Tenacibaculum skagerrakense sp. nov., a marine bacterium isolated from the pelagic zone in Skagerrak, Denmark.
Frette, L., Jørgensen, N. O. G., Irming, H. & Kroer, N. (2004). International Journal of Systematic and Evolutionary Microbiology, 54(2), 519-524.
A number of bacteria were isolated from sea water in Skagerrak, Denmark, at 30 m depth. Two of the isolates, strains D28 and D30T, belonged to the Flavobacteriaceae within the Cytophaga–Flavobacterium–Bacteroides group. Sequencing of 16S rRNA genes of the two strains indicated strongly that they belonged to the genus Tenacibaculum and that they showed greatest similarity to the species Tenacibaculum amylolyticum and Tenacibaculum mesophilum. DNA–DNA hybridization values, DNA base composition and phenotypic characteristics separated the Skagerrak strains from the other species within Tenacibaculum. Thus, it is concluded that the strains belong to a novel species within the genus Tenacibaculum, for which the name Tenacibaculum skagerrakense sp. nov. is proposed, with strain D30T (=ATCC BAA-458T=DSM 14836T) as the type strain.
Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates.
Ten, L. N., Im, W. T., Kim, M. K., Kang, M. S. & Lee, S. T. (2004). Journal of Microbiological Methods, 56(3), 375-382.
A plate assay based on the visible solubilization of small substrate particles and the formation of haloes on Petri dishes, containing a mixture of different dye-labelled polysaccharides as substrates, provides a specific, reliable and rapid simultaneous detection of corresponding polysaccharide-degrading microorganisms. It has potential for increasing the efficacy of screening of microorganisms, utilizing different polysaccharides, in large numbers of natural samples. Diversely colored insoluble forms of amylose, xylan and hydroxyethyl-cellulose (HE-cellulose) were prepared as chromogenic substrates by using the cross-linking reagent 1,4-butanediol diglycidyl ether and the dyes Brilliant Red 3B-A, Cibacron Blue 3GA and Reactive Orange 14. Using the method, the bacteria with amylase or xylanase or cellulase or a combination of these activities were screened from soil and sludge samples, selected and identified according to 16S rDNA sequencing.
Verminephrobacter aporrectodeae sp. nov. subsp. tuberculatae and subsp. caliginosae, the specific nephridial symbionts of the earthworms Aporrectodea tuberculata and A. caliginosa.
Lund, M. B., Schätzle, S., Schramm, A. & Kjeldsen, K. U. (2012). Antonie van Leeuwenhoek, 101(3), 507-514.
Clone library-based studies have shown that almost all lumbricid earthworm species harbour host-specific symbiotic bacteria belonging to the novel genus Verminephrobacter in their nephridia (excretory organs). To date the only described representative from this genus is Verminephrobacter eiseniae, the specific symbiont of the earthworm Eisenia fetida. In this study two novel rod-shaped, non-endosporeforming, betaproteobacterial symbionts were isolated from the nephridia of two closely related earthworm species. Both isolates were affiliated with the genus Verminephrobacter by 16SrRNA gene sequence analysis. Similarly to V. eiseniae, the two isolates grew aerobically with a preference for low oxygen concentrations on a range of sugars, fatty acids and amino acids and fermentatively on glucose and pyruvate. These phenotypes match well with the conditions reported or inferred for the nephridial environment. Based on 16S rRNA gene similarity, DNA–DNA hybridization value and phenotypic characteristics the two isolates are clearly distinct from V. eiseniae. Phenotypic characteristics could not clearly differentiate the two strains as separate species but a low DNA–DNA hybridization value of 57.3%, their earthworm host specificity, differing temperature ranges and pH optima suggest that they represent two subspecies of a novel species of Verminephrobacter. For this species, the name V. aporrectodeae sp. nov. is proposed, with the two subspecies V. aporrectodeae subsp. tuberculatae (type strain, At4T = DSM 21361T = LMG 25313T) and V. aporrectodeae subsp. caliginosae (type strain, Ac9T = DSM 21895T = LMG 25312T) isolated from the nephridia of the earthworms Aporrectodea tuberculate and A. caliginosa, respectively.
The use of plant cell wall degrading enzymes from a newly isolated Penicillium ochrochloron Biourge for viscosity reduction in ethanol production with fresh sweet potato tubers as feedstock.
Huang, Y., Jin, Y., Shen, W., Fang, Y., Zhang, G. & Zhao, H. (2014). Biotechnology and Applied Biochemistry, 61(4), 480-491.
Penicillium ochrochloron Biourge, which was isolated from rotten sweet potato, can produce plant cell wall degrading enzymes (PCWDEs) with high viscosity reducing capability for ethanol production using fresh sweet potato tubers as feedstock. The enzyme preparation was characterized by a broad enzyme spectrum including 13 kinds of enzymes with the activity to hydrolyze cellulose, hemicellulose, pectin, starch and protein. The maximum viscosity reducing capability was observed when the enzyme preparation was obtained after five days fermentation using 20 g/L corncob as a sole carbon source, 4.5 g/L NH4NO3 as sole nitrogen source, and an initial medium pH of 6.5. The sweet potato mash treated with the enzyme preparation exhibited much higher fermentation efficiency (92.58%) compared with commercial cellulase (88.06%) and control (83.5%). The enzyme production was then scaled up to 0.5, 5, and 100 L, and the viscosity reducing rates were found to be 85%, 90%, and 91%, respectively. Thus, P. ochrochloron Biourge displays potential viscosity reducing capability for ethanol production.
Patterns of functional enzyme activity in fungus farming ambrosia beetles.
Licht, H. H. D. F. & Biedermann, P. H. (2012). Frontiers in Zoology, 9(1), 13.
Introduction: In wood-dwelling fungus-farming weevils, the so-called ambrosia beetles (Curculionidae: Scolytinae and Platypodinae), wood in the excavated tunnels is used as a medium for cultivating fungi by the combined action of digging larvae (which create more space for the fungi to grow) and of adults sowing and pruning the fungus. The beetles are obligately dependent on the fungus that provides essential vitamins, amino acids and sterols. However, to what extent microbial enzymes support fungus farming in ambrosia beetles is unknown. Here we measure (i) 13 plant cell-wall degrading enzymes in the fungus garden microbial consortium of the ambrosia beetle Xyleborinus saxesenii, including its primary fungal symbionts, in three compartments of laboratory maintained nests, at different time points after gallery foundation and (ii) four specific enzymes that may be either insect or microbially derived in X. saxesenii adult and larval individuals. Results: We discovered that the activity of cellulases in ambrosia fungus gardens is relatively small compared to the activities of other cellulolytic enzymes. Enzyme activity in all compartments of the garden was mainly directed towards hemicellulose carbohydrates such as xylan, glucomannan and callose. Hemicellulolytic enzyme activity within the brood chamber increased with gallery age, whereas irrespective of the age of the gallery, the highest overall enzyme activity were detected in the gallery dump material expelled by the beetles. Interestingly endo-β-1,3(4)-glucanase activity capable of callose degradation was identified in whole-body extracts of both larvae and adult X. saxesenii, whereas endo-β-1,4-xylanase activity was exclusively detected in larvae. Conclusion: Similar to closely related fungi associated with bark beetles in phloem, the microbial symbionts of ambrosia beetles hardly degrade cellulose. Instead, their enzyme activity is directed mainly towards comparatively more easily accessible hemicellulose components of the ray-parenchyma cells in the wood xylem. Furthermore, the detection of xylanolytic enzymes exclusively in larvae (which feed on fungus colonized wood) and not in adults (which feed only in fungi) indicates that only larvae (pre-) digest plant cell wall structures. This implies that in X. saxesenii and likely also in many other ambrosia beetles, adults and larvae do not compete for the same food within their nests - in contrast, larvae increase colony fitness by facilitating enzymatic wood degradation and fungus cultivation.
Metatranscriptomics Reveals the Functions and Enzyme Profiles of the Microbial Community in Chinese Nong-Flavor Liquor Starter.
Huang, Y., Yi, Z., Jin, Y., Huang, M., He, K., Liu, D., Luo, H., Zhao, D., He, H., Fang, Y. & Zhao, H. (2017). Frontiers in Microbiology, 8, 1747.
Chinese liquor is one of the world's best-known distilled spirits and is the largest spirit category by sales. The unique and traditional solid-state fermentation technology used to produce Chinese liquor has been in continuous use for several thousand years. The diverse and dynamic microbial community in a liquor starter is the main contributor to liquor brewing. However, little is known about the ecological distribution and functional importance of these community members. In this study, metatranscriptomics was used to comprehensively explore the active microbial community members and key transcripts with significant functions in the liquor starter production process. Fungi were found to be the most abundant and active community members. A total of 932 carbohydrate-active enzymes, including highly expressed auxiliary activity family 9 and 10 proteins, were identified at 62°C under aerobic conditions. Some potential thermostable enzymes were identified at 50, 62, and 25°C (mature stage). Increased content and overexpressed key enzymes involved in glycolysis and starch, pyruvate and ethanol metabolism were detected at 50 and 62°C. The key enzymes of the citrate cycle were up-regulated at 62°C, and their abundant derivatives are crucial for flavor generation. Here, the metabolism and functional enzymes of the active microbial communities in NF liquor starter were studied, which could pave the way to initiate improvements in liquor quality and to discover microbes that produce novel enzymes or high-value added products.