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PubMed2003

Microbial community structure in biofilms and water of a drinking water distribution system determined by lipid biomarkers.

The development of microbial communities in biofilms of a drinking water distribution system was monitored, and compared to the microbial communities in water. The microbial communities were studied by phospholipid fatty acid (PLFA) profiles. In drinking water samples the most common PLFAs, with the proportion of 60.9%, were monoenoic fatty acids, such as 16:1omega7c and 18:1omega7c, indicating high abundance of gram-negative bacteria. Instead, in biofilm samples saturated fatty acids, such as 16:0 and 18:0, indicating general biomass, accounted for 54.9-78.4% of the total PLFAs. The proportions of monoenoic fatty acids in biofilm increased from 11.5% to 31.2% with water aging from 22 h to 62 h in the distribution system. In conclusion, water aging affected the structure of microbial communities in biofilms, and the microbes in water differed from those in biofilms. These differences might also reflect the differences in the physiological state of the microbes, which is influenced by water chemistry and by the growth environment, i.e. water or biofilm.

Bacteria↗

PubMed2006

Effects of lactose on colon microbial community structure and function in a four-stage semi-continuous culture system.

A semi-continuous four-channel colon simulator was used to study the effects of lactose for the first time on the growth and fermentation dynamics of colonic microbiota. In six separate simulations, lactose supplementation increased the total SCFA concentration by 3-5 fold as compared with the baseline in the respective vessels. The total bacterial density was inversely correlated with lactic acid production (P = 0.003), while production of butyrate (P = 0.007) and propionate (P = 0.02) correlated with higher numbers of bacteria. A major shift in the microbial community structure in the lactose supplemented vessels was demonstrated by bacterial genomic %G+C-profiling of the total population, where lactose supplementation induced a clearly dominant peak in the bifidobacteria prominent area, %G+C 60-65. The transient shift to increased numbers of bifidobacteria (23-27%) of all bacteria in the first two vessels was also confirmed by the bifidobacteria-specific QPCR-method. In conclusion, lactose produced dramatic changes in microbiota composition and activity as compared with the baseline fermentation.

Base Composition↗

PubMed2003

Microbial community structure in midgut and hindgut of the humus-feeding larva of Pachnoda ephippiata (Coleoptera: Scarabaeidae).

The guts of soil-feeding macroinvertebrates contain a complex microbial community that is involved in the transformation of ingested soil organic matter. In a companion paper (T. Lemke, U. Stingl, M. Egert, M. W. Friedrich, and A. Brune, Appl. Environ. Microbiol. 69:6650-6658, 2003), we show that the gut of our model organism, the humivorous larva of the cetoniid beetle Pachnoda ephippiata, is characterized by strong midgut alkalinity, high concentrations of microbial fermentation products, and the presence of a diverse, yet unstudied microbial community. Here, we report on the community structure of bacteria and archaea in the midgut, hindgut, and food soil of P. ephippiata larvae, determined with cultivation-independent techniques. Clone libraries and terminal restriction fragment length polymorphism analysis of 16S rRNA genes revealed that the intestines of P. ephippiata larvae contain a complex gut microbiota that differs markedly between midgut and hindgut and that is clearly distinct from the microbiota in the food soil. The bacterial community is dominated by phylogenetic groups with a fermentative metabolism (Lactobacillales, Clostridiales, Bacillales, and Cytophaga-Flavobacterium-Bacteroides [CFB] phylum), which is corroborated by high lactate and acetate concentrations in the midgut and hindgut and by the large numbers of lactogenic and acetogenic bacteria in both gut compartments reported in the companion paper. Based on 16S rRNA gene frequencies, Actinobacteria dominate the alkaline midgut, while the hindgut is dominated by members of the CFB phylum. The archaeal community, however, is less diverse. 16S rRNA genes affiliated with mesophilic Crenarchaeota, probably stemming from the ingested soil, were most frequent in the midgut, whereas Methanobacteriaceae-related 16S rRNA genes were most frequent in the hindgut. These findings agree with the reported restriction of methanogenesis to the hindgut of Pachnoda larvae.

Animals↗

PubMed2002

The microbial community structure of drinking water biofilms can be affected by phosphorus availability.

Microbial communities in biofilms grown for 4 and 11 weeks under the flow of drinking water supplemented with 0, 1, 2, and 5 microg of phosphorus liter(-1) and in drinking and warm waters were compared by using phospholipid fatty acids (PLFAs) and lipopolysaccharide 3-hydroxy fatty acids (LPS 3-OH-FAs). Phosphate increased the proportion of PLFAs 16:1 omega 7c and 18:1 omega 7c and affected LPS 3-OH-FAs after 11 weeks of growth, indicating an increase in gram-negative bacteria and changes in their community structure. Differences in community structures between biofilms and drinking and warm waters can be assumed from PLFAs and LPS 3-OH-FAs, concomitantly with adaptive changes in fatty acid chain length, cyclization, and unsaturation.

Bacteria↗

PubMed2003

Effects of glucose overloading on microbial community structure and biogas production in a laboratory-scale anaerobic digester.

This study characterizes the response of the microbial communities of a laboratory-scale mesophilic biogas process, fed with a synthetic substrate based on cellulose and egg albumin, to single pulses of glucose overloading (15 or 25 times the daily feed based on VS). The microbial biomass and community structure were determined from analyses of membrane phospholipids. The ratio between phospholipid fatty acids (PLFAs; eubacteria and eucaryotes) and di-ethers (PLEL; archaea) suggested that methanogens constituted 4-8% of the microbial biomass. The glucose addition resulted in transient increases in the total biomass of eubacteria while there were only small changes in community structure. The total gas production rate increased, while the relative methane content of the biogas and the alkalinity decreased. However, the biomass of methanogens was not affected by the glucose addition. The results show that the microbial communities of biogas processes can respond quickly to changes in the feeding rate. The glucose overload resulted in a transient general stimulation of degradation rates and almost a doubling of eubacterial biomass, although the biomass increase corresponded to only 7% of the glucose C added.

Anaerobiosis↗

PubMed2001

Rhizosphere effects on microbial community structure and dissipation and toxicity of polycyclic aromatic hydrocarbons (PAHs) in spiked soil.

Phytoremediation of soils polluted with polycyclic aromatic hydrocarbons (PAHs) has so far neglected the possible role of the ubiquitous symbiotic associations between plant roots and fungi known as arbuscular mycorrhizas. A time course laboratory experiment with clover and ryegrass grown on spiked [500 + 500 + 50 mg kg-1 of anthracene, chrysene and dibenz(a,h)anthracene] soil demonstrated for the first time that dissipation of condensed PAHs may be enhanced in the presence of arbuscular mycorrhiza [66 and 42% reductions in chrysene and dibenz(a,h)anthracene, respectively, versus 56 and 20% reductions in nonmycorrhizal controls]. Addition of a surfactant accelerated initial PAH dissipation but did not attain final PAH concentrations below those obtained with nonmycorrhizal plants. Toxicity tests (earthworm survival and bioluminescence inhibition in Vibrio fischeri) indicated that mycorrhiza reduced the toxicity of PAHs and/or their metabolites and counteracted a temporally enhanced toxicity mediated by surfactant addition. Phospholipid fatty acid profiles demonstrated that the imposed treatments altered the microbial community structure and indicated that the mycorrhiza-associated microflora was responsible for the observed reductions in PAH concentrations in the presence of mycorrhiza.

Animals↗

PubMed1996

Effects of phenol feeding pattern on microbial community structure and cometabolism of trichloroethylene.

Cometabolism of trichloroethylene (TCE) by phenol-fed enrichments was evaluated in four reactors with distinct phenol feeding patterns. The reactors were inoculated from the same source, operated at the same average dilution rate, and received the same mass of phenol over time. Only the timing of phenol addition differed. Reactor C received phenol continuously; reactor SC5 received phenol semicontinuously--alternating between 5 h of feed and 3 h without feed; reactor SC2 alternated between 2 h of feed and 6 h without feed; and reactor P received a single pulse every 24 h. The structure of the enrichments and their capacity for TCE transformation were analyzed. In long-term operation, reactors C and SC5 were dominated by fungi, had higher levels of predators, were more susceptible to biomass fluctuations, and exhibited reduced capacity for TCE transformation. Reactors P and SC2 were characterized by lower levels of fungi, higher bacterial biomass, higher concentrations of TCE-degrading organisms, and higher rates of TCE transformation. After 200 days of operation, rates of TCE transformation increased 10-fold in reactor P, resulting in TCE transformation rates that were 20 to 100 times higher than the rates of the other reactor communities. The cause of this shift is unknown. Isolates capable of the highest rates of TCE transformation were obtained from reactor P. We conclude that cometabolic activity depends upon microbial community structure and that the community structure can be manipulated by altering the growth substrate feeding pattern.

Journal Article↗

PubMed2005

Microbial community structure and density under different tree species in an acid forest soil (Morvan, France).

Overexploitation of forests to increase wood production has led to the replacement of native forest by large areas of monospecific tree plantations. In the present study, the effects of different monospecific tree cover plantations on density and composition of the indigenous soil microbial community are described. The experimental site of "Breuil-Chenue" in the Morvan (France) was the site of a comparison of a similar mineral soil under Norway spruce (Picea abies), Douglas fir (Pseudotuga menziesii), oak (Quercus sessiflora), and native forest [mixed stand dominated by oak and beech (Fagus sylvatica)]. Sampling was performed during winter (February) at three depths (0-5, 5-10, and 10-15 cm). Abundance of microorganisms was estimated via microbial biomass measurements, using the fumigation-extraction method. The genetic structure of microbial communities was investigated using the bacterial- and fungal-automated ribosomal intergenic spacer analysis (B-ARISA and F-ARISA, respectively) DNA fingerprint. Only small differences in microbial biomass were observed between tree species, the highest values being recorded under oak forest and the lowest under Douglas fir. B- and F-ARISA community profiles of the different tree covers clustered separately, but noticeable similarities were observed for soils under Douglas fir and oak. A significant stratification was revealed under each tree species by a decrease in microbial biomass with increasing depths and by distinct microbial communities for each soil layer. Differences in density and community composition according to tree species and depth were related to soil physicochemical characteristics and organic matter composition.

Bacteria↗

PubMed2001

Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments.

A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.

Bacteria↗

PubMed2000

Whole-cell versus total RNA extraction for analysis of microbial community structure with 16S rRNA-targeted oligonucleotide probes in salt marsh sediments.

rRNA-targeted oligonucleotide probes have become powerful tools for describing microbial communities, but their use in sediments remains difficult. Here we describe a simple technique involving homogenization, detergents, and dispersants that allows the quantitative extraction of cells from formalin-preserved salt marsh sediments. Resulting cell extracts are amenable to membrane blotting and hybridization protocols. Using this procedure, the efficiency of cell extraction was high (95.7% +/- 3.7% [mean +/- standard deviation]) relative to direct DAPI (4',6'-diamidino-2-phenylindole) epifluorescence cell counts for a variety of salt marsh sediments. To test the hypothesis that cells were extracted without phylogenetic bias, the relative abundance (depth distribution) of five major divisions of the gram-negative mesophilic sulfate-reducing delta proteobacteria were determined in sediments maintained in a tidal mesocosm system. A suite of six 16S rRNA-targeted oligonucleotide probes were utilized. The apparent structure of sulfate-reducing bacteria communities determined from whole-cell and RNA extracts were consistent with each other (r(2) = 0.60), indicating that the whole-cell extraction and RNA extraction hybridization approaches for describing sediment microbial communities are equally robust. However, the variability associated with both methods was high and appeared to be a result of the natural heterogeneity of sediment microbial communities and methodological artifacts. The relative distribution of sulfate-reducing bacteria was similar to that observed in natural marsh systems, providing preliminary evidence that the mesocosm systems accurately simulate native marsh systems.

Ecosystem↗

PubMed2003

Molecular characterization of the microbial community structure in two activated sludge systems for the advanced treatment of domestic effluents.

Although activated sludge systems with enhanced biological phosphorus removal (EBPR) represent state-of-the-art technology for phosphate removal from wastewater it is still unknown which species of bacteria are responsible for the EBPR process. The aim of this study was to compare the bacterial composition of activated sludge from two laboratory plants with different modes of operation, anoxic/oxic- (EBPR, no nitrification) and Phoredox-system (EBPR, nitrification and denitrification) with particular emphasis on microorganisms responsible for EBPR process. In addition to fluorescence in situ hybridization (FISH), we applied further rRNA-based molecular techniques like terminal restriction-fragment length polymorphism analysis and comparative 16S rDNA analysis to yield additional information and to verify the results from FISH analysis, like e.g. for the identification of polyphosphate accumulating organisms (PAO). Despite the different modes of operation only minor differences in the bacterial composition were detected by FISH analysis based on the probes used in this study. In contrast T-RFLP analysis yielded characteristic community fingerprints for each of the investigated plants and comparative 16S rDNA analysis indicated highly diverse microbial communities in both plants suggesting substantial differences in the microbial structure. The results obtained by FISH analysis with specific probes for PAOs support the presumption that not only one specific organism is responsible for the EBPR. In our case Tetrasphaera spp. dominated the PAO community, but other possible PAOs, like Microlunatus spp. and members of the Rhodocyclus group, were also detected.

Bacteria↗

PubMed2002

Soil microbial community structure across a thermal gradient following a geothermal heating event.

In this study microbial species diversity was assessed across a landscape in Yellowstone National Park, where an abrupt increase in soil temperature had occurred due to recent geothermal activity. Soil temperatures were measured, and samples were taken across a temperature gradient (35 to 65 degrees C at a 15-cm depth) that spanned geothermally disturbed and unimpacted soils; thermally perturbed soils were visually apparent by the occurrence of dead or dying lodgepole pine trees. Changes in soil microbial diversity across the temperature gradient were qualitatively assessed based on 16S rRNA sequence variation as detected by denaturing gradient gel electrophoresis (DGGE) using both ribosomal DNA (rDNA) and rRNA as PCR templates and primers specific for the Bacteria or Archaea domain. The impact of the major heating disturbance was apparent in that DGGE profiles from heated soils appeared less complex than those from the unaffected soils. Phylogenetic analysis of a bacterial 16S rDNA PCR clone library from a recently heated soil showed that a majority of the clones belonged to the Acidobacterium (51%) and Planctomyces (18%) divisions. Agar plate counts of soil suspensions cultured on dilute yeast extract and R2A agar media incubated at 25 or 50 degrees C revealed that thermophile populations were two to three orders of magnitude greater in the recently heated soil. A soil microcosm laboratory experiment simulated the geothermal heating event. As determined by both RNA- and DNA-based PCR coupled with DGGE, changes in community structure (marked change in the DGGE profile) of soils incubated at 50 degrees C occurred within 1 week and appeared to stabilize after 3 weeks. The results of our molecular and culture data suggest that thermophiles or thermotolerant species are randomly distributed in this area within Yellowstone National Park and that localized thermal activity selects for them.

Bacteria↗

PubMed2003

The isotope array, a new tool that employs substrate-mediated labeling of rRNA for determination of microbial community structure and function.

A new microarray method, the isotope array approach, for identifying microorganisms which consume a (14)C-labeled substrate within complex microbial communities was developed. Experiments were performed with a small microarray consisting of oligonucleotide probes targeting the 16S rRNA of ammonia-oxidizing bacteria (AOB). Total RNA was extracted from a pure culture of Nitrosomonas eutropha grown in the presence of [(14)C]bicarbonate. After fluorescence labeling of the RNA and microarray hybridization, scanning of all probe spots for fluorescence and radioactivity revealed that specific signals were obtained and that the incorporation of (14)C into rRNA could be detected unambiguously. Subsequently, we were able to demonstrate the suitability of the isotope array approach for monitoring community composition and CO(2) fixation activity of AOB in two nitrifying activated-sludge samples which were incubated with [(14)C]bicarbonate for up to 26 h. AOB community structure in the activated-sludge samples, as predicted by the microarray hybridization pattern, was confirmed by quantitative fluorescence in situ hybridization (FISH) and comparative amoA sequence analyses. CO(2) fixation activities of the AOB populations within the complex activated-sludge communities were detectable on the microarray by (14)C incorporation and were confirmed independently by combining FISH and microautoradiography. AOB rRNA from activated sludge incubated with radioactive bicarbonate in the presence of allylthiourea as an inhibitor of AOB activity showed no incorporation of (14)C and thus was not detectable on the radioactivity scans of the microarray. These results suggest that the isotope array can be used in a PCR-independent manner to exploit the high parallelism and discriminatory power of microarrays for the direct identification of microorganisms which consume a specific substrate in the environment.

Ammonia↗

PubMed2006

Microbial community structure during oxygen-stimulated bioremediation in phenol-contaminated groundwater.

This research explored the changes in genetic diversity and spatial distribution of microbial communities in association with the changes in phenol concentration during a bioremediation process. Results using the traditional plate count method indicated an increase of average bacteria densities in groundwater from 10(4) to 10(7)CFUml(-1) initially to 10(7) to 10(9)CFUml(-1) after remediation. The diversity and stability of phenol-degrading bacterial communities were investigated by using single-strand-conformation polymorphism (SSCP) genetic profile analysis of 16S rDNA fragments amplified from groundwater samples. The molecular data showed a high degree of genetic similarity between communities from certain monitoring wells during the early phases of remediation, probably due to similar initial physical conditions among wells. Molecular signatures of several cultivated phenol-degrading bacterial strains could be seen in most groundwater profiles throughout the study period, suggesting that these strains were indigenous to the study site. It was also observed that the species diversity of these microbial communities increased as the phenol levels in the groundwater decreased during the 9-month study period, and recovered to the pre-treatment levels after the remediation program was completed.

Bacteria↗

PubMed2006

Microbial community structure in polluted Baltic Sea sediments.

Nearly half the seabed of the Baltic Proper is incapable of supporting life of higher organisms as a consequence of oxygen depletion resulting from eutrophication. However, these areas are actually teeming with microbial life. Here we used terminal-restriction fragment length polymorphism (T-RFLP) to investigate the dominant archaeal and bacterial groups, with respect to community structure, in surface layers of bottom sediments of the Baltic Sea along a coastal pollution gradient. Both archaeal and bacterial communities formed distinct clusters along the pollution gradient and the community compositions were different at the polluted sites compared with the relatively clean reference sites. The structures of the bacterial communities were most strongly correlated to water depth, followed by organic carbon, oxygen, salinity and silicate levels. In contrast, the structures of the archaeal communities were most strongly correlated to oxygen, salinity, organic carbon, silicate and nitrate levels. Some members of the microbial communities were identified using a combination of traditional and molecular approaches. Isolates obtained on different culture media were identified by partial sequencing of their 16S rRNA genes and some novel species were found. In addition, we developed a computer program, aplaus, to elucidate the putative identities of the most dominant community members by T-RFLP.

Bacteria↗

PubMed2000

Rhizosphere microbial community structure in relation to root location and plant iron nutritional status.

Root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. To examine this question, we performed an experiment with barley (Hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. Plants were grown in an iron-limiting soil in root box microcosms. One-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter root exudate composition. After 30 days, the bacterial communities associated with different root zones, including the primary root tips, nonelongating secondary root tips, sites of lateral root emergence, and older roots distal from the tip, were characterized by using 16S ribosomal DNA (rDNA) fingerprints generated by PCR-denaturing gradient gel electrophoresis (DGGE). Our results showed that the microbial communities associated with the different root locations produced many common 16S rDNA bands but that the communities could be distinguished by using correspondence analysis. Approximately 40% of the variation between communities could be attributed to plant iron nutritional status. A sequence analysis of clones generated from a single 16S rDNA band obtained at all of the root locations revealed that there were taxonomically different species in the same band, suggesting that the resolving power of DGGE for characterization of community structure at the species level is limited. Our results suggest that the bacterial communities in the rhizosphere are substantially different in different root zones and that a rhizosphere community may be altered by changes in root exudate composition caused by changes in plant iron nutritional status.

Bacteria↗

PubMed2005

Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays.

The ecophysiology of microorganisms has been at the heart of microbial ecology since its early days, but only during the past decade have methods become available for cultivation-independent, direct identification of microorganisms in complex communities and for the simultaneous investigation of their activity and substrate uptake patterns. The combination of fluorescence in situ hybridization (FISH) and microautoradiography (MAR) is currently the most widely applied tool for revealing physiological properties of microorganisms in their natural environment with single-cell resolution. For example, this technique has been used in wastewater treatment and marine systems to describe the functional properties of newly discovered species, and to identify microorganisms responsible for key physiological processes. Recently, the scope of FISH-MAR was extended by rendering it quantitative and by combining it with microelectrode measurements or stable isotope probing. Isotope arrays have also been developed that exploit the parallel detection offered by DNA microarrays to measure incorporation of labelled substrate into the rRNA of many community members in a single experiment.

Archaea↗

PubMed2005

Characterization of microbial community structure in Gulf of Mexico gas hydrates: comparative analysis of DNA- and RNA-derived clone libraries.

The characterization of microbial assemblages within solid gas hydrate, especially those that may be physiologically active under in situ hydrate conditions, is essential to gain a better understanding of the effects and contributions of microbial activities in Gulf of Mexico (GoM) hydrate ecosystems. In this study, the composition of the Bacteria and Archaea communities was determined by 16S rRNA phylogenetic analyses of clone libraries derived from RNA and DNA extracted from sediment-entrained hydrate (SEH) and interior hydrate (IH). The hydrate was recovered from an exposed mound located in the northern GoM continental slope with a hydrate chipper designed for use on the manned-submersible Johnson Sea Link (water depth, 550 m). Previous geochemical analyses indicated that there was increased metabolic activity in the SEH compared to the IH layer (B. N. Orcutt, A. Boetius, S. K. Lugo, I. R. Macdonald, V. A. Samarkin, and S. Joye, Chem. Geol. 205:239-251). Phylogenetic analysis of RNA- and DNA-derived clones indicated that there was greater diversity in the SEH libraries than in the IH libraries. A majority of the clones obtained from the metabolically active fraction of the microbial community were most closely related to putative sulfate-reducing bacteria and anaerobic methane-oxidizing archaea. Several novel bacterial and archaeal phylotypes for which there were no previously identified closely related cultured isolates were detected in the RNA- and DNA-derived clone libraries. This study was the first phylogenetic analysis of the metabolically active fraction of the microbial community extant in the distinct SEH and IH layers of GoM gas hydrate.

Archaea↗