Application of good laboratory practice (GLP) to culture collections of microbial and cell cultures

Although the principles and the necessity for good laboratory practice (GLP) guidelines to confirm the credibility, integrity, and quality of non-clinical laboratory studies have been known for more than a decade, culture collection activities are not subject to them. Because of recent advances in biotechnology, culture collections face increased demands not only for quality cultures but also current information. When applied in culture collections, GLP guidelines prove to be an excellent management tool as well as a cost-effective system of providing authentic and reliable microbial and cell cultures and associated data.     

Elevated ozone decreases the multifunctionality of belowground ecosystems

Elevated tropospheric ozone (O₃) affects the allocation of biomass aboveground and belowground and influences terrestrial ecosystem functions. However, how belowground functions respond to elevated O₃ concentrations ([O₃]) remains unclear at the global scale. Here, we conducted a detailed synthesis of belowground functioning responses to elevated [O₃] by performing a meta-analysis of 2395 paired observations from 222 publications. We found that elevated [O₃] significantly reduced the primary productivity of roots by 19.8%, 16.3%, and 26.9% for crops, trees and grasses, respectively. Elevated [O₃] strongly decreased the root/shoot ratio by 11.3% for crops and by 4.9% for trees, which indicated that roots were highly sensitive to O₃. Elevated [O₃] impacted carbon and nitrogen cycling in croplands, as evidenced by decreased dissolved organic carbon, microbial biomass carbon, total soil nitrogen, ammonium nitrogen, microbial biomass nitrogen, and nitrification rates in association with increased nitrate nitrogen and denitrification rates. Elevated [O₃] significantly decreased fungal phospholipid fatty acids in croplands, which suggested that O₃ altered the microbial community and composition. The responses of belowground functions to elevated [O₃] were modified by experimental methods, root environments, and additional global change factors. Therefore, these factors should be considered to avoid the underestimation or overestimation of the impacts of elevated [O₃] on belowground functioning. The significant negative relationships between O₃-treated intensity and the multifunctionality index for croplands, forests, and grasslands implied that elevated [O₃] decreases belowground ecosystem multifunctionality.     

The interaction of rockphosphate,Bradyrhizobium, vesicular-arbuscular mycorrhizae and phosphate-solubilizing microbes on soybean grown in a sub-Himalayan mollisol

A factorial design 2³ × 4 with two levels of Mussorie rockphosphate (RP) with or without vesicular-arbuscular mycorrhizal (VAM) fungi and Bradyrhizobium japonicum, and four treatments of phosphate-solubilizing microbes (PSM) Pseudomonas striata, Bacillus polymyxa, Aspergillus awamori was employed using Patharchatta sandy loam soil (Typic Hapludoll). The observations included mycorrhization, nodulation, grain and straw yield, N and P uptake, available soil P and the PSM population in the soil after crop harvest. Inoculation with endophytes alone caused about 70% root colonization. Addition of rockphosphate or inoculation with PSM, except B. polymyxa, stimulated root infection of native as well as introduced VAM endophytes. Application of RP or inoculation with Bradyrhizobium japonicum, mycorrhizal fungi or phosphate-solubilizing microorganisms significantly increased nodulation, N uptake, available soil P and the PSM population in the soil after the crop harvest. The grain and straw yields did not increase following RP addition or mycorrhizal inoculation but increased significantly after inoculation wit Bradyrhizobium or PSM. In general, the application of RP, Bradyrhizobium, VAM and PSM in combinations of any two or three resulted in significant increases in nodulation, plant growth, grain yield and uptake of N and P. Among the four factor interactions, rockphosphate, Bradyrhizobium and P. striata in the absence of VAM resulted in maximal nodulation, grain and straw yields and N uptake by soybean. The highest P uptake by soybean grain was recorded with Bradyrhizobium and A. awamori in the absence of rockphosphate and VAM. Generally, available soil P and PSM population after crop harvest were not significantly increased by the treatment combinations giving the maximal uptake of nutrients. However, they increased significantly in response to PSM, which produced no significant increase in total uptake of nutrients.Research paper no. 7498     

Examination of thirteen petroliferous formations for hydrocarbon-utilizing sulfate-reducing microorganisms

Virgin cores and production fluids were obtained from seven wells, ranging in depth from 805 ft to 14 492 ft, and examined for the presence of sulfate-reducing bacteria (SRB) using Rosenfeld's sulfate-reducing medium modified by using crude oil in place of lactate. Cores from an additional six wells, ranging in depth from 1160 ft to 13 337 ft were tested for SRB using the modified Rosenfeld medium and API-sulfate-reducing medium. Produced waters from five of the six wells were tested also. All of the eleven produced water samples were positive for SRB while H₂S production was not detected from the core samples.     

Potential and pitfalls of trying to extend symbiotic interactions of nitrogen-fixing organisms to presently non-nodulated plants,such as rice

It has been a long-standing goal in the field of biological nitrogen fixation to extend nitrogen-fixing symbioses to presently non-nodulated cereal plants, such as rice. A number of researchers have recently described the induction of nodule-like structures on the roots of cereals primarily by rhizobia, in either the presence or absence of plant cell-wall-degrading enzymes or plant hormones. We briefly review this research and discuss the potential problems associated with the introduction of nitrogen-fixing microbes in novel physiological environments, such as rice roots. The results of experiments carried out in China on the induction of nodule-like structures on rice roots by rhizobia are highlighted. In addition, we present preliminary results of a series of experiments designed to repeat and evaluate these results using a variety of microscopic techniques and molecular genetic approaches.     

Allelopathic effects ofEupatorium riparium on population regulation of two species ofGalinsoga and soil microbes

Summary Allelopathic effect ofEupatorium riparium Regel, a dominant ruderal weed at higher altitudes in Meghalaya state in north-eastern India, was studied on two common sympatric annual weeds,Galinsoga ciliata (Raf.) andG. parviflora Cav. and on soil microbes. Seed germination and radicle and plumule growth of both species ofGalinsoga were suppressed by the aqueous extract and leachate ofE. riparium. Although the leaf leachate, leaf and litter extracts and litter bed caused considerable reduction in leaf area and seed and dry matter production in both species ofGalinsoga, the effect was much more pronounced onG. parviflora. The inhibitory effect was directly correlated with the concentration of the extract and leachate. The soil microbial population and growth of theGalinsoga spp. declined considerably in the experimental pots where the soil had earlier received leachate of different plant parts ofE. riparium growing in it. The presence of the partly decomposed litter ofE. riparium in the pots reduced soil microbial population and growth of the two weeds much more strongly as compared to the litter in the advanced stages of decomposition. The study also revealed that the abundance and colony growth of the two test fungiviz. Trichoderma viride andAspergillus flavus were differentially affected by the allelopathy ofE. riparium; T. viride being favoured andA. flavus inhibited.     

Kinetics of aerobic biodegradation of benzene and toluene in sandy aquifer material

Monod's equation adequately described aerobic biodegradation rates of benzene and toluene by the microbial population of a sandy aquifer when these compounds were initially present at concentrations lower than 100 mg/l each. Concentrations higher than 100 mg/l were inhibitory, and no benzene or toluene degradation was observed when these compounds were initially present at 250 mg/l each. The Monod coefficients were calculated as k = 8.3 g-benzene/g-cells/day and Ks = 12.2 mg/l for benzene, and k = 9.9 g-toluene/g-cells/day and Ks = 17.4 mg/l for toluene. Specific first-order coefficients would be 0.68 l/mg.day for benzene and 0.57 l.mg.day for toluene.     

Dietary Mannan-oligosaccharides potentiate the beneficial effects of Bifidobacterium bifidum in broiler chicken

This study investigated the effects of dietary Bifidobacterium bifidum (BFD) and mannan-oligosaccharide (MOS), as a synbiotic, on the production performance, gut microbiology, serum biochemistry, antioxidant profile and health indices of broiler chicken. Six dietary treatments were T1 (negative control), T2 (positive control-20 mg antibiotic BMD kg⁻¹ diet; BMD: bacitracin methylene disalicylate), T3 (0·1% MOS + 10⁶ CFU BFD per g feed), T4 (0·1% MOS + 10⁷ CFU BFD per g feed), T5 (0·2% MOS + 10⁶ CFU BFD per g feed) and T6 (0·2% MOS + 10⁷ CFU BFD per g feed). Significantly (P < 0·01) better growth performance and efficiency was observed in birds supplemented with 0·2% MOS along with 10⁶ CFU BFD per g of feed compared to BMD and control birds. Supplementation with 0·2% MOS along with either 10⁶ or 10⁷ CFU BFD per g feed reduced (P < 0·01) the gut coliform, Escherichia coli, total plate count, and Clostridium perfringens count and increased the Lactobacillus and Bifidobacterium count. Significantly (P < 0·01) higher serum and liver antioxidant enzyme pool, serum HDL cholesterol and lower serum glucose, triglyceride, total cholesterol, cardiac risk ratio, atherogenic coefficient and atherogenic index of plasma were observed in birds supplemented with 0·2% MOS along with 10⁶ CFU BFD per g of feed compared to control or BMD supplemented birds. Better production performance, gut microbial composition, serum biochemistry, antioxidant profile and health indices were depicted by broiler chicken supplemented with 0·2% MOS and 10⁶ CFU BFD per g of feed.     

MicroPhenoDB Associates Metagenomic Datawith Pathogenic Microbes,Microbial Core Genes,and Human Disease Phenotypes

Microbes play important roles in human health and disease. The interaction between microbes and hosts is a reciprocal relationship, which remains largely under-explored. Current computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We developed the MicroPhenoDB database by manually curating and consistently integrating microbe-disease association data. MicroPhenoDB provides 5677 non-redundant associations between 1781 microbes and 542 human disease phenotypes across more than 22 human body sites. MicroPhenoDB also provides 696,934 relationships between 27,277 unique clade-specific core genes and 685 microbes. Disease phenotypes are classified and described using the Experimental Factor Ontology (EFO). A refined score model was developed to prioritize the associations based on evidential metrics. The sequence search option in MicroPhenoDB enables rapid identification of existing pathogenic microbes in samples without running the usual metagenomic data processing and assembly. MicroPhenoDB offers data browsing, searching, and visualization through user-friendly web interfaces and web service application programming interfaces. MicroPhenoDB is the first database platform to detail the relationships between pathogenic microbes, core genes, and disease phenotypes. It will accelerate metagenomic data analysis and assist studies in decoding microbes related to human diseases. MicroPhenoDB is available through http://www.liwzlab.cn/microphenodb and http://lilab2.sysu.edu.cn/microphenodb.     

Identification,biochemical composition and phycobiliproteins production of Chroococcidiopsis sp. from arid environment

Molecular and microscopic studies were performed to identify Chroococcidiopsis sp., an endolithic cyanobacterium, isolated from gypsum rocks of Atacama Desert (Chile). It was adapted to grow in mineral liquid medium, with 9 mM nitrate, bubbled with CO₂-enriched air (2.5 % v/v), and continuously illuminated with a white light of 70 μmol photons m^–2 s^–1. The obtained biomass (productivity of 0.21 g L^–1 d^–1) had a C/N ratio of 6.67, and it contained carbohydrates (45.40 % of dry weight), proteins (36.72 %), lipids (5.60 %) nucleic acids (3.90 %) and ashes (8.28 %). The lipid fraction was particularly rich in palmitic (29.86 % of total fatty acids), linoleic (18.20 %), palmitoleic (12.75 %), linolenic (10.92 %), stearic (9.64 %) and capric acid (6.29 %). Chroococcidiopsis sp. accumulated phycobiliproteins in a light-dependent process and produced 204 mg g^–1, under incident light of 10 μmol photons·m^–2·s^–1, with a relative abundance of 40.9 % for phycocyanin, 23.3 % for phycoerythrin, and 35.8 % for allophycocyanin. The biomass from this cyanobacterium can be a good source of these pigments, especially APC (maximum of 95 mg g dw⁻¹), which are of interest for pharmacological, cosmetic, and food industries.