Isolates of Thermoanaerobacter thermohydrosulfuricus from decaying wood compost display genetic and phenotypic microdiversity

In this study, 12 strains of Thermoanaerobacter were isolated from a single decaying wood compost sample and subjected to genetic and phenotypic profiling. The 16S rRNA encoding gene sequences suggested that the isolates were most similar to strains of either Thermoanaerobacter pseudethanolicus or Thermoanaerobacter thermohydrosulfuricus. Examination of the lesser conserved chaperonin-60 (cpn60) universal target showed that some isolates shared the highest sequence identity with T.?thermohydrosulfuricus; however, others to Thermoanaerobacter wiegelii and Thermoanaerobacter sp. Rt8.G4 (formerly Thermoanaerobacter brockii Rt8.G4). BOX-PCR fingerprinting profiles identified differences in the banding patterns not only between the isolates and the reference strains, but also among the isolates themselves. To evaluate the extent these genetic differences were manifested phenotypically, the utilization patterns of 30 carbon substrates were examined and the niche overlap indices (NOI) calculated. Despite showing a high NOI (>?0.9), significant differences existed in the substrate utilization capabilities of the isolates suggesting that either a high degree of niche specialization or mechanisms allowing for non-competitive co-existence, were present within this ecological context. Growth studies showed that the isolates were physiologically distinct in both growth rate and the fermentation product ratios. Our data indicate that phenotypic diversity exists within genetically microdiverse Thermoanaerobacter isolates from a common environment.     

Feeding on fungi: genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass

Dead fungal biomass is an abundant source of nutrition in both litter and soil of temperate forests largely decomposed by bacteria. Here, we have examined the utilization of dead fungal biomass by the five dominant bacteria isolated from the in situ decomposition of fungal mycelia using a multiOMIC approach. The genomes of the isolates encoded a broad suite of carbohydrate-active enzymes, peptidases and transporters. In the extracellular proteome, only Ewingella americana expressed chitinases while the two Pseudomonas isolates attacked chitin by lytic chitin monooxygenase, deacetylation and deamination. Variovorax sp. expressed enzymes acting on the side-chains of various glucans and the chitin backbone. Surprisingly, despite its genomic potential, Pedobacter sp. did not produce extracellular proteins to decompose fungal mycelia but presumably feeds on simple substrates. The ecological roles of the five individual strains exhibited complementary features for a fast and efficient decomposition of dead fungal biomass by the entire bacterial community.     

Physiological and phylogenetic diversity of bacteria growing on resin acids

Resin acids are tricyclic diterpenes which are synthesized by trees and are a major cause of toxicity of pulp mill effluents. Bacterial strains isolated from three different sources and which grow on resin acids were physiologically characterized. Eleven strains, representating distinct groups, were further characterized physiologically and phylogenetically. The isolates had distinct specificities for use, as growth substrates, of the different resin acids tested. The isolates also used fatty acids but were generally limited in use of other diverse substrates tested. According to their 16S rDNA sequences, the representative isolates are related to members of the genera, Sphingomonas, Zoogloea, Ralstonia, Burkholderia, Pseudomonas and Mycobacterium. Analysis of whole-cell fatty acid profiles generally supported those phylogenetic relationships. However, most of the isolated did not have high similarities to reference strains in the Microbial Identification System database of fatty acid profiles or in the Biolog database of substrate oxidation patterns. Described species of Sphingomonas, Zoolgoea, Burkholderia Pseudomonas, most closely related to the isolates we characterized, failed to grow on, or degrade, resin acids. We propose recognition of Zoogloea resiniphila sp. nov., Pseudomonas vancouverensis sp. nov., P. abietaniphila sp. nov. and P. multiresinivorans sp. nov.     

Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions,and description of Thauera phenylacetica sp. nov., Thauera aminoaromaticasp. nov., and Azoarcus buckelii sp. nov

Six strains of denitrifying bacteria isolated from various oxic and anoxic habitats on different monocyclic aromatic substrates were characterized by sequencing 16S rRNA genes, determining physiological and morphological traits, and DNA-DNA hybridization. According to these criteria, strains S100, SP and LG356 were identified as members of Thauera aromatica. Strains B5-1 and B5-2 were tentatively affiliated to the species Azoarcus tolulyticus. Strains B4P and S2 were only distantly related to each other and to other described Thauera species. These two strains are proposed as the type strains of two new species, Thauera phenylacetica sp. nov. and Thauera aminoaromaticasp. nov., respectively. By 16S rRNA gene analysis, strain U120 was highly related to the type strains of Azoarcus evansii and Azoarcus anaerobius, whereas corresponding DNA-DNA reassociation values indicated only a low degree of genomic relatedness. Based upon a low DNA similarity value and the presence of distinguishing physiological properties, strain U120 is proposed as the type strain of a new species, Azoarcus buckelii sp. nov. Almost all of the new isolates were obtained with different substrates. The highly varied substrate spectra of the isolates indicates that an even higher diversity of denitrifying bacteria degrading aromatic compounds would be discovered in the different habitats by using a larger spectrum of aromatic substrates for enrichment and isolation.     

Occurrence and characterization of psychrotolerant hydrocarbon-oxidizing bacteria from surface seawater along the Victoria Land coast (Antarctica)

A total of 253 hydrocarbon-oxidizing bacterial isolates were achieved from eight Antarctic surface seawater samples enriched on diesel oil at 4°C. Isolates were screened by amplified ribosomal DNA restriction analysis prior to 16S rRNA gene sequencing. Sequences were compared to those in available databases using the Basic Local Alignment Search Tool network service to determine their approximate phylogenetic affiliations. The majority of the isolates were affiliated to the Actinobacteria (75.9%) and the Gamma-Proteobacteria (22.9%). The Alpha- and Beta-Proteobacteria represented 0.8 and 0.4% of total isolates, respectively. The Actinobacteria were predominantly allocated to the genera Arthrobacter, Cryobacterium and Rhodococcus. The Gamma-Proteobacteria were mainly found to be related to the genus Pseudomonas. Conversely, the Alpha- and Beta-Proteobacterial isolates shared the highest degree of sequence identity with unclassified bacteria. Differences in the distribution of the detected phylotypes were observed among the analyzed samples. Isolates representing each phylotype were selected for further characterization, including phenotypic assays and screening for the growth ability in the presence of individual hydrocarburic substrates as the sole supplied carbon and energy source. Isolates possessed different patterns of substrate utilization. Aliphatic hydrocarbons supported the growth of a higher number of isolates than aromatics. Results confirm the ability of our Antarctic marine bacteria to utilize hydrocarbons at low temperature and therefore suggesting that isolates with different substrate specificities can act in nature as a consortium in the utilization of complex hydrocarburic mixtures.     

Antifungal efficacy of bacteria isolated from marine sedentary organisms

The antibiotic-producing ability of 57 bacteria isolated from 8 marine sedentary organisms, 6 sponges (Spirastrella sp.,Phyllospongia sp.,Ircinia sp.,Aaptos sp.,Azorica sp.,Axinella sp.), 1 soft coral (Lobophytum sp.) and 1 alga (Sargassum sp.), was evaluated against 6 phytopathogenic fungi (Helminthosporium oryzae, Rhizoctonium solani, Pyricularia oryzae, Fusarium oxysporum, Aspergillus oryzae andA. fumigatus). Bacteria of the genusBacillus (20%),Pseudomonas (33%) andFlavobacterium (40%) were predominant among the heterotrophic bacteria isolated from the marine sponges, soft coral and alga, respectively. Bioassay results revealed that 36 (63%) bacterial isolates displayed antifungal activity against at least one fungus, the alga (Sargassum sp.) being the source of highest number (80%) of producer strains. Twelve bacterial isolates inhibited all fungi. The MIC of the organic extracts of 12 bacteria ranged from 0.3 to 22.8 mg/L.     

Genetic and phenotypic microdiversity of Ochrobactrum spp

The diversity of Ochrobactrum anthropi, Ochrobactrum intermedium, Ochrobactrum tritici and Ochrobactrum grignonense in agricultural soil and on the wheat rhizoplane was investigated. O. anthropi was isolated both from soil and from the rhizoplane, O. intermedium and grignonense only from bulk soil, and O. tritici only from the wheat rhizoplane. On the genetic level, the immunotrapped isolates and a number of strains from culture collection mainly of clinical origin were compared with rep-PCR profiling using BOX primers, and a subset of these isolates and strains using REP primers. The isolates clustered according to their species affiliation. There was no correlation between rep clusters of O. anthropi isolates and habitat (place of isolation). The genetic diversity of Ochrobactrum at the species level as well as microdiversity of O. anthropi (number of BOX groups) was higher in soil than on the rhizoplane. Similarity values from genetic rep-PCR profiles correlated positively with DNA-DNA reassociation percentages. Isolates with >80.7% similarity in BOX profile and >86.4% in rep profile clustered within the same species. Similarity analysis of rep-PCR profiles is hence an alternative to DNA-DNA hybridization as a genomic criterion for species delineation within the genus Ochrobactrum. We used the substrate utilization system BIOLOG-GN to compare the immunotrapped isolates on the phenetic level. For the isolates from bulk soil, substrate utilization versatility (number of utilized substrates) and substrate utilization capacity (mean conversion rate of substrates) were slightly but significantly higher than for the isolates from the rhizoplane. This trend was also seen using API 20E and 20NE systems. Plate counts of total bacteria and the number of immunotrapped Ochrobactrum isolates per gram dry weight were higher for the rhizoplane than for the soil samples. The results of genetic and phenotypic analyses indicated a 'rhizosphere effect'; the diversity and metabolic capacity of Ochrobactrum isolates were higher in bulk soil, and the population density was higher on the wheat rhizoplane.     

Production of Industrial Enzymes (Amylase,Carboxymethylcellulase and Protease) by Bacteria Isolated from Marine Sedentary Organisms

The abilities of bacteria isolated from eight marine sedentary organisms, six marine sponges (Spirastrella sp., Phyllospongia sp., Ircinia sp., Aaptos sp., Azorica sp. and Axinella sp.), one soft coral (Lobophytum sp.) and one alga (Sargassum sp.) to produce industrial enzymes (amylase, carboxymethylcellulase and protease) were examined. The mean total viable counts of the bacterial isolates ranged from 8.7 × 10⁴ to 8.4 × 10⁵ cfu/g wet weight of the organism. All eight organisms harboured amylase (0.05–0.5 IU/ml), carboxymethylcellulase (0.05–0.5 IU/ml) and protease (0.1–0.5 IU/ml) producing bacteria. Of 56 bacterial strains tested, as many as 60 to 83% of the strains produced at least one of the three enzymes, and 47% of strains were able to produce all three enzymes. High activities (> 0.5 IU/ml) of the three enzymes were recorded in bacterial strains belonging to the genera Alcaligenes and Bacillus. From the results of this study, it appears that bacteria associated with marine sedentary organisms are the novel source of industrial enzymes for possible commercial applications and may play an important role in enzyme‐catalysed organic matter cycling in marine environments.     

Screening and Characterization of Several 2,2-Dicholoropropionic Acid–Degrading Bacteria Isolated from Marine Sediment of Danga Bay and East Coast of Singapore Island

Industries and agriculture activities extensively utilize halogenated compounds. These compounds were found to be toxic and pollute the environment. Thus, many studies have been done on microbial degradation of these chemicals. In this study, an attempt was made to isolate bacterial strains EK1–EK5 from marine sediments collected at Danga Bay and east coast of Singapore island. The 16S rRNA analysis suggested that the isolated bacteria had more than 96% sequence identity to the sequence in the database; therefore, they were designated as Bacillus sp., Rhodococcus sp., Lysinibacillus sp., Microbacterium sp., and Aminobacter sp. The results of molecular analysis were supported by biochemical and microscopic examinations. Bacterial isolates were able to grow slowly in minimal medium containing only 2,2-dichloropropionate as the sole carbon source. The cellular doubling times were 39.60 ± 0.1, 36.60 ± 0.2, 30.71 ± 0.1, 41.23 ± 0.1, and 36.70 ± 0.3 h for EK1, EK2, EK3, EK4, and EK5, respectively. In the future, it will be important to further investigate the presence of the dehalogenase gene in their genomic DNA for further characterization.     

Bacterial diversity and their metabolic profiles in the sedimentary environments of Ny-Ålesund,Arctic

Sedimentary environments in the Arctic are known to harbor diverse microbial communities playing a crucial role in the remineralization of organic matter and associated biogeochemical cycles. In this study, we used a combination of culture-dependent and culture-independent approaches to understanding the bacterial community composition associated with the sediments of a terrestrial versus fjord system in the Svalbard Arctic. Community-level metabolic profiling and growth response of retrieved bacterial isolates towards different carbon substrates at varying temperatures were also studied to assess the metabolic response of communities and isolates in the system. Bacterial species belonging to Cryobacterium and Psychrobacter dominated the terrestrial and fjord sediment retrievable fraction. Amplicon sequencing analysis revealed higher bacterial diversity in the terrestrial sediments (Shannon index; 8.135 and 7.935) as compared to the fjord sediments (4.5–5.37). Phylum Proteobacteria and Bacteroidetes dominated both terrestrial and fjord sediments. Phylum Verrucomicrobia and Cyanobacteria were abundant in terrestrial sediments while Epsilonbacteraeota and Fusobacteriia dominated the fjord sediments. Significant differences were observed in the carbon substrate utilization profiles between the terrestrial and fjord sediments at both 4 °C and 20 °C incubations (p?<?0.005). Utilization of N-acetyl-D-glucosamine, D-mannitol and Tween-80 by the sediment communities and bacterial isolates from both systems, irrespective of their temperature incubations implies the affinity of bacteria for such substrates as energy sources and for their survival in cold environments. Our results suggest the ability of sediment bacterial communities to adjust their substrate utilization profiles according to condition changes in the ecosystems and are found to be less influenced by their phylogenetic relatedness.

     

Extremophile Culture Collection from Andean Lakes: Extreme Pristine Environments that Host a Wide Diversity of Microorganisms with Tolerance to UV Radiation

A total of 88 bacterial strains were isolated from six Andean lakes situated at altitudes ranging from 3,400 to 4,600 m above sea level: L. Aparejos (4,200 m), L. Negra (4,400 m), L. Verde (4,460 m), L. Azul (4,400 m), L. Vilama (4,600 m), and Salina Grande (3,400 m). Salinity ranged from 0.4 to 117 ppm. General diversity was determined by denaturing gradient gel electrophoresis (DGGE) analysis. From the excised DGGE bands, 182 bacterial sequences of good quality were obtained. Gammaproteobacteria and Cytophaga/Flavobacterium/Bacteroides (CFB) were the most abundant phylogenetic groups with 42% and 18% of identified bands, respectively. The isolated strains were identified by sequence analysis. Isolated bacteria were subjected to five different UV-B exposure times: 0.5, 3, 6, 12, and 24 h. Afterwards, growth of each isolate was monitored and resistance was classified according to the growth pattern. A wide interspecific variation among the 88 isolates was observed. Medium and highly resistant strains accounted for 43.2% and 28.4% of the isolates, respectively, and only 28.4% was sensitive. Resistance to solar radiation was equally distributed among the isolates from the different lakes regardless of the salinity of the lakes and pigmentation of isolates. Of the highly resistant isolates, 44.5% belonged to gammaproteobacteria, 33.3% to betaproteobacteria, 40% to alphaproteobacteria, 50% to CFB, and among gram-positive organisms, 33.3% were HGC and 44.5% were Firmicutes. Most resistant strains belonged to genera like Exiguobaceterium sp., Acinetobacter sp., Bacillus sp., Micrococcus sp., Pseudomonas sp., Sphyngomonas sp., Staphylococcus sp., and Stenotrophomonas sp. The current study provides further evidence that gammaproteobacteria are the most abundant and the most UV-B-resistant phylogenetic group in Andean lakes and that UV resistance in bacteria isolated from these environments do not depend on pigmentation and tolerance to salinity.     

Fermentation of trihydroxybenzenes by Pelobacter acidigallici gen. nov. sp. nov., a new strictly anaerobic,non-sporeforming bacterium

Five strains of rod-shaped, Gram-negative, non-sporing, strictly anaerobic bacteria were isolated from limnic and marine mud samples with gallic acid or phloroglucinol as sole substrate. All strains grew in defined mineral media without any growth factors; marine isolates required salt concentrations higher than 1% for growth, two freshwater strains only thrived in freshwater medium. Gallic acid, pyrogallol, 2,4,6-trihydroxybenzoic acid, and phloroglucinol were the only substrates utilized and were fermented stoichiometrically to 3 mol acetate (and 1 mol CO₂) per mol with a growth yield of 10g cell dry weight per mol of substrate. Neither sulfate, sulfur, nor nitrate were reduced. The DNA base ratio was 51.8% guanine plus cytosine. A marine isolate, Ma Gal 2, is described as type strain of a new genus and species, Pelobacter acidigallici gen. nov. sp. nov., in the family Bacteroidaceae. In coculture with Acetobacterium woodii, the new isolates converted also syringic acid completely to acetate. Cocultures with Methanosarcina barkeri converted the respective substrates completely to methane and carbon dioxide.     

Isolation and characterization of algicidal bacteria from <Emphasis Type="Italic">Cochlodinium polykrikoides</Emphasis> culture

In this study, we analyzed a bacterial community closely associated with Cochlodinium polykrikoides that caused harmful algal blooming in the sea. Filtration using a plankton mesh and percoll gradient centrifugation were performed to eliminate free-living bacteria. Attached bacteria were analyzed by culture-dependent and culture-independent methods. Five culturable bacterial strains were isolated and identified from the C. polykrikoides mixed bacterial community. The isolates belonged to α-Proteobacteria (Nautella sp., Sagittula sp., and Thalassobius sp.) and γ-Proteobacteria (Alteromonas sp. and Pseudoalteromonas sp.). All of the 5 isolates showed algicidal activity against C. polykrikoides and produced extracellular compounds responsible for algicidal properties after entering the stationary phase. The algicidal compounds produced by the 5 isolates were heat-stable and had molecular masses of less than 10,000 Da. Furthermore, the algicidal compounds were relatively specific for C. polykrikoides in terms of their algicidal activities. Culture-independent analysis of the bacterial community in association with C. polykrikoides was performed using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). On the basis of the PCR-DGGE profile, Sagittula sp. was identified as a dominant species in the bacterial community of C. polykrikoides.     

Phenotypic,genomic and phylogenetic characteristics of rhizobia isolated from root nodules of <Emphasis Type="Italic">Robinia pseudoacacia</Emphasis> (black locust) growing in Poland and Japan

Rhizobial strains, rescued from the root nodules of Robinia pseudoacacia growing in Japan and Poland, were characterized for the phenotypic properties, genomic diversity as well as phylogeny and compared with the reference strains representing different species and genera of nodule bacteria. They had a moderately slow growth rate, a low tolerance to antibiotics, a moderate resistance to NaCl and produced acid in yeast mannitol agar. Cluster analysis based on the phenotypic features divided all bacteria involved in this study into four phena, comprising: (1) Rhizobium sp. + Sinorhizobium sp., (2) Bradyrhizobium sp., (3) R. pseudoacacia microsymbionts + Mesorhizobium sp., and (4) Rhizobium galegae strains at similarity coefficient of 74%. R. pseudoacacia nodule isolates and Mesorhizobium species were placed on a single branch clearly distinct from other rhizobium genera lineages. Strains representing R. pseudoacacia microsymbionts shared 98–99% 16S rDNA sequence identity with Mesorhizobium species and in 16S rDNA phylogenetic tree all these bacteria formed common cluster. The rhizobia tested are genomically heterogeneous as indicated by the AFLP (Amplified Fragment Length Polymorphism) method. The bacteria studied exhibited high degree of specificity for nodulation. Nitrogenase structural genes in these strains were located on 771–961 kb megaplasmids. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Evidence for an enhanced substrate requirement by marine mesophilic bacterial isolates at minimal growth temperatures

Bacterial isolates from the subtropical southeastern continental shelf were cultured in a matrix of temperature and substrate concentrations encompassing a range of temperature and substrate concentrations equal to and exceeding natural ones. At the annual minimum temperature, marine heterotrophic bacterial isolates required higher concentrations of dissolved substrates for active growth than are usually found in seawater. We show this to result from a nonlinear interaction of the combined effects of temperature and substrate concentration on bacterial growth and respiratory rate. As a result, bacterial and protozoan utilization of phytoplankton production during winter and early spring is low, permitting greater energy flow to zooplankton and benthic animals, while in late spring, summer, and fall, the microbial loop dominates energy flux and organic carbon utilization. Escherichia coli shows a similar nonlinear response to temperature at minimal substrate concentrations, albeit at a higher range of concentrations than were utilized by the marine isolates. Thus, bacteria from subtropical regions are shown to have a differential growth response near the minimum temperature for growth, depending on the concentration of available substrates. Offprint requests to: W.J. Wiebe.     

The bacterial microflora of witloof chicory (Cichorium intybus L. var.foliosum Hegi) leaves

The bacterial flora on the heads of four different witloof chicory varieties was examined. The 590 isolates were characterized by their SDS-PAGE protein profiles; they revealed 149 different protein fingerprint types. The fluorescentPseudomonas fingerprint type CH001 was abundantly found on all heads examined. Fourteen other fingerprint types occurred in high densities more than twice. Among these, the following were identified: fluorescentPseudomonas, nonfluorescentPseudomonas sp.,Erwinia herbicola, Erwinia sp., andFlavobacterium sp. The majority of the fingerprint types (90%) was found only once. It was also our objective to isolate bacteria applicable in the biological control of chicory phytopathogens. Isolates of all fingerprint types were tested for in vitro antagonistic activity and for possible deleterious effect on plant growth. FluorescentPseudomonas andSerratia liquefaciens isolates were antagonistic against fungi. Among the 161 fluorescentPseudomonas strains, five were able to produce disease symptoms on chicory leaves upon inoculation. Comparison of the results of this study with those obtained in two previous analyses revealed that the leaf microflora showed some similarities with the bacterial flora of chicory roots. The chicory seed microflora differed from that of both leaves and roots.     

Metabolism of select amino acids in bacteria from the pig small intestine

This study investigated the metabolism of select amino acids (AA) in bacterial strains (Streptococcus sp., Escherichia coli and Klebsiella sp.) and mixed bacterial cultures derived from the jejunum and ileum of pigs. Cells were incubated at 37°C for 3 h in anaerobic media containing 0.5–5 mM select AA plus [U-¹⁴C]-labeled tracers to determine their decarboxylation and incorporation into bacterial protein. Results showed that all types of bacteria rapidly utilized glutamine, lysine, arginine and threonine. However, rates of the utilization of AA by pure cultures of E. coli and Klebsiella sp. were greater than those for mixed bacterial cultures or Streptococcus sp. The oxidation of lysine, threonine and arginine accounted for 10% of their utilization in these pure bacterial cultures, but values were either higher or lower in mixed bacterial cultures depending on AA, bacterial species and the gut segment (e.g., 15% for lysine in jejunal and ileal mixed bacteria; 5.5 and 0.3% for threonine in jejunal mixed bacteria and ileal mixed bacteria, respectively; and 20% for arginine in ileal mixed bacteria). Percentages of AA used for bacterial protein synthesis were 50–70% for leucine, 25% for threonine, proline and methionine, 15% for lysine and arginine and 10% for glutamine. These results indicate diverse metabolism of AA in small-intestinal bacteria in a species- and gut compartment-dependent manner. This diversity may contribute to AA homeostasis in the gut. The findings have important implications for both animal and human nutrition, as well as their health and well-beings.     

Bacterial spoilage of bleached-flax rove treated with sub-lethal concentration of biocides

Summary Bacterial species capable of causing spoilage of biocide-treated and untreated-bleached flax roves were present in gutters, troughs and splash boards of spinning frames and also in the atmosphere around these frames. The common bacterial isolates can stain the bleached-rove treated with a sub-lethal concentration of a range of biocides or they can also reduce strength of the untreated-bleached-roves by degrading the residual non-cellulosic polysaccharides present on the fibre. However, the bacterial isolates did not cause staining on non-biocidetreated roves. The seven main bacteria isolated were Bacillus cereus mycoides, B. subtilis, Enterobacter cloacae, Klebsiella oxytoca, Micrococcus sp., Pseudomonas fluorescens and P. putida and all the isolates produced pectate-lyase on both sterilized-bleached fibre and in liquid culture. B. subtilis also produced xylanase on both substrates tested. None of the isolates produced cellulase on either substrate. Infra-red analysis of the stain produced by the bacteria suggested that compounds present were similar to melanin. Of the seven biocides tested (Dodigen {226X}, Durocid VA, AAS, SOPP, Preventol WB, Resista 4102, Rustol HEK and Sandocide), Dodigen (226X), Preventol WB, Resista 4102 and Rustol HEK offered the best protection of roves against bacterial staining.     

Isolation and molecular characterization of thiosulfate-oxidizing bacteria from an Italian rice field soil

In rice paddy soils an active cycling of sulfur compounds takes place. To elucidate the diversity of thiosulfate-oxidizing bacteria these organisms were enriched from bulk soil and rice roots by the most probable number method in liquid medium. From the MPN enrichment cultures 21 bacterial strains were isolated on solid mineral medium, and could be further shown to produce sulfate from thiosulfate. These strains were characterized by 16S rDNA analyses. The isolates were affiliated to seven different phylogenetic groups within the alpha- and beta-subclass of Proteobacteria. Two of these phylotypes were already described as S-oxidizers in this environment (Xanthobacter sp. and Bosea sp. related strains), but five groups represented new S-oxidizers in rice field soil. These isolates were closely related to Mesorhizobium loti, to Hydrogenophaga sp., to Delftia sp., to Pandoraea sp. or showed sequence similarity to a strain of Achromobacter sp.     

Regulatory role for l-arginine in the utilization of amino acids by pig small-intestinal bacteria

We recently reported that bacteria from the pig small intestine rapidly utilize and metabolize amino acids (AA). This study investigated the effect of L-arginine on the utilization of AA by pure bacterial strains (Streptococcus sp., Escherichia coli and Klebsiella sp.) and mixed bacterial cultures derived from the pig small intestine. Bacteria were incubated at 37°C for 3 h in anaerobic AA media containing 0-5 mmol/L of arginine to determine the effect of arginine on the bacterial utilization of AA. Amino acids in the medium plus cell extracts were analyzed by high-performance liquid chromatography. Results indicated concentration-dependent increases in the bacterial utilization of arginine and altered fluxes of arginine into ornithine and citrulline in the bacteria. Net glutamine utilization increased in pure bacterial strains with increased concentrations of arginine. With the addition of arginine, net utilization of threonine, glycine, phenylalanine and branched-chain AA increased (P<0.05) in Streptococcus sp. and Klebsiella sp., but decreased in E. coli. Net utilization of lysine, threonine, isoleucine, leucine, glycine and alanine by jejunal or ileal mixed bacteria decreased (P<0.05) with the addition of arginine. Complete utilization of asparagine, aspartate and serine were observed in pig small-intestinal bacteria after 3 h of incubation. Overall, the addition of arginine affected the metabolism of the arginine-family of AA and the serine- and aspartate-family of AA in small-intestinal bacteria and reduced the utilization of most AA in ileal mixed bacteria. These novel findings indicate that arginine exerts its beneficial effects on swine nutrition partially by regulating AA utilization and metabolism in the small-intestinal microbiota.