Actinocatenispora comari sp. nov., an endophytic actinomycete isolated from aerial parts of Comarum salesowianum.

A novel actinomycete, designated NUM-2625T, was isolated as an endophytic bacterium in aerial parts of Comarum salesowianum, an endemic species in the Altai, Himalaya mountain chain area, collected from Khasagt Khairkhan Mountain in Mongolia. The 16S rRNA gene sequence of strain NUM-2625T showed the highest similarity to Actinocatenispora thailandica TT2-10T (99.4 %), Actinocatenispora sera KV-744T (99.3 %), and Actinocatenispora rupis CS5-AC17T (97.7 %). Chemotaxonomic properties of strain NUM-2625T were essentially consistent with those of the genus Actinocatenispora, such as the presence of meso-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan, MK-9(H4) and MK-9(H6) as the major menaquinones, and iso-C16 : 0, iso-C15 : 0, iso-C14 : 0 3-OH, and anteiso-C17 : 0 as the major fatty acids. Meanwhile, digital DNA-DNA hybridization and average nucleotide identity values revealed a low relatedness between strain NUM-2625T and the other type strains of the genus Actinocatenispora. In addition, strain NUM-2625T exhibited several phenotypic properties that could be used to distinguish it from its closest relatives. Based on the results of polyphasic analyses, strain NUM-2625T represents a novel species in the genus Actinocatenispora, for which the name Actinocatenispora comari sp. nov. is proposed. The type strain is NUM-2625T (=NBRC 114660T=TBRC 13496T).

Physicochemical profile of microbial-assisted composting on empty fruit bunches of oil palm trees.

This study was carried out to investigate the physicochemical properties of compost from oil palm empty fruit bunches (EFB) inoculated with effective microorganisms (EM∙1™). The duration of microbial-assisted composting was shorter (∼7 days) than control samples (2 months) in a laboratory scale (2 kg) experiment. The temperature profile of EFB compost fluctuated between 26 and 52 °C without the presence of consistent thermophilic phase. The pH of compost changed from weak acidic (pH ∼5) to mild alkaline (pH ∼8) because of the formation of nitrogenous ions such as ammonium (NH4 (+)), nitrite (NO2 (-)), and nitrate (NO3 (-)) from organic substances during mineralization. The pH of the microbial-treated compost was less than 8.5 which is important to prevent the loss of nitrogen as ammonia gas in a strong alkaline condition. Similarly, carbon mineralization could be determined by measuring CO2 emission. The microbial-treated compost could maintain longer period (∼13 days) of high CO2 emission resulted from high microbial activity and reached the threshold value (120 mg CO2-C kg(-1) day(-1)) for compost maturity earlier (7 days). Microbial-treated compost slightly improved the content of minerals such as Mg, K, Ca, and B, as well as key metabolite, 5-aminolevulinic acid for plant growth at the maturity stage of compost. Graphical Abstract Microbial-assisted composting on empty fruit bunches.

Candida utilis assimilates oligomeric sugars in rice straw hydrolysate via the Calcium-Capturing-by-Carbonation (CaCCO) process for glutathione- and cell-biomass production.

Rice-straw hydrolysate (RSH) prepared via the CaCCO (Calcium Capturing by Carbonation) process contains not only monosaccharides but also significant amounts of oligosaccharides. In this study, a glutathione-producing yeast, Candida utilis NBRC 0626, was found to assimilate those oligosaccharides. The yields of reduced glutathione (GSH) and dry cell weight (DCW) per consumed sugars in a medium with RSH after 72h incubation were 10.1mg/g-sugars and 0.49g/g-sugars, respectively. The yields were comparative to those in a medium containing a model monosaccharide mix, suggesting that the assimilated oligosaccharides contribute to additional GSH and DCW production. Glycosyl linkage analysis indicated that the yeast could cleave xylose-, galactose-, and arabinose residues as well as glucose residues at the non-reducing ends. After 72h incubation, 99.1% of the total glucose residues and 84.2% of the total xylose residues in RSH were depleted. Thus the yeast could be applied for efficient utilization of lignocellulosic hydrolysates.

Condensed tannin accumulation and nitrogen fixation potential of Onobrychis viciifolia Scop. grown in a Mediterranean environment.

BACKGROUND: Sainfoin (Onobrychis viciifolia Scop.) is a forage legume found in temperate areas but is less widespread in Mediterranean environments. Compared with other perennial legumes, it has the advantage of containing condensed tannins (CT) that can be important for their implications on ruminant nutrition and health. Data on nitrogen (N) fixation by sainfoin in the literature originate from very different environments and only a few field data are available, so it is important to improve knowledge on the N fixation potential of this species, particularly under a Mediterranean climate. Here the accumulation pattern of polyphenolic compounds (total, non-tannic polyphenols and CT) and the N fixation potential of sainfoin were studied in order to contribute to its valorisation for sustainable farming management in Mediterranean environments. RESULTS: CT concentrations were always in the range considered beneficial for animals, not exceeding 50 g delphinidin equivalent kg⁻¹ dry matter (DM). The regression of aerial fixed N on aerial DM showed a relationship of 22 kg fixed N t⁻¹ aerial DM in a Mediterranean environment. CONCLUSION: A wider exploitation of sainfoin is suggested for production under rain-fed conditions, thus enlarging the limited set of available perennial legumes suitable for Mediterranean environments.

Total bacterial load within Echinacea purpurea, determined using a new PCR-based quantification method, is correlated with LPS levels and in vitro macrophage activity.

Our previous studies indicate that the majority of in vitro monocyte/macrophage activation exhibited by extracts of Echinacea depends on bacterial components. In the present study, total bacterial load was determined within E. purpurea samples and ranged from 6.4 × 10(6) to 3.3 × 10(8) bacteria/g of dry plant material. To estimate total bacterial load, we developed a PCR-based quantification method that circumvents the problems associated with nonviable/nonculturable cells (which precludes using plate counts) or the coamplification of mitochondrial or chloroplast DNA with the use of universal bacterial primers (which precludes the use of qPCR). Differences in total bacterial load within Echinacea samples were strongly correlated with the activity (NF-κB activation in THP-1 cells) and content of bacterial lipopolysaccharides within extracts of this plant material. These results add to the growing body of evidence that bacteria within Echinacea are the main source of components responsible for enhancing innate immune function.

The effect of microwave pretreatment on biogas production from agricultural straws.

Biogas production from microwave-pretreated agricultural residual straws that are used as feedstock was investigated in a laboratory batch study. Barley, spring wheat, winter wheat and oat straw were examined. To investigate the effect of changing the physicochemical structure of the straws on biogas production, the pretreatment processes were applied to two sample groups. The first group contained milled straw and the second group comprised milled wet straw that was prepared by the addition of deionized water. Both groups were subjected to microwave irradiation until oven temperatures of 200 or 300 °C were attained. Sixty-six identical batch anaerobic reactors were run under mesophilic conditions for 60 days. Preliminary test results showed that the microwave pretreatment of the different straws did not improve their anaerobic digestion. An increase in the treatment temperature led to lower biogas production levels. An inverse relationship between the thermal conversion yield and cumulative biogas production was observed.

Unipept: tryptic peptide-based biodiversity analysis of metaproteome samples.

The Unipept web application (http://unipept.ugent.be) supports biodiversity analysis of large and complex metaproteome samples using tryptic peptide information obtained from shotgun MS/MS experiments. Its underlying index structure is designed to quickly retrieve all occurrences of a tryptic peptide in UniProtKB records. Taxon-specificity of the tryptic peptide is successively derived from these occurrences using a novel lowest common ancestor approach that is robust against taxonomic misarrangements, misidentifications, and inaccuracies. Not taking into account this identification noise would otherwise result in drastic loss of information. Dynamic treemaps visualize the biodiversity of metaproteome samples, which eases the exploration of samples with highly complex compositions. The potential of Unipept to gain novel insights into the biodiversity of a sample is evaluated by reanalyzing publicly available metaproteome data sets taken from the bacterial phyllosphere and the human gut.

Efficient ethanol production from separated parenchyma and vascular bundle of oil palm trunk.

For efficient utilization of both starchy and cellulosic materials, oil palm trunk was separated into parenchyma (PA) and vascular bundle (VB). High solid-state simultaneous saccharification and fermentation (HSS-SSF) using 30% (w/v) PA, containing 46.7% (w/w) starch, supplemented with amylases and Saccharomyces cerevisiae K3, produced 6.1% (w/v) ethanol. Subsequent alkali-pretreatment using sodium hydroxide was carried out with starch-free PA (sfPA) and VB. Enzymatic digestibility of 5% (w/v) pretreated sfPA and VB was 92% and 97%, respectively, using 18 FPU of commercial cellulase supplemented with 10 U of Novozyme-188 per gram of substrate. Likewise, HSS-SSF using 30% (w/v) alkali-pretreated sfPA and VB, with cellulases and yeast, resulted in high ethanol production (8.2% and 8.5% (w/v), respectively). These results show that HSS-SSF using separated PA and VB is a useful fermentation strategy, without loss of starchy and cellulosic materials, for oil palm trunk.