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PubMed2000

Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA).

Amplified ribosomal DNA restriction analysis (ARDRA) is a simple method based on restriction endonuclease digestion of the amplified bacterial 16S rDNA. In this study we have evaluated the suitability of this method to detect differences in activated sludge bacterial communities fed on domestic or industrial wastewater, and subject to different operational conditions. The ability of ARDRA to detect these differences has been tested in modified Ludzack-Ettinger (MLE) configurations. Samples from three activated sludge wastewater treatment plants (WWTPs) with the MLE configuration were collected for both oxic and anoxic reactors, and ARDRA patterns using double enzyme digestions AluI+MspI were obtained. A matrix of Dice similarity coefficients was calculated and used to compare these restriction patterns. Differences in the community structure due to influent characteristics and temperature could be observed, but not between the oxic and anoxic reactors of each of the three MLE configurations. Other possible applications of ARDRA for detecting and monitoring changes in activated sludge systems are also discussed.

Aerobiosis↗
PubMed2003

Community structure of microbial biofilms associated with membrane-based water purification processes as revealed using a polyphasic approach.

The microbial communities of membrane biofilms occurring in two full-scale water purification processes employing microfiltration (MF) and reverse osmosis (RO) membranes were characterized using a polyphasic approach that employed bacterial cultivation, 16S rDNA clone library and fluorescence in situ hybridization techniques. All methods showed that the alpha-Proteobacteria was the largest microbial fraction in the samples, followed by the gamma-Proteobacteria. This suggested that members of these two groups could be responsible for the biofouling on the membranes studied. Furthermore, the microbial community structures between the MF and RO samples were considerably different in composition of the most predominant 16S rDNA clones and bacterial isolates from the alpha-Proteobacteria and only shared two common groups ( Bradyrhizobium, Bosea) out of more than 17 different bacterial groups observed. The MF and RO samples further contained Planctomycetes and Fibroacter/ Acidobacteria as the second predominant bacterial clones, respectively, and differed in minor bacterial clones and isolates. The community structure differences were mainly attributed to differences in feed water, process configurations and operating environments, such as the pressure and hydrodynamic conditions present in the water purification systems.

Alphaproteobacteria↗
PubMed2001

The Structure of Microbial Communities in Soil and the Lasting Impact of Cultivation.

The structure of microbial communities was examined as a function of community composition and the relative abundance of specific microbial groups to examine the effects that plant community composition and land-use history have on microbial communities in the soil. The sites sampled were part of the Long Term Ecological Research (LTER) project in agricultural ecology at the W.K. Kellogg Biological Station of Michigan State University (Hickory Corners, MI) and included both active and abandoned agricultural fields as well as nearby fields that had never been cultivated. Microbial community structure was assessed by extracting total RNA from soil samples and using 16S rRNA-targeted oligonucleotide probes to quantify the abundance of rRNA from the alpha, beta, and gamma Proteobacteria, the Actinobacteria (Gram positive bacteria with a high mol % G+C genome), the Bacteria, and the Eukarya. In addition, soil microbial communities were characterized by examining fluorescently tagged terminal restriction fragment length polymorphisms (T-RFLP) in PCR amplified 16S rDNA. Microbial community structure was observed to be remarkably similar among plots that shared a long-term history of agricultural management despite differences in plant community composition and land management that have been maintained on the plots in recent years. In contrast, microbial community structure differed significantly between fields that had never been cultivated and those having a long-term history of cultivation.

Journal Article↗
PubMed2003

Diversity and dynamics of microbial communities in soils from agro-ecosystems.

Soil microbial communities are integrally involved in biogeochemical cycles and their activities are crucial to the productivity of terrestrial ecosystems. Despite the importance of soil microorganisms, little is known about the distribution of microorganisms in the soil or the manner in which microbial community structure responds to changes in land management. We investigated the structure of microbial communities in the soil over two years in a series of replicated plots, that included, cultivated fields, fields abandoned from cultivation and fields with no history of cultivation. Microbial community structure was examined by monitoring the relative abundance of ribosomal RNA (rRNA) from seven of the most common bacterial groups in soil (the Alpha and Beta Proteobacteria, Actinobacteria, Cytophagales, Planctomycetes, Verrucomicrobia and the Acidobacteria) and the Eukarya. These data reveal that soil microbial communities are dynamic, capable of significant change at temporal scales relative to seasonal events. However, despite temporal change in microbial community structure, the rRNA relative abundance of particular microbial groups is affected by the local environment such that recognizable patterns of community structure exist in relation to field management.

Agriculture↗
PubMed2004

[Microbial eco-characterization and its restoration in copper reclaimed wasteland in red soil area of China. II. Effects on soil microbial characteristics and community structure].

Soil microbial features in Lipu copper mining and non-mine soil were studied comparatively. The results indicated that mine soil possessed obviously different microbial features such as lower microbial biomass carbon and soil basal respiration strength, Cmic/Corg decreasing, and higher microbial ecophysiological parameters qCO2, indicating that heavy metal had a depressive impact on soil microbial eco-characteristics. Biolog data showed that mine soil microbial community structure was changed obviously, the speed and quantity of carbon consuming were increased significantly, and the kinds of carbon sources which soil microorganism used were changed, led to consume much more energies for maintaining the normal needs of its life. But the utilization efficiency was lower compared with the control. All the results showed that soil microbial eco-characteristics could be used as a sensitive, effective and liable index of mine soil environment qualities.

Bacteria↗
PubMed1995

Structural differences of the microbial community in two sites of the Terra Nova Bay (Ross Sea, Antarctica): a statistical analysis.

The microbial community structure was investigated in a one month survey at two sampling stations located in the Terra Nova Bay (Antarctica). The microbial assemblage was studied by direct counts with epifluorescent microscopy (picoplankton and picophytoplankton), fractionated adenosine-triphosphate, lipopolysaccarides and bacterial growth on cultural medium. The results underwent the Spearman rank correlation and the principal component analysis together with other environmental parameters (temperature, salinity, nutrient salts and chlorophyll a) with the aim of revealing differences in the microbial community structure between the in-shore and off-shore sites.

Antarctic Regions↗
PubMed2005

Soil bacterial and fungal community structure across a range of unimproved and semi-improved upland grasslands.

Changes in soil microbial community structure due to improvement are often attributed to concurrent shifts in floristic community composition. The bacterial and fungal communities of unimproved and semi-improved (as determined by floristic classification) grassland soils were studied at five upland sites on similar geological substrata using both broad-scale (microbial activity and fungal biomass) and molecular [terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA)] approaches. It was hypothesized that microbial community structure would be similar in soils from the same grassland type, and that grassland vegetation classifications could thus be used as predictors of microbial community structure. Microbial community measurements varied widely according to both site and grassland type, and trends in the effect of grassland improvement differed between sites. These results were consistent with those from similar studies, and indicated that floristic community composition was not a stable predictor of microbial community structure across sites. This may indicate a lack of correlation between grassland plant composition and soil microbial community structure, or that differences in soil chemistry between sites had larger impacts on soil microbial populations than plant-related effects.

Bacteria↗
PubMed1998

Structure of a microbial community in soil after prolonged addition of low levels of simulated acid rain

Humus samples were collected 12 growing seasons after the start of a simulated acid rain experiment situated in the subarctic environment. The acid rain was simulated with H2SO4, a combination of H2SO4 and HNO3, and HNO3 at two levels of moderate acidic loads close to the natural anthropogenic pollution levels of southern Scandinavia. The higher levels of acid applications resulted in acidification, as defined by humus chemistry. The concentrations of base cations decreased, while the concentrations of exchangeable H+, Al, and Fe increased. Humus pH decreased from 3.83 to 3.65. Basal respiration decreased with decreasing humus pH, and total microbial biomass, measured by substrate-induced respiration and total amount of phospholipid fatty acids (PLFA), decreased slightly. An altered PLFA pattern indicated a change in the microbial community structure at the higher levels of acid applications. In general, branched fatty acids, typical of gram-positive bacteria, increased in the acid plots. PLFA analysis performed on the bacterial community growing on agar plates also showed that the relative amount of PLFA specific for gram-positive bacteria increased due to the acidification. The changed bacterial community was adapted to the more acidic environment in the acid-treated plots, even though bacterial growth rates, estimated by thymidine and leucine incorporation, decreased with pH. Fungal activity (measured as acetate incorporation into ergosterol) was not affected. This result indicates that bacteria were more affected than fungi by the acidification. The capacity of the bacterial community to utilize 95 different carbon sources was variable and only showed weak correlations to pH. Differences in the toxicities of H2SO4 and HNO3 for the microbial community were not found.

Journal Article↗
PubMed1995

Fluorescently Labeled Virus Probes Show that Natural Virus Populations Can Control the Structure of Marine Microbial Communities.

Fluorescently stained viruses were used as probes to label, identify, and enumerate specific strains of bacteria and cyanobacteria in mixed microbial assemblages. Several marine virus isolates were fluorescently stained with YOYO-1 or POPO-1 (Molecular Probes, Inc.) and added to seawater samples that contained natural microbial communities. Cells to which the stained viruses adsorbed were easily distinguished from nonhost cells; typically, there was undetectable binding of stained viruses to natural microbial assemblages containing >10(sup6) bacteria ml(sup-1) but to which host cells were not added. Host cells that were added to natural seawater were quantified with 99% (plusmn) 2% (mean (plusmn) range) efficiency with fluorescently labeled virus probes (FLVPs). A marine bacterial isolate (strain PWH3a), tentatively identified as Vibrio natriegens, was introduced into natural microbial communities that were either supplemented with nutrients or untreated, and changes in the abundance of the isolate were monitored with FLVPs. Simultaneously, the concentrations of viruses that infected strain PWH3a were monitored by plaque assay. Following the addition of PWH3a, the concentration of viruses infecting this strain increased from undetectable levels (<1 ml(sup-1)) to 2.9 x 10(sup7) and 8.3 x 10(sup8) ml(sup-1) for the untreated and nutrient-enriched samples, respectively. The increase in viruses was associated with a collapse in populations of strain PWH3a from ca. 30 to 2% and 43 to 0.01% of the microbial communities in untreated and nutrient-enriched samples, respectively. These results clearly demonstrate that FLVPs can be used to identify and quantify specific groups of bacteria in mixed microbial communities. The data show as well that viruses which are present at low abundances in natural aquatic viral communities can control microbial community structure.

Journal Article↗
PubMed2005

[Spatial variation of microbial properties in a creosote-contaminated soil].

By the methods of geostatistics, this paper studied the spatial variation of microbial biomass, microbial community structure and microbial activity in a creosote-contaminated soil. The microbial biomass was indicated by the total amount of 26 examined phospholipid fatty acids (totPLFA), the microbial community structure was characterized by the first two principal components (PC1 and PC2) of the PLFA patterns through subjecting the PLFAs to principal component analysis, and the total amount of CO2-C respired (C(re)) during incubation was used to describe the soil microbial activity. The results showed that most of the variables exhibited various degrees of spatial autocorrelation, and spherical models with nugget could fit their semivariograms. The estimated spatial dependence distances of the variables varied from 2.50 to 16.60 m. The PLFA PC1, totPLFA and C(re) displayed relatively high spatial dependences, their relative structural variance, i.e., the proportion of total variance that can be attributed to the spatial autocorrelation, being 82.3%, 79.6% and 64.7%, respectively, while PLFA PC2 was not spatially autocorrelated. The kriged maps showed that there were several hot spots with relatively high microbial biomass and high microbial activity located in the study site. Gram- negative bacteria characterized by PLFAs 16:1omega7t, cyl7:0, 18:1omega7 and cyl9:0 were the dominant community in these hot spots. The concentration and spatial distribution of polycyclic aromatic hydrocarbons as the main contaminants in the soil could be one of the important factors affecting the spatial variation of soil microbial properties.

Biodegradation, Environmental↗
PubMed2006

Dissolved organic matter concentration and quality influences upon structure and function of freshwater microbial communities.

Past studies have suggested that the concentration and quality of dissolved organic matter (DOM) may influence microbial community structure. In this study, we cross-inoculated the bacterial communities from two streams and a dystrophic lake that varied in DOM concentration and chemistry, to yield nine fully crossed treatments. We measured dissolved organic carbon (DOC) concentration and heterotrophic microbial community productivity throughout a 72-h incubation period, characterized DOM quality by molecular weight, and determined microbial community structure at the initial and final time points. Our results indicate that all bacterial inoculate sources had similar effects upon DOC concentration and DOM quality, regardless of the DOM source. These effects included an overall decrease in DOM M (W) and an initial period of DOC concentration variability between 0-24h. In contrast, microbial communities and their metabolic rates converged to profiles that reflected the DOM source upon which they were growing, regardless of the initial bacterial inoculation. The one exception was that the bacterial community from the low-concentration and low-molecular-weight DOM source exhibited a greater denaturing gradient gel electrophoresis (DGGE) band richness when grown in its own DOM source than when grown in the highest concentration and molecular weight DOM source. This treatment also exhibited a higher rate of productivity. In general, our data suggest that microbial communities are selected by the DOM sources to which they are exposed. A microbial community will utilize the low-molecular-weight (or labile) DOM sources as well as parts of the high-molecular-weight (refractory) DOM, until a community develops that can efficiently metabolize the more abundant high-molecular-weight source. This experiment examines some of the complex interactions between microbial community selection and the combined factors of DOM quality and concentration. Our data suggest that the roles of aerobic aquatic heterotrophic bacteria in carbon cycling, as well as the importance of high-molecular-weight DOM as a carbon source, may be more complex than is conventionally recognized.

Bacteria↗
PubMed2003

Structure of microbial communities in Sphagnum peatlands and effect of atmospheric carbon dioxide enrichment.

Little is known about the structure of microbial communities in Sphagnum peatlands, and the potential effects of the increasing atmospheric CO2 concentration on these communities are not known. We analyzed the structure of microbial communities in five Sphagnum-dominated peatlands across Europe and their response to CO2 enrichment using miniFACE systems. After three growing seasons, Sphagnum samples were analyzed for heterotrophic bacteria, cyanobacteria, microalgae, heterotrophic flagellates, ciliates, testate amoebae, fungi, nematodes, and rotifers. Heterotrophic organisms dominated the microbial communities and together represented 78% to 97% of the total microbial biomass. Testate amoebae dominated the protozoan biomass. A canonical correspondence analysis revealed a significant correlation between the microbial community data and four environmental variables (Na+, DOC, water table depth, and DIN), reflecting continentality, hydrology, and nitrogen deposition gradients. Carbon dioxide enrichment modified the structure of microbial communities, but total microbial biomass was unaffected. The biomass of heterotrophic bacteria increased by 48%, and the biomass of testate amoebae decreased by 13%. These results contrast with the absence of overall effect on methane production or on the vegetation, but are in line with an increased below-ground vascular plant biomass at the same sites. We interpret the increase in bacterial biomass as a response to a CO2-induced enhancement of Sphagnum exudation. The causes for the decrease of testate amoebae are unclear but could indicate a top-down rather than a bottom-up control on their density.

Amoeba↗
PubMed2005

Link between spatial structure of microbial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters.

AIMS: To investigate the relationships between the operation of the volatile organic compound (VOC) removal biofilter and the structure of microbial communities, and to study the impact on degradation activities and the structuring of microbial communities of biofilter malfunctions related to the qualitative composition of the polluted air. METHODS AND RESULTS: A microbiological study and a measurement of biodegradation activities were simultaneously carried out on two identical peat-packed columns, seeded with two different inocula, treating polluted air containing 11 VOCs. For both reactors, the spatial structure of the microbial communities was investigated by means of single-strand conformation polymorphism (SSCP) analysis. For both reactors, stratification of degradation activities in function of depth was observed. Oxygenated compounds were removed at the top of the column and aromatics at the bottom. Comparison of SSCP patterns clearly showed a shift in community structure in function of depth inside both biofilters. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity. Although the operating conditions of both reactors were identical and the biodegradation activities similar, the composition of microflora differed for biofilters A and B. Subdivision of biofilter B into two independent parts supplied with polluted air containing the complex VOC mixture showed that the microflora having colonized the bottom of biofilter B retained their potential for degrading oxygenated compounds. CONCLUSIONS: This work highlights the spatialization of biodegradation functions in a biofilter treating a complex mixture of VOCs. This distribution of biodegradation activities correlates with the spatialization of microbial density and diversity. SIGNIFICANCE AND IMPACT OF THE STUDY: This vertical structure of microbial communities must be taken into consideration when dealing with the malfunctioning of bioreactors. These results are also useful information about changes in microbial communities following natural or anthropogenic alterations in different ecosystems (soils and sediments) where structuring of microbial communities according to depth has been observed.

Air Microbiology↗
PubMed2000

Microbial Biomass and Community Structure in a Sequence of Soils with Increasing Fertility and Changing Land Use.

The microbial biomass and community structure of eight Chinese red soils with different fertility and land use history was investigated. Two community based microbiological measurements, namely, community level physiological profiling (CLPP) using Biolog sole C source utilization tests and phospholipid fatty acid (PLFA) profiles, were used to investigate the microbial ecology of these soils and to determine how land use alters microbial community structure. Microbial biomass-C and total PLFAs were closely correlated to organic carbon and total nitrogen, indicating that these soil microbial measures are potentially good indices of soil fertility in these highly weathered soils. Metabolic quotients and C source utilization were not correlated with organic carbon or microbial biomass. Multivariate analysis of sole carbon source utilization patterns and PLFAs demonstrated that land use history and plant cover type had a significant impact on microbial community structure. PLFAs showed these differences more than CLPP methods. Consequently, PLFA analysis was a better method for assessing broad-spectrum community differences and at the same time attempting to correlate changes with soil fertility. Soils from tea orchards were particularly distinctive in their CLPP. A modified CLPP method, using absorbance readings at 405 nm and different culture media at pH values of 4.7 and 7.0, showed that the discrimination obtained can be influenced by the culture conditions. This method was used to show that the distinctive microbial community structure in tea orchard soils was not, however, due to differences in pH alone.

Journal Article↗
PubMed2002

Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms.

A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive below-ground microbial diversity, but to date very little is known as to how plant species composition and diversity influence the community composition of micro-organisms in the soil. We examined this relationship in fields subjected to different above-ground biodiversity treatments and in field experiments designed to examine the influence of plant species on soil-borne microbial communities. Culture-independent strategies were applied to examine the role of wild or native plant species composition on bacterial diversity and community structure in bulk soil and in the rhizosphere. In comparing the influence of Cynoglossum officinale (hound's tongue) and Cirsium vulgare (spear thistle) on soil-borne bacterial communities, detectable differences in microbial community structure were confined to the rhizosphere. The colonisation of the rhizosphere of both plants was highly reproducible, and maintained throughout the growing season. In a separate experiment, effects of plant diversity on bacterial community profiles were also only observed for the rhizosphere. Rhizosphere soil from experimental plots with lower macrophyte diversity showed lower diversity, and bacterial diversity was generally lower in the rhizosphere than in bulk soil. These results demonstrate that the level of coupling between above-ground macrophyte communities and below-ground microbial communities is related to the tightness of the interactions involved. Although plant species composition and community structure appear to have little discernible effect on microbial communities inhabiting bulk soil, clear and reproducible changes in microbial community structure and diversity are observed in the rhizosphere.

Bacteria↗
PubMed2005

Structure and function of alpine and arctic soil microbial communities.

Cultivation-independent molecular phylogenetic techniques are now widely employed to examine environmental microbial diversity; however, the relationship between microbial community structure and ecosystem function is unclear. This review synthesizes cultivation-independent views of microbiological diversity with our current understanding of nutrient dynamics in alpine and arctic soils. Recently, we have begun to explore connections between microbial community structure and function in soils from the alpine Niwot Ridge LTER site in Colorado, USA, whose ecology has been extensively investigated for over 50 years. We examined the diversity of bacterial, eucaryal, and archaeal small subunit rRNA genes in tundra and talus soils across seasons in the alpine. This work has provided support for spatial and seasonal shifts in specific microbial groups, which correlate well with previously documented transitions in microbial processes. In addition, these preliminary results suggest that the physiologies of certain groups of organisms may scale up to the ecosystem level, providing the basis for testable hypotheses about the function of specific microbes in this system. These studies have also expanded on the known diversity of life, as these soils harbor bacterial and eucaryotic lineages that are distantly related to other known organisms. In contrast to the alpine, microbial diversity in the arctic has been little explored; only three published studies have used molecular techniques to examine these soils. Because of the importance of these systems, particularly to the global C cycle, and their vulnerability to current and impending climate change, the microbial diversity of these soils needs to be further investigated.

Archaea↗
PubMed2003

Use of a similarity index based on microbial fatty acid (MFA) analysis to monitor biological wastewater treatment systems.

Estimating the stability of microbial community structures may be useful in advanced biological wastewater treatment system design and operation. In this research, a monitoring method using fatty acid profiles was evaluated for detecting changes in microbial community structures. For the evaluation, the operating parameters such as pH, organic loading, and chlorine addition were varied in two identical laboratory scale conventional activated sludge systems. A similarity index based on microbial fatty acid analysis was used to express the stability of microbial community structures in the systems. Experiments using a model microbial community showed that microbial compositions changed daily even under constant operating conditions and that the rate of change increased under dynamic operating conditions. Substrate changes brought about a relatively large change in a microbial community structure, eventually resulting in a very different microbial community. After only 7 days following a substrate change in a lab-scale bioreactor, the biomass exhibited only 45% similarity to the original structure. The analysis of microbial fatty acids conveys additional information, in that it could be used for the calculation of biomass concentrations in a wastewater treatment system if microbial fatty acid analyses are executed on a routine basis as a monitoring tool for biological wastewater treatment systems. The total fatty acid concentrations were about 0.61% of the biomass concentration as mixed liquor volatile suspended solid concentrations in this research.

Bacteria↗