Tullio Brusa

Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline

The chemical composition of the Bannock basin has been studied in some detail. We recently showed that unusual microbial populations, including a new division of Archaea (MSBL1), inhabit the NaCl-rich hypersaline brine. High salinities tend to reduce biodiversity, but when brines come into contact with fresher water the natural haloclines formed frequently contain gradients of other chemicals, including permutations of electron donors and acceptors, that may enhance microbial diversity, activity and biogeochemical cycling. Here we report a 2.5-m-thick chemocline with a steep NaCl gradient at 3.3 km within the water column betweeen Bannock anoxic hypersaline brine and overlying sea water. The chemocline supports some of the most biomass-rich and active microbial communities in the deep sea, dominated by Bacteria rather than Archaea, and including four major new divisions of Bacteria. Significantly higher metabolic activities were measured in the chemocline than in the overlying sea water and underlying brine; functional analyses indicate that a range of biological processes is likely to occur in the chemocline. Many prokaryotic taxa, including the phylogenetically new groups, were confined to defined salinities, and collectively formed a diverse, sharply stratified, deep-sea ecosystem with sufficient biomass to potentially contribute to organic geological deposits.

Isolation and characterization ofMethanobrevibacter oralis sp. nov.

A new coccobacillary, nonmotile, Gram-positive, methane-producing organism was isolated from human subgingival plaque. Both hydrogen and carbon dioxide were required for growth. No methane was produced from acetate, formate, or methanol. The optimum pH was 6.9–7.4, and the optimum temperature was 36–38°C. Fecal extract was required for growth, and a volatile fatty acid mixture was highly stimulatory. The DNA G+C content was 28 mol%. On the basis of these characteristics, DNA-DNA hybridization studies, and electrophoretic analysis of cellular proteins, the isolate was considered a new species and namedMethanobrevibacter oralis.

Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin

Urania basin in the deep Mediterranean Sea houses a lake that is >100 m deep, devoid of oxygen, 6 times more saline than seawater, and has very high levels of methane and particularly sulfide (up to 16 mM), making it among the most sulfidic water bodies on Earth. Along the depth profile there are 2 chemoclines, a steep one with the overlying oxic seawater, and another between anoxic brines of different density, where gradients of salinity, electron donors and acceptors occur. To identify and differentiate the microbes and processes contributing to the turnover of organic matter and sulfide along the water column, these chemoclines were sampled at a high resolution. Bacterial cell numbers increased up to a hundredfold in the chemoclines as a consequence of elevated nutrient availability, with higher numbers in the upper interface where redox gradient was steeper. Bacterial and archaeal communities, analyzed by DNA fingerprinting, 16S rRNA gene libraries, activity measurements, and cultivation, were highly stratified and metabolically more active along the chemoclines compared with seawater or the uniformly hypersaline brines. Detailed analysis of 16S rRNA gene sequences revealed that in both chemoclines δ- and ε-Proteobacteria, predominantly sulfate reducers and sulfur oxidizers, respectively, were the dominant bacteria. In the deepest layers of the basin MSBL1, putatively responsible for methanogenesis, dominated among archaea. The data suggest that the complex microbial community is adapted to the basins extreme chemistry, and the elevated biomass is driven largely by sulfur cycling and methanogenesis.

Methanogens in the human intestinal tract and oral cavity

The incidence and concentration of methanobacteria in the human intestinal tract have not been well evaluated. Only recently were such microorganisms found in the oral cavity. We determined the counts of methanogens in the feces of healthy subjects on a Mediterranean diet and evaluated whether individuals with methanobacteria in the intestine also harbor such bacteria in the oral cavity. Methanobacteria were observed in the feces of 18 of the 20 subjects, at a level ranging from 103 to 1010/g dry wt. Only 45% of the subjects harbored methanobacteria in the plaque and saliva, showing that the presence of methanogens in the oral cavity was not correlated with their presence in the feces. The presence and number of methanobacteria appeared to remain constant after 3 months. A short rod arranged in chains, similar to theMethanobrevibacter smithii which predominates in feces, was the methanogenic form present in the mouth.

Aromatic hydrocarbon degradation patterns and catechol 2,3-dioxygenase genes in microbial cultures from deep anoxic hypersaline lakes in the eastern Mediterranean sea.

Several mixed cultures able to grow on different aromatic hydrocarbons were obtained from different depths (between 3500 and 3660 m under the sea surface) of water/brine interfaces (1 to 5 m over the estimated brine surface) of three deep hypersaline anoxic basins (Urania, Discovery and Atalante) in the eastern Mediterranean sea. Eight strains which completely removed toluene from the medium in six to 10 days were isolated from one of the mixed cultures obtained from the Urania basin. The strains grew on toluene and yeast extract in the presence of NaCl concentrations of up to 50 and 100 g l(-1), respectively, indicating that they are halotolerant rather than halophilic. Even though DNA fingerprinting methods showed that the strains were strictly related, two groups could be found on the basis of the plasmid profile. Metabolic profiling and partial sequencing (350 bp) of the 16S rDNA showed that the strains were related to Pseudomonas mendocina. A 320 bp fragment of the catechol 2,3-dioxygenase gene from all the strains was aimplified by PCR. The sequence of the fragment showed 100% identity with xylE from pWW53 of Pseudomonas putida MT53 isolated from soil. Southern hybridisation experiments showed that catechol 2,3-dioxygenase is plasmid encoded.

Methanogenic bacteria: presence in foodstuffs

Methanogenic bacteria are anaerobic, oxygen‐intolerant microorganisms, and it is only by studying the different habitats of such bacteria that fundamental information about their ecology becomes available. This research has evaluated methanogenic bacteria in apparently aerobic ecosystems, in foodstuffs not subjected to chemical‐physical reclamation processes, where the presence of methanogenic bacteria has never been investigated.

Influence of the herbicide bentazon on soil microbial community.

Changes in microbial numbers and activities in a soil in response to bentazon applied at 10 and 100 ppm were studied after 4 and 30 weeks of incubation in laboratory conditions. As regards the eight general and functional microbial groups studied (aerobic and anaerobic bacteria, fungi, aerobic and anaerobic N2-fixing bacteria, nitrifiers, aerobic and anaerobic cellulolytic microorganisms), only the number of anaerobic N2-fixing bacteria significantly decreased, in the presence of the highest herbicide concentration for 30 weeks. At both the incubation times, only the higher dose of bentazon markedly inhibited soil nitrification and CO2 emission. Methanogenesis was inhibited by 1000 ppm bentazon added to anaerobic liquid cultures containing 5% soil for at least 2 weeks. There was an incomplete recovery of the herbicide at the two incubation times: < 5% of 10 ppm after 4 weeks and about 30% of 100 ppm after 30 weeks. No biodegradation of the compound was observed in liquid cultures under aerobic or anaerobic conditions. It is concluded that a bentazon concentration no higher than the field rate distributed within a 2-cm layer of soil does not considerably affect the microflora even in the absence of microbial degradation.

Quantitative determination of methanogenic bacteria in the feces of different mammals

In this research on fresh human, cattle, swine, and rabbit feces, methanogenic bacteria were found in all samples examined, at the following concentrations per gram dry weight: swine, 108; human, 107; cattle, 106; and rabbit, 104. Anaerobic heterotrophic bacteria were found in the following concentrations per gram dry weight: human, 1011; swine, 1011; cattle, 1011; and rabbit, 1010. The total number of O2-intolerant was higher than that of O2-tolerant bacteria: about 10–100 times for methanogenic and 100–1000 times for anaerobic heterotrophic bacteria.

Oxygen tolerance of anaerobic bacteria isolated from human feces

The large bowel intestinal flora of mammals is made up mostly of O2-intolerant anaerobic microorganisms which are irreversibly damaged by brief exposure to air. The aim of our work was to investigate the effect of atmospheric O2 on human intestinal anaerobic microorganisms. Thirty O2-intolerant bacterial strains that reached 100% mortality after 120 min of air exposure were isolated. Ten of these strains were tested for their atmospheric O2 sensitivity as a function of air exposure time; all tested microorganisms showed a similar mortality trend on exposure to air. In fact, 50% of cells survive, on the average, after 4–5 min of atmospheric O2; this percentage decreases to 3–5% after only 20 min, and after 40 min only one cell in a thousand survives; all strains reached 100% mortality in a time range of 100–120 min. The strains examined were identified as belonging to the generaEubacterium, Peptostreptococcus, andCoprococcus.

Influence of long-term feeding of different purified dietary fibers on cecal microflora composition and its metabolizing activity on bile acids

Abstract The aim of the study was to investigate the effect of four weeks ingestion of 10% fiber diets (cellulose, lignocellulose, pectin and guar gum) and a fiber-free diet on cecal microflora composition and its primary bile acid metabolizing activity in vitro in female Sprague Dawley rats. There was no difference in the qualitative and quantitative cecal microflora composition in rats fed cellulose and lignocellulose diets and those fed fiber-free diet. Guar gum and pectin diets significantly increased Bacteroidaceae compared to cellulose and lignocellulose diets. The counts of bifidobacteria were significantly higher in rats fed guar gum than in all the other groups. Clostridia were present in high counts in rats fed guar gum and pectin and generally absent in all the other groups. As regards 7α-dehydroxylating cholic and chenodeoxycholic microorganisms, cellulose and lignocellulose diets significantly decreased these microbial counts compared to all the diets. The results show that dietary fiber can induce alterations of cecal microflora composition and intestinal bile acid metabolism.