Autotrophic production of polyhydroxyalkanoates using acidogenic-derived H2 and CO2 from fruit waste

The environmental concerns regarding fossil plastics call for alternative biopolymers such as polyhydroxyalkanoates (PHAs) whose manufacturing costs are however still too elevated. Autotrophic microbes like Cupriavidus necator, able to convert CO2 and H2 into PHAs, offer an additional strategy. Typically, the preferred source for CO2 and H2 are expensive pure gases or syngas, which has toxic compounds for most PHAs-accumulating strains. In this work, for the first time, H2 and CO2 originating from an acidogenic reactor were converted autotrophically into poly(3-hydroxybutyrate) P(3HB). During the first stage, a mixed microbial community continuously catabolized melon waste into H2 (26.7 %) and CO2 (49.2 %) that were then used in a second bioreactor by C. necator DSM 545 to accumulate 1.7 g/L P(3HB). Additionally, the VFAs (13 gCOD/L) produced during acidogenesis were processed into 2.7 g/L of P(3HB-co-3HV). This is the first proof-of-concept of using acidogenic-derived H2 and CO2 from fruit waste to produce PHAs.

Renewing Lost Genetic Variability with a Classical Yeast Genetics Approach

Due to their long domestication time course, many industrial Saccharomyces cerevisiae strains are adopted in numerous processes mostly for historical reasons instead of scientific and technological needs. As such, there is still significant room for improvement for industrial yeast strains relying on yeast biodiversity. This paper strives to regenerate biodiversity with the innovative application of classic genetic methods to already available yeast strains. Extensive sporulation was indeed applied to three different yeast strains, specifically selected for their different origins as well as backgrounds, with the aim of clarifying how new variability was generated. A novel and easy method to obtain mono-spore colonies was specifically developed, and, to reveal the extent of the generated variability, no selection after sporulation was introduced. The obtained progenies were then tested for their growth in defined mediums with high stressor levels. A considerable and strain-specific increase in both phenotypic and metabolomic variability was assessed, and a few mono-spore colonies were found to be of great interest for their future exploitation in selected industrial processes.

Innovative co-production of polyhydroxyalkanoates and methane from broken rice

Broken rice, a low-cost starchy residue of the rice industry, can be an interesting substrate to reduce the polyhydroxyalkanoates (PHAs) production cost. However, since the most common PHAs-producing strains lack amylases, this waste must be firstly hydrolysed by additional commercial enzymes. In this work, the acidogenesis phase of the anaerobic digestion was exploited as efficient hydrolysis step to convert broken rice into volatile fatty acids (VFAs) to be used as PHAs carbon source by Cupriavidus necator DSM 545, one of the most promising PHAs-producing microbes. Broken rice, both non-hydrolysed and enzymatically hydrolysed, was processed in two continuous stirred tank reactors, at hydraulic retention times (HRT) of 5, 4 and, 3 days, to produce VFAs. The highest VFAs levels were obtained from non-hydrolysed broken rice which was efficiently exploited for PHAs accumulation by C. necator DSM 545. PHAs contents were higher after 96 h of incubation and, noteworthy, reached the highest value of 0.95 g/L in the case of 4 days HRT without any chemicals supplementation, except vitamins. Moreover, in view of a biorefinery approach, the residual solid fraction was used for methane production resulting in promising CH₄ levels. Methane yields were very promising again for 4 days HRT. As such, this HRT resulted to be the most suitable to obtain effluents with high promise in terms of both PHAs accumulation and CH₄ production. In addition, these results demonstrate that broken rice could be efficiently processed into two valuable products without any costly enzymatic pre-treatment and pave the way for future biorefining approaches where this by-product can be converted in a cluster of added-value compounds. Techno-economical estimations are in progress to assess the feasibility of the entire process, in view of supporting the low-cost conversion of organic waste into valuable products.

Engineering Cupriavidus necator DSM 545 for the one-step conversion of starchy waste into polyhydroxyalkanoates

Starch-rich by-products could be efficiently exploited for polyhydroxyalkanoates (PHAs) production. Unfortunately, Cupriavidus necator DSM 545, one of the most efficient PHAs producers, is not able to grow on starch. In this study, a recombinant amylolytic strain of C. necator DSM 545 was developed for the one-step PHAs production from starchy residues, such as broken rice and purple sweet potato waste. The glucodextranase G1d from Arthrobacter globiformis I42 and the α-amylase amyZ from Zunongwangia profunda SM-A87 were co-expressed into C. necator DSM 545. The recombinant C. necator DSM 545 #11, selected for its promising hydrolytic activity, produced high biomass levels with noteworthy PHAs titers: 5.78 and 3.65 g/L from broken rice and purple sweet potato waste, respectively. This is the first report on the engineering of C. necator DSM 545 for efficient amylase production and paves the way to the one-step conversion of starchy waste into PHAs.

Natural Saccharomyces cerevisiae Strain Reveals Peculiar Genomic Traits for Starch-to-Bioethanol Production: the Design of an Amylolytic Consolidated Bioprocessing Yeast

Natural yeast with superior fermentative traits can serve as a platform for the development of recombinant strains that can be used to improve the sustainability of bioethanol production from starch. This process will benefit from a consolidated bioprocessing (CBP) approach where an engineered strain producing amylases directly converts starch into ethanol. The yeast Saccharomyces cerevisiae L20, previously selected as outperforming the benchmark yeast Ethanol Red, was here subjected to a comparative genomic investigation using a dataset of industrial S. cerevisiae strains. Along with Ethanol Red, strain L20 was then engineered for the expression of α-amylase amyA and glucoamylase glaA genes from Aspergillus tubingensis by employing two different approaches (delta integration and CRISPR/Cas9). A correlation between the number of integrated copies and the hydrolytic abilities of the recombinants was investigated. L20 demonstrated important traits for the construction of a proficient CBP yeast. Despite showing a close relatedness to commercial wine yeast and the benchmark Ethanol Red, a unique profile of gene copy number variations (CNVs) was found in L20, mainly encoding membrane transporters and secretion pathway proteins but also the fermentative metabolism. Moreover, the genome annotation disclosed seven open reading frames (ORFs) in L20 that are absent in the reference S288C genome. Genome engineering was successfully implemented for amylase production. However, with equal amylase gene copies, L20 proved its proficiency as a good enzyme secretor by exhibiting a markedly higher amylolytic activity than Ethanol Red, in compliance to the findings of the genomic exploration. The recombinant L20 dT8 exhibited the highest amylolytic activity and produced more than 4 g/L of ethanol from 2% starch in a CBP setting without the addition of supplementary enzymes. Based on the performance of this strain, an amylase/glucoamylase ratio of 1:2.5 was suggested as baseline for further improvement of the CBP ability. Overall, L20 showed important traits for the future construction of a proficient CBP yeast. As such, this work shows that natural S. cerevisiae strains can be used for the expression of foreign secreted enzymes, paving the way to strain improvement for the starch-to-bioethanol route.

Selection of Superior Yeast Strains for the Fermentation of Lignocellulosic Steam-Exploded Residues

The production of lignocellulosic ethanol calls for a robust fermentative yeast able to tolerate a wide range of toxic molecules that occur in the pre-treated lignocellulose. The concentration of inhibitors varies according to the composition of the lignocellulosic material and the harshness of the pre-treatment used. It follows that the versatility of the yeast should be considered when selecting a robust strain. This work aimed at the validation of seven natural Saccharomyces cerevisiae strains, previously selected for their industrial fitness, for their application in the production of lignocellulosic bioethanol. Their inhibitor resistance and fermentative performances were compared to those of the benchmark industrial yeast S. cerevisiae Ethanol Red, currently utilized in the second-generation ethanol plants. The yeast strains were characterized for their tolerance using a synthetic inhibitor mixture formulated with increasing concentrations of weak acids and furans, as well as steam-exploded lignocellulosic pre-hydrolysates, generally containing the same inhibitors. The eight non-diluted liquors have been adopted to assess yeast ability to withstand bioethanol industrial conditions. The most tolerant S. cerevisiae Fm17 strain, together with the reference Ethanol Red, was evaluated for fermentative performances in two pre-hydrolysates obtained from cardoon and common reed, chosen for their large inhibitor concentrations. S. cerevisiae Fm17 outperformed the industrial strain Ethanol Red, producing up to 18 and 39 g/L ethanol from cardoon and common reed, respectively, with ethanol yields always higher than those of the benchmark strain. This natural strain exhibits great potential to be used as superior yeast in the lignocellulosic ethanol plants.

Efficient production of polyhydroxybutyrate from slaughterhouse waste using a recombinant strain of Cupriavidus necator DSM 545

Slaughterhouse residues are greatly available and can pose a threat to the environment if not disposed of correctly. Such by-products can be proficiently processed into polyhydroxyalkanoates by accurately selected and developed bacterial strains. Cupriavidus necator DSM 545, one of the most efficient polyhydroxyalkanoates-producing strain, cannot grow well on fatty substrates. In this work, a recombinant lipolytic C. necator microbe was developed for the efficient conversion of slaughtering by-products into polyhydroxyalkanoates. Two lipase sequences, lipC and lipH of Pseudomonas stutzeri BT3, were effectively expressed in C. necator DSM 545. The engineered strain C. necator DSM 545 JR11, selected for the outstanding extracellular lipolytic activity, produced high levels of polyhydroxyalkanoates (nearly 65% of cell dry mass) from udder, jowl and membrane caul fat. This research is crucial to the cost-effective one-step processing of slaughterhouse waste into polyhydroxyalkanoates with useful applications in several industrial and medical sectors.

Internal medicine inpatients' prevalence of misdiagnosed severe osteoporosis

Vertebral fractures (VF) related to osteoporosis (i.e., severe OP) increase the risk of disability and mortality, but they are often neglected. We observed a severe OP misdiagnosis in 28.9% of inpatients with previous spinal imaging positive for VFs. Diagnosing severe OP is crucial to reduce the health care costs of inpatients.

INTRODUCTION

Vertebral fractures (VFs) related to osteoporosis (OP) increase the risk of additional fractures and death. In inpatients, VFs are often neglected with consequent delay in OP treatments, prolongation of hospitalization, and reduction of life expectancy. The aim of this study was to evaluate the prevalence of a misdiagnosed severe OP (i.e., with VF) in general medicine inpatients.

METHODS

We evaluated inpatients of a Medicine Unit between January 2019 and December 2019 without severe OP diagnosis, who had spinal imaging. For each patient, we collected demographic data, previous or current OP treatment, and presence/number of VFs. Descriptive data were presented by medians (interquartile range [IQR]) for continuous data or as numbers (percentages) for categorical data. Differences between subgroups were analyzed with chi-square or Kruskal-Wallis tests as appropriate. p-values <0.05 were considered statistically significant.

RESULTS

793 subjects were admitted to inpatient's clinic: 235 (135 females and 100 males with a median age of 76.0 [64.0-83.0] years) were enrolled. One or more vertebral fractures were present in 28.9% (68/235) subjects; 47% (32/68) had two or more vertebral fractures. The majority of patients (55/68) with VFs had not previously received a severe OP diagnosis.

CONCLUSIONS

Severe OP was misdiagnosed in at least 8.6% of inpatients. The prevalence dramatically increases (about 29%) in subjects with previous spinal imaging showing one or more VFs. More attention should be given to this co-morbidity, which is known to be an additional risk factor for disability and mortality.

Light excess stimulates Poly-beta-hydroxybutyrate yield in a mangrove-isolated strain of Synechocystis sp

Poly-β-hydroxybutyrate (PHB) is a biodegradable biopolymer that may replace fossil-based plastics reducing its negative environmental impact. One highly sustainable strategy to produce these biopolymers is the exploitation of photosynthetic microorganisms that use sunlight and CO₂ to produce biomass and subsequently, PHB. Exploring environmental biological diversity is a powerful tool to find resilient microorganisms potentially exploitable to produce bioproducts. In this work, a cyanobacterium (Synechocystis sp.) isolated from a contaminated area close to an important industrial complex was shown to produce PHB under different culture conditions. Carbon, nutrients supply and light intensity impact on biomass and PHB productivity were assessed, showing that the highest yield of PHB achieved was 241 mg L^-1 (31%_dcw) under high light intensity. Remarkably this condition not only stimulated PHB accumulation by 70% compared to other conditions tested but also high cellular duplication rate, maximizing the potential of this strain for PHB production.

Conversion of Starchy Waste Streams into Polyhydroxyalkanoates Using Cupriavidus necator DSM 545

Due to oil shortage and environmental problems, synthetic plastics have to be replaced by different biodegradable materials. A promising alternative could be polyhydroxyalkanoates (PHAs), and the low-cost abundant agricultural starchy by-products could be usefully converted into PHAs by properly selected and/or developed microbes. Among the widely available starchy waste streams, a variety of residues have been explored as substrates, such as broken, discolored, unripe rice and white or purple sweet potato waste. Cupriavidus necator DSM 545, a well-known producer of PHAs, was adopted in a simultaneous saccharification and fermentation (SSF) process through an optimized dosage of the commercial amylases cocktail STARGEN™ 002. Broken rice was found to be the most promising carbon source with PHAs levels of up to 5.18 g/L. This research demonstrates that rice and sweet potato waste are low-cost feedstocks for PHAs production, paving the way for the processing of other starchy materials into bioplastics.

Metabolomic Alterations Do Not Induce Metabolic Burden in the Industrial Yeast M2n[pBKD2-Pccbgl1]-C1 Engineered by Multiple δ-Integration of a Fungal β-Glucosidase Gene

In the lignocellulosic yeast development, metabolic burden relates to redirection of resources from regular cellular activities toward the needs created by recombinant protein production. As a result, growth parameters may be greatly affected. Noteworthy, Saccharomyces cerevisiae M2n[pBKD2-Pccbgl1]-C1, previously developed by multiple δ-integration of the β-glucosidase BGL3, did not show any detectable metabolic burden. This work aims to test the hypothesis that the metabolic burden and the metabolomic perturbation induced by the δ-integration of a yeast strain, could differ significantly. The engineered strain was evaluated in terms of metabolic performances and metabolomic alterations in different conditions typical of the bioethanol industry. Results indicate that the multiple δ-integration did not affect the ability of the engineered strain to grow on different carbon sources and to tolerate increasing concentrations of ethanol and inhibitory compounds. Conversely, metabolomic profiles were significantly altered both under growing and stressing conditions, indicating a large extent of metabolic reshuffling involved in the maintenance of the metabolic homeostasis. Considering that four copies of BGL3 gene have been integrated without affecting any parental genes or promoter sequences, deeper studies are needed to unveil the mechanisms implied in these metabolomic changes, thus supporting the optimization of protein production in engineered strains.

A yeast metabolome-based model for an ecotoxicological approach in the management of lignocellulosic ethanol stillage

Lignocellulosic bioethanol production results in huge amounts of stillage, a potentially polluting by-product. Stillage, rich in heavy metals and, mainly, inhibitors, requires specific toxicity studies to be adequately managed. To this purpose, we applied an FTIR ecotoxicological bioassay to evaluate the toxicity of lignocellulosic stillage. Two weak acids and furans, most frequently found in lignocellulosic stillage, have been tested in different mixtures against three Saccharomyces cerevisiae strains. The metabolomic reaction of the test microbes and the mortality induced at various levels of inhibitor concentration showed that the strains are representative of three different types of response. Furthermore, the relationship between concentrations and FTIR synthetic stress indexes has been studied, with the aim of defining a model able to predict the concentrations of inhibitors in stillage, resulting in an optimized predictive model for all the strains. This approach represents a promising tool to support the ecotoxicological management of lignocellulosic stillage.

Nuclease expression in efficient polyhydroxyalkanoates-producing bacteria could yield cost reduction during downstream processing

Industrial manufacturing of polyhydroxyalkanoates (PHAs) requires purification of PHAs granules from high-cell-density cultures. Cells are broken by homogenization and PHAs granules are cleansed and treated to obtain PHAs latexes. However, cell lysis releases large amounts of DNA which results in an increasing viscosity of the medium, hampering the following downstream steps. Drop in viscosity is generally achieved by costly procedures such as heat treatment or the supplementation of hypochlorite and commercially available nucleases. Searching for a cost-effective solution to this issue, a nuclease gene from Staphylococcus aureus has been integrated into two efficient PHAs-producing bacteria: Cupriavidus necator DSM 545 and Delftia acidovorans DSM 39. Staphylococcal nuclease has been proficiently expressed in both microbial hosts without affecting PHAs production. Moreover, the viscosity of the lysates of recombinant C. necator cells was greatly reduced, indicating that the engineered strain is expected to yield large reduction cost in PHAs downstream processing.

Production of bioethanol from multiple waste streams of rice milling

This work describes the feasibility of using rice milling by-products as feedstock for bioethanol. Starch-rich residues (rice bran, broken, unripe and discolored rice) were individually fermented (20%w/v) through Consolidated Bioprocessing by two industrial engineered yeast secreting fungal amylases. Rice husk (20%w/v), mainly composed by lignocellulose, was pre-treated at 55°C with alkaline peroxide, saccharified through optimized dosages of commercial enzymes (Cellic® CTec2) and fermented by the recombinant strains. Finally, a blend of all the rice by-products, formulated as a mixture (20%w/v) according to their proportions at milling plants, were co-processed to ethanol by optimized pre-treatment, saccharification and fermentation by amylolytic strains. Fermenting efficiency for each by-product was high (above 88% of the theoretical) and further confirmed on the blend of residues (nearly 52g/L ethanol). These results demonstrated for the first time that the co-conversion of multiple waste streams is a promising option for second generation ethanol production.

A novel FTIR-based approach to evaluate the interactions between lignocellulosic inhibitory compounds and their effect on yeast metabolism

FTIR analysis revealed antagonistic effects between lignocellulosic inhibitory compounds through the metabolomic alterations induced on differentS. cerevisiaestrains.

Consolidated bioprocessing of starchy substrates into ethanol by industrial Saccharomyces cerevisiae strains secreting fungal amylases

The development of a yeast strain that converts raw starch to ethanol in one step (called Consolidated Bioprocessing, CBP) could significantly reduce the commercial costs of starch-based bioethanol. An efficient amylolytic Saccharomyces cerevisiae strain suitable for industrial bioethanol production was developed in this study. Codon-optimized variants of the Thermomyces lanuginosus glucoamylase (TLG1) and Saccharomycopsis fibuligera α-amylase (SFA1) genes were δ-integrated into two S. cerevisiae yeast with promising industrial traits, i.e., strains M2n and MEL2. The recombinant M2n[TLG1-SFA1] and MEL2[TLG1-SFA1] yeast displayed high enzyme activities on soluble and raw starch (up to 8118 and 4461 nkat/g dry cell weight, respectively) and produced about 64 g/L ethanol from 200 g/L raw corn starch in a bioreactor, corresponding to 55% of the theoretical maximum ethanol yield (g of ethanol/g of available glucose equivalent). Their starch-to-ethanol conversion efficiencies were even higher on natural sorghum and triticale substrates (62 and 73% of the theoretical yield, respectively). This is the first report of direct ethanol production from natural starchy substrates (without any pre-treatment or commercial enzyme addition) using industrial yeast strains co-secreting both a glucoamylase and α-amylase.

Exploring grape marc as trove for new thermotolerant and inhibitor-tolerant Saccharomyces cerevisiae strains for second-generation bioethanol production

BACKGROUND

Robust yeasts with high inhibitor, temperature, and osmotic tolerance remain a crucial requirement for the sustainable production of lignocellulosic bioethanol. These stress factors are known to severely hinder culture growth and fermentation performance.

RESULTS

Grape marc was selected as an extreme environment to search for innately robust yeasts because of its limited nutrients, exposure to solar radiation, temperature fluctuations, weak acid and ethanol content. Forty newly isolated Saccharomyces cerevisiae strains gave high ethanol yields at 40°C when inoculated in minimal media at high sugar concentrations of up to 200 g/l glucose. In addition, the isolates displayed distinct inhibitor tolerance in defined broth supplemented with increasing levels of single inhibitors or with a cocktail containing several inhibitory compounds. Both the fermentation ability and inhibitor resistance of these strains were greater than those of established industrial and commercial S. cerevisiae yeasts used as control strains in this study. Liquor from steam-pretreated sugarcane bagasse was used as a key selective condition during the isolation of robust yeasts for industrial ethanol production, thus simulating the industrial environment. The isolate Fm17 produced the highest ethanol concentration (43.4 g/l) from the hydrolysate, despite relatively high concentrations of weak acids, furans, and phenolics. This strain also exhibited a significantly greater conversion rate of inhibitory furaldehydes compared with the reference strain S. cerevisiae 27P. To our knowledge, this is the first report describing a strain of S. cerevisiae able to produce an ethanol yield equal to 89% of theoretical maximum yield in the presence of high concentrations of inhibitors from sugarcane bagasse.

CONCLUSIONS

This study showed that yeasts with high tolerance to multiple stress factors can be obtained from unconventional ecological niches. Grape marc appeared to be an unexplored and promising substrate for the isolation of S. cerevisiae strains showing enhanced inhibitor, temperature, and osmotic tolerance compared with established industrial strains. This integrated approach of selecting multiple resistant yeasts from a single source demonstrates the potential of obtaining yeasts that are able to withstand a number of fermentation-related stresses. The yeast strains isolated and selected in this study represent strong candidates for bioethanol production from lignocellulosic hydrolysates.

Designing industrial yeasts for the consolidated bioprocessing of starchy biomass to ethanol

Consolidated bioprocessing (CBP), which integrates enzyme production, saccharification and fermentation into a one step process, is a promising strategy for the effective ethanol production from cheap lignocellulosic and starchy materials. CBP requires a highly engineered microbial strain able to both hydrolyze biomass with enzymes produced on its own and convert the resulting simple sugars into high-titer ethanol. Recently, heterologous production of cellulose and starch-degrading enzymes has been achieved in yeast hosts, which has realized direct processing of biomass to ethanol. However, essentially all efforts aimed at the efficient heterologous expression of saccharolytic enzymes in yeast have involved laboratory strains and much of this work has to be transferred to industrial yeasts that provide the fermentation capacity and robustness desired for large scale bioethanol production. Specifically, the development of an industrial CBP amylolytic yeast would allow the one-step processing of low-cost starchy substrates into ethanol. This article gives insight in the current knowledge and achievements on bioethanol production from starchy materials with industrial engineered S. cerevisiae strains.

Effects of heat treatment on microbial communities of granular sludge for biological hydrogen production

Dark fermentation shares many features with anaerobic digestion with the exception that to maximize hydrogen production, methanogens and hydrogen-consuming bacteria should be inhibited. Heat treatment is widely applied as an inoculum pre-treatment due to its effectiveness in inhibiting methanogenic microflora but it may not exclusively select for hydrogen-producing bacteria. This work evaluated the effects of heat treatment on microbial viability and structure of anaerobic granular sludge. Heat treatment was carried out on granular sludge at 100 °C with four residence times (0.5, 1, 2 and 4 h). Hydrogen production of treated sludges was studied from glucose by means of batch test at different pH values. Results indicated that each heat treatment strongly influenced the granular sludge resulting in microbial communities having different hydrogen productions. The highest hydrogen yields (2.14 moles of hydrogen per mole of glucose) were obtained at pH 5.5 using the sludge treated for 4 h characterized by the lowest CFU concentration (2.3 × 10(3)CFU/g sludge). This study demonstrated that heat treatment should be carefully defined according to the structure of the sludge microbial community, allowing the selection of highly efficient hydrogen-producing microbes.

Polyhydroxyalkanoates production by engineered Cupriavidus necator from waste material containing lactose

Cupriavidus necator DSM 545 is a well-known polyhydroxyalkanoates (PHAs) producer, but unable to grow on lactose. The aim of this study was to construct a recombinant strain of C. necator that can use lactose-containing waste material such as cheese whey, to produce PHAs. One of the intracellular PHA depolymerases (phaZ1) of C. necator was chosen to insert the lacZ, lacI and lacO genes of Escherichia coli. This would have the effect to allow polymer production on lactose and, at the same time, to remove part of the PHA intracellular degradation system. Disruption of phaZ1 was achieved by gene replacement after isolating a fragment of this gene and interrupting it with a cartridge containing the lac genes and a synthetic promoter. Growth and polymer production studies of the genetically modified (GM) strain mRePT in lactose, whey permeate and hydrolyzed whey permeate as carbon sources, were performed. Lower PHA degradation and higher yields were obtained compared to the wild-type strain. Inactivation of the putative depolymerase gene phaZ3 on mRePT recombinant strain was also reported.

New evidence for nitrogen fixation within the Italian white truffle Tuber magnatum

Diversity of nitrogen-fixing bacteria and the nitrogen-fixation activity was investigated in Tuber magnatum, the most well-known prized species of Italian white truffle. Degenerate PCR primers were applied to amplify the nitrogenase gene nifH from T. magnatum ascomata at different stages of maturation. Putative amino acid sequences revealed mainly the presence of Alphaproteobacteria belonging to Bradyrhizobium spp. and expression of nifH genes from Bradyrhizobia was detected. The nitrogenase activity evaluated by acetylene reduction assay was 0.5-7.5μmolC(2)H(4)h(-1)g(-1), comparable with early nodules of legumes associated with specific nitrogen-fixing bacteria. This is the first demonstration of nitrogenase expression gene and activity within truffle.

Pseudomonas fluorescens 134 as a Biological Control Agent (BCA) Model in Cell Immobilization Technology

Antifungal activity against Rhizoctonia solani was achieved in vivo through the application of Pseudomonas fluorescens strain 134 encapsulated in sodium alginate beads of different sizes (0.5, 1, and 2 mm). The activity was compared to that obtainable with chemical treatments and bead-derived liquid formulations. The latter was obtained by dissolving alginate beads of 1 and 0.5 mm in 1% Na-citrate solution before application, without any significant (P < 0.05) reduction of bacterial numbers during the dissolution process. The dry bead formulations were applied next to the seeds in plant inoculation experiments, resulting in a reduction of disease symptoms, which were markedly reduced when the liquid formulation was applied. Moreover, the rate of disease symptoms related to liquid formulations from both 1 and 0.5 mm beads was comparable (near to 10%) to that of chemical treatment. Pseudomonas fluorescens strain 134 delivered as both dry and liquid formulations was able to colonize cotton root at a population density of about 10(8) CFU/g fresh root, 15 days after sowing.

Selenite-reducing capacity of the copper-containing nitrite reductase ofRhizobium sullae

Rhizobium sullae strain HCNT1 contains a nitric oxide-producing nitrite reductase of unknown function due to the absence of a complementary nitric oxide reductase. HCNT1 had the ability to grow on selenite concentrations as high as 50 mM, and during growth, selenite was reduced to the less toxic elemental selenium. An HCNT1 mutant lacking nitrite reductase grew poorly in the presence of 5 mM selenite, was unable to grow in the presence of 25 or 50 mM selenite and also showed no evidence of selenite reduction. A naturally occurring nitrite reductase-deficient R. sullae strain, CC1335, also showed little growth on the higher concentrations of selenite. Mobilization of a plasmid containing the HCNT1 gene encoding nitrite reductase into CC1335 increased its resistance to selenite. To confirm that this ability to grow in the presence of high concentrations of selenite correlated with nitrite reductase activity, a new nitrite reductase-containing strain was isolated from the same location where HCNT1 was isolated. This strain was also resistant to high concentrations of selenite. Inactivation of the gene encoding nitrite reductase in this strain increased selenite sensitivity. These data suggest that the nitrite reductase of R. sullae provides resistance to selenite and offers an explanation for the radically truncated denitrification found uniquely in this bacterium.

Resuscitation of Viable But Not Culturable Sinorhizobium meliloti 41 pRP4-luc: Effects of Oxygen and Host Plant

A plasmid-borne, firefly-derived, luciferase gene (luc) was inserted and stably inherited in Sinorhizobium meliloti 41 as a reporter gene. The strain obtained, S. meliloti 41/pRP4-luc, and its parental strain served as a model system for viable but not culturable (VBNC) resuscitation experiments in both in vitro and soil samples. Incubation under oxygen (02) concentrations varying from 1% to atmospheric levels did not result in resuscitation. A demonstration of recovery was attained through exposure to the appropriate concentrations of antibiotics, bacteriostatic chloramphenicol, and bactericidal ampicillin. The resuscitation ratio was 1 recovered VBNC cell in every 10(5) 5-cyano-2,3-di-4-tolyl-tetrazolium chloride (CTC+) bacteria. Although isolated VBNC rhizobia were unable to nodulate Medicago sativa, which apparently did not enhance VBNC reversion, resuscitated bacteria maintained their symbiotic properties. Soil experiments showed that the lack of O2 leads to onset of VBNC status as in liquid microcosm, but the number of recoverable and culturable cells decreased more drastically in soil.

Investigation into the role of the truncated denitrification chain in Rhizobium sullae strain HCNT1

Most denitrifying bacteria reduce nitrate to the inert gases nitrous oxide or nitrogen. A remarkable exception to this is Rhizobium sullae strain HCNT1, which catalyses only a single step in the denitrification pathway, the reduction of nitrite to the reactive molecule nitric oxide. Further study demonstrated that HCNT1 does not encode the genes for NO reductase. Prolonged incubation of HCNT1 under anoxic conditions revealed that the cells had reduced culturability but not viability when nitrite was present. This may indicate an adaptation to anoxic conditions to provide resistance to environmental stresses. A closely related strain of R. sullae, strain CC1335, which is unable to denitrify, was found to lose culturability but not viability irrespective of the presence of nitrite. When the gene for nitrite reductase was mobilized into CC1335, this increased culturability with or without nitrite. These results indicate that the presence of nitrite reductase can influence the long-term survival of R. sullae strains and may provide an explanation as to why HCNT1 possesses this unusual truncation of its denitrification electron transport chain.

Survival, root colonisation and biocontrol capacities of Pseudomonas fluorescens F113 LacZY in dry alginate microbeads

Cells of Pseudomonas fluorescens F113 LacZY were encapsulated in alginate and their survival and ability to colonise sugar beet were evaluated. To assess survival, the formulation, composed of dry alginate microbeads of 300- to 700-microm diameter, was stored 1 year at 28+/-2 and 4+/-2 degrees C and then tested against pathogenic fungi Pythium ultimum and Rhizoctonia solani in in vitro inhibition experiments. The same material was also used as inoculant for protection of sugar beet against Py. ultimum in microcosm experiments. The results obtained indicated that, although drying alginate beads resulted in a significant reduction of bacterial viability, the use of microbeads enabled a satisfactory level of root colonisation and protection, at least under microcosm conditions. The capability of the encapsulated cells to produce the antifungal metabolite 2,4-diacetylphloroglucinol (Phl) was not significantly affected by 12 months storage.

Aspects of Marker/Reporter Stability and Selectivity in Soil Microbiology

Based on several experiences of microbial release using genetically modified Rhizobium leguminosarum, we have highlighted a number of aspects related to the suitability of introduced markers such as resistance to mercury and b-galactosidase activity, the latter serving the function of high-expression level reporter gene obtained by the introduction of a synthetic promoter conferring strong inducible expression in Gram-negative bacteria. In vitro expression and in vivo performances of the chosen examples have been followed in model strains comparing gene dosage and expression levels. The technical possibility of unambiguously monitoring the marked GMM has been evaluated in medium- and long-term experiments carried out both in microcosms and soil, also including the presence of the plant symbiotic host. Marker stability, regardless the nature of the gene, was shown to be dependent on the location of the genetic modification and on its degree of gene expression regulation. Reporter strength was found to be an advantage allowing the distinction of marker-bearing bacteria while negatively affecting their genetic stability. Plasmid-borne regulated reporters were found to be stable up to the stages of rhizosphere colonization, but were more critically selected against upon symbiotic host invasion.

Identification, sequencing and mutagenesis of the gene for a D-carbamoylase from Agrobacterium radiobacter

A clone positive for D-carbamoylase activity (2.7 kb HindIII-BamHI DNA fragment) was obtained by screening a genomic library of Agrobacterium radiobacter in Escherichia coli. This DNA fragment contains an open reading frame of 912 bp which is predicted to encode a peptide of 304 amino acids with a calculated molecular mass of 34247 Da. The D-carbamoylase gene, named cauA, was placed under the control of T7 RNA-dependent promoter and expressed in E. coli BL21(DE3). After induction with isopropyl-thio-beta-D-galactopyranoside, the synthesis of D-carbamoylase in E. coli reached about 40% of the total protein. The expressed protein was shown to possess a molecular mass, on SDS-PAGE, of 36 kDa and showed an enhanced stability with respect to that of the wild-type enzyme derived from A. radiobacter. Site-directed mutagenesis experiments allowed us to establish that a Pro14-->Leu14 exchange leads to an inactive enzyme species, while a Cys279-->Ser279 exchange did not impair the functional properties of the enzyme.

Fate of genetically modified Rhizobium leguminosarum biovar viciae during long-term storage of commercial inoculants

A study was carried out to assess the behaviour, in terms of strain survival and genetic stability, of genetically modified micro-organisms (GEMs) during their storage in commercial-type agricultural inoculants. Three genetically modified Rhizobium leguminosarum biovar viciae strains were constructed, using a gene cassette containing an inducible lacZ gene from Escherichia coli and mercury resistance determinants from transposon Tn 1831. In the first case the genes have been integrated into the chromosome, the second strain contains the inducible cassette on a plasmid, in the third case the cassette is carried by the same plasmid, but the lacZ is constitutively expressed at high levels, due to the removal of the regulatory structure (lac operator) between the gene and its promoter. Three inoculum formulations, based on liquid, vermiculite and peat carriers, were prepared using the genetically modified strains, and were monitored during a period of up to 16 months. Results indicate a high stability of the chromosomally integrated markers. The plasmid-borne modification also was very stable, though the presence of the plasmid affected the strain growth kinetics. In contrast, the strain containing the highly expressed lacZ showed dramatic marker instability. Strain behaviour in stored inoculant packages reflected that observed in batch cultures; moreover, prolonged storage appeared to magnify differences found in in vitro cultures.

Enhanced degradation of ammonium-pretreated wheat straw by lignocellulolytic Streptomyces spp

Eleven actinomycetes, isolated from the gut of worker termites (Macrotermes, Armitermes, Microcerotermes, Odontotermes), were identified as Streptomyces chromofuscus, S. chromogenus, S. diastaticus, and S. rochei. Their ability to grow on natural lignocellulosic substrates was tested in solid state fermentation experiments using wheat straw (C/N = 49.8) as a sole carbon source. Weight loss was 4.7–20.9% of the initial substrate, after 5 weeks at 30 °C; lignin and cellulose content decreased 2.0–16.1 and 3.5–32.9%, respectively. When the 11 Streptomyces were grown on wheat straw pretreated with (NH4)HCO3 (C/N = 28.2), weight loss was 9.3–29.9% of the initial substrate, indicating an overall enhancement of lignocellulose degradation. Weight, lignin, and cellulose losses were enhanced when S. chromofuscus (strain A2 and A11) and S. rochei A4 were grown on pretreated wheat straw instead of the untreated substrate. With S. rochei A10 the weight loss and lignin degradation were enhanced, while cellulolysis was slightly depressed. Weight loss and cellulose degradation were both enhanced when the remaining strains were grown on pretreated wheat straw. In this case, lignin degradation was depressed (S. chromofuscus A6 and A8, S. diastaticus A12, S. rochei A14) or remained essentially the same (S. diastaticus A3 and S. chromogenus A7). Key words: Streptomyces, wheat straw, degradation, lignin, cellulose.

Bactericidal-activities of human polymorphonuclear leukocyte proteins against Escherichia coli O111:B4 coated with C5 or C8

The postnuclear supernatant of disrupted polymorphonuclear leukocytes exhibited bactericidal activity on Escherichia coli O111:B4 coated with immunoglobulin M antibodies and C5 or C8 but not on C3- or C7-coated bacteria. To characterize this antimicrobial activity further, granules obtained from the postnuclear supernatant were extracted with sodium acetate (pH 4) and the soluble extract was subsequently fractionated through carboxymethyl cellulose and Sephacryl S-200. Over 90% of the activity present in the starting material was recovered in the soluble granule extract. Kinetic and dose-response analyses of the bacterial activity of the polymorphonuclear leukocyte extract on BAC1-5 and BAC1-8 revealed different susceptibilities to killing of these two bacterial intermediates; they also differed for their susceptibilities to killing at 37 degrees C and at room temperature. The suggestion raised by these data, that BAC1-5 and BAC1-8 could be killed by different bactericidal factors, was confirmed by the findings that separate fractions of the soluble granule extract obtained by carboxymethyl cellulose and Sephacryl S-200 chromatography exhibited specific activity on either BAC1-5 or BAC1-8, whereas other fractions were active on both intermediates.

Selective C3 deficiency due to C3 nephritic factor in an apparently healthy girl

Routine laboratory investigations performed on the serum of an 8-year-old girl examined because of a moderate degree of iron-deficiency anemia showed a markedly reduced C3 level. More detailed complement studies revealed a selective C3 deficiency, as indicated by the almost undetectable C3 concentration tested by both hemolytic and immunochemical assays and by the normal or slightly reduced levels of all the other complement components. The hemolytic activity of the serum was restored by the addition of partially purified C3 component. The isolated C3 deficiency could be attributed to the presence of a C3-cleaving activity in the serum of the propositus. This activity was identified as C3 nephritic factor (C3NeF) since it was heat-stable, was absorbed by Cowan I strain of Staphylococcus aureus and was-eluted in the IgG fraction after DEAE-chromatography of the serum. The levels of H and I factors of the alternative pathway in the serum of the propositus and of C3 in the serum samples of her parents and two siblings were found to be within the normal range. The previous clinical history of the girl and the follow-up for a period of approximately 5 years showed that she was apparently healthy and did not reveal clinical and/or laboratory evidence of glomerulonephritis, lipodystrophy or repeated bacterial infections usually associated with the presence of C3NeF in the serum.

Kinetics of assembly and decay of complement components on Escherichia coli O111:B4 preparation of stable intermediates

The preparation of bacterial intermediates bearing complement components at various steps of the complement sequence was investigated by suspending immunoglobulin M-opsonized Escherichia coli O111:B4 cells in complement-deficient sera at different temperatures and ionic strengths. The optimal conditions for the formation of the intermediates at Tmax were found to be an ionic strength of 0.091 mu and a temperature of 37 degrees C, except for BAC142, which could be formed equally well at room temperature. In contrast to all the other intermediates, which, once formed at Tmax, were stable in the presence of the whole serum, BAC142 decayed with a half-life of 10 min due to the lability of bound C2. Washing with a buffer of either 0.091 or 0.046 mu did not affect the bacterial intermediates, with the exception of BAC1-3 formed either in the presence of C5-deficient serum or with purified C3 added to BAC142. All the intermediates were found to be stable after incubation in 0.091-mu buffer for 30 min at 37 degrees C.

[Phenotypic relations with regard to pyocin sensitivity, of 191 strains of Pseudomonas aeruginosa isolated in a hospital environment]

191 strains of Pseudomonas aeruginosa, isolated from clinical specimens, were tested by passive and active pyocin typing. The results of passive typing were computerized and a final dendrogram, with its peculiar similarity levels between the single strains, was obtains. This study will permit to build a system, to mark out the Pseudomonas strains, through active pyocin typing or through passive pyocin typing.