A taxonomic study of bacteria isolated from grasses: a proposed new species Pseudomonas graminis sp. nov.
The taxonomic position of a yellow-pigmented group of bacteria, isolated from the phyllosphere of grasses was investigated. Results obtained from restriction analysis of amplified 16S rDNA with seven endonucleases (CfoI, HaeIII, AluI, HinfI, MspI, Sau3A and ScrFI) showed identical restriction patterns for each enzyme of all isolates studied, which suggests that all strains belong to the same species. The grass isolates displayed the characteristics of the genus Pseudomonas. They were Gram-negative, aerobic and rod-shaped with polar flagella. Isolates were catalase-positive and oxidase-negative, and unable to oxidize or ferment glucose with the production of acid. The isolates did not reduce nitrate to nitrite but were able to utilize a wide range of compounds individually as a sole carbon source, with preference being given to the utilization of monosaccharides. The disaccharides tested were not utilized as substrates. The DNA base compositions of the tested strains ranged from 60 to 61 mol% G+C. The major isoprenoid quinone of each was ubiquinone Q-9 and hydroxy fatty acids were represented by 3-hydroxydodecanoic acid and 2-hydroxydodecanoic acid. Comparison of 16S rDNA sequences showed that the bacteria were members of the genus Pseudomonas, with similarity values between 91.5 and 97.7%. DNA-DNA hybridization studies with closely related neighbours revealed a low level of homology (< 27%), indicating that the isolates represent an individual species. On the basis of phenotypic and phylogenetic analyses a new species, Pseudomonas graminis sp. nov. (type strain DSM 11363T), is proposed. (+info)
Evolutionary dynamics of Ty1-copia group retrotransposons in grass shown by reverse transcriptase domain analysis.
The evolutionary dynamics of Ty1-copia group retrotransposons in grass were examined by reverse transcriptase (RT) domain analysis. Twenty-three rice RT sequences were newly determined for this report. Phylogenetic analysis of 177 RT sequences, mostly derived from wheat, rice, and, maize, showed four distinct families, which were designated G1, G2, G3, and G4. Three of these families have elements obtained from distantly related species, indicative of origins prior to the radiation of grass species. Results of Southern hybridization and detailed comparisons between the wheat and rice sequences indicated that each of the families had undergone a distinct pattern of evolution. Multiple families appear to have evolved in parallel in a host species. Analyses of synonymous and nonsynonymous substitutions suggested that there is a low percentage of elements carrying functional RT domains in the G4 family, indicating that the production of new G4 elements has been controlled by a small number of elements carrying functional RT domains. (+info)
Identification of Epichloe endophytes in planta by a microsatellite-based PCR fingerprinting assay with automated analysis.
Epichloe endophytes are a group of filamentous fungi that include both sexual (Epichloe) and asexual (Neotyphodium) species. As a group they are genetically diverse and form both antagonistic and mutualistic associations with temperate grasses. We report here on the development of a microsatellite-based PCR system for fingerprinting this group of fungi with template isolated from either culture or infected plant material. M13mp19 partial genomic libraries were constructed for size-fractionated genomic DNA from two endophyte strains. These libraries were screened with a mixture of DIG-labeled dinucleotide and trinucleotide repeat probes. Positive clones were sequenced, and nine unique microsatellite loci were identified. An additional microsatellite was serendipitously identified in the 3' untranscribed region of the 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase gene from N. lolii Lp19. Primers were designed for each locus and a panel of endophytes, from different taxonomic groupings, was screened to determine the degree of polymorphism. On the basis of these results a multiplex assay was developed for strain identification with fluorescently labeled primers for five of these loci. Using this system the size of the products amplified can be precisely determined by automated analysis, and an allele profile for each strain can be readily generated. The assay was shown to resolve endophyte groupings to the level of known isozyme phenotype groupings. In a blind test the assay was used successfully to identify a set of endophytes in planta. A reference database of allele sizes has been established for the panel of endophytes examined, and this will be expanded as new strains are analyzed. (+info)
Postweaning performance of calves from Angus, Brahman, and reciprocal-cross cows grazing endophyte-infected tall fescue or common bermudagrass.
Data from 403 Polled Hereford-sired calves from Angus, Brahman, and reciprocal-cross cows were used to evaluate the effects of preweaning forage environment on postweaning performance. Calves were spring-born in 1991 to 1994 and managed on either endophyte-infected tall fescue (E+) or common bermudagrass (BG) during the preweaning phase. After weaning, calves were shipped to the Grazinglands Research Laboratory, El Reno, OK and stratified to one of two winter stocker treatments by breed and preweaning forage; stocker treatments were winter wheat pasture (WW) or native range plus supplemental CP (NR). Each stocker treatment was terminated in March, calves grazed cool-season grasses, and calves were then moved to a feedlot phase in June. In the feedlot phase, calves were fed to approximately 10 mm fat over the 12th rib and averaged approximately 115 d on feed. When finished, calves were weighed and shipped to Amarillo, TX for slaughter. Averaged over calf breed group, calves from E+ gained faster during the stocker phase (P<.10), had lighter starting and finished weights on feed (P< .01), lighter carcass weights (P<.01), and smaller longissimus muscle areas (P<.05) than calves from BG. Calves from E+ were similar to calves from BG in feedlot ADG, percentage kidney, heart, and pelvic fat, fat thickness over 12th rib, yield grade, marbling score, and dressing percentage. Maternal heterosis was larger in calves from E+ for starting weight on feed (P<.01), finished weight (P<.10), and carcass weight (P<.16). These data suggest that few carryover effects from tall fescue preweaning environments exist, other than lighter, but acceptable, weights through slaughter. These data further suggest that the tolerance to E+ in calves from reciprocal-cross cows, expressed in weaning weights, moderated postweaning weight differences between E+ and BG compared to similar comparisons in calves from purebred cows. (+info)
The mechanism of rhythmic ethylene production in sorghum. The role of phytochrome B and simulated shading.
Mutant sorghum (Sorghum bicolor [L.] Moench) deficient in functional phytochrome B exhibits reduced photoperiodic sensitivity and constitutively expresses a shade-avoidance phenotype. Under relatively bright, high red:far-red light, ethylene production by seedlings of wild-type and phytochrome B-mutant cultivars progresses through cycles in a circadian rhythm; however, the phytochrome B mutant produces ethylene peaks with approximately 10 times the amplitude of the wild type. Time-course northern blots show that the mutant's abundance of the 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase mRNA SbACO2 is cyclic and is commensurate with ethylene production, and that ACC oxidase activity follows the same pattern. Both SbACO2 abundance and ACC oxidase activity in the wild-type plant are very low under this regimen. ACC levels in the two cultivars did not demonstrate fluctuations coincident with the ethylene produced. Simulated shading caused the wild-type plant to mimic the phenotype of the mutant and to produce high amplitude rhythms of ethylene evolution. The circadian feature of the ethylene cycle is conditionally present in the mutant and absent in the wild-type plant under simulated shading. SbACO2 abundance in both cultivars demonstrates a high-amplitude diurnal cycle under these conditions; however, ACC oxidase activity, although elevated, does not exhibit a clear rhythm correlated with ethylene production. ACC levels in both cultivars show fluctuations corresponding to the ethylene rhythm previously observed. It appears that at least two separate mechanisms may be involved in generating high-amplitude ethylene rhythms in sorghum, one in response to the loss of phytochrome B function and another in response to shading. (+info)
Quantifying the risks of TB infection to cattle posed by badger excreta.
Despite strong circumstantial evidence to suggest that the main route of TB transmission from badgers to cattle is via contaminated badger excreta, it is unclear whether the associated risks are high enough to account for the prevalence of the disease in south-west England. To decide whether this was a viable route of transmission, cattle contact with badger excreta was investigated using a deterministic approach to quantify the risks to cattle posed by badger excreta. Levels of investigative and grazing contacts between cattle and badger urine and faeces could each account for the disease prevalence in south-west England. An infection probability of 3.7 x 10(-4) per bite from pasture contaminated with badger urine infected with Mycobacterium bovis could account for the prevalence of TB in cattle in south-west England. Infection probabilities of 6.9 x 10(-7) per investigation and 1.1 x 10(-7) per bite from badger latrines could each account for the prevalence of TB in cattle in the south-west. When considering only the high risk areas of south-west England these bounds fell by a factor of eight. However, badger excreta may still constitute a high level of risk to cattle. The levels of cattle contact with badger excreta are far higher than previously thought, suggesting that it is the probability of infection per given contact with infected badger excreta which has the greater influence on the probability of transmission and not the level of contact. The infection probability per cattle contact with infected badger excreta is in all likelihood extremely low. (+info)
Fractionation of fiber and crude protein in fresh forages during the spring growth.
The composition of the fiber and CP of alfalfa, bromegrass, and endophyte-free and -infected tall fescue forages was compared during the spring growth from vegetative to reproductive stages. Forages were sampled from April 27 to June 6 in 1994, and from April 27 to June 11 in 1995, with 11 and 12 harvest dates, respectively. Total dietary fiber (TDF) was fractionated into insoluble and soluble fiber (SF). The CP of the forages was fractionated into nonprotein N (A), soluble CP (B1), insoluble CP that was soluble in neutral detergent (B2), CP insoluble in neutral detergent but soluble in acid detergent (B3), and CP insoluble in acid detergent (C). Effects of year, forage species, and harvest dates (day as a covariable) were included in the model. Across harvest dates, alfalfa (A) had lower (P < .01) TDF and higher (P < .01) SF concentrations than grasses (GR) (A: 49.9 and 14.4% and GR: 60.4 and 4.5% [OM basis] for TDF and SF, respectively). Alfalfa had higher (P < .01) CP (20.6% DM) than GR (15.3%). The rate of decrease in CP (% DM) across days was higher (P < .01) for bromegrass (-.4%/d) than for the other forages (-.29%/d). Fraction A (% of CP) was not different (P = .24) among forages (22.5%), but B1 was higher (P < .01) in A (17.1%) than in GR (13.2%). The B2 fraction (% of CP) was higher (P < .01) in A compared with GR (51.6 vs 45.9%, respectively). Alfalfa had lower (P < .01) B3 (3.0% of CP) than bromegrass (18.6%) and tall fescue (13.2%). Fraction C was not different (P = .23) among forages (3.8%). Fractions A, B1, and C (% of CP) did not change (P > .05) across days for all forages. Fraction B2 (% of CP) decreased across days in A (-.21%/d) but was not affected in GR. Fraction B3 (% of CP) increased (P < .05) in A (.1%/d), decreased in endophyte-infected tall fescue (-.20%/d), and did not change (P > .05) in the other forages. Crude protein and fiber composition were affected more by forage species than by maturity. The CP and NDF concentrations were more affected by maturity. Insoluble fractions but not soluble fractions of CP were affected by maturity. (+info)
Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures.
Bacterial community structure and diversity in rhizospheres in two types of grassland, distinguished by both plant species and fertilization regimen, were assessed by performing a 16S ribosomal DNA (rDNA) sequence analysis of DNAs extracted from triplicate soil plots. PCR products were cloned, and 45 to 48 clones from each of the six libraries were partially sequenced. Phylogenetic analysis of the resultant 275 clone sequences indicated that there was considerable variation in abundance in replicate unfertilized, unimproved soil samples and fertilized, improved soil samples but that there were no significant differences in the abundance of any phylogenetic group. Several clone sequences were identical in the 16S rDNA region analyzed, and the clones comprised eight pairs of duplicate clones and two sets of triplicate clones. Many clones were found to be most closely related to environmental clones obtained in other studies, although three clones were found to be identical to culturable species in databases. The clones were clustered into operational taxonomic units at a level of sequence similarity of >97% in order to quantify diversity. In all, 34 clusters containing two or more sequences were identified, and the largest group contained nine clones. A number of diversity, dominance, and evenness indices were calculated, and they all indicated that diversity was high, reflecting the low coverage of rDNA libraries achieved. Differences in diversity between sample types were not observed. Collector's curves, however, indicated that there were differences in the underlying community structures; in particular, there was reduced diversity of organisms of the alpha subdivision of the class Proteobacteria (alpha-proteobacteria) in improved soils. (+info)