Bacterial and fungal diversity in the starter production process of Fen liquor, a traditional Chinese liquor

Fermented foods and beverages are important parts of human diet. Fen liquor, a Chinese liquor is a fermented beverage that uses a traditional fermentation process. Starters are the main microbial source and also provide nutrients for microorganisms during fermentation. In this study, starters of Fen liquor were produced through a complex traditional fermentation process. To investigate the community structure and the composition of microorganisms in the starter production process, bacterial 16S rRNA and fungal internal transcribed spacer (ITS) regions were sequenced using clone libraries and pyrosequencing, respectively. There was much higher diversity among the bacteria than among the fungi in the starter production process. Bacteria on the surface of the starters belonged mostly to the Lactobacillaceae family, while members of the Bacillacae family were dominant in the interior of the samples that lacked access to air and water. In the fungi population, diversity was high only in the raw material. In all other samples, nearly all of the fungal sequences were from Pichia kudriavzevii, a member of the Saccharomycetaceae family. Nearly all samples showed similar fungal community structures, indicating that there was little change in the fungal community. To the best of our knowledge, this is the first report to reveal the whole process of the starter production of Chinese traditional liquor. The findings obtained in this study provide new insights into understanding the composition of the microbial community during the traditional Chinese liquor starter production process and information about the production process control and monitoring.     

Impact of two bacterial biocontrol agents on bacterial and fungal culturable groups associated with the roots of field-grown maize

Aims:  To assess the impact of Bacillus amyloliquefaciens and Microbacterium oleovorans on bacterial and fungal groups associated to the roots of field-grown maize.
Methods and Results:  Identification and count of bacterial and fungal culturable populations associated to the roots of maize seedlings, changes in culturable community structure according to the richness and diversity indexes concept and shifts in microbial activity through analysis of cellulolytic, ammonification and nitrification potentials were determined, in relation to kernel treatment with biological control agents. Following the treatment of maize kernels with B. amyloliquefaciens at 10⁷ CFU ml⁻¹, an increase in bacterial diversity was observed at the rhizoplane of resultant seedlings. Bacterial richness was significantly increased at the root inner tissues of seedlings treated with Mic. oleovorans . Fusarium , Aspergillus , Penicillium and Trichoderma were the main fungal genera isolated and there population sizes were unequally affected by the addition of biocontrol agents.
Conclusions:  Numbers and types of isolated bacteria and fungi changed in response to the addition of biocontrol agents, while microbial activity remained unchanged with respect to control.
Significance and Impact of the Study:  This study provides an insight of the effects of proven biocontrol agents on micro-organisms naturally associated to the target crop.     

Isolation, characterization and identification of lactic acid bacteria and yeasts from sour Mifen, a traditional fermented rice noodle from China

Aims:  Considering the effect of natural fermentation on the textural improvement of fermented rice noodles in China and South Asia, and given the lack of reports concerning microbial populations and structure in the fermentation process, this study aims to determine the number of viable micro-organisms and identify the species isolated from the local factories, and to assess their potential use as a starter culture from their enzymatic profiles.
Methods and Results:  Fourteen samples from three local factories were analysed for the presence of micro-organisms. A total of 170 lactic acid bacteria (LAB) and 96 yeasts were isolated from the factories. The isolates were phenotypically characterized by using API 50 CHL kits, API 20 Strep kits, API ID 32 C kits and by performing additional biochemical tests. The enzymatic profiles of isolates were assessed by using API ZYM kits. Lactobacillus plantarum and Saccharomyces cerevisiae were identified as predominant species in the fermented supernatants. A majority of the isolates of LAB and yeasts displayed activities of α-glucosidase, β-glucosidase, lipase and trypsin.
Conclusions:  The microbial composition and strain characteristics present in the fermentation supernatant demonstrate that a majority of micro-organisms have the ability to digest starch, sugar, protein or lipid. It supports our previous work in which the rice starch was modified and purified by fermentation and thus improves the texture of rice noodles.
Significance and Impact of the Study:  The dominant strains would be important in developing a starter culture. The results can form the basis for the improvement of product quality and consistency.     

The microbial signature of aerosols produced during the thermophilic phase of composting

Aims:  The microbial diversity of bioaerosols released during operational activities at composting plants is poorly understood. Identification of bacteria and fungi present in such aerosols is the prerequisite for the definition of microbial indicators that could be used in dispersal and exposure studies.
Methods and Results:  A culture-independent analysis of composting bioaerosols collected at five different industrial open sites during the turning of composting piles in fermentation was performed by building 16S rDNA and 18S rDNA libraries. More than 800 sequences were analysed. Although differences in the phylotypes distribution were observed from one composting site to another, similarities in the structure of microbial diversity were remarkable. The same phyla dominated in the five bioaerosols: Ascomycota among fungi, Firmicutes and Actinobacteria among bacteria. For each phylum, some dominant phylotypes were common to at least four bioaerosols. These common phylotypes belonged to Thermomyces , Aspergillus , Penicillium , Geobacillus, Planifilum , Thermoactinomyces , Saccharopolyspora , Thermobifida and Saccharomonospora .
Conclusions:  The microbial signature of aerosols produced during the thermophilic phase of composting was determined. The similarities observed may be explained by the selection of thermophilic and sporulating species.
Significance and Impact of the Study:  Several bacteria and fungi identified in this study may represent potential indicators of composting bioaerosols in air.     

Identification of yeast and bacteria involved in the mezcal fermentation of Agave salmiana

Aims:  To identify the yeast and bacteria present in the mezcal fermentation from Agave salmiana .
Methods and Results:  The restriction and sequence analysis of the amplified region, between 18S and 28S rDNA and 16S rDNA genes, were used for the identification of yeast and bacteria, respectively. Eleven different micro-organisms were identified in the mezcal fermentation. Three of them were the following yeast: Clavispora lusitaniae , Pichia fermentans and Kluyveromyces marxianus. The bacteria found were Zymomonas mobilis subsp. mobilis and Zymomonas mobilis subsp. pomaceae, Weissella cibaria , Weissella paramesenteroides , Lactobacillus pontis , Lactobacillus kefiri , Lactobacillus plantarum and Lactobacillus farraginis .
Conclusions:  The phylogenetic analysis of 16S rDNA and ITS sequences showed that microbial diversity present in mezcal is dominated by bacteria, mainly lactic acid bacteria species and Zymomonas mobilis . Pichia fermentans and K. marxianus could be micro-organisms with high potential for the production of some volatile compounds in mezcal.
Significance and Impact of the Study:  We identified the community of bacteria and yeast present in mezcal fermentation from Agave salmiana.     

Genetic characterization of microbial communities living at the surface of building stones

Aims:  The aim of the present study was to reveal the microbial genetic diversity of epilithic biofilms using a DNA-based procedure.
Methods and Results:  A DNA extraction protocol was first selected to obtain PCR-amplifiable metagenomic DNA from a limestone biofilm. Extracted DNA was used to amplify either 16S rRNA genes or ITS regions from prokaryotic and eukaryotic genomes, respectively. Amplified DNAs were subsequently cloned, amplified by colony PCR and screened by restriction analysis [restriction analyses of amplified ribosomal DNA (ARDRA)] for DNA sequencing. Phylogenetic analysis using 16S rDNA sequences showed that predominating bacteria were Alphaproteobacteria belonging to the genera Sphingomonas , Erythrobacter , Porphyrobacter , Rhodopila and Jannashia ; Cyanobacteria and Actinobacteria were also identified. Analysis of ITS rDNA sequences revealed the presence of algae of the Chlorophyceae family and fungi related either to Rhinocladiella or to a melanized ascomycete. Statistical analysis showed that the specific richness evidenced was representative of the original sampled biofilm.
Conclusions:  The molecular methodology developed here constitutes a valuable tool to investigate the genetic diversity of microbial biofilms from building stone.
Significance and Impact of the Study:  The easy-to-run molecular method described here has practical importance to establish microbiological diagnosis and to define strategies for protection and restoration of stone surfaces.     

Factors affecting the attachment of micro-organisms isolated from ultrafiltration and reverse osmosis membranes in dairy processing plants

Aims:  To identify the types of micro-organisms involved in the formation of biofilms on dairy ultrafiltration and reverse osmosis membranes and investigate factors affecting the attachment of those isolates.
Methods and Results:  Micro-organisms isolated from industrial membranes following standard cleaning were identified using the API culture identification system. Thirteen different isolates representing eight genera were isolated and their ability to attach to surfaces was compared using a microtitre plate assay. Three Klebsiella strains attached best, while mixed strains of Pseudomonas and Klebsiella attached better than individual strains. Whey enhanced the attachment of the isolates. The micro-organisms were characterized according to cell surface hydrophobicity using the microbial adhesion to hydrocarbon (MATH) test, and cell surface charge by measuring the zeta potential. These cell surface characteristics did not show a clear relationship with the attachment of our strains.
Conclusions:  A variety of different micro-organisms is associated with dairy ultrafiltration and reverse osmosis membranes after cleaning, suggesting several possible sources of contamination. The cleaning of these membranes may be inadequate. The attachment of the different isolates is highly variable and enhanced in the presence of whey.
Significance and Impact of the Study:  Knowledge of persistent microflora colonizing dairy membrane systems will help develop strategies to mitigate biofilm development in this environment, improving hygiene in membrane processing plants.     

小蓬竹根际土壤微生物及内生真菌多样性分析

为了解喀斯特典型物种-小蓬竹根际土壤微生物及不同部位内生真菌多样性,采用沿等高线等距离取样法采集小蓬竹根际土壤及健康植株,通过可培养对根际土微生物及内生菌进行分离,利用分子技术对其进行鉴定,根据鉴定结果构建系统发育树,并计算小蓬竹根际土壤微生物和根茎叶内生真菌多样性。结果如下：（1）共从根际土壤、根、茎、叶分离得到139个真菌菌株,隶属于27属,其中根际土壤分离得到34个真菌菌株隶属于12属,根部分离得到的63个内生真菌菌株隶属于17个属,茎部分离得到的14个内生真菌菌株隶属于8个属,叶部分离得到28个内生真菌菌株隶属于9个属;（2）根际土壤共分离得到41株细菌菌株,隶属于7个属26个种,20株放线菌菌株,隶属于1属15种;从Shannon-Wiener多样性指数、均匀度指数、Simpson指数排序来看,真菌主要表现为根 > 根际土壤 > 茎 > 叶,细菌和放线菌多样性均较低。（3）按层次聚类分析可分别将真菌、细菌、放线菌聚为3支。小蓬竹根际土壤、根、茎和叶具有丰富的微生物多样性,不同部位菌群组成存在差异性（P<0.05）,且存在以假单胞菌属、芽孢杆菌属等为优势属的抗盐耐旱菌群,这有助于揭示小蓬竹对喀斯特生境的适应性,以及为微生物-植物群落之间相互关系提供一定基础数据,为后期寻找小蓬竹相关耐性功能菌奠定基础。     

Feather micro-organisms and uropygial antimicrobial defences in a colonial passerine bird

1.  The relationship between the composition of communities of micro-organisms and their hosts remains poorly understood. We conducted extensive field studies of feather-degrading bacteria, other cultivable bacteria, and fungi on the plumage of a migratory bird, the barn swallow Hirundo rustica Linnaeus, to understand the association between micro-organisms, host sociality and host antimicrobial defences, as reflected by the size of the uropygial gland.
2.  The abundance of feather-degrading bacteria, but not other cultivable bacteria or fungi, decreased with increasing size of the uropygial gland.
3.  Females had more feather-degrading bacteria than males.
4.  Barn swallows living in larger colonies had more feather-degrading bacteria than less social conspecifics.
5.  These findings suggest that the uropygial gland plays a specific role in regulating the abundance of feather-degrading bacteria that furthermore depends on the social environment of the host.     

Effect of starter culture inoculation on feed hygiene and microbial population development in fermented pig feed composed of a cereal grain mix with wet wheat distillers' grain

Aims:  Investigating the influence of an added starter culture on the properties of fermented liquid pig feed.
Methods and Results:  Diets of cereal grain blended with wet wheat distillers' grain that were either not inoculated (WWDG), inoculated with a silage starter culture at start (WWDGsc1) or at start and at each backslopping (replacement of 80% the content with fresh mixture, simulating feed outtake, WWDGsc5) were fermented for 5 days, followed by 5 days of daily backslopping. Numbers of undesirable micro-organisms (enterobacteria, moulds) were reduced in all fermentations; particularly enterobacteria in the starter culture inoculated diets. Lactobacillus plantarum present in the starter culture became dominant in diets WWDGsc1 and WWDGsc5. However, Lactobacillus panis that was dominating WWDG was also abundant in WWDGsc1 and WWDGsc5. Yeast populations were not influenced by the starter culture, with Pichia fermentans dominating all fermentations. All diets had similar chemical characteristics with the exception of a significant increase of all tested organic acids in WWDGsc5.
Conclusions:  The addition of a starter culture influences the bacterial population in fermented liquid feed, but there is also a strong impact of the flora already present in the feed ingredients. The yeast population is not influenced by adding a lactic acid bacteria (LAB) starter culture. A consortium of LAB and yeast strains adapted to the fermentation should be used as starter culture.
Significance and Impact of the Study:  The results suggest that it is possible to influence the current unpredictable and spontaneous process of feed fermentation when appropriate starter cultures are used. For this purpose, LAB and yeasts with desirable characteristics should be isolated.     

In vitro antibacterial activity and antifungal mode of action of flocculosin, a membrane-active cellobiose lipid

Aims:  To investigate the in vitro antibacterial activity and antifungal mode of action of flocculosin, a cellobiose lipid produced by Pseudozyma flocculosa .
Methods and Results:  When tested against clinical bacterial isolates, the compound was particularly active against Gram-positive bacteria and its effect was not mitigated against isolates known as resistant to other antibiotics. The antifungal activity of flocculosin was found to be rapid and concentration-dependent. At lethal concentrations against Candida albicans , flocculosin caused a rapid leakage of intracellular potassium and inhibited acidification of the medium by plasma membrane ATPases suggesting a physical rather than a biochemical effect. TEM observations of cells exposed 6 h to flocculosin revealed disrupted membranes and disorganized mitochondria.
Conclusions:  Data obtained in this study confirm that flocculosin acts by disrupting the membrane surface of sensitive micro-organisms.
Significance and Impact of the Study:  The elucidation of an antifungal mode of action of flocculosin can be exploited in furthering its antimicrobial potential against fungi and bacteria whose cell membranes are particularly sensitive to the action of the molecule.     

Initial in vitro evaluations of the antibacterial activities of glucosinolate enzymatic hydrolysis products against plant pathogenic bacteria

Aims:  The aim of the study was to evaluate the in vitro antibacterial effects of glucosinolate hydrolysis products (GHP) against plant pathogenic micro-organisms namely Agrobacterium tumefaciens , Erwinia chrysanthemi , Pseudomonas cichorii , Pseudomonas tomato , Xanthomonas campestris and Xanthomonas juglandis .
Methods and Results:  Using a disc diffusion assay, seven different doses of 10 GHP were tested against each bacteria. The results showed that the isothiocyanates were potent antibacterials, whilst the other GHP were much less efficient. Moreover, the antibacterial effects were dose-dependent, increasing with the dose applied; 2-phenylethylisothiocyanate and sulforaphane showed the strongest inhibitory effects. The overall results show a great potential for using the isothiocyanates as an alternative tool to control undesired bacterial growth in plants.
Conclusions:  Glucosinolate hydrolysis products and more specifically the isothiocyanates: benzylisothiocyanate, 2-phenylethylisothiocyanate, the isothiocyanate Mix and sulforaphane, were effective phytochemicals against the in vitro growth of the phytopathogenic bacteria. The antibacterial activity exhibited by these phytochemicals reinforces their potential as alternatives to the traditional chemical control of phytopathogenic bacteria.
Significance and Impact of the Study:  This current in vitro study is the first providing comparative data on GHP as potential control agents for plant pathogenic bacteria. However, more studies are needed to determine their possible allelopathic impacts e.g. inhibition of plant growth and negative effects on beneficial soil bacteria and fungi (mycorrhizae).     

Sedimentary arsenite-oxidizing and arsenate-reducing bacteria associated with high arsenic groundwater from Shanyin, Northwestern China

Aims:  Shanyin County is one of the most severe endemic arsenism affected areas in China but micro-organisms that potentially release arsenic from sediments to groundwater have not been studied. Our aim was to identify bacteria with the potential to metabolize or transform arsenic in the sediments.
Methods and Results:  Culture and nonculture-based molecular methods were performed to identify arsenite-oxidizing bacteria, arsenate-reducing bacteria and arsenite oxidase genes. Arsenite-oxidizing bacteria were identified only from the land surface to 7 m underground that were affiliated to α- and β-Proteobacteria. Arsenate-reducing bacteria were found in almost all the sediment samples with different depths (0–41 m) and mainly belong to γ-Proteobacteria. Several novel arsenite oxidase genes ( aoxBs ) were identified from the upper layers of the sediments (0–7 m) and were found to be specific for arsenite-oxidizing bacteria.
Conclusions:  The distribution of arsenite-oxidizing bacteria in upper layers and arsenate-reducing bacteria in different depths of the sediments may impact the arsenic release into the nearby tubewell groundwater.
Significance and Impact of the Study:  This study provides valuable sources of micro-organisms (and genes) that may contribute to groundwater arsenic abnormality and may be useful to clean arsenic contaminated groundwater.     

Maturing dynamics of surface microflora in Fontina PDO cheese studied by culture-dependent and -independent methods

Aims:  To study the evolution of rind microbial communities in Fontina PDO cheese.
Methods and Results:  Four batches were examined for their surface microflora during ripening, carried out in two different maturing caves, at Ollomont and Pré-Saint-Didier, Aosta Valley region, Northwest of Italy. Culture-dependent methodologies were combined with culture-independent analysis (PCR-DGGE). Yeasts were found to increase from 10³ to 10⁶ CFU cm⁻² in 28 days, with consequent rise of surface pH, which allowed the growth of salt-tolerant bacteria, in particular coryneforms which reached 10⁹ CFU cm⁻² at the end of 3 months. Coagulase-negative cocci and lactic acid bacteria reached 10⁷ CFU cm⁻² in the same period. Debaryomyces hansenii and Candida sake were the species more constantly present throughout the whole maturing process. As early as after 1 day since manufacture, Lactococcus lactis subsp. lactis and Streptococcus thermophilus were detected on cheese rinds. Arthrobacter nicotianae , Brevibacterium casei and Corynebacterium glutamicum were found after 7–28 days .
Conclusions:  According to cluster analysis of DGGE profiles, the maturing environment seemed to influence the dynamics of microbial groups on Fontina surfaces.
Significance and Impact of the Study:  These results represent a first picture of micro-organisms colonizing Fontina PDO rinds. Further studies are in progress to better understand the origin of this surface microflora and to formulate surface starters.     

Identification of lactic acid bacteria in Moroccan raw milk and traditionally fermented skimmed milk 'lben'

Aims:  To identify lactic acid bacteria (LAB) present in Moroccan dairy products to establish and preserve their microbial species diversity.
Methods and Results:  Thirty-seven samples were collected from different farms. A total of 146 LAB were isolated and subjected to (GTG)₅-PCR analysis. Comparison of the profiles with data available at the Moroccan Coordinated Collections of Micro-organisms allowed identification of 85 isolates. The remaining 61 were subjected to SDS-PAGE analysis of whole cell proteins. Comparison of the profiles with data available at the Belgian Coordinated Collections of Micro-organisms allowed identification of 43 isolates. Several of the remaining 18 isolates exhibited identical protein electrophoretic fingerprints. Therefore, eight representatives of them were subjected to partial pheS gene sequencing which allowed identification of all remaining isolates. In raw milk, six genera were found while in 'lben', three were found. This is the first report of Leuconostoc kimchii in dairy products.
Conclusions:  LAB diversity was established using a stepwise polyphasic identification approach. It used the expertise of both research bodies involved in this study and proved to be cost-effective for the identification of all isolates.
Significance and Impact of the Study:  To establish LAB diversity in Moroccan dairy products which could be a source of strains with specific properties.     

Effect of the tropical forage calliandra on microbial protein synthesis and ecology in the rumen

C.S. MCSWEENEY, B. PALMER, R. BUNCH AND D.O. KRAUSE. 2001 .
Aims: To determine the effect of condensed tannins in Calliandra calothyrsus (calliandra) on rumen microbial function.
Methods and Results: Microbial populations, ruminal protein synthesis and fermentation end-products were measured in sheep fed roughage hay supplemented with calliandra (30%), with and without inclusions of polyethylene glycol (PEG) to counteract the effect of tannin. Molecular and conventional enumeration techniques were used to quantify rumen bacteria, fungi and protozoa, and protein synthesis was predicted from estimates of urinary purine excretion. The total number of cellulolytic bacteria, including populations of Fibrobacter succinogenes and Ruminococcus spp., was significantly lower in sheep supplemented with calliandra and these populations increased when animals were treated with PEG. By contrast, protozoa and fungi and the microbial group containing Bacteroides - Porphyromonas - Prevotella bacteria appeared to be less affected. The efficiency of microbial protein synthesis in the rumen was not altered significantly.
Conclusions: Calliandra caused significant shifts in rumen microbial populations without changing the efficiency of protein synthesis.
Significance and Impact of the Study: The effect of calliandra tannins on rumen digestion may result more from complexing with nutrients than direct inhibition of micro-organisms.     

Potential use of Tunisian Pituranthos chloranthus essential oils as a natural disinfectant

Aims:  To highlight the bactericidal and fungicidal activities of Tunisian Pituranthos chloranthus essential oils and to study their potential use as powerful and natural disinfectant.
Methods and Results:  The essential oils were obtained by hydro-distillation of the aerial part of P. chloranthus . The bactericidal and fungicidal properties of essential oils were investigated by using the NCCLS broth dilution method and the EN 1275 and EN 1276 European standard methods. High bactericidal and fungicidal effects of 1·87–3·75 and 7·5 mg l⁻¹ were obtained, respectively. Essential oils concentrations of 0·5% and 1% (w/v) allowed reductions in viability higher than 5 and 4 log units per ml for standard bacteria and fungi, respectively, within a contact time of 5 min under dirty conditions.
Conclusions:  Our results support the traditional uses of P. chloranthus as a natural disinfectant and insecticide. It could be used to manage life-threatening pathogens as well as food preservative.
Significance and Impact of the Study:  This natural disinfectant could play a vital role in alleviating the spread of pathogenic micro-organisms and environmental problems associated with the indiscriminate use of synthetic chemicals.     

Electrochemical checking of aerobic isolates from electrochemically active biofilms formed in compost

Aims:  To design a cyclic voltammetry (CV) procedure to check the electrochemical activity of bacterial isolates that may explain the electrochemical properties of biofilms formed in compost.
Methods and Results:  Bacteria catalysing acetate oxidation in garden compost were able to form electrochemically active biofilms by transferring electrons to an electrode under chronoamperometry. They were recovered from the electrode surface and identification of the isolates using 16S rRNA sequencing showed that most of them were Gammaproteobacteria, mainly related to Enterobacter and Pseudomonas spp. A CV procedure was designed to check the electrochemical activity of both groups of isolates. Preliminary CVs suggested that the bacteria were not responsible for the catalysis of acetate oxidation. In contrast, both groups of isolates were found to catalyse the electrochemical reduction of oxygen under experimental conditions that favoured adsorption of the microbial cells on the electrode surface.
Conclusions:  Members of the genera Enterobacter and Pseudomonas were found to be able to catalyse the electrochemical reduction of oxygen.
Significance and Impact of the Study:  This study has shown the unexpected efficiency of Enterobacter and Pseudomonas spp. in catalysing the reduction of oxygen, suggesting a possible involvement of these species in biocorrosion, or possible application of these strains in designing bio-cathode for microbial fuel cells.     

Polaromonas and Hydrogenophaga species are the predominant bacteria cultured from granular activated carbon filters in water treatment

Aim:  Identification of the predominating cultivable bacteria in granular activated carbon (GAC) filters used in a variety of water treatment plants for selecting representative strains to study the role of bacteria in the removal of dissolved organic matter.
Methods and Results:  Bacterial isolates were collected from 21 GAC filters in nine water treatment plants treating either ground water or surface water with or without oxidative pretreatment. Enrichment of samples in dilute liquid medium improved culturability of the bacteria by approximately log unit, to 9% up to 70% of the total cell counts. Genomic fingerprinting and 16S rDNA sequence analysis revealed that most (68%) of the isolates belonged to the Betaproteobacteria and 25% were identified as Alphaproteobacteria . The number of different genera within the Betaproteobacteria was higher in the GAC filters treating ozonated water than in the filters treating nonozonated water. Polaromonas was observed in nearly all of the GAC filters (86%), and the genera Hydrogenophaga , Sphingomonas and Afipia were observed in 43%, 33% and 29% of the filter beds, respectively. AFLP analysis revealed that the predominating genus Polaromonas included a total of 23 different genotypes.
Conclusions:  This study is the first to demonstrate that Polaromonas , which has mainly been observed in ultraoligotrophic freshwater environments, is a common component of the microbial community in GAC filters used in water treatment.
Significance and Impact of the Study:  The predominance of ultraoligotrophic bacteria in the GAC filters indicates that very low concentrations of substrates are available for microbial growth. Polaromonas species are suited for further studies on the nutritional versatility and growth kinetics enabling the modelling of biodegradation processes in GAC filters.     

Molecular ecology of a facultative swine waste lagoon

Aims:  To investigate the microbial ecology of three facultative swine waste lagoons.
Methods and Results:  Phylogenetic analysis of sequences in a 16S rRNA gene clone library and fluorescence in situ hybridization (FISH) analyses were used to assess bacterial diversity in a swine waste lagoon. FISH analysis and Gram-staining were used to compare the microbial communities of all three swine waste lagoons. Six operational taxonomic units were in high relative abundance and corresponded to the following phylotypes; Thiolamprovum , Verrucomicrobia , Acholeplasma , Turicibacter , Clostridium and Bacteroides . PCR was employed to detect the genes apsA and dsrAB which encode for enzymes specifically associated with dissimilatory sulfate-reduction within sulfate-reducing bacteria (SRB). Amplification of these genes confirmed their presence within the lagoons.
Conclusions:  All lagoons were dominated by purple sulfur bacteria, affiliated to Thiolamprovum pedioforme . The molecular identification of fermentative bacteria and SRB indicate the following metabolic processes within such facultative ponds: sulfur-cycling, fermentation, inter-species hydrogen transfer and carbon cycling.
Significance and Impact of the Study:  This study provides the first molecular evidence for the existence of a sulfur cycle which is linked to phototrophic sulfide oxidation by purple bacteria and organotrophic sulfate-reduction by SRB.