Denaturing Gradient Gel Electrophoresis Patterns Research Articles

Changes in rhizosphere bacterial populations during phytoextraction of heavy metal contaminated soil with poplar

The objective of this paper was to study the response of rhizosphere ammonia‐oxidizing bacterial (AOB) populations during phytoextraction. Hybrid poplars were grown in compartmented root containers with an aged heavy metal (HM)‐contaminated soil for 13 weeks. Bulk and poplar rhizosphere soils were analyzed by denaturing gradient gel electrophoresis (DGGE) of amoA gene fragments. DGGE patterns revealed that amoA‐containing populations in the contaminated soils were markedly different from those in the uncontaminated soils. AmoA profiles appeared to be stable over time in the bulk soils. In contrast, contaminated rhizosphere soils revealed a clear shift of populations with removal of HMs. Rhizosphere AOB populations of the HM‐contaminated soils became similar to the populations of the uncontaminated soils during phytoextraction. The effect of phytoextraction was, however, not evident in the bulk samples, which still contained large amounts of HMs. This study suggests that rhizosphere AOB populations are able to recover after the relief of HM stress by phytoextraction practices.

Phytoremediation and microbial community structure of soil from a metal-contaminated military shooting range: Comparisons of field and pot experiments

In this study, the heavy metal uptake ability of two plant species, barnyard grass and Indian mallow, and the effects of associated micro-communities on the rhizosphere of these plants were investigated in metal-contaminated sites. In addition, the effectiveness of phytoremediation using these plants was compared under field and pot conditions. To accomplish this analysis, phytoremediation of general military shooting range soil was conducted for 8 weeks under the two conditions. The results showed that metal uptake by plants and reductions in soil metal concentration were lower in the field than in pots. However, soil dehydrogenase activities and microbial diversity increased in response to phytoremediation in the field. Specifically, the soil dehydrogenase activities of barnyard grass in field soils were 3-fold higher than those of potted soils. Moreover, the denaturing gradient gel electrophoresis patterns revealed that groups formed according to plant species. Finally, the Shannon-Weaver diversity index and Simpson dominance index were higher in the rhizosphere of barnyard grass than in the rhizosphere of Indian mallow under field conditions. These results indicate that it is difficult to apply the results obtained from pot experiments to field conditions. These findings can be used to inform future studies conducted to determine if field sites are suitable for phytoremediation based on the results of pot studies.

Microbial Population and Activity in Wetland Microcosms Constructed for Improving Treated Municipal Wastewater

The idea of using constructed wetlands for the treatment and improving of wastewater emerged in the second half of the last century. Despite relatively wide use of this environmentally friendly technology, relatively little is known about the microbial populations involved in biotransformation and removal of contaminants in this system. The aim of the current study was to investigate the assembly and function of microbial populations in vertical-flow constructed wetland microcosms designed to improve the quality of wastewater after activated sludge treatment. Also, the performance of 3-year-old wetland ponds was investigated. Even though the quality of the influent water was relatively high, improvement in water parameters such as coliform level, ammonia concentration, BOD, and TSS was observed. The performance of the wetland ponds was comparable to that of the microcosms. The microbial community composition of the biofilm formed on the surface of gravel particles in vegetated and plant-free microcosms was studied by denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene fragments. Highly complex bacterial diversity was observed in the biofilm. Cluster analysis of DGGE patterns demonstrated that depth within the wetland microcosm has a stronger effect on microbial community composition of the biofilm formed on wetland matrix than vegetation. Measurements of fluorescein diacetate hydrolysis activity and nitrification potential revealed that hydrolytic activity was affected by both microcosm depth and vegetation presence, whereas nitrification potential was mostly influenced by depth. Resolving the bacterial assemblage of wetland biofilm, which often is considered a black box, will help to understand the interactions involved in the development of diverse and mature biofilm and its function.

Diversity ofpufMgenes, involved in aerobic anoxygenic photosynthesis, in the bacterial communities associated with colonial ascidians

Ascidians are invertebrate filter feeders widely distributed in benthic marine environments. A total of 14 different ascidian species were collected from the Western Mediterranean and their bacterial communities were analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene. Results showed that ascidian tissues harbored Bacteria belonging to Gamma- and Alphaproteobacteria classes, some of them phylogenetically related to known aerobic anoxygenic phototrophs (AAPs), such as Roseobacter sp. In addition, hierarchical cluster analysis of DGGE patterns showed a large variability in the bacterial diversity among the different ascidians analyzed, which indicates that they would harbor different bacterial communities. Furthermore, pufM genes, involved in aerobic anoxygenic photosynthesis in marine and freshwater systems, were widely detected within the ascidians analyzed, because nine out of 14 species had pufM genes inside their tissues. The pufM gene was only detected in those specimens that inhabited shallow waters (<77 m of depth). Most pufM gene sequences were very closely related to that of uncultured marine bacteria. Thus, our results suggest that the association of ascidians with bacteria related to AAPs could be a general phenomenon and that ascidian-associated microbiota could use the light that penetrates through the tunic tissue as an energy source.

Effect of monoculture soybean on soil microbial community in the Northeast China

Monoculture (MC) soybean, a common practice in the Northeast China, causes significant declines in soybean yield and quality. The objective of this study was to evaluate the responses of the soil microbial community and soybean yield to different soybean cropping systems. Three cropping systems were compared, (1) corn-soybean rotation (corn-corn-soybean, CS), (2) MC soybean for 3 years (S3), (3) MC soybean for 9 years (S9). Both bulk and rhizosphere soil samples were collected at three growth stages: two trifoliate (V2), full bloom (R2), and full seed (R6), respectively. Soil microbial DNA was analyzed using polymerase chain reaction (PCR)—denaturing gradient gel electrophoresis (DGGE) to assess changes in composition of bacterial and fungal communities. Prominent DGGE bands were excised and sequenced to gain insight into the identities of the predominant microbial populations. Some prominent differences were observed in bacterial DGGE patterns of amplified 16S rDNA (V3 region) among rhizosphere soils. These major differences included one DGGE band (showing 100% similarity to Arthrobacter sp.) that was enriched at R2 stages in CS and S9, and another band with 97% sequence similarity to an uncultured actinobacterium was detected at R6 stage in CS, and at R2 and R6 stages in S9. The bacterial community from bulk soil showed no significant band change in DGGE patterns among different cropping systems. In fungal DGGE patterns of the amplified 18S rDNA partial fragment, one specific band (showing 98% similarity to Trichoderma viride) occurred in rhizosphere soil of treatment CS at V2 and R6 stages and treatment S9 at R6 stage. None of the above bands were detected in treatment S3. The soybean yields and plant heights from CS and S9 were greater than those from S3. Moreover, catalase activities from CS and S9 at V2 and R2 stages were higher than those tested from S3 at the corresponding times in rhizosphere soil. The present results showed that DGGE patterns were not able to detect significant differences in diversity or evenness among microbial communities, but significant differences were found in the composition of bacterial and fungal community structures. Some distinguished bands from bacterial and fungal DGGE patterns were only enriched in CS and S9 soil, which could potentially play an important role in soybean growth development.

Characterization of copper-resistant bacteria and assessment of bacterial communities in rhizosphere soils of copper-tolerant plants

Thirteen copper-resistant bacteria were isolated from copper-tolerant plant species growing on a copper mine wasteland. The isolates were identified by 16S rRNA gene sequence analysis and characterized by their resistance to heavy metals and plant growth-promoting characteristics. The assessment of the bacterial communities in the rhizosphere soils of copper-tolerant plants was measured as bands in denaturing gradient gel electrophoresis (DGGE) obtained directly from rhizosphere soil DNA extracts. The isolates were found to exhibit different multiple heavy metal resistance characteristics. Strains SZY6, YJ7 and JYC17 were found to produce indole acetic acid (IAA), siderophore, 1-aminocyclopropane-1-carboxylate (ACC) deaminase or to solubilize phosphate. Root elongation assay conducted on rape under gnotobiotic conditions with strains MT16, JYC17, SZY6, GZC24, and YJ7 demonstrated increase (from 16 to 41%) in root elongation of inoculated rape seedlings compared to the control plants. In the rhizosphere soil samples the DGGE profiles of the direct DNA extracts were similar. The DGGE profiles indicated that there was no significant correlation between the concentration of available copper in the rhizosphere soils and the number of the visible bands in the DGGE pattern.

Effect of continuous olive mill wastewater applications, in the presence and absence of nitrogen fertilization, on the structure of rhizosphere-soil fungal communities

Olive mill wastewater (OMW) is rich in potentially toxic organics precluding its disposal into water receptors. However, land application of diluted OMW may result in safe disposal and fertilization. In order to investigate the effects of OMW on the structure of soil fungal groups, OMW was applied daily to pepper plants growing in a loamy sand and a sandy loam at two doses for a period of 3 months (total OMW equivalents 900 and 1800 m(3) ha(-1)). Nitrogen (N) fertilization alleviated N scarcity and considerably enhanced plant biomass production; however, when applied in combination with the high OMW dose, it induced plant stress. OMW applications resulted in marked changes in the denaturing gradient gel electrophoresis patterns of soil basidiomycete communities, while concurrent N fertilization reduced these effects. In contrast, the ascomycete communities required N fertilization to respond to OMW addition. Cloning libraries for the basidiomycete communities showed that Cryptococcus yeasts and Ceratobasidium spp. dominated in the samples treated with OMW. In contrast, certain plant pathogenic basidiomycetes such as Thanatephorus cucumeris and Athelia rolfsii were suppressed. The observed changes may be reasonably explained by the capacity of OMW to enrich soils in organic substrates, to induce N immobilization and to directly introduce OMW-derived basidiomycetous yeasts.

A nested PCR approach for improved recovery of archaeal 16S rRNA gene fragments from freshwater samples

In a survey on the presence of archaea in a number of European lakes, it was found that known archaeal primer sets for PCR were not suited for use in freshwater environment, as some lack selectivity, while others were too selective. A nested PCR was developed for denaturing gradient gel electrophoresis (DGGE) with primer sets 21F-958R and Parch519f-Arch915r, respectively. After sequencing of the DGGE bands obtained by this nested method, 93% of the sequences were of archaeal origin. More diverse archaeal DGGE patterns were found as compared with other PCR methods. The nested PCR-DGGE method presented here is therefore a reliable tool to analyze the archaeal diversity in freshwater habitats, revealing even more widespread diversity of the archaea.

Response of bacterioplankton community structures to hydrological conditions and anthropogenic pollution in contrasting subtropical environments

Bacterioplankton community structures under contrasting subtropical marine environments (Hong Kong waters) were analyzed using 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) and subsequent sequencing of predominant bands for samples collected bimonthly from 2004 to 2006 at five stations. Generally, bacterial abundance was significantly higher in the summer than in the winter. The general seasonal variations of the bacterial community structure, as indicated by cluster analysis of the DGGE pattern, were best correlated with temperature at most stations, except for the station close to a sewage discharge outfall, which was best explained by pollution-indicating parameters (e.g. biochemical oxygen demand). Anthropogenic pollutions appear to have affected the presence and the intensity of DGGE bands at the stations receiving discharge of primarily treated sewage. The relative abundance of major bacterial species, calculated by the relative intensity of DGGE bands after PCR amplification, also indicated the effects of hydrological or seasonal variations and sewage discharges. For the first time, a systematic molecular fingerprinting analysis of the bacterioplankton community composition was carried out along the environmental and pollution gradient in a subtropical marine environment, and it suggests that hydrological conditions and anthropogenic pollutions altered the total bacterial community as well as the dominant bacterial groups.

Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill

The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaromatic hydrocarbon (PAH) degraders and the differences in denaturing gradient gel electrophoresis patterns compared with those of the reference site. Members of the classes Alphaproteobacteria and Actinobacteria were the prevailing groups of bacteria detected in both matrices, although the sand bacterial community exhibited higher species richness than the rock bacterial community did. Culture-dependent and -independent approaches suggested that the genus Rhodococcus could play a key role in the in situ degradation of the alkane fraction of the Prestige fuel together with other members of the suborder Corynebacterineae. Moreover, other members of this suborder, such as Mycobacterium spp., together with Sphingomonadaceae bacteria (mainly Lutibacterium anuloederans), were related as well to the degradation of the aromatic fraction of the Prestige fuel. The multiapproach methodology applied in the present study allowed us to assess the complexity of autochthonous microbial communities related to the degradation of heavy fuel from the Prestige and to isolate some of their components for a further physiological study. Since several Corynebacterineae members related to the degradation of alkanes and PAHs were frequently detected in this and other supralittoral environments affected by the Prestige oil spill along the northwestern Spanish coast, the addition of mycolic acids to bioremediation amendments is proposed to favor the presence of these degraders in long-term fuel pollution-affected areas with similar characteristics.

Characterization of bacterial and fungal communities in composted biosolids over a 2 year period using denaturing gradient gel electrophoresis

Composting is a microbial process that converts organic waste into a nutrient-rich end product used in horticultural and agricultural applications. The diversity and long-term succession of microorganisms found in composted biosolids has been less characterized than other composts. In this study, bacterial and fungal communities found in composted biosolids aging from 1 to 24 months were studied using denaturing gradient gel electrophoresis (DGGE) and sequencing. The results revealed high levels of diversity, where 53 bacterial species belonging to 10 phyla and 21 fungal species belonging to 4 phyla were identified. Significant differences were observed when comparing the bacterial DGGE patterns of young compost samples, whereas no differences were observed in samples over 8 months. For fungal patterns, no significant differences were observed during the first 4 months of composting, but the diversity then significantly shifted until 24 months. The results indicate that patterns of bacterial species vary during the first few months of composting, whereas fungal patterns generally vary throughout the whole process, except during early stages. The description of the main microbial groups found in composted biosolids could find various applications, including the discovery of biotechnologically relevant microorganisms and the development of novel markers allowing quantitative monitoring of key microorganisms.

Study of microbial diversity in raw milk and fresh curd used for Fontina cheese production by culture-independent methods

The bacterial populations of raw milk employed for the production of Fontina cheese in alpine farms located in different valleys and altitudes (from 700 to 2246 m above sea level) were investigated by culture independent techniques. Total microbial DNA was isolated from milk and curd samples and used as template in Polymerase Chain Reaction (PCR) to study the hypervariable V3 region of the bacterial 16S rRNA gene and analyzed by Denaturing Gradient Gel Electrophoresis (DGGE). Representative bands of DGGE patterns were sequenced for identification purposes. The use of universal primer for PCR-DGGE allowed the description of the bacterial community, not only for the presence of lactic acid bacteria, but also for other adventitious species. DGGE profiles obtained from milk and fresh curd samples were generally different and typical for each farm, although some recurrent bands were observed. Cluster analysis of DGGE profiles did not show high similarity among samples and it was probably dependent on the different geographical areas of pastures. Some Lactic Acid Bacteria (LAB) recurred in many samples ( Streptococcus thermophilus, Enterococcus faecium, Enterococcus faecalis, Lactococcus lactis, Leuconostoc lactis) indicating that alpine milk is a preferential niche for their colonization. The microbiota included not only mesophilic and thermoresistant LAB but also adventitious bacteria ( Macrococcus caseolyticus, Rothia spp.) and psychrotrophic bacteria ( Chryseobacterium spp ., Pseudomonas spp.), that were found in almost all samples, but disappeared after the warming up at 47–48 °C of coagulated milk. Pantoea spp. was primarily found in curds and only with a low incidence in milk samples, indicating the environmental origin. Finally the sequencing data confirmed the presence of E. faecium, E. faecalis and S. thermophilus as major species present in the curd. These species were found also in raw milk, proving its importance as source of the typical fermenting microflora.

Powdery Mildew-Infection Changes Bacterial Community Composition in the Phyllosphere

To investigate changes in bacterial communities associated with a fungal foliar disease, epiphytic bacteria from powdery mildew-infected and uninfected leaves of cucumber and Japanese spindle were analyzed using both culture-dependent and -independent methods. Dilution plate counting suggested that powdery mildew-infected leaves likely accommodated larger populations of phyllosphere bacteria than uninfected leaves. Community-level physiological profiles (CLPP) also indicated that functional diversity, richness, and evenness of bacterial communities were significantly greater in the phyllosphere of powdery mildew-infected leaves. Genotype diversity and richness based on band patterns of denaturing gradient gel electrophoresis (DGGE) of the phyllosphere bacterial community were greater for leaves infected by powdery mildew. A principle component analysis of CLPP and DGGE patterns revealed a clear difference between infected and uninfected leaves of both plant species. These results suggest that powdery mildew-infection results in larger bacterial populations, and greater diversity and richness, and also changes the structure of the phyllosphere bacterial community. Furthermore, DNA sequences of the DGGE bands that showed greater intensity in the infected than uninfected leaves, differed between cucumber and Japanese spindle. This suggests that specific bacteria are associated with the plant species accompanying this fungal infection.

Polymorphism of mytilin B mRNA is not translated into mature peptide

Diversity of mRNAs from mytilin B, one of the five mytilins identified in the Mediterranean mussel, Mytilus galloprovincialis, has been investigated from circulating hemocytes. One mussel expressed simultaneously two to ten different mytilin B mRNAs as observed in denaturing gradient gel electrophoresis (DGGE), defining 10 individual DGGE patterns (named A to J) within the mussels from Messina, Sicily (Italy). Three patterns accounted for 79% of the individuals whereas other patterns were found in only 2–7% of the 57 analyzed mussels. Base mutations were observed at specific locations, mainly within COOH-terminus and 3′UTR, leading to 36 nucleotide sequence variants and 21 different coding sequences (cds) segregating in two different clusters. Most of the base mutations were silent, and the number of pro-peptide variants was restricted to four. Finally, as the two amino acid replacements occurred within COOH-terminus, mature peptide from mytilin B appeared unique. Multiple sequencing of partial mytilin B gene from one mussel revealed that one to four randomly distributed mutation points occurred within intron-3. Only one sequence out of the 91 analyzed contained 16 mutation points. In addition, this sequence was the only one containing four out of the six mutation points occurring within exon-4, that code for most of the COOH-terminus domain, including the unique amino acid replacement. Statistical tests for neutrality indicated negative selection pressure on signal and mature peptide domains, but possible positive selection pressure for COOH-terminus domain.

Extraction of DNA from Soil for Analysis of Bacterial Diversity in Transgenic and Nontransgenic Papaya Sites

The influence of transgenic crops on the soil diversity of microorganisms is one of the major risk assessments being conducted in Taiwan since 2007, and a reliable soil DNA extraction method for denaturing gradient gel electrophoresis (DGGE) is required. Six soils of different type, organic matter content, cation exchange capacity, and pH were tested, and four previously reported soil DNA extraction methods were applied to these soils. Soil DNA extracts by Zhou's CS method plus QIAquick gel was recommended in our laboratory for DGGE to monitor the microbial diversity in soil. There were some differences on the bacterial diversity based on DGGE patterns at the beginning of planting, and the difference decreased after six months. The results also indicated that clay content (10.8-25.0%) and pH (4.4-6.9) of different soil samples we tested did not affect the DNA extraction efficiencies, but positive correlations were found between the organic matter content (1.2-3.9%) of soils and the DNA yields in Widmer's GS method (r = 0.93, p = 0.005) and the MoBio UC method (r = 0.92, p = 0.007). Coefficient of determinations between organic matter content and DNA yield were higher than those between clay content, CEC, and pH, indicating that organic matter content was more correlated with DNA yield than that clay content, CEC, and pH in our soil samples tested.

Flavobacterial Community Structure in a Hardwater Rivulet and Adjacent Forest Soil, Harz Mountain, Germany

The great increase in the abundance and phylogenetic diversity of Flavobacterium spp. within a few hundred meters downstream of the discharge site of the Westerhöfer Bach, a hardwater rivulet, raised the question whether adjacent soil may serve as a reservoir of bacteria not detected in discharge water. To address this question, denaturing gradient gel electrophoresis (DGGE) analyses of the V3 region of Flavobacterium 16S rRNA genes were performed on DNA from nine soil samples and five rivulet sites. The resulting patterns were tested for the significance of differences between the sampling habitats using the nonparametric analysis of similarities and multidimensional scaling procedures. Even though both habitats were sampled in two consecutive years DGGE patterns of soil and downstream water samples showed significant overlap (R = 0.614). Sequencing of 57 DGGE bands resulted in 30 different sequences, which, on the basis of BLAST analyses, were between 96% and 100% similar to published clone, DGGE, and strain sequences from a wide range of different habitats. Forty-five percent of the highly similar sequences included those of isolates from the Westerhöfer Bach, while the other sequences were more closely related to clones and cultures from other habitats, especially agricultural soil. Based on these results we suggest that the increase in flavobacterial strain diversity and abundance in the rivulet may originate from soil microflora.

Predicting a clinical/biochemical phenotype for PKU/MHP patients with PAH gene mutations

Phenylketonuria (PKU) and mild hyperphenylalaninemia (MHP) are allelic disorders caused by mutations in the gene encoding phenylalanine hydroxylase (PAH). In this study, a total of 218 independent PAH chromosomes (109 unrelated patients with PKU residing in Lithuania) were investigated. All 13 exons of the PAH gene of all PKU probands were scanned for DNA alterations by denaturing gradient gel electrophoresis (DGGE). In the cases of a specific DGGE pattern recognised, mutations were identified by direct fluorescent automated sequencing or by restriction enzyme digestion analysis of a relevant exons. 25 different PAH gene mutations were identified in Lithuania. We estimated a connection between individual PAH locus mutations and biochemical and metabolic phenotypes in patients in whom the mutant allele acts on its own, i.e., in functionally hemizygous patients and using the assigned value (AV) method to determine the severity of both common and rare mutant alleles, as well as to check a model to predict the combined phenotypic effect of two mutant PAH alleles.

The use of denaturing gradient gel electrophoresis with fully degenerate pufM primers to monitor aerobic anoxygenic phototrophic assemblages

Aerobic Anoxygenic Photosynthetic bacteria (AAnP) were recently proposed to be significant contributors to the global ocean carbon and energy cycles, but relatively little is known about the spatial and temporal distribution of AAnP populations. Here, we report on the development of denaturing gradient gel electrophoresis (DGGE) analyses to monitor naturally occurring marine AAnP populations using the pufM gene. We developed an approach using fully degenerate universal pufM primers, and tested the effect of different primers and PCR conditions on DGGE band resolution and migration. PufM‐DGGE analyses of eastern Mediterranean environmental DNA samples show that AAnP composition was coherent among stations and seasons. Furthermore, samples from different depths of stratified water columns resulted in clearly different DGGE patterns, while very similar DGGE patterns at varying depths were observed under well‐mixed conditions. These results demonstrate the potential use of DGGE with fully degenerate primers as a tool for rapid analyses of natural marine AAnP communities.

Spatio-temporal variations of the bacterioplankton community composition in Chaohu Lake, China

Despite considerable attention paid to Chaohu Lake in China, the dynamics of bacterioplankton community composition (BCC) on spatial and seasonal scales are poorly understood. In this study, water samples were collected from autumn 2006 to summer 2007 at five positions in Chaohu Lake with different trophic status. BCC of these samples was determined by both the PCR amplification of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE). The abundance and diversity of bacterioplankton communities at different sampling positions showed similar seasonal patterns. The BCCs in the samples varied substantially, and the pattern of changes indicated that the seasonal difference might have a significant impact on the BCC’s structure in the lake. Canonical correspondence analysis (CCA) on the DGGE patterns and physicochemical parameters indicated that the temperature and the levels of 5-d biochemical O 2 demand (BOD 5), NH 3–N, COD Mn, total nitrogen, total phosphorous, and dissolved oxygen significantly influenced the BCC, and four of the seven variables were related to the level of eutrophication. Our results indicate that eutrophic status and season are the most influential factors in determining BCC in Chaohu Lake.

Lipid biomarkers, pigments and cyanobacterial diversity of microbial mats across intertidal flats of the arid coast of the Arabian Gulf (Abu Dhabi, UAE)

Variations in morphology, fatty acids, pigments and cyanobacterial community composition were studied in microbial mats across intertidal flats of the arid Arabian Gulf coast. These mats experience combined extreme conditions of salinity, temperature, UV radiation and desiccation depending on their tidal position. Different mat forms were observed depending on the topology of the coast and location. The mats contained 63 fatty acids in different proportions. The increased amounts of unsaturated fatty acids (12-39%) and the trans/cis ratio (0.6-1.6%) of the cyanobacterial fatty acid n-18:1omega9 in the higher tidal mats suggested an adaptation of the mat microorganisms to environmental stress. Chlorophyll a concentrations suggested lower cyanobacterial abundance in the higher than in the lower intertidal mats. Scytonemin concentrations were dependent on the increase in solar irradiation, salinity and desiccation. The mats showed richness in cyanobacterial species, with Microcoleus chthonoplastes and Lyngbya aestuarii morphotypes as the dominant cyanobacteria. Denaturing gradient gel electrophoresis patterns suggested shifts in the cyanobacterial community dependent on drainage efficiency and salinity from lower to higher tidal zones. We conclude that the topology of the coast and the variable extreme environmental conditions across the tidal flat determine the distribution of microbial mats as well as the presence or absence of different microorganisms.