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PubMed1980

Characterization of benthic microbial community structure by high-resolution gas chromatography of Fatty Acid methyl esters.

Fatty acids are a widely studied group of lipids of sufficient taxonomic diversity to be useful in defining microbial community structure. The extraordinary resolution of glass capillary gas-liquid chromatography can be utilized to separate and tentatively identify large numbers of fatty acid methyl esters derived from the lipids of estuarine detritus and marine benthic microbiota without the bias of selective methods requiring culture or recovery of the microbes. The gas-liquid chromatographic analyses are both reproducible and highly sensitive, and the recovery of fatty acids is quantitative. The analyses can be automated, and the diagnostic technique of mass spectral fragmentation analysis can be readily applied. Splitless injection on glass capillary gas chromatographic columns detected by mass spectral selective ion monitoring provides an ultrasensitive and definitive monitoring system. Reciprocal mixtures of bacteria and fungi, when extracted and analyzed, showed progressive changes of distinctive fatty acid methyl esters derived from the lipids. By manipulating the environment of an estuarine detrital microbial community with antibiotics and culture conditions, it was possible to produce a community greatly enriched in eucaryotic fungi, as evidenced by scanning electron microscopic morphology. The fatty acid methyl esters from the lipids in the fungus-enriched detritus showed enrichment of the C(18) dienoic and the C(18) and C(20) polyenoic esters. Manipulation of the detrital microbiota that increased the procaryotic population resulted in an absence of large structures typical of fungal mycelia or diatoms, as evidenced by scanning electron microscopy, and a significantly larger proportion of anteiso- and isobranched C(15) fatty acid esters, C(17) cyclopropane fatty acid esters, and the cis-vaccenic isomer of the C(18) monoenoic fatty acid esters. As determined by these techniques, a marine settling community showed greater differences in bacterial as contrasted to microeucaryotic populations when compared with the microbial communities of benthic cores.

Journal Article↗
PubMed2004

Microbial community structure of membrane fouling film in an intermittently and continuously aerated submerged membrane bioreactor treating domestic wastewater.

There was an observable difference in microbial community structure between suspended microorganisms and membrane biofouling film in intermittently and continuously aerated SMBRs. The dominant quinone type of membrane biofouling film in an intermittently aerated SMBR was ubiquinone (UQs)-8, -10 followed by menaquinone (MKs)-8(H4) and -8(H2). But that of the continuously aerated SMBR was UQs-10, -8 followed by MKs-6 and -8(H4). The experimental results also showed that the conditions of an intermittently aerated SMBR may contribute to biofouling by Pseudomonas, Moraxella, Vibrio (quinone type UQ-8), Staphylococcus warneri (quinone type MK-7), Micrococcus sp. (quinone type MK-8(H2)) and Nocardia sp. (quinone type MK-8(H4)), but biofouling in a continuously aerated SMBR may be due to Paracoccus sp. (quinone type: UQ-10) and Flavobacterium species (quinone type: MK-6). The microbial diversities in the intermittently aerated SMBR were 10.9 and 9.4 for biofouling film and suspended microorganisms, respectively. For the continuously aerated SMBR, the results were 10.4 and 10.5 for biofouling film and suspended microorganisms, respectively.

Bacteria↗
PubMed2005

Physiology and microbial community structure in soil at extreme water content.

A sandy loam soil was brought to 6 water contents (13-100% WHC) to study the effects of extreme soil moistures on the physiological status of microbiota (represented by biomass characteristics, specific respiration, bacterial growth, and phospholipid fatty acid, PLFA, stress indicators) and microbial community structure (assessed using PLFA fingerprints). In dry soils, microbial biomass and activity declined as a consequence of water and/or nutrient deficiency (indicated by PLFA stress indicators). These microbial communities were dominated by G+ bacteria and actinomycetes. Oxygen deficits in water-saturated soils did not eliminate microbial activity but the enormous accumulation of poly-3-hydroxybutyrate by bacteria showed the unbalanced growth in excess carbon conditions. High soil water content favored G bacteria.

Actinobacteria↗
PubMedDate not supplied

Microbial community structures in foaming and nonfoaming full-scale wastewater treatment plants.

A survey of full-scale activated-sludge plants in Illinois revealed that filamentous foaming is a widespread problem in the state, and that the causes and consequences of foaming control strategies are not fully understood. To link microbial community structure to foam occurrence, microbial populations in eight foaming and nine nonfoaming full-scale activated-sludge systems were quantified using oligonucleotide hybridization probes targeting the ribosomal RNA (rRNA) of the mycolata; Gordonia spp.; Gordonia amarae; "Candidatus Microthrix parvicella"; the alpha-, beta-, and gamma-subclasses of the Proteobacteria, and members of the Cytophaga-Flavobacteria. Parallel measurements of microbial population abundance using hybridization of extracted RNA and fluorescence in situ hybridization (FISH) showed that the levels of mycolata, particularly Gordonia spp., were higher in most foaming systems compared with nonfoaming systems. Fluorescence in situ hybridization and microscopy suggested the involvement of "Candidatus Microthrix parvicella" and Skermania piniformis in foam formation in other plants. Finally, high numbers of "Candidatus Microthrix parvicella" were detected by FISH in foam and mixed liquor samples of one plant, whereas the corresponding levels of rRNA were low. This finding implies that inactive "Candidatus Microthrix parvicella" cells (i.e., cells with low rRNA levels) can cause foaming.

Bacteria↗
PubMed2006

Effects of the internal recycling rate on biological nutrient removal and microbial community structure in a sequential anoxic/anaerobic membrane bioreactor.

This study investigated the effects of the internal recycling rate on nutrients removal in a sequential anoxic/anaerobic membrane bioreactor (SAM). Microbial community structure in sludge from the SAM was studied using quinone profile method. Above 98% COD, 68% nitrogen, and 55% phosphorus removal efficiencies were achieved when the internal recycling rate was 2.5 times influent flow. At that rate, the optimum specific nitrate loading rate and COD/NO(3)-N ratio were found to be 2.24 mgNO(3)-N g(-1) MLSS h(-1) and 9.13, respectively. Batch tests demonstrated that anoxic condition suppressed phosphorus release, and that denitrification was also influenced by initial substrate concentration. Denitrification appeared to have some priority over phosphorus release for substrate uptake. Microbial community analysis revealed a predominance of the subclass beta-Proteobacteria. Furthermore, it was found that Rhodocyclus-related bacteria were efficient at phosphorus removal than Actinobacteria.

Aerobiosis↗
PubMed2000

An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics.

A systematic evaluation of the value and potential of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure has been undertaken. The reproducibility and robustness of the method has been assessed using environmental DNA samples isolated directly from PCB-polluted or pristine soil, and subsequent polymerase chain reaction (PCR) amplification of total community 16S rDNA. An initial investigation to assess the variability both within and between different polyacrylamide gel electrophoresis (PAGE) runs showed that almost identical community profiles were consistently produced from the same sample. Similarly, very little variability was observed as a result of variation between replicate restriction digestions, PCR amplifications or between replicate DNA isolations. Decreasing concentrations of template DNA produced a decline in both the complexity and the intensity of fragments present in the community profile, with no additional fragments detected in the higher dilutions that were not already present when more original template DNA was used. Reducing the number of cycles of PCR produced similar results. The greatest variation between profiles generated from the same DNA sample was produced using different Taq DNA polymerases, while lower levels of variability were found between PCR products that had been produced using different annealing temperatures. Incomplete digestion by the restriction enzyme may, as a result of the generation of partially digested fragments, lead to an overestimation of the overall diversity within a community. The results obtained indicate that, once standardized, T-RFLP analysis is a highly reproducible and robust technique that yields high-quality fingerprints consisting of fragments of precise sizes, which, in principle, could be phylogenetically assigned, once an appropriate database is constructed.

DNA Primers↗
PubMed2005

In situ identification and characterization of the microbial community structure of full-scale enhanced biological phosphorous removal plants in Japan.

Fluorescent in situ hybridization (FISH) and polyphosphate (polyP) staining methods were used to characterize the microbial community structure of 13 activated sludge samples taken from nine different Japanese wastewater treatment plants with and without enhanced biological phosphorous removal (EBPR) activities. FISH with published rRNA-targeted oligonucleotide probes for important bacterial groups involving in the EBPR process revealed that Rhodocyclus-related polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms from a gammaproteobacterial lineage GB were the predominant populations detected, representing 4-18% and 10-31% of EUBmix-stained cells, respectively, in those samples. However, a considerable proportion of Rhodocyclus-related PAO cells were observed with no polyP granules accumulated based on polyP staining. This was further supported by a poor correlation between Rhodocyclus-related PAO population and sludge total phosphorous (TP) contents. In contrast, high correlations between polyP-stained cells and sludge TP contents were observed. In particular, among those polyP-stained cells in samples Ariake_A2O and Nakano_AO, more than 85% of them could not be targeted by probe PAOmix. These non-Rhodocyclus-related PAOs included populations from other bacterial divisions and members of the Betaproteobacteria other than those in Rhodocyclus-related group.

Bacteria↗
PubMed2004

Effects of hydroxylamine on microbial community structure and function of autotrophic nitrifying biofilms determined by in situ hybridization and the use of microelectrodes.

Effects of hydroxylamine (NH2OH), an intermediate of NH4+ oxidation, on microbial community structure and function of two autotrophic nitrifying biofilms fed with and without NH2OH were analyzed by a 16S rRNA approach and the use of microelectrodes. In the NH2OH-added biofilm, partial oxidation of NH4+ to NO2- was observed, whereas complete oxidation of NH4+ to NO3- was achieved in the control biofilm. In situ hybridization results revealed that no nitrite-oxidizing bacteria (NOB) hybridized with any specific probes were detected in the NH2OH-added biofilm. Thus, the addition of low concentrations of NH2OH (250 microM) completely inhibited the growth of NOB. Phylogenetic analysis of 16S rDNA indicated that the ammonia-oxidizing bacteria (AOB) detected in both biofilms were closely related to Nitrosomonas europaea, and that the clone sequences from both biofilm libraries have more than 99% similarity to each other. However, in situ hybridization results revealed that the addition of NH2OH changed the form of growth pattern of the dominant Nitrosomonas spp. from dense clusters mode to single scattered cells mode. Microelectrode measurements revealed that the average NH4+ consumption rate calculated in the NH2OH-added biofilm was two times higher than that in the control biofilm. This clearly demonstrated that the oxidation of NH4+ was stimulated by NH2OH addition.

Biofilms↗
PubMed2006

Microbial community structure and dynamics of dark fire-cured tobacco fermentation.

The Italian Toscano cigar production includes a fermentation step that starts when dark fire-cured tobacco leaves are moistened and mixed with ca. 20% prefermented tobacco to form a 500-kg bulk. The dynamics of the process, lasting ca. 18 days, has never been investigated in detail, and limited information is available on microbiota involved. Here we show that Toscano fermentation is invariably associated with the following: (i) an increase in temperature, pH, and total microbial population; (ii) a decrease in reducing sugars, citric and malic acids, and nitrate content; and (iii) an increase in oxalic acid, nitrite, and tobacco-specific nitrosamine content. The microbial community structure and dynamics were investigated by culture-based and culture-independent approaches, including denaturing gradient gel electrophoresis and single-strand conformational polymorphism. Results demonstrate that fermentation is assisted by a complex microbial community, changing in structure and composition during the process. During the early phase, the moderately acidic and mesophilic environment supports the rapid growth of a yeast population predominated by Debaryomyces hansenii. At this stage, Staphylococcaceae (Jeotgalicoccus and Staphylococcus) and Lactobacillales (Aerococcus, Lactobacillus, and Weissella) are the most commonly detected bacteria. When temperature and pH increase, endospore-forming low-G+C content gram-positive bacilli (Bacillus spp.) become evident. This leads to a further pH increase and promotes growth of moderately halotolerant and alkaliphilic Actinomycetales (Corynebacterium and Yania) during the late phase. To postulate a functional role for individual microbial species assisting the fermentation process, a preliminary physiological and biochemical characterization of representative isolates was performed.

Bacteria↗
PubMed2004

Analysis of microbial community structure in a biofilm on membrane surface in the submerged membrane bioreactor treating domestic wastewater on the basis of respiratory quinone profiles.

The objective of this study was to investigate the microbial community structure of the biofouling film formed on hollow-fiber membrane surfaces in the submerged membrane bioreactor (SMBR) with a nitrification-denitrification process. In this experiment, aeration was conducted intermittently (60 min off, 90 min on) cyclic anoxic and oxic conditions in the SMBR. The dominant quinone types of biofilm on the membrane surface in an intermittently aerated SMBR were ubiquinone (UQs)-8, -10, followed by menaquinones (MKs)-8(H4), -8(H2) and -7, but those of suspended microorganisms were UQ-8, UQ-10 followed by MKs-8, -9(H4) and -6. The change in quinone profiles of biofilm on the membrane surface suggested that UQ-9, MK-7, MK-8(H2) and MK-8(H4) contributed to microbiological fouling in the intermittently aerated SMBR treating domestic wastewater. The microbial diversities of suspended microorganisms and biofilm, calculated based on the composition of all quinones, were 9.5 and 10.9, respectively.

Bacteria↗
PubMed2026

Elucidation of microbial community structure, small-molecule metabolic and flavor profile characteristics in Xuanwei ham under different processing techniques.

This study systematically compared the impacts of traditional (TH) and modern (MH) processing techniques on the physicochemical properties, microbial community structure, metabolome, and volatile aroma compounds of Xuanwei ham. The results showed that the TH group had higher moisture content and water activity, along with a more tender texture, whereas the MH group exhibited greater hardness and chewiness. Microbiological analysis revealed that the interior of the MH group had higher species richness of both fungi and bacteria, while the TH group maintained higher fungal diversity. Metabolomic analysis identified 112 differential metabolites, with sweet amino acids and certain lipids being more enriched in modern ham, whereas traditional ham contained higher levels of umami amino acids, polyunsaturated fatty acids, and flavor compounds such as carnosine. KEGG pathway enrichment indicated that the differences were primarily concentrated in amino acid biosynthesis and metabolism-related pathways. Volatile flavoromics analysis identified 45 odor-active compounds and screened 15 key aroma-active substances. Among them, modern processed ham was significantly enriched in fatty aldehydes such as (E)-2-nonenal, hexanal, nonanal, and octanal, whereas traditional processed ham was characterized by 1-octen-3-ol, (E,E)-2,4-decadienal, methional, acetoin, and benzeneacetaldehyde. Correlation analysis confirmed that dominant microbes in Xuanwei ham were significantly associated with differential metabolites and characteristic aroma compounds, respectively. This study provides a scientific basis for standardizing production processes, enabling precise quality control, and promoting high-quality industrial development of Xuanwei ham.

Animals↗
PubMed1997

Variation in microbial community structure in two boreal peatlands as determined by analysis of phospholipid Fatty Acid profiles.

Analyses of phospholipid fatty acids (PLFAs) were used to assess variation in community structure and total microbial biomass in two boreal peatlands in Sweden. The total PLFA concentration in peat ranged from 0.16 to 7.0 nmol g of wet peat(sup-1) (median, 0.70 nmol g of wet peat(sup-1)). Principal-component analysis of PLFA data revealed that the degree of depth-related variation in PLFA composition was high among peatland habitats, with general differences between wet sites, with water tables within a few centimeters of the moss surface, and dry sites, with water tables >10 cm below the moss surface. However, variation in PLFA composition over the growing season was negligible. In the principal-component analyses, most PLFAs were determined to be parts of clusters of covarying fatty acids, suggesting that they originated in the same functional groups of microorganisms. Major clusters were formed by monounsaturated (typical of gram-negative eubacteria), terminally branched (gram-positive or anaerobic gram-negative eubacteria), methyl-branched and branched unsaturated (sulfate-reducing bacteria and/or actinomycetes), (omega)8 monounsaturated (methane-oxidizing bacteria), and polyunsaturated (eucaryotes) PLFAs. Within the clusters, PLFAs had rather distinct concentration-depth distributions. For example, PLFAs from sulfate-reducing bacteria and/or actinomycetes and those from methane-oxidizing bacteria had maximum concentrations slightly below and at the average water table depth, respectively.

Journal Article↗
PubMed2006

Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea.

Molecular biological methods were used to investigate the microbial diversity and community structure in intertidal sandy sediments near the island of Sylt (Wadden Sea) at a site which was characterized for transport and mineralization rates in a parallel study (D. de Beer, F. Wenzhöfer, T. Ferdelman, S.E. Boehme, M. Huettel, J.E.E. van Beusekom, M.E. Böttcher, N. Musat, N. Dubilier, Transport and mineralization rates in North Sea sandy intertidal sediments, Sylt-Romo Basin, Wadden Sea, Limnol. Oceanogr. 50 (2005) 113-127). Comparative 16S rRNA sequence analysis revealed a high bacterial diversity. Most sequences retrieved by PCR with a general bacterial primer set were affiliated with Bacteroidetes, Gammaproteobacteria, Deltaproteobacteria and the Pirellula cluster of Planctomycetales. Fluorescence in situ hybridization (FISH) and slot-blot hybridization with group-specific rRNA-targeted oligonucleotide probes were used to characterize the microbial community structure over depth (0-12 cm) and seasons (March, July, October). We found high abundances of bacteria with total cell numbers up to 3 x 10(9) cells ml(-1) and a clear seasonal variation, with higher values in July and October versus March. The microbial community was dominated by members of the Planctomycetes, the Cytophaga/Flavobacterium group, Gammaproteobacteria, and bacteria of the Desulfosarcina/Desulfococcus group. The high abundance (1.5 x 10(7)-1.8 x 10(8) cells ml(-1) accounting for 3-19% of all cells) of presumably aerobic heterotrophic polymer-degrading planctomycetes is in line with the high permeability, deep oxygen penetration, and the high rates of aerobic mineralization of algal biomass measured in the sandy sediments by de Beer et al. (2005). The high and stable abundance of members of the Desulfosarcina/Desulfococcus group, both over depth and season, suggests that these bacteria may play a more important role than previously assumed based on low sulfate reduction rates in parallel cores (de Beer et al., 2005).

Bacteria↗
PubMed2005

Methane production and microbial community structure in single-stage batch and sequential batch systems anaerobically co-digesting food waste and biosolids.

Anaerobic co-digestion of food waste and biosolids was carried out in sequential batch and single-stage batch systems in four treatments. Methane yield, which was used as a functional process parameter, differed between treatments, with the single-stage batch system generating lower volumes than the sequential batch systems. Volatile fatty acid (VFA) concentrations and pH in the leachate also differed between treatments. VFA concentrations were highest and methane generation yields lowest in the single-stage batch system in comparison to the sequential batch systems. The anaerobic microbial community structure of the domains Archaea and Bacteria, determined by denaturing gradient gel electrophoresis, differed between treatments and was correlated to a number of environmental parameters such as pH, VFA concentration and methane generation rate. Methane generation rate was significantly correlated to the community structure of Bacteria but not Archaea. This indicated that the substrates that are produced by acetogens (Bacteria) are important for the growth and community structure of the methanogens (Archaea). Community structure of Archaea changed over time, but this had no observable effect on functional ability based on methane yields. Microbial diversity (H') was shown to be not important in developing a functionally successful anaerobic microbial community.

Anaerobiosis↗
PubMed2006

Microbial community structure in soils with decomposing residues from plants with genetic modifications to lignin biosynthesis.

Lignin is a major determinant of the decomposition of plant materials in soils. Advances in transgenic technology have led to the possibility of modifying lignin to improve the pulping properties of plant materials for papermaking. Previous studies have shown that lignin modifications also affect the rate of plant material decay in soil. The aim of this work was to investigate short-term changes in soil microbial community structures when tobacco residues with reduced activity of enzymes in the monolignol pathway decompose. The residues from lignin-modified plants all decomposed faster than unmodified plant materials. The relative proportions of some of the structural groups of microbial phospholipid fatty acids were affected by genetic modifications, especially the proportion of double unsaturated chain fatty acids, indicative of fungi.

Alcohol Oxidoreductases↗
PubMed2006

The effects of stubble retention and nitrogen application on soil microbial community structure and functional gene abundance under irrigated maize.

The effects of agronomic management practices on the soil microbial community were investigated in a maize production system in New South Wales, Australia. The site has been intensively studied to measure the impact of stubble management and N-fertilizer application on greenhouse gas emissions (CO(2) and N(2)O), N-cycling, pathology, soil structure and yield. As all of these endpoints can be regulated by microbial processes, the microbiology of the system was examined. Soil samples were taken after a winter fallow period and the diversity of the bacterial and fungal communities was measured using PCR-denaturing gradient gel electrophoresis. Stubble and N shifted the structure of bacterial and fungal communities with the primary driver being stubble addition on the fungal community structure (P<0.05 for all effects). Changes in C, N (total and NO(3)), K and Na, were correlated (P<0.05) with variation in the microbial community structure. Quantitative PCR showed that nifH (nitrogen fixation) and napA (denitrification) gene abundance increased upon stubble retention, whereas amoA gene numbers were increased by N addition. These results showed that the management of both stubble and N have significant and long-term impacts on the size and structure of the soil microbial community at phylogenetic and functional levels.

Agriculture↗
PubMed2003

Multi-scale variation in spatial heterogeneity for microbial community structure in an eastern Virginia agricultural field.

To better understand the distribution of soil microbial communities at multiple spatial scales, a survey was conducted to examine the spatial organization of community structure in a wheat field in eastern Virginia (USA). Nearly 200 soil samples were collected at a variety of separation distances ranging from 2.5 cm to 11 m. Whole-community DNA was extracted from each sample, and community structure was compared using amplified fragment length polymorphism (AFLP) DNA fingerprinting. Relative similarity was calculated between each pair of samples and compared using geostatistical variogram analysis to study autocorrelation as a function of separation distance. Spatial autocorrelation was found at scales ranging from 30 cm to more than 6 m, depending on the sampling extent considered. In some locations, up to four different correlation length scales were detected. The presence of nested scales of variability suggests that the environmental factors regulating the development of the communities in this soil may operate at different scales. Kriging was used to generate maps of the spatial organization of communities across the plot, and the results demonstrated that bacterial distributions can be highly structured, even within a habitat that appears relatively homogeneous at the plot and field scale. Different subsets of the microbial community were distributed differently across the plot, and this is thought to be due to the variable response of individual populations to spatial heterogeneity associated with soil properties.

Bacteria↗