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PubMed2026

Pilot metaproteomic profiling reveals bacterial diversity and potential medical and veterinary relevance of tick microbiomes in northern Algeria.

Ticks are major ectoparasites and vectors of pathogens affecting humans, livestock, and wildlife. They harbor diverse microbial communities that may influence tick biology and interactions with microorganisms; however, functional information on tick-associated microbiomes remains limited, particularly in North Africa. In this pilot study, we applied a metaproteomic approach based on high-resolution tandem mass spectrometry to characterize bacterial communities associated with three tick species collected in Algeria: Rhipicephalus sanguineus sensu lato, Hyalomma aegyptium, and Hyalomma dromedarii. Peptide spectra were assigned to taxa using a two-step database search strategy based on NCBInr, and bacterial composition and relative abundance were compared across tick species and sampling locations. A total of 40 bacterial genera belonging to 32 families and four phyla were identified. Microbiome composition differed significantly between tick genera and collection locations, suggesting an influence of species-specific and geographical factors on microbial community structure. Dominant genera included Streptomyces, Bacillus, Clostridium, Escherichia, Flavobacterium, Paenibacillus, and Providencia. Peptides related to Coxiella spp. were frequently detected, consistent with previous reports of Coxiella-like endosymbionts in ticks. This pilot study provides a first metaproteomic characterization of tick-associated communities in Algeria. The results reveal species- and location-associated differences in microbial composition and highlight the potential of metaproteomics for exploring tick-associated microbiomes in North Africa.

Animals↗
PubMed2001

Impact of fumigants on soil microbial communities.

Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity, H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, H increased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. and Heliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.

Allyl Compounds↗
PubMed2005

Proteogenomic approaches for the molecular characterization of natural microbial communities.

At the present time we know little about how microbial communities function in their natural habitats. For example, how do microorganisms interact with each other and their physical and chemical surroundings and respond to environmental perturbations? We might begin to answer these questions if we could monitor the ways in which metabolic roles are partitioned amongst members as microbial communities assemble, determine how resources such as carbon, nitrogen, and energy are allocated into metabolic pathways, and understand the mechanisms by which organisms and communities respond to changes in their surroundings. Because many organisms cannot be cultivated, and given that the metabolisms of those growing in monoculture are likely to differ from those of organisms growing as part of consortia, it is vital to develop methods to study microbial communities in situ. Chemoautotrophic biofilms growing in mine tunnels hundreds of meters underground drive pyrite (FeS(2)) dissolution and acid and metal release, creating habitats that select for a small number of organism types. The geochemical and microbial simplicity of these systems, the significant biomass, and clearly defined biological-inorganic feedbacks make these ecosystem microcosms ideal for development of methods for the study of uncultivated microbial consortia. Our approach begins with the acquisition of genomic data from biofilms that are sampled over time and in different growth conditions. We have demonstrated that it is possible to assemble shotgun sequence data to reveal the gene complement of the dominant community members and to use these data to confidently identify a significant fraction of proteins from the dominant organisms by mass spectrometry (MS)-based proteomics. However, there are technical obstacles currently restricting this type of "proteogenomic" analysis. Composite genomic sequences assembled from environmental data from natural microbial communities do not capture the full range of genetic potential of the associated populations. Thus, it is necessary to develop bioinformatics approaches to generate relatively comprehensive gene inventories for each organism type. These inventories are critical for expression and functional analyses. In proteomic studies, for example, peptides that differ from those predicted from gene sequences can be measured, but they generally cannot be identified by database matching, even if the difference is only a single amino acid residue. Furthermore, many of the identified proteins have no known function. We propose that these challenges can be addressed by development of proteogenomic, biochemical, and geochemical methods that will be initially deployed in a simple, natural model ecosystem. The resulting approach should be broadly applicable and will enhance the utility and significance of genomic data from isolates and consortia for study of organisms in many habitats. Solutions draining pyrite-rich deposits are referred to as acid mine drainage (AMD). AMD is a very prevalent, international environmental problem associated with energy and metal resources. The biological-mineralogical interactions that define these systems can be harnessed for energy-efficient metal recovery and removal of sulfur from coal. The detailed understanding of microbial ecology and ecosystem dynamics resulting from the proposed work will provide a scientific foundation for dealing with the environmental challenges and technological opportunities, and yield new methods for analysis of more complex natural communities.

Ecosystem↗
PubMed2005

Modulation of gut mucosal biofilms.

Non-digestible inulin-type fructans, such as oligofructose and high-molecular-weight inulin, have been shown to have the ability to alter the intestinal microbiota composition in such a way that members of the microbial community, generally considered as health-promoting, are stimulated. Bifidobacteria and lactobacilli are the most frequently targeted organisms. Less information exists on effects of inulin-type fructans on the composition, metabolism and health-related significance of bacteria at or near the mucosa surface or in the mucus layer forming mucosa-associated biofilms. Using rats inoculated with a human faecal flora as an experimental model we have found that inulin-type fructans in the diet modulated the gut microbiota by stimulation of mucosa-associated bifidobacteria as well as by partial reduction of pathogenic Salmonella enterica subsp. enterica serovar Typhimurium and thereby benefit health. In addition to changes in mucosal biofilms, inulin-type fructans also induced changes in the colonic mucosa stimulating proliferation in the crypts, increasing the release of mucins, and altering the profile of mucin components in the goblet cells and epithelial mucus layer. These results indicate that inulin-type fructans may stabilise the gut mucosal barrier. Dietary supplementation with these prebiotics could offer a new approach to supporting the barrier function of the mucosa.

Animals↗
PubMed2005

Effects of fire on properties of forest soils: a review.

Many physical, chemical, mineralogical, and biological soil properties can be affected by forest fires. The effects are chiefly a result of burn severity, which consists of peak temperatures and duration of the fire. Climate, vegetation, and topography of the burnt area control the resilience of the soil system; some fire-induced changes can even be permanent. Low to moderate severity fires, such as most of those prescribed in forest management, promote renovation of the dominant vegetation through elimination of undesired species and transient increase of pH and available nutrients. No irreversible ecosystem change occurs, but the enhancement of hydrophobicity can render the soil less able to soak up water and more prone to erosion. Severe fires, such as wildfires, generally have several negative effects on soil. They cause significant removal of organic matter, deterioration of both structure and porosity, considerable loss of nutrients through volatilisation, ash entrapment in smoke columns, leaching and erosion, and marked alteration of both quantity and specific composition of microbial and soil-dwelling invertebrate communities. However, despite common perceptions, if plants succeed in promptly recolonising the burnt area, the pre-fire level of most properties can be recovered and even enhanced. This work is a review of the up-to-date literature dealing with changes imposed by fires on properties of forest soils. Ecological implications of these changes are described.

Animals↗
PubMed2004

Sulfate-reducing bacteria in tubes constructed by the marine infaunal polychaete Diopatra cuprea.

Marine infaunal burrows and tubes greatly enhance solute transport between sediments and the overlying water column and are sites of elevated microbial activity. Biotic and abiotic controls of the compositions and activities of burrow and tube microbial communities are poorly understood. The microbial communities in tubes of the marine infaunal polychaete Diopatria cuprea collected from two different sediment habitats were examined. The bacterial communities in the tubes from a sandy sediment differed from those in the tubes from a muddy sediment. The difference in community structure also extended to the sulfate-reducing bacterial (SRB) assemblage, although it was not as pronounced for this functional group of species. PCR-amplified 16S rRNA gene sequences recovered from Diopatra tube SRB by clonal library construction and screening were all related to the family Desulfobacteriaceae. This finding was supported by phospholipid fatty acid analysis and by hybridization of 16S rRNA probes specific for members of the genera Desulfosarcina, Desulfobacter, Desulfobacterium, Desulfobotulus, Desulfococcus, and Desulfovibrio and some members of the genera Desulfomonas, Desulfuromonas, and Desulfomicrobium with 16S rRNA gene sequences resolved by denaturing gradient gel electrophoresis. Two of six SRB clones from the clone library were not detected in tubes from the sandy sediment. The habitat in which the D. cuprea tubes were constructed had a strong influence on the tube bacterial community as a whole, as well as on the SRB assemblage.

Animals↗
PubMed2006

Antibodies to periodontal organisms are associated with decreased kidney function. The Dental Atherosclerosis Risk In Communities study.

BACKGROUND/AIMS: Increasing evidence suggests that clinical signs of periodontal disease are independently associated with renal impairment. However, no studies have examined the possible linkage of kidney disease with serum antibody to oral pathogens. METHODS: The periodontal disease status was assessed in an older community-dwelling population (Dental Atherosclerosis Risk in Communities) to include: clinical measurements; oral biofilm microbial composition by DNA checkerboard, and serum antibody immunoglobulin-gamma (IgG) titers to specific bacteria by immunocheckerboard. Baseline characteristics were used to compute estimated glomerular filtration rate defining eGFR <60 ml/min/1.73 m(2) as impaired renal function in 103 of 5,032 subjects. Levels of serum IgG to specific oral bacteria were categorized by quartiles (comparing upper vs. lower three) as high titer and GFR <60 as the dependent variable in logistic regression models, adjusting for multiple comparisons (Hotelling T(2)) and traditional risk factors including age, race, smoking, diabetes, hypertension, body mass, waist-to-hip ratio, serum triglycerides, HDL, and LDL cholesterol. RESULTS: High levels of serum IgG to selected periodontal pathogens including Porphyromonas gingivalis, Treponema denticola and Aggregobacter actinomycetemcomitans were associated with an increased odds for GFR <60 ml/min/1.73 m(2), adjusted odds ratio ranging from 1.6 to 1.8 and p < 0.05. CONCLUSIONS: Elevated IgG to periodontal pathogens is significantly associated with impaired kidney function, independent of traditional risk factors. Prospective studies are necessary to confirm these findings.

Aged↗
PubMed1988

Mychonastes desiccatus Brown sp. nova (Chlorococcales, Chlorophyta)--an intertidal alga forming achlorophyllous desiccation-resistant cysts.

An intertidal Chlorella-like alga Mychonastes desiccatus Brown sp. nova, capable of forming achlorophyllous desiccation-resistant cysts, has been grown in unialgal culture. This small alga was first isolated from a dried sample of a well-studied microbial mat. The mat, located at North Pond, Laguna Figueroa, San Quintin, Baja California, Mexico, is a vertically-stratified microbial community which forms laminated sediments. Morphology, pigment composition and G+C content are within the range typical for the genus Chlorella s. 1. Unlike other chlorellae, however, upon desiccation M. desiccatus forms an achlorophyllous, lipid-filled cyst (thick-walled resting stage) in which no plastid is evident. Rewetting leads to chloroplast differentiation, excystment and recovery of the fully green alga. During desiccation, sporopollenin is deposited within a thickening cell wall. Encystment cannot be induced by growth in the dark. The formation of desiccation-induced cysts allows the alga to survive frequent and intermittent periods of dryness. These chlorellae tolerate wide ranges of acidity and temperature; they both grow and form cysts in media in which sodium ions are replaced with potassium. Although the cysts tolerate crystalline salts, the cell grow optimally in concentrations corresponding from three-quarters to full-strength seawater.

Biopolymers↗
PubMed2006

Rapid quantitative profiling of complex microbial populations.

Diverse and complex microbial ecosystems are found in virtually every environment on earth, yet we know very little about their composition and ecology. Comprehensive identification and quantification of the constituents of these microbial communities--a 'census'--is an essential foundation for understanding their biology. To address this problem, we developed, tested and optimized a DNA oligonucleotide microarray composed of 10,462 small subunit (SSU) ribosomal DNA (rDNA) probes (7167 unique sequences) selected to provide quantitative information on the taxonomic composition of diverse microbial populations. Using our optimized experimental approach, this microarray enabled detection and quantification of individual bacterial species present at fractional abundances of <0.1% in complex synthetic mixtures. The estimates of bacterial species abundance obtained using this microarray are similar to those obtained by phylogenetic analysis of SSU rDNA sequences from the same samples--the current 'gold standard' method for profiling microbial communities. Furthermore, probes designed to represent higher order taxonomic groups of bacterial species reliably detected microbes for which there were no species-specific probes. This simple, rapid microarray procedure can be used to explore and systematically characterize complex microbial communities, such as those found within the human body.

Adult↗
PubMed2005

Microbial community activities during establishment, performance, and decline of bench-scale passive treatment systems for mine drainage.

Permeable reactive barrier (PRB) technology, in which sulfate-reducing bacteria (SRB) facilitate precipitation of metal sulfides, is a promising approach for remediation of sulfate- and metal-laden mine drainage. While PRBs are easily established, they often decline for reasons not well understood. SRB depend on or compete with multiple dynamic microbial populations within a PRB; as a result, performance depends on the changing PRB chemical composition and on succession and competition within the microbial community. To investigate these interactions, we constructed and monitored eight bench-scale PRBs to define periods of establishment, performance, and decline. We then conducted short-term batch studies, using substrate-supplemented column materials, on Days 0 (pre-establishment), 27 (establishment), 41 (performance), and 99 (decline) to reveal potential activities of cellulolytic bacteria, fermenters + anaerobic respirers, SRB, and methanogens. PRBs showed active sulfate reduction, with sulfate removal rates (SRR) of approximately 1-3 mol/m3/d, as well as effective removal of Zn2+. Potential activities of fermentative + anaerobic respiratory bacteria were initially high but diminished greatly during establishment and dropped further during performance and decline. In contrast, potential SRB activity rose during establishment, peaked during performance, and diminished as performance declined. Potential methanogen activity was low; in addition, SRB-methanogen substrate competition was shown not to limit SRB activity. Cellulolytic bacteria showed no substrate limitation at any time. However, fermenters experienced substrate limitation by Day 0, SRB by Day 27, and methanogens by Day 41, showing the dependence of each group on upstream populations to provide substrates. All potential activities, except methanogenesis, were ultimately limited by cellulose hydrolysis; in addition, all potential activities except methanogenesis declined substantially by Day 99, showing that long-term substrate deprivation strongly diminished the intrinsic capacity of the PRB community to perform.

Alkalies↗
PubMed2005

Sulfide-oxidizing activity and bacterial community structure in a fluidized bed reactor from a zero-discharge mariculture system.

In the present work we describe a comprehensive analysis of sulfide oxidation in a fluidized bed reactor (FBR) from an environmentally sustainable, zero-discharge mariculture system. The FBR received oxygen-depleted effluent from a digestion basin (DB) that is responsible for gasification of organic matter and nitrogen. The FBR is a crucial component in this recirculating system because it safeguards the fish from the toxic sulfide produced in the DB. Microscale sulfide oxidation potential and bacterial community composition within FBR biofilms were correlated to biofilter performance by integrating bulk chemical, microsensor (O2, pH, and H2S), and molecular microbial community analyses. The FBR consistently oxidized sulfide during two years of continuous operation, with an estimated average sulfide removal rate of 1.3 g of sulfide-S L(FBR)(-1) d(-1). Maximum sulfide oxidation rates within the FBR biofilms were 0.36 and 0.21 mg of sulfide-S cm(-3) h(-1) in the oxic and anoxic layers, respectively, indicating that both oxygen and nitrate serve as electron acceptors for sulfide oxidation. The estimated anoxic sulfide removal rate, as extrapolated from bench scale, autotrophic, nitrate-amended experiments, was 0.7 g of sulfide-S L(FBR)(-1) d(-1), which is approximately 50% of the total estimated sulfide removal in the FBR. Community composition analyses using denaturing gradient gel electrophoresis (DGGE) of bacterial 16S rRNA gene fragments from FBR samples taken at six-month intervals revealed several sequences that were closely affiliated with sulfide-oxidizing bacteria. These included the denitrifying, sulfide-oxidizing bacteria Thiomicrospira denitrificans, members of the filamentous Thiothrix genus, and sulfide-oxidizing symbionts from the Gammaproteobacteria. In addition, marine Alphaproteobacteria and Bacteroidetes species were present in all of the DGGE profiles examined. DGGE analyses showed significant shifts in the bacterial community composition between profiles over two years of sampling, indicating the presence of a diverse and dynamic microbial community within the functionally stable FBR. The FBR's combined capacity for both oxic and anoxic sulfide oxidation, as indicated by bulk chemical, microsensor, and molecular microbial analyses, gives it significant functional elasticity, which is crucial for proper performance in the dynamic environment of this mariculture system.

Aquaculture↗
PubMed2003

Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of periodontitis patients.

Bacteria are involved in the onset and progression of periodontitis. A promising molecular technique, denaturing gradient gel electrophoresis (DGGE), to study microbial population dynamics in the subgingival pocket is presented. Twenty-three samples were taken from the subgingival pockets of nine patients and six healthy family members. From four periodontitis patients, 12 samples were evaluated before, 1 day after and 3 months after treatment. Part of the 16S rRNA gene of all bacteria was amplified by PCR and separated by DGGE, creating banding patterns representative of the community structure. Shifts in composition and diversity of the microbial population could be determined semiquantitatively, and this showed that treatment resulted in a decrease in the diversity of the population. After 3 months a microbial population 33-47% different from the population before treatment had re-established. Intense bands representing Exiguobacterium aurantiacum were present in 13 out of 25 samples, indicating that this species may play a role in periodontal disease.

Actinomyces↗
PubMed2006

Microbial community related to volatile organic compound (VOC) emission in household biowaste.

Malodorous emissions and potentially pathogenic microorganisms which develop during domestic organic waste collection are not only a nuisance but may also pose health risks. The aim of the present study was to determine whether the presence of specific microorganisms in biowastes is directly related to the composition of the emitted volatile organic compounds (VOCs). The succession of microbial communities during 16 days of storage in organic waste collection bins was studied by denaturing gradient gel electrophoresis (DGGE) of amplified 16S ribosomal DNA in parallel with a classical cultivation and isolation approach. Approximately 60 different bacterial species and 20 different fungal species were isolated. Additionally, some bacterial species were identified through sequencing of excised DGGE bands. Proton transfer reaction mass spectrometry (PTR-MS) was used to detect VOCs over the sampling periods, and co-inertia analyses of VOC concentrations with DGGE band intensities were conducted. Positive correlations, indicating production of the respective VOC or enhancement of microbial growth, and negative correlations, indicating the use of, or microbial inhibition by the respective compound, were found for the different VOCs. Measurement of the VOC emission pattern from a pure culture of Lactococcus lactis confirmed the positive correlations for the protonated masses 89 (tentatively identified as butyric acid), 63 (tentatively identified as dimethylsulfide), 69 (likely isoprene) and 73 (likely butanone).

Bacteria↗
PubMed2006

Annually reoccurring bacterial communities are predictable from ocean conditions.

Factors influencing patterns in the distribution and abundance of plant and animal taxa modulate ecosystem function and ecosystem response to environmental change, which is often taken to infer low functional redundancy among such species, but such relationships are poorly known for microbial communities. Using high-resolution molecular fingerprinting, we demonstrate the existence of extraordinarily repeatable temporal patterns in the community composition of 171 operational taxonomic units of marine bacterioplankton over 4.5 years at our Microbial Observatory site, 20 km off the southern California coast. These patterns in distribution and abundance of microbial taxa were highly predictable and significantly influenced by a broad range of both abiotic and biotic factors. These findings provide statistically robust demonstration of temporal patterning in marine bacterial distribution and abundance, which suggests that the distribution and abundance of bacterial taxa may modulate ecosystem function and response and that a significant subset of the bacteria exhibit low levels of functional redundancy as documented for many plant and animal communities.

Bacteria↗
PubMedDate not supplied

Protistan diversity estimates based on 18S rDNA from seawater incubations in the Western North Atlantic.

Cloning/sequencing and fragment analysis of ribosomal RNA genes (rDNA) are becoming increasingly common methods for the identification of microbial taxa. Sequences of these genes provide many additional taxonomic characters for species that otherwise have few distinctive morphological features, or that require involved microscopy or laboratory culture and testing. These same approaches are now being applied with great success in ecological studies of natural communities of microorganisms. Extensive information on the composition of natural microbial assemblages is being amassed at a rapid pace through genetic analyses of environmental samples and comparison of the resulting genetic information with well-established (and rapidly growing) public databases. We examined microbial eukaryote diversity in a natural seawater sample from the coastal western North Atlantic Ocean using two molecular biological approaches: the cloning and sequencing of rRNA genes and by fragment analysis of these genes using the terminal restriction fragment length polymorphism (T-RFLP) method. A simple experiment was carried out to examine changes in the overall eukaryote (largely protistan) diversity and species composition (phylotype diversity) of a natural microbial assemblage when a seawater sample is placed in a container and incubated at ambient light and temperature for 72 h. Containment of the natural seawater sample resulted in relatively minor changes in the overall eukaryote diversity (species richness) obtained by either molecular method at three time points (time-zero, time-24 h, time-72 h). However, substantial changes in the dominance of particular eukaryote phylotypes took place between the three sampling times. Only 18% of the total number of phylotypes observed in the study were observed at all three time points, while 65% (108 of 165) phylotypes were observed only at a single time point (54 unique phylotypes initially, 37 more unique phylotypes at 24 h, and 17 more at 72 h). The results of this study indicate that a high diversity of protistan taxa existed in the original seawater sample at very low abundance, and thus were not observed in the initial characterization of community structure. Containment resulted in significant shifts in the dominance of these taxa, enabling the presence of previously unobserved phylotypes to be documented after 24 or 72 h of incubation.

Animals↗
PubMed2006

Resource availability controls fungal diversity across a plant diversity gradient.

Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales.

Biodiversity↗
PubMed2001

Structure of microbial communities in activated sludge: potential implications for assessing the biodegradability of chemicals.

Various methods used to assess the biodegradability of chemicals often employ activated sludge as an inoculum since chemicals that ultimately enter the environment are often discharged through wastewater. Differences in the structure and function of activated sludge microbial communities that may complicate interpretation of biodegradation tests could arise from differences in wastewater composition, wastewater treatment plant (WWTP) operation, or manipulations done after collection of the activated sludge. In this study, various methods were used to characterize the structure of microbial communities found in freshly collected activated sludge from WWTPs in Japan, Europe, and the United States, as well as sludge that had been continuously fed either sewage or a glucose-peptone mixture for several weeks after collection. Comparisons of biomass levels, whole-community substrate utilization (determined using Biolog GN and GP plates), and phospholipid fatty acid (PLFA) profiles indicated there were both geographical and temporal differences among freshly collected activated sludge samples. Moreover, marked shifts in the structure of activated sludge microbial communities occurred upon continuous cultivation in the laboratory for 5 weeks using a glucose-peptone feed. These shifts were evident from whole-community substrate utilization and PLFA profiles as well as differences in the profiles of 16S rDNA genes from numerically dominant populations obtained by denaturing gradient gel electrophoresis and terminal restriction fragment analyses. Further studies are needed to better define the variability within and between activated sludge from wastewater treatment plants and laboratory reactors and to assess the impact of such differences on the outcome of biodegradability tests.

Bacteria↗
PubMed2002

Analysis of the differences in microbial community structures between suspended and sessile microorganisms in rivers based on quinone profile.

In this study, a quinone profiling method was applied to clarify the differences in community structure between suspended and sessile microorganisms in rivers. The compositions of microbial quinone of 6 sites for 4 rivers were analyzed. Ubiquinone (UQ)-8, UQ-10, menaquinone (MK)-7, and plastoquinone (PQ)-9 were observed in all samples of suspended and sessile microorganisms for the sites investigated. The dominant quinone species in suspended microorganisms was ubiquinone, and that in sessile microorganism was photosynthetic quinones (namely PQ-9 and vitamin K1). This indicated that aerobic bacteria were abundant in the suspended microorganisms, and photosynthetic microorganisms such as micro-algae and cyanobacteria dominated in the sessile microorganisms. The quinone concentration in the river waters tested, which reflects the concentration of suspended microorganisms, ranged from 0.045 to 1.813 nmol/L. The microbial diversities of suspended and sessile microorganisms calculated based on the composition of all quinones were in the range from 3.4 to 7.5, which was lower than those for activated sludge and soils. Moreover, the diversity of heterotrophic bacteria for sessile microorganisms in the rivers was higher than that for the suspended microorganisms.

Fresh Water↗