Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

Background: Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results: Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion: Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree.

Abundance and Genetic Diversity of nifH Gene Sequences in Anthropogenically Affected Brazilian Mangrove Sediments

Although mangroves represent ecosystems of global importance, the genetic diversity and abundance of functional genes that are key to their functioning scarcely have been explored. Here, we present a survey based on the nifH gene across transects of sediments of two mangrove systems located along the coast line of Sao Paulo state (Brazil) which differed by degree of disturbance, i.e., an oil-spill-affected and an unaffected mangrove. The diazotrophic communities were assessed by denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR), and clone libraries. The nifH gene abundance was similar across the two mangrove sediment systems, as evidenced by qPCR. However, the nifH-based PCR-DGGE profiles revealed clear differences between the mangroves. Moreover, shifts in the nifH gene diversities were noted along the land-sea transect within the previously oiled mangrove. The nifH gene diversity depicted the presence of nitrogen-fixing bacteria affiliated with a wide range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and also a group of anaerobic sulfate-reducing bacteria. We also detected a unique mangrove-specific cluster of sequences denoted Mgv-nifH. Our results indicate that nitrogen-fixing bacterial guilds can be partially endemic to mangroves, and these communities are modulated by oil contamination, which has important implications for conservation strategies.

The Selection Exerted by Oil Contamination on Mangrove Fungal Communities

Mangrove ecosystems are tropical environments that are characterized by the interaction between the land and the sea. As such, this ecosystem is vulnerable to oil spills. Here, we show a culture-independent survey of fungal communities that are found in the sediments of the following two mangroves that are located on the coast of Sao Paulo State (Brazil): (1) an oil-spill-affected mangrove and (2) a nearby unaffected mangrove. Samples were collected from each mangrove forest at three distinct locations (transect from sea to land), and the samples were analyzed by quantitative PCR and internal transcribed spacer (ITS)-based PCR-DGGE analysis. The abundance of fungi was found to be higher in the oil-affected mangrove. Visual observation and correspondence analysis (CA) of the ITS-based PCR-DGGE profiles revealed differences in the fungal communities between the sampled areas. Remarkably, the oil-spilled area was quite distinct from the unaffected sampling areas. On the basis of the ITS sequences, fungi that are associated with the Basidiomycota and Ascomycota taxa were most common and belonged primarily to the genera Epicoccum, Nigrospora, and Cladosporium. Moreover, the Nigrospora fungal species were shown to be sensitive to oil, whereas a group that was described as "uncultured Basidiomycota" was found more frequently in oil-contaminated areas. Our results showed an increase in fungal abundance in the oil-polluted mangrove regions, and these data indicated potential fungal candidates for remediation of the oil-affected mangroves.

A Two-Stage Aerobic/Anaerobic Denitrifying Horizontal Bioreactor Designed for Treating Ammonium and H2S Simultaneously

A two-stage bioreactor was operated for a period of 140 days in order to develop a post-treatment process based on anaerobic bioxidation of sulfite. This process was designed for simultaneously treating the effluent and biogas of a full-scale UASB reactor, containing significant concentrations of NH4 and H2S, respectively. The system comprised of two horizontal-flow bed-packed reactors operated with different oxygen concentrations. Ammonium present in the effluent was transformed into nitrates in the first aerobic stage. The second anaerobic stage combined the treatment of nitrates in the liquor with the hydrogen sulfide present in the UASB-reactor biogas. Nitrates were consumed with a significant production of sulfate, resulting in a nitrate removal rate of 0.43 kg N m(3) day(-1) and a parts per thousand yen92 % efficiency. Such a removal rate is comparable to those achieved by heterotrophic denitrifying systems. Polymeric forms of sulfur were not detected (elementary sulfur); sulfate was the main product of the sulfide-based denitrifying process. S-sulfate was produced at a rate of about 0.35 kg m(3) day(-1). Sulfur inputs as S-H2S were estimated at about 0.75 kg m(3) day(-1) and Chemical Oxygen Demand (COD) removal rates did not vary significantly during the process. DGGE profiling and 16S rRNA identified Halothiobacillus-like species as the key microorganism supporting this process; such a strain has not yet been previously associated with such bioengineered systems.

Lactobacillus acidophilus CRL 1014 improved “gut health” in the SHIME® reactor

Abstract Background How to maintain “gut health” is a goal for scientists throughout the world. Therefore, microbiota management models for testing probiotics, prebiotics, and synbiotics have been developed. Methods The SHIME® model was used to study the effect of Lactobacillus acidophilus 1014 on the fermentation pattern of the colon microbiota. Initially, an inoculum prepared from human feces was introduced into the reactor vessels and stabilized over 2-wk using a culture medium. This stabilization period was followed by a 2-wk control period during which the microbiota was monitored. The microbiota was then subjected to a 4-wk treatment period by adding 5 mL of sterile peptone water with L. acidophilus CRL1014 at the concentration of 108 CFU/mL to vessel one (the stomach compartment). Plate counts, Denaturing Gradient Gel Electrophoresis (DGGE), short-chain fatty acid (SCFA) and ammonium analyses were carried out for monitoring of the microbial community from the colon compartments. Results A significant increase (p < 0.01) in the Lactobacillus spp. and Bifidobacterium spp. populations was observed during the treatment period. The DGGE obtained showed changes in the lactobacilli community from the colon compartments of the SHIME® reactor. The (SCFA) concentration increased (p < 0.01) during the treatment period, due mainly to significant increased levels of acetic, butyric, and propionic acids. However, ammonium concentrations decreased during the same period (p < 0.01). Conclusions This study showed the beneficial influence of L. acidophilus CRL 1014 on microbial metabolism and lactobacilli community composition for improving human health.

Comparison of different protocols for the extraction of microbial DNA from reef corals

This study aimed to test different protocols for the extraction of microbial DNA from the coral Mussismilia harttii. Four different commercial kits were tested, three of them based on methods for DNA extraction from soil (FastDNA SPIN Kit for soil, MP Bio, PowerSoil DNA Isolation Kit, MoBio, and ZR Soil Microbe DNA Kit, Zymo Research) and one kit for DNA extraction from plants (UltraClean Plant DNA Isolation Kit, MoBio). Five polyps of the same colony of M. harttii were macerated and aliquots were submitted to DNA extraction by the different kits. After extraction, the DNA was quantified and PCR-DGGE was used to study the molecular fingerprint of Bacteria and Eukarya. Among the four kits tested, the ZR Soil Microbe DNA Kit was the most efficient with respect to the amount of DNA extracted, yielding about three times more DNA than the other kits. Also, we observed a higher number and intensities of DGGE bands for both Bacteria and Eukarya with the same kit. Considering these results, we suggested that the ZR Soil Microbe DNA Kit is the best adapted for the study of the microbial communities of corals.

Interspecific variation of the bacterial community structure in the phyllosphere of the three major plant components of mangrove forests

Mangrove forests encompass a group of trees species that inhabit the intertidal zones, where soil is characterized by the high salinity and low availability of oxygen. The phyllosphere of these trees represent the habitat provided on the aboveground parts of plants, supporting in a global scale, a large and complex microbial community. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonizers, which is influenced by numerous environmental factors in addition to leaf physical and chemical properties. Here, a combination of culture-base methods with PCR-DGGE was applied to test whether local or plant specific factors shape the bacterial community of the phyllosphere from three plant species (Avicenia shaueriana, Laguncularia racemosa and Rhizophora mangle), found in two mangroves. The number of bacteria in the phyllosphere of these plants varied between 3.62 x 10(4) in A. schaeriana and 6.26 x 10³ in R. mangle. The results obtained by PCR-DGGE and isolation approaches were congruent and demonstrated that each plant species harbor specific bacterial communities in their leaves surfaces. Moreover, the ordination of environmental factors (mangrove and plant species), by redundancy analysis (RDA), also indicated that the selection exerted by plant species is higher than mangrove location on bacterial communities at phyllosphere.

Impatto di rifaximina sul microbiota intestinale: selezione di bifidobatteri antibiotico resistenti

The ideal approach for the long term treatment of intestinal disorders, such as inflammatory bowel disease (IBD), is represented by a safe and well tolerated therapy able to reduce mucosal inflammation and maintain homeostasis of the intestinal microbiota. A combined therapy with antimicrobial agents, to reduce antigenic load, and immunomodulators, to ameliorate the dysregulated responses, followed by probiotic supplementation has been proposed. Because of the complementary mechanisms of action of antibiotics and probiotics, a combined therapeutic approach would give advantages in terms of enlargement of the antimicrobial spectrum, due to the barrier effect of probiotic bacteria, and limitation of some side effects of traditional chemiotherapy (i.e. indiscriminate decrease of aggressive and protective intestinal bacteria, altered absorption of nutrient elements, allergic and inflammatory reactions). Rifaximin (4-deoxy-4’-methylpyrido[1’,2’-1,2]imidazo[5,4-c]rifamycin SV) is a product of synthesis experiments designed to modify the parent compound, rifamycin, in order to achieve low gastrointestinal absorption while retaining good antibacterial activity. Both experimental and clinical pharmacology clearly show that this compound is a non systemic antibiotic with a broad spectrum of antibacterial action, covering Gram-positive and Gram-negative organisms, both aerobes and anaerobes. Being virtually non absorbed, its bioavailability within the gastrointestinal tract is rather high with intraluminal and faecal drug concentrations that largely exceed the MIC values observed in vitro against a wide range of pathogenic microorganisms. The gastrointestinal tract represents therefore the primary therapeutic target and gastrointestinal infections the main indication. The little value of rifaximin outside the enteric area minimizes both antimicrobial resistance and systemic adverse events. Fermented dairy products enriched with probiotic bacteria have developed into one of the most successful categories of functional foods. Probiotics are defined as “live microorganisms which, when administered in adequate amounts, confer a health benefit on the host” (FAO/WHO, 2002), and mainly include Lactobacillus and Bifidobacterium species. Probiotic bacteria exert a direct effect on the intestinal microbiota of the host and contribute to organoleptic, rheological and nutritional properties of food. Administration of pharmaceutical probiotic formula has been associated with therapeutic effects in treatment of diarrhoea, constipation, flatulence, enteropathogens colonization, gastroenteritis, hypercholesterolemia, IBD, such as ulcerative colitis (UC), Crohn’s disease, pouchitis and irritable bowel syndrome. Prerequisites for probiotics are to be effective and safe. The characteristics of an effective probiotic for gastrointestinal tract disorders are tolerance to upper gastrointestinal environment (resistance to digestion by enteric or pancreatic enzymes, gastric acid and bile), adhesion on intestinal surface to lengthen the retention time, ability to prevent the adherence, establishment and/or replication of pathogens, production of antimicrobial substances, degradation of toxic catabolites by bacterial detoxifying enzymatic activities, and modulation of the host immune responses. This study was carried out using a validated three-stage fermentative continuous system and it is aimed to investigate the effect of rifaximin on the colonic microbial flora of a healthy individual, in terms of bacterial composition and production of fermentative metabolic end products. Moreover, this is the first study that investigates in vitro the impact of the simultaneous administration of the antibiotic rifaximin and the probiotic B. lactis BI07 on the intestinal microbiota. Bacterial groups of interest were evaluated using culture-based methods and molecular culture-independent techniques (FISH, PCR-DGGE). Metabolic outputs in terms of SCFA profiles were determined by HPLC analysis. Collected data demonstrated that rifaximin as well as antibiotic and probiotic treatment did not change drastically the intestinal microflora, whereas bacteria belonging to Bifidobacterium and Lactobacillus significantly increase over the course of the treatment, suggesting a spontaneous upsurge of rifaximin resistance. These results are in agreement with a previous study, in which it has been demonstrated that rifaximin administration in patients with UC, affects the host with minor variations of the intestinal microflora, and that the microbiota is restored over a wash-out period. In particular, several Bifidobacterium rifaximin resistant mutants could be isolated during the antibiotic treatment, but they disappeared after the antibiotic suspension. Furthermore, bacteria belonging to Atopobium spp. and E. rectale/Clostridium cluster XIVa increased significantly after rifaximin and probiotic treatment. Atopobium genus and E. rectale/Clostridium cluster XIVa are saccharolytic, butyrate-producing bacteria, and for these characteristics they are widely considered health-promoting microorganisms. The absence of major variations in the intestinal microflora of a healthy individual and the significant increase in probiotic and health-promoting bacteria concentrations support the rationale of the administration of rifaximin as efficacious and non-dysbiosis promoting therapy and suggest the efficacy of an antibiotic/probiotic combined treatment in several gut pathologies, such as IBD. To assess the use of an antibiotic/probiotic combination for clinical management of intestinal disorders, genetic, proteomic and physiologic approaches were employed to elucidate molecular mechanisms determining rifaximin resistance in Bifidobacterium, and the expected interactions occurring in the gut between these bacteria and the drug. The ability of an antimicrobial agent to select resistance is a relevant factor that affects its usefulness and may diminish its useful life. Rifaximin resistance phenotype was easily acquired by all bifidobacteria analyzed [type strains of the most representative intestinal bifidobacterial species (B. infantis, B. breve, B. longum, B. adolescentis and B. bifidum) and three bifidobacteria included in a pharmaceutical probiotic preparation (B. lactis BI07, B. breve BBSF and B. longum BL04)] and persisted for more than 400 bacterial generations in the absence of selective pressure. Exclusion of any reversion phenomenon suggested two hypotheses: (i) stable and immobile genetic elements encode resistance; (ii) the drug moiety does not act as an inducer of the resistance phenotype, but enables selection of resistant mutants. Since point mutations in rpoB have been indicated as representing the principal factor determining rifampicin resistance in E. coli and M. tuberculosis, whether a similar mechanism also occurs in Bifidobacterium was verified. The analysis of a 129 bp rpoB core region of several wild-type and resistant bifidobacteria revealed five different types of miss-sense mutations in codons 513, 516, 522 and 529. Position 529 was a novel mutation site, not previously described, and position 522 appeared interesting for both the double point substitutions and the heterogeneous profile of nucleotide changes. The sequence heterogeneity of codon 522 in Bifidobacterium leads to hypothesize an indirect role of its encoded amino acid in the binding with the rifaximin moiety. These results demonstrated the chromosomal nature of rifaximin resistance in Bifidobacterium, minimizing risk factors for horizontal transmission of resistance elements between intestinal microbial species. Further proteomic and physiologic investigations were carried out using B. lactis BI07, component of a pharmaceutical probiotic preparation, as a model strain. The choice of this strain was determined based on the following elements: (i) B. lactis BI07 is able to survive and persist in the gut; (ii) a proteomic overview of this strain has been recently reported. The involvement of metabolic changes associated with rifaximin resistance was investigated by proteomic analysis performed with two-dimensional electrophoresis and mass spectrometry. Comparative proteomic mapping of BI07-wt and BI07-res revealed that most differences in protein expression patterns were genetically encoded rather than induced by antibiotic exposure. In particular, rifaximin resistance phenotype was characterized by increased expression levels of stress proteins. Overexpression of stress proteins was expected, as they represent a common non specific response by bacteria when stimulated by different shock conditions, including exposure to toxic agents like heavy metals, oxidants, acids, bile salts and antibiotics. Also, positive transcription regulators were found to be overexpressed in BI07-res, suggesting that bacteria could activate compensatory mechanisms to assist the transcription process in the presence of RNA polymerase inhibitors. Other differences in expression profiles were related to proteins involved in central metabolism; these modifications suggest metabolic disadvantages of resistant mutants in comparison with sensitive bifidobacteria in the gut environment, without selective pressure, explaining their disappearance from faeces of patients with UC after interruption of antibiotic treatment. The differences observed between BI07-wt e BI07-res proteomic patterns, as well as the high frequency of silent mutations reported for resistant mutants of Bifidobacterium could be the consequences of an increased mutation rate, mechanism which may lead to persistence of resistant bacteria in the population. However, the in vivo disappearance of resistant mutants in absence of selective pressure, allows excluding the upsurge of compensatory mutations without loss of resistance. Furthermore, the proteomic characterization of the resistant phenotype suggests that rifaximin resistance is associated with a reduced bacterial fitness in B. lactis BI07-res, supporting the hypothesis of a biological cost of antibiotic resistance in Bifidobacterium. The hypothesis of rifaximin inactivation by bacterial enzymatic activities was verified by using liquid chromatography coupled with tandem mass spectrometry. Neither chemical modifications nor degradation derivatives of the rifaximin moiety were detected. The exclusion of a biodegradation pattern for the drug was further supported by the quantitative recovery in BI07-res culture fractions of the total rifaximin amount (100 μg/ml) added to the culture medium. To confirm the main role of the mutation on the β chain of RNA polymerase in rifaximin resistance acquisition, transcription activity of crude enzymatic extracts of BI07-res cells was evaluated. Although the inhibition effects of rifaximin on in vitro transcription were definitely higher for BI07-wt than for BI07-res, a partial resistance of the mutated RNA polymerase at rifaximin concentrations > 10 μg/ml was supposed, on the basis of the calculated differences in inhibition percentages between BI07-wt and BI07-res. By considering the resistance of entire BI07-res cells to rifaximin concentrations > 100 μg/ml, supplementary resistance mechanisms may take place in vivo. A barrier for the rifaximin uptake in BI07-res cells was suggested in this study, on the basis of the major portion of the antibiotic found to be bound to the cellular pellet respect to the portion recovered in the cellular lysate. Related to this finding, a resistance mechanism involving changes of membrane permeability was supposed. A previous study supports this hypothesis, demonstrating the involvement of surface properties and permeability in natural resistance to rifampicin in mycobacteria, isolated from cases of human infection, which possessed a rifampicin-susceptible RNA polymerase. To understand the mechanism of membrane barrier, variations in percentage of saturated and unsaturated FAs and their methylation products in BI07-wt and BI07-res membranes were investigated. While saturated FAs confer rigidity to membrane and resistance to stress agents, such as antibiotics, a high level of lipid unsaturation is associated with high fluidity and susceptibility to stresses. Thus, the higher percentage of saturated FAs during the stationary phase of BI07-res could represent a defence mechanism of mutant cells to prevent the antibiotic uptake. Furthermore, the increase of CFAs such as dihydrosterculic acid during the stationary phase of BI07-res suggests that this CFA could be more suitable than its isomer lactobacillic acid to interact with and prevent the penetration of exogenous molecules including rifaximin. Finally, the impact of rifaximin on immune regulatory functions of the gut was evaluated. It has been suggested a potential anti-inflammatory effect of rifaximin, with reduced secretion of IFN-γ in a rodent model of colitis. Analogously, it has been reported a significant decrease in IL-8, MCP-1, MCP-3 e IL-10 levels in patients affected by pouchitis, treated with a combined therapy of rifaximin and ciprofloxacin. Since rifaximin enables in vivo and in vitro selection of Bifidobacterium resistant mutants with high frequency, the immunomodulation activities of rifaximin associated with a B. lactis resistant mutant were also taken into account. Data obtained from PBMC stimulation experiments suggest the following conclusions: (i) rifaximin does not exert any effect on production of IL-1β, IL-6 and IL-10, whereas it weakly stimulates production of TNF-α; (ii) B. lactis appears as a good inducer of IL-1β, IL-6 and TNF-α; (iii) combination of BI07-res and rifaximin exhibits a lower stimulation effect than BI07-res alone, especially for IL-6. These results confirm the potential anti-inflammatory effect of rifaximin, and are in agreement with several studies that report a transient pro-inflammatory response associated with probiotic administration. The understanding of the molecular factors determining rifaximin resistance in the genus Bifidobacterium assumes an applicative significance at pharmaceutical and medical level, as it represents the scientific basis to justify the simultaneous use of the antibiotic rifaximin and probiotic bifidobacteria in the clinical treatment of intestinal disorders.

Dealogenazione riduttiva dei policlorobifenili (PCB) in sedimenti anaerobici marini della laguna di Venezia: arricchimento e identificazione dei microrganismi dealogenanti

I policlorobifenili (PCB) sono inquinanti tossici e fortemente recalcitranti che contaminano suoli e sedimenti di acqua dolce e marini. Le tecnologie attualmente impiegate per la loro rimozione (dragaggio e trattamento chimoco-fisico o conferimento in discarica) sono molto costose, poco efficaci o ad alto impatto ambientale. L’individuazione di strategie alternative, di natura biologica, consentirebbe lo sviluppo di un processo alternativo più sostenibile. Nel processo di declorurazione riduttiva i congeneri di PCB a più alto grado di clorurazione, che sono i più tossici, recalcitranti e maggiormente tendenti al bioaccumulo, vengono utilizzati da alcuni microrganismi anaerobici come accettori finali di elettroni nella catena respiratoria e bioconvertiti in congeneri a minor grado di clorurazione, meno pericolosi, che possono essere mineralizzati da parte di batteri aerobi. La declorurazione riduttiva dei PCB è stata spesso studiata in colture anaerobiche di arricchimento in terreno minerale ottenute a partire da sedimenti di acqua dolce; questi studi hanno permesso di dimostrare che batteri del phylum dei Chloroflexi e appartenenti al genere Dehalococcoides o filogeneticamente facenti parte del gruppo dei Dehalococcoides-like sono i decloruranti. Sono tuttavia scarse le informazioni riguardanti l'occorrenza della declorurazione dei PCB in ambienti marini, nei quali l'alta salinità e concentrazione di solfati influenzano diversamente l'evoluzione delle popolazioni microbiche. In sedimenti contaminati della laguna di Venezia è stata osservata declorurazione sia dei PCB preesistenti che di congeneri esogeni; questi studi hanno permesso l'ottenimento di colture di arricchimento fortemente attive nei confronti di 5 congeneri di PCB coplanari. In questa tesi, a partire dalle colture capaci di declorurare i PCB coplanari, sono stati allestiti nuovi passaggi di arricchimento su Aroclor®1254, una miscela di PCB più complessa e che meglio rappresenta la contaminazione ambientale. Le colture sono state allestite come microcosmi anaerobici in fase slurry, preparati risospendendo il sedimento nell'acqua superficiale, ricreando in tal modo in laboratorio le stesse condizioni biogeochimiche presenti in situ; gli slurry sterili sono stati inoculati per avviare le colture. Per favorire la crescita dei microrganismi decloruranti e stimolare così la decloruraazione dei PCB sono stati aggiunti inibitori selettivi di metanogeni (Bromoetansulfonato o BES) e solfato-riduttori (molibdato), sono state fornite fonti di carbonio ed energia (eD), quali acidi grassi a corta catena e idrogeno, utilizzate di batteri decloruranti noti, e per semplificare la comunità microbica sono stati aggiunti antibiotici cui batteri decloruranti del genere Dehalococcoides sono resistenti. Con questo approccio sono stati allestiti passaggi di arricchimento successivi e le popolazioni microbiche delle colture sono state caratterizzate con analisi molecolari di fingerprinting (DGGE). Fin dal primo passaggio di arricchimento nei microcosmi non ammendati ha avuto luogo un'estesa declorurazione dell'Aroclor®1254; nei successivi passaggi si è notato un incremento della velocità del processo e la scomparsa della fase di latenza, mentre la stessa stereoselettività è stata mantenuta a riprova dell’arricchimento degli stessi microrganismi decloruranti. Le velocità di declorurazione ottenute sono molto alte se confrontate con quelle osservate in colture anaerobiche addizionate della stessa miscela descritte in letteratura. L'aggiunta di BES o molibdato ha bloccato la declorurazione dei PCB ma in presenza di BES è stata riscontrata attività dealogenante nei confronti di questa molecola. La supplementazione di fonti di energia e di carbonio ha stimolato la metanogenesi e i processi fermentativi ma non ha avuto effetti sulla declorurazione. Ampicillina e vancomicina hanno incrementato la velocità di declorurazione quando aggiunte singolarmente, insieme o in combinazione con eD. E' stato però anche dimostrato che la declorurazione dei PCB è indipendente sia dalla metanogenesi che dalla solfato-riduzione. Queste attività respiratorie hanno avuto velocità ed estensioni diverse in presenza della medesima attività declorurante; in particolare la metanogenesi è stata rilevata solo in dipendenza dall’aggiunta di eD alle colture e la solfato-riduzione è stata inibita dall’ampicillina in microcosmi nei quali un’estesa declorurazione dei PCB è stata osservata. La caratterizzazione delle popolazioni microbiche, condotte mediante analisi molecolari di fingerprinting (DGGE) hanno permesso di descrivere le popolazioni batteriche delle diverse colture come complesse comunità microbiche e di rilevare in tutte le colture decloruranti la presenza di una banda che l’analisi filogenetica ha ascritto al batterio m-1, un noto batterio declorurante in grado di dealogenare un congenere di PCB in colture di arricchimento ottenute da sedimenti marini appartenente al gruppo dei Dehalococcoides-like. Per verificare se la crescita di questo microrganismo sia legata alla presenza dei PCB, l'ultimo passaggio di arricchimento ha previsto l’allestimento di microcosmi addizionati di Aroclor®1254 e altri analoghi privi di PCB. Il batterio m-1 è stato rilevato in tutti i microcosmi addizionati di PCB ma non è mai stato rilevato in quelli in cui i PCB non erano presenti; la presenza di nessun altro batterio né alcun archebatterio è subordinata all’aggiunta dei PCB. E in questo modo stato dimostrato che la presenza di m-1 è dipendente dai PCB e si ritiene quindi che m-1 sia il declorurante in grado di crescere utilizzando i PCB come accettori di elettroni nella catena respiratoria anche in condizioni biogeochimiche tipiche degli habitat marini. In tutte le colture dell'ultimo passaggio di arricchimento è stata anche condotta una reazione di PCR mirata alla rilevazione di geni per dealogenasi riduttive, l’enzima chiave coinvolto nei processi di dealogenazione. E’ stato ottenuto un amplicone di lughezza analoga a quelle di tutte le dealogenasi note in tutte le colture decloruranti ma un tale amplificato non è mai stato ottenuto da colture non addizionate di PCB. La dealogenasi ha lo stesso comportamento di m-1, essendo stata trovata come questo sempre e solo in presenza di PCB e di declorurazione riduttiva. La sequenza di questa dealogenasi è diversa da tutte quelle note sia in termini di sequenza nucleotidica che aminoacidica, pur presentando due ORF con le stesse caratteristiche e domini presenti nelle dealogenasi note. Poiché la presenza della dealogenasi rilevata nelle colture dipende esclusivamente dall’aggiunta di PCB e dall’osservazione della declorurazione riduttiva e considerato che gran parte delle differenze genetiche è concentrata nella parte di sequenza che si pensa determini la specificità di substrato, si ritiene che la dealogenasi identificata sia specifica per i PCB. La ricerca è stata condotta in microcosmi che hanno ricreato fedelmente le condizioni biogeochimiche presenti in situ e ha quindi permesso di rendere conto del reale potenziale declorurante della microflora indigena dei sedimenti della laguna di Venezia. Le analisi molecolari condotte hanno permesso di identificare per la prima volta un batterio responsabile della declorurazione dei PCB in sedimenti marini (il batterio m-1) e una nuova dealogenasi specifica per PCB. L'identificazione del microrganismo declorurante permette di aprire la strada allo sviluppo di tecnologie di bioremediation mirata e il gene della dealogenasi potrà essere utilizzato come marker molecolare per determinare il reale potenziale di declorurazione di miscele complesse di PCB in sedimenti marini.

Phylogenetische Charakterisierung von Mikroorganismen aus dem Intestinaltrakt von Insekten

Zusammenfassung Die komplexe Lebensgemeinschaft des Termitendarms fasziniert die Biologen schon seit langem. Es ist bekannt, dass Termiten ihre Nahrung mit Hilfe von symbiontischen Bakterien und Protozoen verdauen können. Ohne ihre Symbionten würden sie verhungern. Das Zusammenspiel von Termiten und darmbewohnenden Mikroorganismen, zu denen Flagellaten, Bakterien, Archaebakterien und Hefen gehören, ist trotz moderner Untersuchungstechniken keineswegs vollständig aufgeklärt. In der vorliegenden Arbeit wurden:1) Einige kultivierte und nicht-kultivierte Bakterien charakterisiert, die an der Darmwand von Mastotermes darwiniensis lokalisiert sind. Die Darmwandbakterien wurden entweder nach Kultivierung oder direkt von der Darmwand für die Analyse der 16S rDNA verwendet. Die Sequenzierung erfolgte entweder nach DGGE oder nach Klonierung der PCR-Produkte. Die identifizierten Bakterien kann man in 7 Gruppen teilen:1: Gram-positive Bakterien mit hohem GC-Gehalt 2: Gram-positive Bakterien mit niedrigem GC-Gehalt 3: Fusobakterien-ähnliche Bakterien 4: ß-Proteobakterien5: Verrucomicrobien6: Bacteroides-ähnliche Bakterien7: Methanogene Bakterien 2) Aufgrund des Vorhandenseins des Coenzyms Deazaflavin-Derivats F420, kann man Methanbakterien mikroskopisch identifizieren und von anderen Bakterien unterscheiden, weil Methanbakterien im kurzwelligen Blaulicht blaugrün aufleuchten. Untersuchungen haben gezeigt, dass mindestens zwei Morphotypen von Methanbakterien an der Darmwand von M. darwiniensis vorkommen. Sie wurden auch über 16S rDNA Sequenzanalyse identifiziert. Ihre Lokalisierung an der Darmwand wurde durch Fluoreszenz-in-situ-Hybridsierung mit spezifischen Oligonukleotiden nachgewiesen. Schließlich konnte gezeigt werden, dass pro Gramm Termite 2,6 µg Methan pro Stunde produziert werden. 3) Bis jetzt wurden aus verschiedenen Termiten sulfatreduzierende Bakterien (SRB) isoliert. Deshalb wurde in dieser Arbeit die Verbreitung der SRB in verschiedenen Insekten untersucht. Insgesamt wurden zwei Sequenzen aus Libellenlarven (FSBO4 und FSBRO2), drei Sequenzen aus Zuckmückenlarven (FSCI, FSCII und FSC4), eine Sequenz aus Rosenkäfern (FSPa4-5) und ebenfalls eine Sequenz aus Eintagsfliegenlarven (FSB6) identifiziert. Alle identifizierten Bakterien ausser Klon FSB6, gehören zur Gattung Desulfovibrio. Klon FSB6 gehört zu der Gram-positiven Gattung Desulfotomaculum.Außerdem wurde die Sulfatreduktionsrate der SRB im Darm von Rosenkäfern (Pachnoda marginata), Holz- bzw. Sulfat-gefütterten Termiten (Mastotermes darwiniensis) und einer Reinkultur von Desulfovibrio intestinalis gemessen. Dabei konnte gezeigt werden, dass die Aktivität pro Zelle in Holz-gefütterten Termite am höchsten ist (4,9 nmol/107 Bakterien x h).

Ottimizzazione dei processi depurativi di reflui ad elevato carico organico a fini di recupero energetico

L’attuale condizione che caratterizza il settore energetico richiede un necessario processo di riconversione che, oltre a favorire il risparmio energetico, riduca la dipendenza dai combustibili fossili ed accresca l’impiego di fonti energetiche rinnovabili, dando un contributo fondamentale alla riduzione delle emissioni di gas serra come diversi accordi internazionali richiedono. Si rende pertanto necessario accelerare i processi che da alcuni anni stanno favorendo l’utilizzo di energia da fonti rinnovabili. Tra queste, le fonti legate ai processi di trattamento biologico dei reflui stanno avendo un interessante sviluppo. Esistono numerosi processi biologici che consentono la produzione di energia in maniera indiretta, quali ad esempio i processi di digestione anaerobica finalizzati alla produzione di biogas e/o produzione biologica di idrogeno. In tale contesto si inserisce la tecnologia delle Microbial Fuel Cell, che consente la produzione diretta di energia elettrica, finalizzata al recupero energetico inteso al miglioramento dell’efficienza energetica e alla riduzione dei costi d’esercizio di impianti di trattamento biologico dei reflui. Il presente lavoro di Tesi di Dottorato sperimentale, svoltosi in collaborazione al laboratorio PROT.-IDR. della sede ENEA di Bologna, riporta i risultati dell’attività di ricerca condotta su una MFC (Microbial Fuel Cell) a doppio stadio biologico per il trattamento di reflui ad elevato carico organico e produzione continua di energia elettrica. E’ stata provata l’applicabilità della MFC con entrambi i comparti biotici utilizzando elettrodi di grafite non trattata ottenendo, con un carico organico in ingresso di circa 9 gd-1, valori di potenza massima prodotta che si attestano su 74 mWm-2, corrente elettrica massima generata di 175 mAm-2 ad una tensione di 421 mV, ed una conversione di COD in elettricità pari a 1,2 gCODm-2d-1. I risultati sono stati molto positivi per quanto riguarda le prestazioni depurative ottenute dalla MFC. L’efficienza di depurazione misurata ha raggiunto un valore massimo del 98% di rimozione del COD in ingresso, mentre e la concentrazione di azoto ammoniacale nell’effluente raccolto all’uscita del sedimentatore è sempre stata inferiore a 1 mgN-NH4+l-1. Tra gli obiettivi posti all’inizio della sperimentazione si è rivelata di notevole interesse la valutazione del possibile utilizzo della MFC come sistema per il monitoraggio on-line del COD e degli acidi grassi volatili (VFA) prodotti all’interno di un digestore anaerobico, attraverso la definizione di una correlazione tra i dati elettrici registrati in continuo e le concentrazioni di CODanaer e VFA misurate in diversi periodi della sperimentazione. L’analisi DGGE della biomassa catodica ha fornito uno strumento analitico utile allo studio della diversità della comunità microbica sospesa ed adesa al catodo e ha confermato la forte similarità delle specie batteriche riconosciute nei campioni analizzati. In particolare, le bande di sequenziamento ottenute sono affiliate ai gruppi batterici Firmicutes, -Proteobacteria,  -Proteobacteria, -Proteobacteria e Bacteroidetes. Da quanto emerso dalla sperimentazione condotta si può pertanto concludere che ad oggi le MFC sono in fase di evoluzione rispetto ai primi prototipi utilizzati per lo studio delle comunità microbiali e per la comprensione dei meccanismi di trasferimento elettronico. Sfruttarne la potenza prodotta in maniera commerciale diviene una grande sfida per il futuro, ed è opinione comune che le prime applicazioni pratiche delle MFC saranno come fonte di recupero energetico per i dispositivi utilizzati per il monitoraggio dell’ambiente e per il trattamento delle acque reflue.

Effetto della temperatura di conservazione del latte, dalla raccolta all'affioramento, sulla microflora del latte, del sieroinnesto e del formaggio Trentingrana

This PhD research is part of a project addressed to improve the quality of Grana Trentino production. The objectives were to evaluated if milk storage and collection procedures may affect cheese-making technology and quality. Actually the milk is collected and delivered to the cheese factory just after milking in 50 L cans without refrigeration or in tanks cooled at 18 °C. This procedure is expensive (two deliveries each day) and the milk quality is difficult to preserve as temperatures are not controlled. The milk refrigeration at the farm could allow a single delivery to the dairy. Therefore it could be a good strategy to preserve raw milk quality and reduce cheese spoilage. This operation may, however, have the drawbacks of favouring the growth of psychrotrophic bacteria and changing the aptitude of milk to coagulation. With the aim of studying the effect on milk and cheese of traditional and new refrigerated technologies of milk storage, two different collection and creaming technologies were compared. The trials were replicated in three cheese factories manufacturing Grana Trentino. Every cheese-making day, about 1000 milk liters were collected from always the same two farms in the different collection procedures (single or double). Milk was processed to produce 2 wheels of Grana trentino every day. During the refrigerated trials, milk was collected and stored at the farm in a mixed tank at 12 or 8 °C and then was carried to the dairy in truck once a day. 112 cheese making day were followed: 56 for traditional technology and 56 for the refrigerated one. Each one of these two thechnologies lead to different ways of creaming: long time in the traditional one and shorter in the new one. For every cheese making day we recorded time, temperatures and pH during the milk processing to cheese. Whole milk before ceraming, cream and skim milk after creaming, vat milk and whey were sampled during every cheese-making day for analysis. After 18 months ripening we opened 46 cheese wheels for further chemical and microbiological analyses. The trials were performed with the aim of: 1 estimate the effect of storage temperatures on microbial communities, physico-chemical or/and rheological differences of milk and skim milk after creaming. 2 detect by culture dependent (plate counts) and indipendent (DGGE) methodolgies the microbial species present in whole, skimmed milk, cream and cheese sampled under the rind and in the core; 3 estimate the physico-chemical characteristics, the proteolytic activity, the content of free aminoacids and volatile compounds in 18 months ripened Grana Trentino cheeses from different storing and creaming of milk technologies. The results presented are remarkable since this is the first in-deep study presenting microbiological and chemical analysis of Grana Trentino that even if belonging to Grana Padano Consortium, it is clearly different in the milk and in the manufacturing technology.

Therapeutic strategies for modulation of the vaginal microbiota

The vaginal microbiota of healthy women consists of a wide variety of anaerobic and aerobic bacteria, dominated by the genus Lactobacillus. The activity of lactobacilli is essential to protect women from genital infections and to maintain the natural healthy balance of the vaginal ecosystem. This role is particularly important during pregnancy because vaginal infection is one of the most important mechanisms for preterm birth. The most common vaginal disorder is bacterial vaginosis (BV). BV is a polymicrobial disorder, characterized by a depletion of lactobacilli and an increase in the concentration of other bacteria, including Gardnerella vaginalis, anaerobic Gram-negative rods, anaerobic Gram-positive cocci, Mycoplasma hominis, and Mobiluncus spp. An integrated molecular approach based on real-time PCR and PCR-DGGE was used to investigate the effects of two different therapeutic approaches on the vaginal microbiota composition. (i) The impact of a dietary supplementation with the probiotic VSL#3, a mixture of Lactobacillus, Bifidobacterium and Streptococcus strains, on the vaginal microbial ecology and immunological profiles of healthy women during late pregnancy was investigated. The intake was associated to a slight modulation of the vaginal microbiota and cytokine secretion, with potential implications in preventing preterm birth. (ii) The efficacy of different doses of the antibiotic rifaximin (100 mg/day for 5 days, 25 mg/day for 5 days, 100 mg/day for 2 days) on the vaginal microbiota of patients with BV enrolled in a multicentre, double-blind, randomised, placebo-controlled study was also evaluated. The molecular analyses demonstrated the ability of rifaximin 25 mg/day for 5 days to induce an increase of lactobacilli and a decrease of the BV-associated bacteria after antibiotic treatment, and a reduction of the complexity of the vaginal microbial communities. Thus, confirming clinical results, it represents the most effective treatment to be used in future pivotal studies for the treatment of BV.

Entwicklung und Anwendung molekularbiologischer Methoden zur Art- und Stamm-Identifizierung pro- und eukaryotischer Organismen

Das Wachstum von Milchsäurebakterien-Arten der Gattungen Lactobacillus, Pediococcus und Leuconostoc während der Weinfermentation kann durch die Bildung verschiedener Stoffwechselprodukte zu Weinfehlern führen. Um rechtzeitig Gegenmaßnahmen ergreifen zu können und einem Weinverderb vorzubeugen, bedarf es geeigneter Identifizierungsmethoden. Klassische mikrobiologische Methoden reichen oft nicht aus, um Mikroorganismen auf Art- und Stammniveau gezielt zu identifizieren. Wegen ihrer schnellen Durchführbarkeit und Zuverlässigkeit sind molekularbiologische Identifizierungsmethoden zur Kontrolle der mikrobiellen Flora während der Lebensmittelfermentierung in der heutigen Zeit unabdingbar. In der vorliegenden Forschungsarbeit wurden die 23S rRNA-Gensequenzen von neun Pediococcus-Typstämmen sequenziert, analysiert und phylogenetische Analysen durchgeführt. Zur Art-Identifizierung der Pediokokken wurden PCR-Primer generiert und ein Multiplex PCR System entwickelt, mit dem alle typischen Arten simultan in einer Reaktion nachgewiesen werden konnten. Die Ergebnisse der Multiplex PCR-Identifizierung von 62 Pediococcus-Stämmen aus Kulturensammlungen und 47 neu isolierten Stämmen aus Wein zeigten, dass einige Stämme unter falschen Artnamen hinterlegt waren, und dass P. parvulus im Weinanbaugebiet Rheinhessen weit verbreitet war. Die Fähigkeit der Pediococcus-Stämme zur Exopolysaccharid-Synthese wurde durch den Nachweis zweier Gene überprüft. Auf Basis der 23S rDNA-Sequenzen wurden rRNA-Sekundärstrukturen mit der neu entwickelten Software Structure Star generiert, die zum Auffinden von Zielbereichen für fluoreszenzmarkierte DNA-Sonden geeignet waren. Die Sequenzunterschiede zwischen den Pediococcus-Arten reichten aus, um zwei Gruppen durch Fluoreszenz in situ Hybridisierung differenzieren zu können. Die Verwendung unmarkierter Helfer-sonden verbesserte die Zugänglichkeit der Sonden an die rRNA, wodurch das Fluoreszenz-Signal verstärkt wurde. Um Milchsäurebakterien durch Denaturierende Gradienten Gel Elektrophorese differenzieren zu können, wurden Primer entwickelt, mit denen ein hochvariabler 23S rDNA-Bereich amplifiziert werden konnte. Die Nested Specifically Amplified Polymorphic DNA (nSAPD)-PCR wurde in der vorliegenden Arbeit zur Art- und Stamm-Differenzierung pro- und eukaryotischer Organismen angewandt. Es wurden vor allem weinrelevante Milchsäurebakterien der Gattungen Oenococcus, Lactobacillus, Pediococcus und Leuconostoc und Hefen der Gattungen Dekkera / Brettanomyces und Saccharomyces untersucht. Die Cluster-Analyse der Pediococcus-Typstämme führte zu einer unterschiedlichen Baum-Topologie im Vergleich zum phylogenetischen 23S rDNA-Stammbaum. Die Verwandtschaftsverhältnisse der untersuchten O. oeni-Stämme aus Starterkulturen konnten in Bezug auf eine frühere Cluster-Analyse reproduziert werden. Die Untersuchung von 40 B. bruxellensis-Stämmen aus rheinhessischen Weinproben zeigte eine Gruppierung der Stämme gemäß dem Ort der Probennahme. Beim Vergleich der Verwandtschaftsverhältnisse von Stämmen der Arten P. parvulus und B. bruxellensis, die aus denselben Weinproben isoliert wurden, konnte eine hohe Übereinstimmung der beiden Baum-Topologien beobachtet werden. Anhand der SAPD-PCR Untersuchung von Sekthefen aus Starterkulturen konnten alle Stämme der Art S. cerevisiae zugeordnet werden. Die nSAPD-PCR war darüber hinaus geeignet, um höhere Eukaryoten wie Weinreben zu differenzieren und es konnten die Verwandtschaftsverhältnisse von Mäusen und menschlichen Individuen durch Cluster-Analysen nachvollzogen werden. Mit Hilfe der Sequence Characterized Amplified Region (SCAR)-Technik wurden (n)SAPD-Marker in SCAR-Marker konvertiert. Die neu generierten SCAR-Primer konnten zur simultanen Art-Identifizierung von sieben weinschädlichen Milchsäurebakterien in einer Multiplex PCR erfolgreich eingesetzt werden. Die in dieser Arbeit entwickelten molekularbiologischen Identifizierungsmethoden können zum Beispiel in der mikrobiologischen Qualitätskontrolle Anwendung finden.