyuania halimionae CPA5T, respectively. The major respiratory quinone was ubiquinone-10(Q-10). The polar lipid profile of NZ-12BT was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyl-N-methyl-ethanolamine, phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, one unknown polar lipid, three unknown phospholipids, and three unknown glycolipids. The major fatty acids of strain NZ-12BT were C18:1ω12t, C16:0, C17:1ω6c, and C14:02-OH. Carotenoids were present. Genome mining analysis revealed a biosynthetic gene cluster encoding for the terpene biosynthesis. Pairwise ANI and dDDH values of strain NZ-12BT and closely related phylogenetic neighbors were below the threshold values of 95% and 70%, respectively. The DNA G+C content was 65.4 mol% (by genome). Based on data obtained by a polyphasic approach, type strain NZ-12BT (=DSM 112810T = NCCB 100841T) represents a novel species of the genus Alteriqipengyuania, for which the name Alteriqipengyuania abyssalis sp. nov. is proposed.

Carotenoid Cocktail Produced by An Antarctic Soil Flavobacterium with Biotechnological Potential

Carotenoids are highly important in pigmentation, and its content in farmed crustaceans and fish correlates to their market value. These pigments also have a nutritional role in aquaculture where they are routinely added as a marine animal food supplement to ensure fish development and health. However, there is little information about carotenoids obtained from Antarctic bacteria and its use for pigmentation improvement and flesh quality in aquaculture. This study identified carotenoids produced by Antarctic soil bacteria. The pigmented strain (CN7) was isolated on modified Luria–Bertani (LB) media and incubated at 4 °C. This Gram-negative bacillus was identified by 16S rRNA analysis as Flavobacterium segetis. Pigment extract characterization was performed through high-performance liquid chromatography (HPLC) and identification with liquid chromatography–mass spectrometry (LC–MS). HPLC analyses revealed that this bacterium produces several pigments in the carotenoid absorption range (six peaks). LC–MS confirms the presence of one main peak corresponding to lutein or zeaxanthin (an isomer of lutein) and several other carotenoid pigments and intermediaries in a lower quantity. Therefore, we propose CN7 strain as an alternative model to produce beneficial carotenoid pigments with potential nutritional applications in aquaculture.

"Candidatus Chlorobium masyuteum," a Novel Photoferrotrophic Green Sulfur Bacterium Enriched From a Ferruginous Meromictic Lake

Anoxygenic phototrophic bacteria can be important primary producers in some meromictic lakes. Green sulfur bacteria (GSB) have been detected in ferruginous lakes, with some evidence that they are photosynthesizing using Fe(II) as an electron donor (i.e., photoferrotrophy). However, some photoferrotrophic GSB can also utilize reduced sulfur compounds, complicating the interpretation of Fe-dependent photosynthetic primary productivity. An enrichment (BLA1) from meromictic ferruginous Brownie Lake, Minnesota, United States, contains an Fe(II)-oxidizing GSB and a metabolically flexible putative Fe(III)-reducing anaerobe. "Candidatus Chlorobium masyuteum" grows photoautotrophically with Fe(II) and possesses the putative Fe(II) oxidase-encoding cyc2 gene also known from oxygen-dependent Fe(II)-oxidizing bacteria. It lacks genes for oxidation of reduced sulfur compounds. Its genome encodes for hydrogenases and a reverse TCA cycle that may allow it to utilize H2 and acetate as electron donors, an inference supported by the abundance of this organism when the enrichment was supplied by these substrates and light. The anaerobe "Candidatus Pseudopelobacter ferreus" is in low abundance (∼1%) in BLA1 and is a putative Fe(III)-reducing bacterium from the Geobacterales ord. nov. While "Ca. C. masyuteum" is closely related to the photoferrotrophs C. ferroooxidans strain KoFox and C. phaeoferrooxidans strain KB01, it is unique at the genomic level. The main light-harvesting molecule was identified as bacteriochlorophyll c with accessory carotenoids of the chlorobactene series. BLA1 optimally oxidizes Fe(II) at a pH of 6.8, and the rate of Fe(II) oxidation was 0.63 ± 0.069 mmol day-1, comparable to other photoferrotrophic GSB cultures or enrichments. Investigation of BLA1 expands the genetic basis for phototrophic Fe(II) oxidation by GSB and highlights the role these organisms may play in Fe(II) oxidation and carbon cycling in ferruginous lakes.

Biotechnological Advances in Lycopene β-Cyclases

Lycopene β-cyclase is one of the key enzymes in the biosynthesis of carotenoids, which catalyzes the β-cyclization of both ends of lycopene to produce β-carotene. Lycopene β-cyclases are found in a wide range of sources, mainly plants and microorganisms. Lycopene β-cyclases have been extensively studied for their important catalytic activity, including for use in genetic engineering to modify plants and microorganisms, as a blocking target for lycopene industrial production strains, and for their genetic and physiological effects related to microorganic and plant biological traits. This review of lycopene β-cyclases summarizes the major studies on their basic classification, functional activity, metabolic engineering, and plant science.

Vegetation affects photoprotective pigments and copepod distribution in the Himalayan lakes: Implication for climate change adaptation

Lakes in the Himalayas host unique biota and biological communities which are highly sensitive to climate change. High penetration of solar UV radiation in clear shallow lake affects the distribution and abundance of the zooplankton communities. Survival of copepods in such habitats often relies on available photoprotective compounds. We estimated species diversity and distribution patterns of copepods with detectable carotenoids in 7 lakes of the central Himalayas along the altitudinal gradients. To determine the factors influencing the accumulation of high-level photoprotective compounds, we analyzed the physicochemical parameters of water and the concentration of Lignin like Compounds (LLCs), Aromaticity (ARO), Humic Compounds (HCs), Degree of Humification (DoH) and percent Total Organic Matter (TOM) in littoral sediments. In the shallow lakes, copepod abundance and diversity correlate with water transparency. Humic compounds (HCs) derived from ligninaceous plants stimulate the accumulation of photoprotective compounds that allow for the domination of diaptomidae. Copepods receive photoprotective compounds from the humic-bounded sediment substrate. The amount of photoprotectants in the aquatic food chain of the central Himalayas is largely influenced by ligninaceous compounds derived from catchment vegetation. In copepods of shallow clear lakes, the remnant of dead trees in the littoral zones helps to minimize hazards caused by exposure effect and climatic stress. The reduction of vegetative covers in the shorelines may alter the community structure of zooplankton, particularly in the upland ecosystem.

Mixed culture purple phototrophic bacteria is an effective fishmeal replacement in aquaculture

Aquaculture is the fastest growing animal food production industry, now producing 50% of all food fish. However, aquaculture feeds remain dependent on fishmeal derived from capture fisheries, which must be reduced for continued sustainable growth. Purple phototrophic bacteria (PPB) efficiently yield biomass from wastewater with high product homogeneity, a relatively high protein fraction, and potential added value as an ingredient for fish feeds. Here we test bulk replacement of fishmeal with PPB microbial biomass in diets for Asian sea bass (Lates calcarifer), a high value carnivorous fish with high protein to energy requirement. Mixed culture PPB were grown in a novel 1 m³ attached photo-biofilm process using synthetic and real wastewater. Four experimental diets were formulated to commercial specifications but with the fishmeal substituted (0%, 33%, 66%, and 100%) with the synthetic grown PPB biomass and fed to a cohort of 540 juvenile fish divided amongst 12 tanks over 47 days. Weight and standard length were taken from individual fish at 18, 28, and 47d. No significant difference in survival was observed due to diet or other factors (94-100%). There was a negative correlation between PPB inclusion level and final weight (p = 5.94 × 10^-5) with diet accounting for 4.1% of the variance over the trial (general linear model, R² = 0.96, p = 1 × 10^-6). Feed conversion ratio was also significantly influenced by diet (p = 6 × 10^-7) with this factor accounting for 89% of variance. Specifically, feed conversion ratio (FCR) rose to 1.5 for the 100% replacement diet during the last sample period, approximately 1.0 for the partial replacement, and 0.8 for the nil replacement diet. However, this study demonstrates that bulk replacement of fishmeal by PPB is feasible, and commercially viable at 33% and 66% replacement.

The Methoxylated, Highly Conjugated C40 Carotenoids, Spirilloxanthin and Anhydrorhodovibrin, Can Be Separated Using High Performance Liquid Chromatography with Safe and Environmentally Friendly Solvents

High performance liquid chromatography (HPLC) is a frequently used technique in carotenoid research. So far, however, little attention has been paid to the fact that many of the organic solvents used in HPLC separation of highly apolar C₄₀ carotenoids impose a significant threat to both health (especially for women) and the general laboratory environment. Here, we developed a solvent combination capable of allowing high-resolution HPLC separation of the C₄₀ carotenoid, spirilloxanthin, and all of its biosynthetic precursors beginning with phytoene, using relatively safe, environmentally friendly solvents. We show that separation of spirilloxanthin and its precursors anhydrorhodovibrin and lycopene using modern ultra-high performance chromatography (UHPLC) poses particular problems for apolar carotenoid separation, due to the long residence times in the sample delivery system, which facilitates carotenoid aggregation. We resolved these problems by developing the solvent delivery combination acetone/acetonitrile/isopropanol/methanol (65/30/5/2 (v/v/v/v)), which allows excellent column separation using the safe isocratic solvent system methanol/tetrahydrofuran (98/2 (v/v)). We also demonstrate that the development strategy for optimizing a solvent system for carotenoid separation can be well-described by the use of the average dielectric constant of the total sample delivery solvent, and present a formal method for analysis of the efficiency of separation.

Development of an Improved Carotenoid Extraction Method to Characterize the Carotenoid Composition under Oxidative Stress and Cold Temperature in the Rock Inhabiting Fungus Knufia petricola A95

Black yeasts are a highly specified group of fungi, which are characterized by a high resistance against stress factors. There are several factors enabling the cells to survive harsh environmental conditions. One aspect is the pigmentation, the melanin black yeasts often display a highly diverse carotenoid spectrum. Determination and characterization of carotenoids depend on an efficient extraction and separation, especially for black yeast, which is characterized by thick cell walls. Therefore, specific protocols are needed to ensure reliable analyses regarding stress responses in these fungi. Here we present both. First, we present a method to extract and analyze carotenoids and secondly we present the unusual carotenoid composition of the black yeast Knufia petricola A95. Mechanical treatment combined with an acetonitrile extraction gave us very good extraction rates with a high reproducibility. The presented extraction and elution protocol separates the main carotenoids (7) in K. petricola A95 and can be extended for the detection of additional carotenoids in other species. K. petricola A95 displays an unusual carotenoid composition, with mainly didehydrolycopene, torulene, and lycopene. The pigment composition varied in dependency to oxidative stress but remained relatively constant if the cells were cultivated under low temperature. Future experiments have to be carried out to determine if didehydrolycopene functions as a protective agent itself or if it serves as a precursor for antioxidative pigments like torulene and torularhodin, which could be produced after induction under stress conditions. Black yeasts are a promising source for carotenoid production and other substances. To unravel the potential of these fungi, new methods and studies are needed. The established protocol allows the determination of carotenoid composition in black yeasts.

Focused Review: Cytotoxic and Antioxidant Potentials of Mangrove-Derived Streptomyces

Human life expectancy is rapidly increasing with an associated increasing burden of chronic diseases, such as neurodegenerative diseases and cancer. However, there is limited progress in finding effective treatment for these conditions. For this reason, members of the genus Streptomyces have been explored extensively over the past decades as these filamentous bacteria are highly efficient in producing bioactive compounds with human health benefits. Being ubiquitous in nature, streptomycetes can be found in both terrestrial and marine environments. Previously, two Streptomyces strains (MUSC 137T and MUM 256) isolated from mangrove sediments in Peninsular Malaysia demonstrated potent antioxidant and cytotoxic activities against several human cancer cell lines on bioactivity screening. These results illustrate the importance of streptomycetes from underexplored regions aside from the terrestrial ecosystem. Here we provide the insights and significance of Streptomyces species in the search of anticancer and/or chemopreventive agents and highlight the impact of next generation sequencing on drug discovery from the Streptomyces arsenal.

Carotenoid Distribution in Nature

Carotenoids are naturally occurring red, orange and yellow pigments that are synthesized by plants and some microorganisms and fulfill many important physiological functions. This chapter describes the distribution of carotenoid in microorganisms, including bacteria, archaea, microalgae, filamentous fungi and yeasts. We will also focus on their functional aspects and applications, such as their nutritional value, their benefits for human and animal health and their potential protection against free radicals. The central metabolic pathway leading to the synthesis of carotenoids is described as the three following principal steps: (i) the synthesis of isopentenyl pyrophosphate and the formation of dimethylallyl pyrophosphate, (ii) the synthesis of geranylgeranyl pyrophosphate and (iii) the synthesis of carotenoids per se, highlighting the differences that have been found in several carotenogenic organisms and providing an evolutionary perspective. Finally, as an example, the synthesis of the xanthophyll astaxanthin is discussed.