Identification of the culturable and nonculturable bacterial population in ground water of a municipal water supply in Germany

Chryseobacterium potabilaquae sp. nov., Chryseobacterium aquaeductus sp. nov. and Chryseobacterium fistulae sp. nov., from drinking water systems

A polyphasic taxonomic study was conducted on three strains isolated from drinking water systems that had previously been deposited as Chryseobacterium species at the Spanish Type Culture Collection in order to complete their classification. Strains CECT 9293^T, CECT 9390^T and CECT 9393^T were isolated from sites in Barcelona, Spain, in the framework of a project aimed at generating the first MALDI-TOF database specific for bacteria present in water for human consumption. Their partial 16S rRNA sequences showed that their closest relatives among the type strains of Chryseobacterium exhibited 98 % similarity or less, supporting their taxonomic novelty. At the same time, comparison between them revealed that strains CECT 9293^T and CECT 9393^T could perhaps be related at the species level as they shared 99.5 % similarity. However, whole genome sequencing was performed and the subsequent calculation of relatedness indices, average nucleotide identity and estimated DNA–DNA hybridization, ruled out that possibility and confirmed instead that each of the strains should be considered a separate species in the genus Chryseobacterium. Having clarified their status, we also performed phylogenomic analyses and searched for possible environmental or non-type material sequences that could be related to any of them at the species level. In parallel, the strains were characterized phenotypically and compared to their closest relatives to determine diagnostic traits to support their formal proposal. The proposed species are Chryseobacterium potabilaquae sp. nov. with the type strain CECT 9293^T (=LMG 32084^T), Chryseobacterium aquaeductus sp. nov. with the type strain CECT 9390^T (=LMG 32085^T) and Chryseobacterium fistulae sp. nov. with the type strain CECT 9393^T (=LMG 32086^T).

Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil

A Gram-stain-negative, asporogenous, aerobic rods, motile by means of a single polar flagellum, catalase- and oxidase-positive, methylotrophic bacterium, designated 17Sr1-28^T, was isolated from gamma ray-irradiated soil. The 16S rRNA gene sequence analysis showed that strain 17Sr1-28^T was phylogenetically related to Methylobacterium currus PR1016A^T (96.8%), Methylobacterium platani PMB02^T (96.2%), Methylobacterium aquaticum DSM 16371^T (96.3%), Methylobacterium tarhaniae N4211^T (96.4%), Methylobacterium frigidaeris IER25-16^T (95.8%), and Methylobacterium organophilum JCM 2833^T (92.7%). The G+C content calculated based on genome sequence was 71.6%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain 17Sr1- 28^T and M. currus, M. platani, M. aquaticum, M. tarhaniae, M. frigidaeris, and M. organophilum were 77.7-90.4% and 22-39.6%, respectively. The major fatty acids of strain 17Sr1-28^T were summed feature 8 (C_18:1ω7c and/or C_18:1ω6c), and summed feature 3 (C_16:1ω7c and/or C_16:1ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. On the basis of the data from phenotypic tests and genotypic differences between strain 17Sr1-28^T and its close phylogenetic relatives, strain 17Sr1-28^T represents a new species belonging to the genus Methylobacterium, for which the name Methylobacterium terrae sp. nov. (= KCTC 52904^T = NBRC 112873^T) is proposed.

Lettuce (Lactuca sativa, variety Salanova) production in decoupled aquaponic systems: Same yield and similar quality as in conventional hydroponic systems but drastically reduced greenhouse gas emissions by saving inorganic fertilizer

Decoupled aquaponic systems have the potential to become one of the most effective sustainable production systems for the combined production of animal protein and plant crops. Here, recirculating aquaculture systems for fish production are combined with hydroponics for soilless plant production thereby recycling dissolved nutrients derived from metabolism of the fish. The aim of the present study was to characterize hydroponic lettuce production using conventional nutrient solution in comparison with decoupled aquaponics using the nutrient rich fish water as basis for the nutrient solution being supplemented by missing nutrients. In addition, one aquaponic treatment became disinfected in order to assess any occurring advantage of the aquaponics derived fish water. For evaluation the temperature, electrical conductivity, pH, and the mineral composition of the nutrient solution, as well as colony forming units in the fish water were monitored. Additionally, plant growth (fresh and dry weight, number and area of leaves) and quality parameters of lettuce leaves (nitrate, mineral content, phenolic compounds) were examined. Carbon sources and microorganisms derived from fish water seem to have neither beneficial nor detrimental effects on plant growth in this study. Except for some differences in the mineral content of the lettuce leaves, all other quality parameters were not significantly different. The use of aquaponic fish water saved 62.8% mineral fertilizer and fully substituted the required water for the nutrient solution in comparison to the control. Additionally, the reduced fertilizer demand using decoupled aquaponics can contribute to reduce greenhouse gas emissions of an annual lettuce production site per ha by 72% due to saving the energy for fertilizer production. This study clearly demonstrates the huge potential of the innovative approach of decoupled aquaponics to foster the transformation of our conventional agriculture towards sustainable production systems saving resources and minimizing emissions.

An Integrative Evaluation Method for the Biological Safety of Down and Feather Materials

Background: Down and feather materials have been commonly used and promoted as natural stuffing for warm clothing and bedding. These materials tend to become more allergenic as they become contaminated with microorganisms, in addition to being subjected to several kinds of chemical treatments. The biological or chemical contaminants in these materials pose a major risk to human health, to consumers and manufacturers alike. Here, we report the development of an integrative evaluation method for down and feather materials to assess bacterial contamination and in vivo toxicity. Methods: To assess bacterial contamination, we quantified 16S ribosomal RNA, performed culture tests, and established a conversion formula. To determine in vivo toxicity, we performed a zebrafish embryo toxicity testing (ZFET). Results: Washing the material appropriately decreases the actual number of bacteria in the down and feather samples; in addition, after washing, 16S rRNA sequencing revealed that the bacterial compositions were similar to those in rinse water. The ZFET results showed that even materials with low bacterial contamination showed high toxicity or high teratogenicity, probably because of the presence of unknown chemical additives. Conclusions: We established an integrative evaluation method for down and feather safety, based on bacterial contamination with in vivo toxicity testing.

Inhibition of Adherence of Mycobacterium avium to Plumbing Surface Biofilms of Methylobacterium spp

Both Mycobacterium spp. and Methylobacterium spp. are opportunistic premise plumbing pathogens that are found on pipe surfaces in households. However, examination of data published in prior microbiological surveys indicates that Methylobacterium spp. and Mycobacterium spp. tend not to coexist in the same household plumbing biofilms. That evidence led us to test the hypothesis that Methylobacterium spp. in biofilms could inhibit the adherence of Mycobacterium avium. Measurements of adherence of M. avium cells to stainless steel coupons using both culture and PCR-based methods showed that the presence of Methylobacterium spp. biofilms substantially reduced M. avium adherence and vice versa. That inhibition of M. avium adherence was not reduced by UV-irradiation, cyanide/azide exposure, or autoclaving of the Methylobacterium spp. biofilms. Further, there was no evidence of the production of anti-mycobacterial compounds by biofilm-grown Methylobacterium spp. cells. The results add to understanding of the role of microbial interactions in biofilms as a driving force in the proliferation or inhibition of opportunistic pathogens in premise plumbing, and provide a potential new avenue by which M. avium exposures may be reduced for at-risk individuals.

Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex

The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR), opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs). The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They were significantly more susceptible to antibiotics than S. maltophilia. We demonstrate that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic resistance profiles and β-lactamase expression phenotypes, as shown by diverse multivariate analyses and robust univariate statistical tests. We discuss our data in light of current models of bacterial speciation, which fit these data well, stressing the implications of species delimitation in ecological, evolutionary and clinical research.

Methylobacterium spp. as an indicator for the presence or absence of Mycobacterium spp

OBJECTIVE/BACKGROUND

A published survey of bacteria in showerhead biofilm samples revealed that Methylobacterium spp. and Mycobacterium spp. seldom coexisted in biofilms.

METHODS

To confirm that information, biofilm samples were collected from household plumbing of Mycobacterium avium patients and Methylobacterium spp. and M. avium numbers were measured by direct colony counts.

RESULTS

The results demonstrated that if Methylobacterium spp. were present, Mycobacterium spp. were absent, and the opposite.

CONCLUSION

The data demonstrate that microbial populations in biofilms can influence the presence or absence of opportunistic premise plumbing pathogens and, thereby, increase the range of strategies to reduce exposure to waterborne pathogens. Finally, by assessing for the visual presence of methylobacteria as pink pigmentation on showers and shower curtains, homeowners and managers of hospitals and other buildings can quickly determine whether a premise plumbing biofilm sample has mycobacteria with a high degree of assurance.

Impact of hydraulic well restoration on native bacterial communities in drinking water wells

The microbial monitoring of drinking water production systems is essential to assure water quality and minimize possible risks. However, the comparative impact of microbes from the surrounding aquifer and of those established within drinking water wells on water parameters remains poorly understood. High pressure jetting is a routine method to impede well clogging by fine sediments and also biofilms. In the present study, bacterial communities were investigated in a drinking water production system before, during, and after hydraulic purging. Variations were observed in bacterial communities between different wells of the same production system before maintenance, despite them having practically identical water chemistries. This may have reflected the distinct usage practices of the different wells, and also local aquifer heterogeneity. Hydraulic jetting of one well preferentially purged a subset of the dominating taxa, including lineages related to Diaphorobacter, Nitrospira, Sphingobium, Ralstonia, Alkanindiges, Janthinobacterium, and Pseudomonas spp, suggesting their tendency for growth in well-associated biofilms. Lineages of potential drinking water concern (i.e. Legionellaceae, Pseudomonadaceae, and Acinetobacter spp.) reacted distinctly to hydraulic jetting. Bacterial diversity was markedly reduced in drinking water 2 weeks after the cleaning procedure. The results of the present study provide a better understanding of drinking water wells as a microbial habitat, as well as their role in the microbiology of drinking water systems.

Structure of bacterial communities in diverse freshwater habitats

The structures and dynamics of bacterial communities from raw source water, groundwater, and drinking water before and after filtration were studied in four seasons of a year, with culture-independent methods. Genomic DNA from water samples was analyzed by the polymerase chain reaction – denaturing gradient gel electrophoresis system and by cloning of the 16S rRNA gene. Water samples exhibited complex denaturing gradient gel electrophoresis genetic profiles composed of many bands, corresponding to a great variety of bacterial taxa. The bacterial communities of different seasons from the four sampling sites clustered into two major groups: (i) water before and after filtration, and (ii) source water and groundwater. Phylogenetic analyses of the clones from the autumn sampling revealed 13 phyla, 19 classes, and 155 operational taxonomic units. Of the clones, 66% showed less than 97% similarities to known bacterial species. Representatives of the phyla Proteobacteria, Bacteroidetes, and Actinobacteria were found at all four sampling sites. Species belonging to the phylum Firmicutes were an important component of the microbial community in filtered water. Representatives of Enterobacteriaceae were not detected, indicating the absence of fecal pollution in the drinking water. Differences were found in the bacterial populations that were sampled from the same sites in different seasons. Each water habitat had a unique bacterial profile. Drinking water harbors diverse and dynamic microbial communities, part of which may be active and resilient to chlorine disinfection. This study provides, for the first time, basic data for uncultivable drinking water bacteria in Israel.

Detection of Helicobacter pylori in biofilms by real-time PCR

Helicobacter pylori is a cause of peptic ulcer disease and a causative agent of gastric cancer. Currently, a possible waterborne route of transmission or a possible survival in drinking water biofilms is discussed. H. pylori, like many other bacterial strains, has the ability to enter the viable but nonculturable state (vbnc) in case of unfavorable conditions. Therefore it is necessary to develop new analysis tools for vbnc bacteria. We established a fast and reliable method to detect H. pylori in drinking water biofilms by quantitative real-time PCR which makes it redundant to use difficult cultivation methods for nonculturable bacteria. With this method it was possible to identify water biofilms as a niche for H. pylori. The real-time PCR analysis targets the ureA subunit of the Helicobacter pylori urea gene which showed high specificity and sensitivity. The quantitative real-time PCR was used to detect H. pylori in biofilms of different age, unspiked and spiked with predetermined levels of cells. The drinking water biofilms were generated in a silicone-tube model. The DNA-sequences for probe and primers showed no cross-homologies to other related bacteria and it was possible to detect less than 10 genomic units of H. pylori. This novel method is a useful tool for a fast screening of drinking water biofilms for H. pylori. The results suggest that drinking water biofilms may act as a reservoir for H. pylori which raises new concerns about the role of biofilms as vectors for pathogens like Helicobacter pylori.

Identification of heterotrophic plate count bacteria isolated from drinking water in Japan by DNA sequencing analysis

Heterotrophic plate count (HPC) test has been employed to indicate the effectiveness of water treatment processes and the microbiological condition of the distribution system. In Japan, because the majority of HPC bacteria are supposed to be harmless and all tap water should maintain residual chlorine, there are few studies of the virulence of HPC bacteria. In this study, we examined HPC bacteria isolated from finished and tap water for hemolytic activity to determine their virulence potential. 34 of 39 colonies expressing hemolytic activity were identified by partial 16S rDNA sequencing, but some of their percent identity were relatively low. This may have been due to the mismatching of the primer pair with some strains, or these strains may be unidentified new species. A total of 30 of 34 isolates identified have been reported to be opportunistic pathogens or food poisoning bacteria. To control the growth of these opportunistic pathogens among HPC bacteria, appropriate water quality control must always be done and residual chlorine must be maintained in every tap for a safe water supply.

Identification of active bacterial communities in a model drinking water biofilm system using 16S rRNA-based clone libraries

Recent phylogenetic studies have used DNA as the target molecule for the development of environmental 16S rRNA gene clone libraries. As DNA may persist in the environment, DNA-based libraries cannot be used to identify metabolically active bacteria in water systems. In this study, an annular reactor was used to generate model drinking water biofilms grown on polycarbonate slides. High-quality RNA was extracted from 2-month-old biofilms and used to generate 16S rRNA-based clones. Sequencing analyses of 16S rRNA-based clones suggested that the active bacterial fraction consisted of a few dominant bacterial groups related to Nevskia ramosa and to uncultured bacteria. Several of these bacterial groups were closely related to clones characterized in a DNA-based clone library also generated in this study. Altogether, these results suggest that some of the predominant drinking water bacteria identified using DNA-based techniques are indeed active.

Waterborne pathogen detection by use of oligonucleotide-based microarrays

A small-oligonucleotide microarray prototype was designed with probes specific for the universal 16S rRNA and cpn60 genes of several pathogens that are usually encountered in wastewaters. In addition to these two targets, wecE-specific oligonucleotide probes were included in the microarray to enhance its discriminating power within the Enterobacteriaceae family. Universal PCR primers were used to amplify variable regions of 16S rRNA, cpn60, and wecE genes directly in Escherichia coli and Salmonella enterica serovar Typhimurium genomic DNA mixtures (binary); E. coli, S. enterica serovar Typhimurium, and Yersinia enterocolitica genomic DNA mixtures (ternary); or wastewater total DNA. Amplified products were fluorescently labeled and hybridized on the prototype chip. The detection sensitivity for S. enterica serovar Typhimurium was estimated to be on the order of 0.1% (10(4) S. enterica genomes) of the total DNA for the combination of PCR followed by microarray hybridization. The sensitivity of the prototype could be increased by hybridizing amplicons generated by PCR targeting genes specific for a bacterial subgroup, such as wecE genes, instead of universal taxonomic amplicons. However, there was evidence of PCR bias affecting the detection limits of a given pathogen as increasing amounts of a different pathogen were spiked into the test samples. These results demonstrate the feasibility of using DNA microarrays in the detection of waterborne pathogens within mixed populations but also raise the problem of PCR bias in such experiments.

Phylogenetic assessment of heterotrophic bacteria from a water distribution system using 16S rDNA sequencing

Determination of a heterotrophic plate count (HPC) for drinking-water samples alone is not enough to assess possible health hazards associated with sudden changes in the bacterial count. Speciation is very crucial to determine whether the population includes pathogens and (or) opportunistic pathogens. Most of the isolates recovered from drinking water samples could not be allocated to a specific phylogenetic branch based on the use of conventional diagnostic methods. The present study had to use phylogenetic analysis, which was simplified by determining and using the first 500-bp sequence of the 16S rDNA, to successfully identify the type and species of bacteria found in the samples. Gram-positive bacteria α-, β-, and γ-Proteobacteria were found to be the major groups representing the heterotrophic bacteria in drinking water. The study also revealed that the presence of sphingomonads in drinking water supplies may be much more common than has been reported so far and thus further studies are merited. The intermittent mode of supply, mainly characterized by water stagnation and flow interruption associated possibly with biofilm detachment, raised the possibility that the studied bacterial populations in such systems represented organisms coming from 2 different niches, the biofilm and the water column.Key words: intermittent water supply, 16S rDNA, biofilm, water column.

Methylobacterium hispanicum sp. nov. and Methylobacterium aquaticum sp. nov., isolated from drinking water

Members of the genus Methylobacterium are ubiquitous in nature and can be isolated from almost any freshwater environment where dissolved oxygen exists. This genus is composed of a variety of pink-pigmented, facultatively methylotrophic (PPFM) bacteria. During a screening programme to monitor the bacterial population present in the drinking water of a municipal water supply in Seville (Spain) during the year 2003, five strains of PPFM bacteria were isolated and characterized. Analysis of their complete 16S rRNA gene sequences revealed that they constituted two separate phylogenetic groups (strains GP34T and GR18, and strains GR16T, GP22 and GP32, respectively) showing highest similarity to members of the genus Methylobacterium. The highest 16S rRNA sequence similarities of strain GP34T were found with respect to the type strains of Methylobacterium radiotolerans (96·6 %) and Methylobacterium fujisawaense (96·4 %) and the highest 16S rRNA sequence similarities of strain GR16T were to the type strains of Methylobacterium extorquens (96·0 %) and Methylobacterium rhodesianum (95·8 %). The G+C content of their DNA ranged from 66·5 to 67·8 mol%. DNA–DNA hybridization studies confirmed that they constituted two separate genospecies. On the basis of this phenotypic, phylogenetic and genotypic study, two novel species of the genus Methylobacterium are proposed: Methylobacterium hispanicum sp. nov., with type strain GP34T (CECT 5997T=CCM 7219T=DSM 16372T=CIP 108332T), and Methylobacterium aquaticum sp. nov., with type strain GR16T (CECT 5998T=CCM 7218T=DSM 16371T=CIP 108333T).

What is life--and how do we search for it in other worlds?

If there is life on distant worlds, how would we go about finding it?