Quinone Profiles Research Articles

The evolution of strictly monofunctional naphthoquinol C-methyltransferases is vital in cyanobacteria and plastids.

Prenylated quinones are membrane-associated metabolites that serve as vital electron carriers for respiration and photosynthesis. The UbiE (EC 2.1.1.201)/MenG (EC 2.1.1.163) C-methyltransferases catalyze pivotal ring methylations in the biosynthetic pathways of many of these quinones. In a puzzling evolutionary pattern, prokaryotic and eukaryotic UbiE/MenG homologs segregate into 2 clades. Clade 1 members occur universally in prokaryotes and eukaryotes, excluding cyanobacteria, and include mitochondrial COQ5 enzymes required for ubiquinone biosynthesis; Clade 2 members are specific to cyanobacteria and plastids. Functional complementation of an Escherichia coli ubiE/menG mutant indicated that Clade 1 members display activity with both demethylbenzoquinols and demethylnaphthoquinols, independently of the quinone profile of their original taxa, while Clade 2 members have evolved strict substrate specificity for demethylnaphthoquinols. Expression of the gene-encoding bifunctional Arabidopsis (Arabidopsis thaliana) COQ5 in the cyanobacterium Synechocystis or its retargeting to Arabidopsis plastids resulted in synthesis of a methylated variant of plastoquinone-9 that does not occur in nature. Accumulation of methylplastoquinone-9 was acutely cytotoxic, leading to the emergence of suppressor mutations in Synechocystis and seedling lethality in Arabidopsis. These data demonstrate that in cyanobacteria and plastids, co-occurrence of phylloquinone and plastoquinone-9 has driven the evolution of monofunctional demethylnaphthoquinol methyltransferases and explains why plants cannot capture the intrinsic bifunctionality of UbiE/MenG to simultaneously synthesize their respiratory and photosynthetic quinones.

Distribution of Phototrophic Purple Nonsulfur Bacteria in Massive Blooms in Coastal and Wastewater Ditch Environments.

The biodiversity of phototrophic purple nonsulfur bacteria (PNSB) in comparison with purple sulfur bacteria (PSB) in colored blooms and microbial mats that developed in coastal mudflats and pools and wastewater ditches was investigated. For this, a combination of photopigment and quinone profiling, pufM gene-targeted quantitative PCR, and pufM gene clone library analysis was used in addition to conventional microscopic and cultivation methods. Red and pink blooms in the coastal environments contained PSB as the major populations, and smaller but significant densities of PNSB, with members of Rhodovulum predominating. On the other hand, red-pink blooms and mats in the wastewater ditches exclusively yielded PNSB, with Rhodobacter, Rhodopseudomonas, and/or Pararhodospirillum as the major constituents. The important environmental factors affecting PNSB populations were organic matter and sulfide concentrations and oxidation–reduction potential (ORP). Namely, light-exposed, sulfide-deficient water bodies with high-strength organic matter and in a limited range of ORP provide favorable conditions for the massive growth of PNSB over co-existing PSB. We also report high-quality genome sequences of Rhodovulum sp. strain MB263, previously isolated from a pink mudflat, and Rhodovulum sulfidophilum DSM 1374T, which would enhance our understanding of how PNSB respond to various environmental factors in the natural ecosystem.

Isoprenoid Quinones Resolve the Stratification of Redox Processes in a Biogeochemical Continuum from the Photic Zone to Deep Anoxic Sediments of the Black Sea.

The stratified water column of the Black Sea serves as a model ecosystem for studying the interactions of microorganisms with major biogeochemical cycles. Here, we provide detailed analysis of isoprenoid quinones to study microbial redox processes in the ocean. In a continuum from the photic zone through the chemocline into deep anoxic sediments of the southern Black Sea, diagnostic quinones and inorganic geochemical parameters indicate niche segregation between redox processes and corresponding shifts in microbial community composition. Quinones specific for oxygenic photosynthesis and aerobic respiration dominate oxic waters, while quinones associated with thaumarchaeal ammonia oxidation and bacterial methanotrophy, respectively, dominate a narrow interval in suboxic waters. Quinone distributions indicate highest metabolic diversity within the anoxic zone, with anoxygenic photosynthesis being a major process in its photic layer. In the dark anoxic layer, quinone profiles indicate the occurrence of bacterial sulfur and nitrogen cycling, archaeal methanogenesis, and archaeal methanotrophy. Multiple novel ubiquinone isomers, possibly originating from unidentified intra-aerobic anaerobes, occur in this zone. The respiration modes found in the anoxic zone continue into shallow subsurface sediments, but quinone abundances rapidly decrease within the upper 50 cm below the sea floor, reflecting the transition to lower energy availability. In the deep subseafloor sediments, quinone distributions and geochemical profiles indicate archaeal methanogenesis/methanotrophy and potentially bacterial fermentative metabolisms. We observed that sedimentary quinone distributions track lithology, which supports prior hypotheses that deep biosphere community composition and metabolisms are determined by environmental conditions during sediment deposition.IMPORTANCE Microorganisms play crucial roles in global biogeochemical cycles, yet we have only a fragmentary understanding of the diversity of microorganisms and their metabolisms, as the majority remains uncultured. Thus, culture-independent approaches are critical for determining microbial diversity and active metabolic processes. In order to resolve the stratification of microbial communities in the Black Sea, we comprehensively analyzed redox process-specific isoprenoid quinone biomarkers in a unique continuous record from the photic zone through the chemocline into anoxic subsurface sediments. We describe an unprecedented quinone diversity that allowed us to detect distinct biogeochemical processes, including oxygenic photosynthesis, archaeal ammonia oxidation, aerobic methanotrophy, and anoxygenic photosynthesis in defined geochemical zones.

INCREASING ROLE OF MICROORGANISM WITH UBIQUINONE-9 IN DENITRIFYING PAO SLUDGE

An anaerobic-aerobic (An-Ox) sequencing batch reactor (SBR) was operated for the growth of phosphate accumulating organisms (PAOs), while an anaerobic-anoxic (An-Ax) SBR was used for the growth of denitrifying PAOs (dPAOs). Both reactors exhibited successful enhanced biological phosphorous removal (EBPR) performance. The sludge P contents in the two reactors increased from approximately 2% at the beginning of the operation to 9.1% (An-Ox SBR) and 7.3% (An-Ax SBR) after 140 d. The results of the quinone profile analysis demonstrated that the proportions of UQ-8, UQ-10, and MK-8 (H4) in the An- Ox sludge increased compared to the beginning of the operation, whereas in the An-Ax sludge, the proportion of UQ-8 was the highest and exhibited the greatest increase, and the mole fraction of UQ-9 more than doubled from 8.3% to 16.9%. Thus, the role of microorganisms with UQ-8 and UQ-9 was found to have significantly increased in the An-Ax sludge. As a result of microbial identification through the fatty acid methyl ester (FAME) analysis, Comamonas testosteroni and Pseudomonas alcaligenes, which produce the UQ-9 in the An-Ax sludge, as well as Psychrobacter immobilis, which produces UQ-8.

Identification and characterization of Burkholderia multivorans CCA53

ObjectiveA lignin-degrading bacterium, Burkholderia sp. CCA53, was previously isolated from leaf soil. The purpose of this study was to determine phenotypic and biochemical features of Burkholderia sp. CCA53.ResultsMultilocus sequence typing (MLST) analysis based on fragments of the atpD, gltD, gyrB, lepA, recA and trpB gene sequences was performed to identify Burkholderia sp. CCA53. The MLST analysis revealed that Burkholderia sp. CCA53 was tightly clustered with B. multivorans ATCC BAA-247T. The quinone and cellular fatty acid profiles, carbon source utilization, growth temperature and pH were consistent with the characteristics of B. multivorans species. Burkholderia sp. CCA53 was therefore identified as B. multivorans CCA53.

Effects of 3,5-dichlorophenol on excess biomass reduction and bacterial community dynamics in activated sludge as revealed by a polyphasic approach

The effects of 3,5-dichlorophenol (DCP) on excess sludge reduction and microbial community dynamics were studied using laboratory-scale activated sludge reactors. The addition of 3,5-DCP at an interval of 7-8 days of operation resulted in effective reduction of growing biomass without a significant decrease in substrate removal activity. However, this uncoupling effect completely disappeared after 30 days of operation. Quinone profiling showed that a drastic component shift from ubiquinone-8 (Q-8) to Q-10 as the major homolog took place during this period of operation, suggesting that Q-10-containing bacteria, i.e., Alphaproteobacteria, became predominant at the uncoupler-ineffective stage. This result was supported by PCR-aided denaturating gradient gel electrophoresis and clone library analyses of 16S rRNA genes and fluorescence in situ hybridization. Among the gene clones detected, those corresponding to Brevundimonas predominated at the uncoupler-ineffective stage. The uncoupler-added reactor yielded 3,5-DCP-resistant Pseudomonas strains as the predominant cultivable bacteria and non-3,5-DCP-resistant Brevundimonas strains as the second most abundant isolates These results suggest that the disappearance of the uncoupling function of 3,5-DCP during the long-term operation of the reactor is related to the drastic community change with increasing populations of Alphaproteobacteria. Most of these alphaproteobacteria represented by Brevundimonas are not resistant to 3,5-DCP but, by an unknown mechanism, may support the bioprotection of the microbial community from the uncoupling effect.

Development of coupled supercritical fluid extraction-high performance liquid chromatography for quinone analysis in activated sludge

ABSTRACTCoupled supercritical fluid extraction-high performance liquid chromatography (Coupled SFE-HPLC) was developed to determine the microbial community dynamics based on the quinone profile. It is a fast (less than 2 h) and high reproducibility (1.6% in coefficient of variation) method. The comparable results were obtained by the developed method and the organic solvent extraction method, it was 603.4 µmol kg−1 and 594.1 µmol kg−1 dry samples, respectively. The low dissimilarity index (0.07) between the two methods indicates that quinone profile obtained by both methods were considered similar. The results show that coupled SFE-HPLC method offers simplification for a rapid and routine analysis.

Supercritical Fluid Extraction of Quinones from Compost for Microbial Community Analysis

Supercritical fluid extraction (SFE) was used to extract quinones from compost to monitor the microbial community dynamics during composting. The 0.3 g of dried compost was extracted using 3 mL min−1of carbon dioxide (90%) and methanol (10%) at 45°C and 25 MPa for a 30 min extraction time. The extracted quinones were analysed using ultra performance liquid chromatography (UPLC) with 0.3 mL min−1of methanol mobile phase for a 50 min chromatographic run time. A comparable detected amount of quinones was obtained using the developed method and an organic solvent extraction method, being 36.06 μmol kg−1and 34.54 μmol kg−1, respectively. Significantly low value of dissimilarity index (D) between the two methods (0.05) indicated that the quinone profile obtained by both methods was considered identical. The developed method was then applied to determine the maturity of the compost by monitoring the change of quinone during composting. The UQ-9 and MK-7 were predominant quinones in the initial stage of composting. The diversity of quinone became more complex during the cooling and maturation stages. This study showed that SFE had successfully extracted quinones from a complex matrix with simplification and rapidity of the analysis that is beneficial for routine analysis.

Soil Microbial Biomass and Diversity Amended with Bagasse Mulch in Tillage and No-tillage Practices in the Sugarcane Plantation

Biomass residues in plantation farms and process industries still have valuable materials and can be recycled as other materials. Gunung Madu Plantation (GMP) in Lampung Province, Indonesia where this study was observed had used bagasse as mulch 80 tons (wet weight) per hectare. This study observed the effect of tillage and bagasse much on soil microbes in sugarcane plantation. Each treatment was used in conjunction with or without bagasse mulch in a split-plot experimental design. Previous study showed bagasse mulch had increased litter fungal biomass and communities in the soil. However soil microbial community structure has not been comprehensively investigated. Quinone profile method was used to analyze the community structure amended with bagasse mulch in the sugarcane plantation. Quinone profile method reflectively estimated the microbial biomass and the diversity. The no-tillage with bagasse mulch had the highest microbial biomass (1.026μmol kg-1 dry soil) compare to the no-tillage without bagasse mulch, the conventional tillage with bagasse mulch and the conventional tillage without bagasse mulch. The Diversity index (DQ) and Shannon-Wiener diversity index (H) was also the highest in the no-tillage amended with bagasse mulch. Therefore mulch treatment in combination with no-tillage is an effective residue management of biomass residue to improve soil quality.

Falsiporphyromonas endometrii gen. nov., sp. nov., isolated from the post-partum bovine uterus, and emended description of the genus Porphyromonas Shah and Collins 1988

Two black-pigmented, anaerobic bacterial strains, designated LMM 40(T) and LMM 41, were isolated from the bovine post-partum endometrium of two Holstein cows. The 16S rRNA gene sequences of the two strains were identical and showed the highest similarity to the 16S rRNA gene sequence of the type strain of Porphyromonas crevioricanis (90.2%) but only 85.1% 16S rRNA gene sequence similarity to the type strain of the type species of the genus Porphyromonas, Porphyromonas asaccharolytica. The major fatty acid profiles of the two strains were similar to those of species of the genus Porphyromonas, containing iso-C(15 : 0) as the major component and moderate amounts of anteiso-C(15 : 0), iso-C(13 : 0), C(15 : 0) and C(16 : 0). Hydroxylated fatty acids, such as iso-C(14 : 0) 3-OH, iso-C(16 : 0) 3-OH and iso-C(17 : 0) 3-OH, were also detected. The quinone profiles were dominated by the menaquinones MK-8 and MK-9, while spermidine was the major polyamine. The polar lipid profiles contained major amounts of phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and two unidentified lipids and minor amounts of phosphatidylglycerol, an unidentified aminolipid, a second unidentified aminophospholipid and an unidentified glycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G+C contents of LMM 40(T) and LMM 41 were 40.7 and 41.3 mol%, respectively. Based on a polyphasic approach, including phylogenetic analysis, physiological and biochemical tests as well as metabolic fingerprinting, it is proposed that the two strains are members of a novel genus and species, for which the name Falsiporphyromonas endometrii gen. nov., sp. nov. is proposed. The type strain of Falsiporphyromonas endometrii is LMM 40(T) ( = DSM 27210(T) = CCUG 64267(T)). An emended description of the genus Porphyromonas is also presented.

Waste sludge reduction with a pilot-scale membrane bioreactor for point source pollution management

It is an important subject to reduce the amount of waste sludge from small-/middle-scale wastewater facilities for the establishment of point source pollution management. In this work, we focused on the development of sludge decomposition system which did not increase organic loading ratio into wastewater treatment units. The excess sludge produced from wastewater treatment plant of a food factory was decomposed by an aerobic digestion technology with a membrane bioreactor (MBR) system. It was composed of digestion tank (500 L) and a membrane filtration unit (350 L). Sludge was decomposed under the following conditions: 25 g L-1 of MLSS, 36.9 d of HRT, average temperature 32.3°C, and 0.565 kg-SS m-3 d-1 of sludge loading rate. The system decomposed 77.2% of the fed sludge to inorganic carbon, and all of average TOC, CODMn and CODCr in the effluent were less than 50 mg L-1. However, the effluent contained T–N and T–P at 200 mg N L-1 and 150 mg-P L-1, respectively. The quinone profile analysis indicated that the consortia of sludge in the reactor were different from the fed sludge.

Preliminary Discussion on the Activity of Denitrifying Phosphorus-Removing Bacteria in Sequencing Batch Reactors by Quinone Profile Analysis

Based on DPBs (Denitrifying Phosphorus-removing Bacteria) obtained from a lab-scale SBR, a quinone profile system had been established to analyze quinones in sludge samples. There existed a positive correlation between the contents of UQ-8 extracted from the sludge samples and the denitrifying and phosphorus removal efficiency of the treating system. With quinone profiles taken as a new important index, it was evidently feasible to determine the removal effect.

Otariodibacter oris gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of pinnipeds

A total of 27 bacterial isolates from California sea lions and a walrus tentatively classified within the family Pasteurellaceae was further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, tentatively designated Bisgaard taxon 57. According to 16S rRNA gene sequences, the most closely related species with a validly published name was Bisgaardia hudsonensis and the most closely related species based on rpoB sequence comparison was Pasteurella multocida subsp. multocida; highest similarities between the isolates and the type strains of B. hudsonensis and P. multocida subsp. multocida were 95.0 and 88.2%. respectively. All isolates of Bisgaard taxon 57 exhibit the phenotypic characters of the family Pasteurellaceae. Members of Bisgaard taxon 57 can be separated from existing genera of the Pasteurellaceae by the following tests: positive reactions for catalase, oxidase, Voges-Proskauer and indole; no X- or V-factor dependency; and acid production from L-arabinose (slow), L-fucose, maltose and trehalose, but not from dulcitol, D-mannitol, D-mannose or sucrose. The main fatty acids of Bisgaard taxon 57 (CCUG 59994(T)) are C(14:0), C(16:0), C(16:1)ω7c and the summed feature C(14:0) 3-OH/iso-C(16:1) I. This fatty acid profile is characteristic of members of the Pasteurellaceae. The quinone profile of Bisgaard taxon 57 (DSM 23800(T)) was similar to that of other genera in the Pasteurellaceae. The DNA G+C content of strain Baika1(T) is 36.2 mol%, which is at the lower end of the range for members of the family Pasteurellaceae. On the basis of both phylogenetic and phenotypic evidence, it is proposed that members of Bisgaard taxon 57 should be classified as representatives of a novel species in a new genus, Otariodibacter oris gen. nov., sp. nov. The type strain of Otariodibacter oris is Baika1(T) (=CCUG 59994(T)=DSM 23800(T)), which was isolated from the oral cavity of a healthy California sea lion in Copenhagen Zoo, Denmark, in 2007.

Rhodanobacter denitrificans sp. nov., isolated from nitrate-rich zones of a contaminated aquifer

Bacterial strains 2APBS1(T) and 116-2 were isolated from the subsurface of a nuclear legacy waste site where the sediments are co-contaminated with large amounts of acids, nitrate, metal radionuclides and other heavy metals. A combination of physiological and genetic assays indicated that these strains represent the first member of the genus Rhodanobacter shown to be capable of complete denitrification. Cells of strain 2APBS1(T) and 116-2 were Gram-negative, non-spore-forming rods, 3-5 µm long and 0.25-0.5 µm in diameter. The isolates were facultative anaerobes, and had temperature and pH optima for growth of 30 °C and pH 6.5; they were able to tolerate up to 2.0 % NaCl, although growth improved in its absence. Strains 2APBS1(T) and 116-2 contained fatty acid and quinone (ubiquinone-8; 100 %) profiles that are characteristic features of the genus Rhodanobacter. Although strains 2APBS1(T) and 116-2 shared high 16S rRNA gene sequence similarity with Rhodanobacter thiooxydans LCS2(T) (>99 %), levels of DNA-DNA relatedness between these strains were substantially below the 70 % threshold used to designate novel species. Thus, based on genotypic, phylogenetic, chemotaxonomic and physiological differences, strains 2APBS1(T) and 116-2 are considered to represent a single novel species of the genus Rhodanobacter, for which the name Rhodanobacter denitrificans sp. nov. is proposed. The type strain is 2APBS1(T) ( = DSM 23569(T) = JCM 17641(T)).

Nitrate Removal Efficiency and Bacterial Community Dynamics in Denitrification Processes Using Poly (<sc>L</sc>-lactic acid) as the Solid Substrate

Laboratory-scale solid-phase denitrification (SPD) reactors for nitrate removal were constructed by acclimating activated sludge with poly (L-lactic acid) (PLLA) having weight-average molecular weights (M(w)) of 9,900, 12,000, and 45,100 g mol(-1). A good nitrate removal rate (3.5-5.3 mg NO(3)(-)-N g [dry wt](-1) h(-1)) was found in the reactor containing PLLA of 9,900 g mol(-1), whereas the other two reactors with the higher M(w) PLLA showed low nitrate removal efficiency. Microbial community dynamics in the low M(w) PLLA-acclimated reactor were studied by 16S rRNA gene-targeted PCR-denaturing gradient gel electrophoresis and quinone profiling. Nonmetric multidimensional scaling analyses of these data sets revealed a marked population shift during acclimation of the SPD reactor with low M(w) PLLA. The 16S rRNA gene clone library and culture-dependent analyses showed that bacteria belonging to the family Comamonadaceae predominated and played the primary role in denitrification in the PLLA-using reactor; however, none of the bacterial isolates from the reactor degraded PLLA. These results suggest that the nitrate removal property of the PLLA-using SPD reactor is attained through the bioavailability of hydrolysates released abiotically from the solid substrate.

Analysis of soil microorganisms determined by the phospholipid fatty acid and quinone profile in organic matter-applied soil

Analysis of soil microorganisms determined by the phospholipid fatty acid and quinone profile in organic matter-applied soil

Approach for Estimating Microbial Growth and Biodegradation of Hydrocarbon Contaminants in Subsoil Based on Field Measurements: 2. Application in a Field Lysimeter Experiment

A new approach was applied to represent the natural attenuation of hydrocarbon (HC) contaminants as observed in a field lysimeter experiment. The approach describes the microbial growth on HC contaminants and linked HC biodegradation under natural precipitation conditions. The HC contaminants contained an inert component (n-dodecane) and soluble components (toluene, ethylbenzene, xylene isomers, and naphthalene), and their attenuation processes were predicted. The respiratory quinone profile method is used to indicate temporary changes in in situ microbial biomass possessed by HC-degrading microorganisms in soils. On the basis of field measurements conducted during the initial 92 days post-HC contamination, the kinetic parameters of HC-degrading microorganisms were estimated, which were used for the prediction of microbial growth and linked HC-contaminant depletion in the contaminated soil for the subsequent 259 days. The prediction was in good agreement with the measured HC concentration and corresponding respiratory quinones from HC-degrading microorganisms. The results indicate that the proposed approach can provide a reliable prediction of HC depletion in subsoil on the basis of field measurements. Further efforts are expected to incorporate the approach into a multiphase flow and multicomponent transport model for application to actual HC-contaminated sites.

Quinone profiles of microbial communities in sediments of Haihe River–Bohai Bay as influenced by heavy metals and environmental factors

A total of 11 sediment samples were collected from the sites along Haihe River-Bohai Bay, with site 1 at the beginning of Haihe River and site 11 in Bohai Bay, about 150km away from site 1. Quinone profiles were used for the analysis of microbial community as influenced by pollutants in water and sediments, such as heavy metals, and other environmental factors. Nineteen species of quinones were found at site 1 while only six species at sites 10 and 11. Both the diversity of quinone species (DQ) and the number of quinones were higher in the sediments from Haihe River and the near-sea area of Bohai Bay than in those from the deep-sea area. The β diversity values were significantly higher, while Jaccard indexes of similarity were much lower among non-contiguous pairs of sites as compared with the contiguous ones. Cluster analysis indicated that quinone profiles may be grouped into two main clusters (sites 1-7 and sites 8-11), and there were higher similarities within the groups than between groups. Quinone species composition varied at different sites. Ubiquinones such as UQ-8, UQ-9, and UQ-10 and menaquinones such as MK-6, MK-7, MK-8 were isolated from all the sites and accounted for the largest proportions. Pearson correlation analysis revealed that both the number of quinone species and DQ correlated positively with total organic carbon contents in water and sediments, but negatively correlated with salinity and electroconductivity and did not correlate significantly with heavy metal contents in water.

Effects of Raw Materials and Bulking Agents on the Thermophilic Composting Process

Three typical biological solid wastes, animal manure, garbage, and sewage sludge, were compared with regard for the composting process and the changes in microbial community structure. The effect of different bulking agents such as rice straw, vermiculite, sawdust, and waste paper were compared in manure compost. The differences in the microbial community were characterized by the quinone profile method. The highest mass reduction was found in garbage composting (56.8%), compared to manure and sludge at 25% and 20.2%, respectively. A quinone content of 305.2 micromol/kg was observed in the late stage of garbage composting, although the diversity index of quinone profile was 9.7, lower than that in manure composting. The predominant quinone species were found to be MK-7, which corresponds to gram positive bacteria with low G+C content such as Bacillus. The predominance of MK-7 was especially found in garbage and sludge composting process, while the increase in quinones with partially saturated long side chain was shown in late composting process of manure, which corresponded to the proliferation of Actinobacteria. The effect of different bulking agents on the composting process was much smaller than the effect of different raw materials. High organic matter content in the raw materials results in a higher microbial biomass and activity, which was connected to the high mass reduction rate.

Intact Phospholipid and Quinone Biomarkers to Assess Microbial Diversity and Redox State in Microbial Mats

Microbial mats are stratified microbial communities composed by highly inter-related populations and therefore are frequently chosen as model systems to study diversity and ecophysiological strategies. The present study describes an integrated approach to analyze microbial quinones and intact polar lipids (IPLs) in microbial mats within layers as thin as 500 microm by liquid chromatography-tandem mass spectrometry. Quinone profiles revealed important depth-related differences in community composition in two mat systems. The higher abundance of ubiquinones, compared to menaquinones, reflected the clear predominance of microorganisms belonging to aerobic alpha-, beta-, and gamma-Proteobacteria in Ebro delta estuarine mats. Hypersaline photosynthetic Camargue mats (France) showed a predominance of menaquinone-9 at the top of the mat, which is consistent with an important contribution of facultative aerobic or anaerobic bacteria in its photic zone. Quinone indices also indicated a higher diversity of non-phototrophs and a more anaerobic character in the hypersaline mats. Besides, the dissimilarity index suggested that the samples were greatly influenced by a depth-related redox state gradient. In the analysis of IPLs, there was a predominance of phosphatidylglycerols and sulfoquinovosyldiacylglycerols, the latter being an abundant biomarker of Cyanobacteria. This combined approach based on quinone and IPL analysis has proven to be a useful method to establish differences in the microbial diversity and redox state of highly structure microbial mat systems at a fine-scale level.