Stimulated activity of the soil nitrifying community accelerates community adaptation to Zn stress

Field data have shown that soil nitrifying communities gradually adapt to zinc (Zn) after a single contamination event with reported adaptation times exceeding 1 year. It was hypothesized that this relatively slow adaptation relates to the restricted microbial diversity and low growth rate of the soil nitrifying community. This hypothesis was tested experimentally by recording adaptation rates under varying nitrification activities (assumed to affect growth rates) and by monitoring shifts in community composition. Soils were spiked at various Zn concentrations (0-4000 mg Zn kg⁻¹) and two NH₄⁺-N doses (N1, N2) were applied to stimulate growth. A control series receiving no extra NH₄⁺-N was also included. Soils were incubated in pots under field conditions with free drainage. The pore water Zn concentration at which nitrification was halved (EC50, mg Zn l⁻¹) did not change significantly during 12 months in the control series (without NH₄⁺-N applications), although nitrification recovered after 12 months at the highest Zn dose only. The EC50 after 12 months incubation increased by more than a factor 10 with increasing NH₄⁺-N dose (p < 0.05) illustrating that increased activity accelerates adaptation to Zn. Zinc tolerance tests confirmed the role of Zn exposure, time and NH₄⁺-N dose on adaptation. Zinc tolerance development was ascribed to the AOB community since the AOB/AOA ratio (AOB = ammonia oxidizing bacteria; AOA = ammonia oxidizing archaea) increased from 0.4 in the control to 1.4 in the most tolerant community. Moreover, the AOB amoA DGGE profile changed during Zn adaptation whereas the AOA amoA DGGE profile remained unaffected. These data confirm the slow but pronounced adaptation of nitrifiers to Zn contamination. We showed that adaptation to Zn was accelerated at higher activity and was associated with a shift in soil AOB community that gradually dominated the nitrifying community.     

Quantitative PCR assays to enumerate Rhizobium leguminosarum strains in soil also target non viable cells and overestimate those detected by the plant infection method

The plant infection method is commonly used to estimate the Most Probable Number (MPN) of soil rhizobia. Here, a qPCR method was set-up and validated with newly developed ANU (strain specific) and RHIZ (more general) primers to quantify the specific Rhizobium leguminosarum bv. trifolii ANU843 strain or general R. leguminosarum strains. Detection limits of qPCR protocols in soil were 1.2 × 10⁴ (ANU) and 4.2 × 10³ (RHIZ) cells per g soil. The qPCR assay appears robust and accurate in freshly inoculated soils but overestimated MPN for indigenous soil rhizobia. An incubation experiment showed that qPCR detected added DNA or non viable cells in soils up to 5 months after addition and incubation at 20 °C in moist conditions.     

Somatic hybridization as a tool for tomato breeding

Protoplast fusion can be used to produce somatic hybrids of species that cannot be obtained by sexual hybridization. The possibility to introgress genes from Solanum species into the cultivated tomato species Lycopersicon esculentum, and to obtain novel cytoplasm-nucleus combinations (cybrids) was considered as an important strategy to extend the genetic variation available for tomato breeding. Somatic hybrids between L. esculentum and other Lycopersicon species, as well as between L. esculentum and Solanum or Nicotiana species, have been produced. Specific mutants, genotypes with antibiotic resistances, and metabolic inhibition by iodoacetate or iodoacetamide and irradiation were used for the selection of hybrids. In addition, the improvement of protoplast culture techniques and the use of the favourable tissue culture traits derived from species such as L. peruvianum, which have been introduced into tomato by classical breeding, allowed the efficient recovery of somatic hybrids. However, the occurrence of somatic incongruity in fusion combinations of L. esculentum and Solanum and even more in L. esculentum and Nicotiana, did not allow the production of true cybrids and/or fertile hybrids, indicating the importance of both cytoplasm-nucleus and nucleus-nucleus interactions in somatic incongruity. Another problem with fusions between distantly related species is the strongly reduced fertility of the hybrids and the very limited homoeologous recombination between chromosomes of the parental species. Partial genome transfer from donor to recipient through microprotoplast (+) protoplast fusion, and the production of monosomic or disomic chromosome addition lines, light overcome some of these problems. In symmetric somatic hybrids between L. esculentum and S. tuberosum the occurrence of limited somatic and meiotic recombination was demonstrated. Fertile progeny plants could be obtained, though at a low frequency, when embryo rescue was performed on a large scale after backcrossing hexaploid somatic tomato (+) potato hybrids with a tetraploid potato genotype. The potential value of genomic in situ hybridization (GISH) and RFLPs for the analysis of the genome/chromosome composition of the hybrids has been demonstrated for intergeneric somatic hybrids between Lycopersicon and Solanum.Abbreviations cpDNA chloroplast DNA - mtDNA mitochondrial DNA     

Reassortment among bovine, porcine and human rotavirus strains results in G8P[7] and G6P[7] strains isolated from cattle in South Korea

Group A rotaviruses (GARVs) cause severe acute gastroenteritis in children and young animals. Although zoonotic infections with bovine-like G6 and G8 GARVs have been reported in many countries, there is little evidence for reassortment between bovine GARVs and GARVs from heterologous species. The finding of bovine GARVs with the G6 and G8 genotypes in combination with the typical porcine P[7] prompted us to characterize all 11 genes of 30 bovine GARVs isolated from clinically infected calves. By the comparison of the full-length ORF of VP7 and NSP1-5, and the partial VP1-4 and VP6 nucleotide sequences between the 30 Korean and other known strains, three different genome constellations were found. Twenty seven strains showed the G8-P[7]-I5-R1-C1-M2-A1-N1-T1-E1-H1 genotypes, a single strain possessed the G6-P[7]-I2-R2-C1-M2-A1-N2-T1-E2-H1 genotype constellation and 2 strains the G6-P[7]-I2-R2-C2-M2-A3-N2-T6-E2-H3 genotype constellation. The complete genome of a single reference strains for each of these three genotype constellations (KJ25, KJ9-1 and KJ19-2) was determined and analyzed. A detailed phylogenetic analysis revealed a complicated picture, with several reassortments among bovine-like, porcine-like and human-like GARV strains, resulting in several different reassortant strains successfully infecting cattle.     

The identification of a barley haze active protein that influences beer haze stability: Cloning and characterisation of the barley SE protein as a barley trypsin inhibitor of the chloroform/methanol type

Previous pilot brewing trials have demonstrated that in the absence of a molecular weight (MW) 12,000 (barley silica eluate (SE) protein), the beer brewed from the malt of these SE −ve varieties formed less haze after accelerated ageing than beers brewed using SE +ve malt varieties. The previously described SE protein was characterised using comparative two-dimensional (2-D) gel electrophoresis immunoblots of barley seed extracts from both SE +ve and SE −ve varieties. The SE protein spot identified was excised and its partial sequence determined, after in-gel cleavage using trypsin and separation of the resulting fragments by reversed-phase high performance liquid chromatography (HPLC). N-terminal sequence analysis of the tryptic peptides from SE +ve and SE −ve varieties identified the SE protein as the barley trypsin inhibitor-CMe precursor (BTI-CMe). The mature BTI-CMe protein is 13.3 kDa and its functional gene is located on chromosome 3H. Cloning of the BTI-CMe protein demonstrated that both SE −ve and SE +ve barley varieties contain a BTI-CMe protein family member that is similar but has a consistently different sequence, primarily in the last 30 amino acid residues of their C-termini.     

Field determination of soil hydraulic properties for simulation of the optimum watertable regime

A field experiment to evaluate accurate cost and time efficient methodologies for determining soil hydraulic properties was done at the NIAB Research Station at Faisalabad, Pakistan. The experiment was performed on a freely draining loamy soil. This soil type is representative of 75% of the topsoil in a tile drainage area known as the Fourth Drainage Project. Redistribution of water was monitored at five locations, for seven depths, following a steady state infiltration for prolonged time. The data were analyzed with Darcian flow analysis, three simplified methods, and two parameter optimization programs to calculate unsaturated hydraulic conductivity. The Darcian flow analysis was used as a reference against which the simplified methods were compared. Two simplified methods produced satisfactory results with less effort. The drawback is that the simplified methods alone do not provide enough information for use in simulation models. The advantage of the two optimization programs — SFIT and RETC — is that they are based on a continuous function which describes complete h() and K() curves. This is a requirement for computer simulation of salt and water movement in the unsaturated soil. The results of the optimizations were evaluated by their correspondence to field measurements and to laboratory measurements and by their ability to simulate soil water flow. Both programs fit the observed field data well, but only the SFIT optimized parameters were suitable for soil water flow simulations.Abbreviations IWASRI International Waterlogging and Salinity Research Institute - NRAP Netherlands Research Assistance Project - NIAB Nuclear Institute for Agriculture and Biology - SSP Soil Survey of Pakistan Revised paper from Field determination of soil hydraulic properties presented in ICID, CIID IDW5, Lahore, Pakistan (1–55 — 1–64).     

Co-tolerance to zinc and copper of the soil nitrifying community and its relationship with the community structure

Soil microbial communities can develop trace metal tolerance upon soil contamination with corresponding metals. A few studies have reported co-tolerance in such cases, i.e. tolerance to other metals than those to which the microbial community had been exposed to. This study was set-up to test for co-tolerance of nitrifying communities to zinc (Zn) and copper (Cu) and to relate tolerances to shifts in community structure using amoA AOB (ammonia oxidizing bacteria) DGGE. Seven sets of soils, each representing a Cu or Zn contamination gradient were sampled from four locations. At two locations, both Cu and Zn had been added as single contaminants. Increased Zn and Cu tolerance of the nitrifying communities was consistently observed in response to corresponding soil contamination. Co-tolerance to Zn was obtained in two of the three Cu gradients and that to Cu in one of the four Zn gradients. DGGE analysis and sequencing showed that contamination with either Zn or Cu selected for identical AOB phylotypes in soils at one location but not at the other location. The nitrifying community structures in soils from different locations did not become more similar upon Zn exposure than those in corresponding uncontaminated soils. Hence, trace metal tolerance development was not due to the emergence of specific AOB phylotypes, but due to the emergence of different AOB phylotypes bearing tolerance mechanisms for Zn, Cu or both metals.     

Secreted antigens of Mycobacterium avium subspecies paratuberculosis as prominent immune targets

We here describe the identification and characterization of three novel secreted Mycobacterium avium subsp. paratuberculosis antigens of 9, 15 and 34 kDa (Map2609, Map2942c and Map0210c, respectively) by screening a genomic expression library with a serum of a naturally infected clinical cow. The 9, 15 and 34 kDa antigens display strong homology to previously described M. tuberculosis antigens, TB8.4, MPT53 and Erp, respectively. Furthermore, these antigens were shown to be recognized by antibodies from infected cattle, when tested with a limited number of sera from subclinical (n=7) and clinical (n=3) infected cattle.