Mineralogical composition and biomass studies of the microbial mats sediments from the Ebro Delta, Spain.

The mineral composition of the microbial mats at La Banya spit was studied. The spit is formed by a narrow sand bar and a peninsula and is located south of the main body of the Ebro Delta (Tarragona, Spain). Although quartz was the predominant mineral component in all sampling sites, clay, feldspars, calcite, aragonite, halite, dolomite and gypsum were also found. An increase in both the fine material (clay) and the halite content was observed in the sites influenced by nearby salterns. The amount of each mineral did not differ significantly along a 55 cm deep profile, except for halite and aragonite, which reached a maximum in the surface and decreased with depth. Dolomite, which ranged from 0.5 to 5% (w/w), is a possible indicator of sulfate-reducing bacteria activity in the past. Organic carbon and total nitrogen were quantified for biomass assessment. Total nitrogen ranged from 0.1 to 0.56% in the uppermost layer, where the microbial mat is active, but was undetectable at deeper layers. Organic carbon ranged from 1 to 5.5% in the active microbial mat layers and decreased to 0.3% at deeper layers. During the summer, both organic carbon and total nitrogen contents (biomass) of the microbial mat samples from some sites increase, whereas other sites show constant concentrations throughout the year, and others have a fluctuant biomass content.     

Sulfide fluxes in a microbial mat from the Ebro Delta, Spain

The sulfur cycle of Ebro Delta microbial mats was studied in order to determine sulfide production and sulfide consumption. Vertical distribution of two major functional groups involved in the sulfur cycle, anoxygenic phototrophic bacteria and dissimilatory sulfate-reducing bacteria (SRB), was also studied. The former reached up to 2.2×10⁸ cfu cm^–3 sediment in the purple layer, and the latter reached about 1.8×10⁵ SRB cm^–3 sediment in the black layer. From the changes in sulfide concentrations under light-dark cycles it can be inferred that the rate of H₂S production was 6.2 μmol H₂S cm^–3 day^–1 at 2.6 mm, and 7.6 μmol H₂S cm^–3 day^–1 at 6 mm. Furthermore, sulfide consumption was also assessed, determining rates of 0.04, 0.13 and 0.005 mmol l^–1 of sulfide oxidized at depths of 2.6, 3 and 6 mm, respectively. Electronic Publication     

Diversity of anoxygenic phototrophic sulfur bacteria in the microbial mats of the Ebro Delta: a combined morphological and molecular approach

The diversity of purple and green sulfur bacteria in the multilayered sediments of the Ebro Delta was investigated. Specific oligonucleotide primers for these groups were used for the selective amplification of 16S rRNA gene sequences. Subsequently, amplification products were separated by denaturing gradient gel electrophoresis and sequenced, which yielded a total of 32 sequences. Six of the sequences were related to different cultivated members of the green sulfur bacteria assemblage, whereas seven fell into the cluster of marine or halophilic Chromatiaceae. Six sequences were clustered with the family Ectothiorhodospiraceae, three of the six being closely related to chemotrophic bacteria grouped together with Halorhodospira genus, and the other three forming a group related to the genus Ectothiorhodospira. The last thirteen sequences constituted a cluster where no molecular isolate from microbial mats has so far been reported. Our results indicate that the natural diversity in the ecosystem studied has been significantly underestimated in the past and point out the presence of novel species not related to all known purple sulfur bacteria. Furthermore, the detection of green sulfur bacteria, after only an initial step of enrichment, suggests that -- with the appropriate methodology -- several genera, such as Prosthecochloris, could be established as regular members of marine microbial mats.     

PCR-DGGE and real-time PCR dsrB-based study of the impact of heavy metals on the diversity and abundance of sulfate-reducing bacteria

Sulfate-reducing bacteria (SRB) are widely used for heavy metal (HM) treatment in bioreactors but their growth and biological activity can be inhibited by such treatment. Here, bioreactor experiments were used to investigate changes in the SRB community and the copy number of the dissimilatory sulfite reductase β-subunit functional gene (dsrB) under high doses of sulfates and HMs. The SRB community was investigated using polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and sequencing techniques, while the dsrB gene abundance was measured by quantitative real-time PCR (qRT-PCR). The sulfate reduction rate was initially much higher in reactors without HMs than in those containing HMs (p = 0.001). Sulfate levels were reduced by 50% within the first 3 days of operation. As a result, the HM removal rate was initially much lower in the reactors containing HMs. Most of the HMs reduced to safe limits within 9 ~ 12 days of operation. The SRB community mainly consisted of Desulfovibrio vulgaris, D. termitidis, D. desulfuricans, D. simplex and Desulfomicrobium baculatum, as determined by PCR-DGGE. qRT-PCR revealed a decreasing trend in the copy numbers of a functional gene (dsrB) after 6 days in samples lacking HMs; however, the opposite trend was observed in the HM-containing samples.     

Isolation and Characterization of Cyanobacteria from Microbial Mats of the Ebro Delta,Spain

Isolation and identification of several strains of cyanobacteria from microbial mats of the Ebro Delta, Spain, are described. A series of tenfold dilutions was the first step of isolation. Self-isolation techniques, which use one or several physiological characteristics of a cyanobacterium, were applied in some cases to obtain enrichment cultures. Twelve filamentous strains were isolated and stored in axenic culture. As only a few cyanobacterial species can be frozen and revived without any cryoprotective agent, preservation of isolated strains was assayed with several cryoprotective solutions. Methanol and glycerol were not suitable as cryoprotective agents for most of the isolates. Dimethyl sulfoxide (DMSO) was apparently the best cryoprotector. A new method, which used a filter paper as a growing substratum that later could be directly stored at −80°C, was successfully used. A morphological study of each strain under light and electron microscopy was made to classify them. All isolated strains belong to phylum BX, Class 1, subsection III of the Bergey's manual of systematic bacteriology, 2nd ed., vol. 1. Most genera are included in the LPP group as Lyngbya aestuarii and Microcoleus chthonoplastes. Received: 30 April 2002 / Accepted: 31 May 2002     

Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities

Here, we describe a three-step nested-PCR-denaturing gradient gel electrophoresis (DGGE) strategy to detect sulfate-reducing bacteria (SRB) in complex microbial communities from industrial bioreactors. In the first step, the nearly complete 16S rRNA gene was amplified using bacterial primers. Subsequently, this product was used as a template in a second PCR with group-specific SRB primers. A third round of amplification was conducted to obtain fragments suitable for DGGE. The largest number of bands was observed in DGGE patterns of products obtained with primers specific for the Desulfovibrio-Desulfomicrobium group, indicating a large diversity of these SRBs. In addition, members of other phylogenetic SRB groups, i.e., Desulfotomaculum, Desulfobulbus, and Desulfococcus-Desulfonema-Desulfosarcina, were detected. Bands corresponding to Desulfobacterium and Desulfobacter were not detected in the bioreactor samples. Comparative sequence analysis of excised DGGE bands revealed the identity of the community members. The developed three-step PCR-DGGE strategy is a welcome tool for studying the diversity of sulfate-reducing bacteria.     

Lipid dynamics in the viperine snake, Natrix maura, from the Ebro Delta (NE Spain)

Body reserves play a major role in several aspects of vertebrate biology. Accurate identification and quantification of body reserves constitute a useful contribution to the better understanding of the energetic costs of reproduction and the implication of food availability in life history traits of organisms. In this study, lipid content in fat bodies, liver and muscle of the viperine snake (Natrix maura) were measured along an active season. Samples were collected monthly from a natural population of the Ebro Delta Natural Park (NE Spain). This methodology pointed out that lipids stored in fat bodies were the main energetic source during reproduction. In addition, lipids stored in liver appeared to be critical for vitellogenesis, while lipids stored in muscle turned out to be a supplementary energetic resource to fuel reproductive effort. Relationships between changes in body reserves and prey availability in canals of the Ebro Delta were also considered. In males, lipid reserves presented a positive correlation with food availability. On the contrary, lipid reserves in female viperine snakes decreased during vitellogenesis even though food availability increased in this period, which suggests a quick transfer of body lipids to clutch. In April, when rice fields of the Ebro Delta were dry and aquatic prey was scarce for viperine snakes, males and females presented a lower lipid content in fat bodies, liver and muscle than they did in other months, showing a clear link between prey availability and body reserves during food shortage. Thus, patterns of variation in fat levels indicated that Natrix maura is a capital breeder since it acquires resources in advance and stores them until they are invested during the reproductive period. Nevertheless, the shortage in April forces Natrix maura to turn into a facultative income breeder to fuel vitellogenesis. Finally, fat reserves in body components were compared with an estimate of body condition calculated by the residuals from the regression of body mass on body length. In male viperine snakes, the estimate of body condition was correlated with fat levels, revealing that this index is useful to measure condition in living individuals. On the contrary, body condition in females was not correlated with fat levels, which suggests that it is not appropriate to infer condition in female viperine snakes since it depends on the reproductive status of the individuals.     

应用特异PCR快速鉴定微生物肥料中4种乳酸菌

【目的】植物乳杆菌(Lactobacillus plantarum)、鼠李糖乳杆菌(L.rhamnosus)、嗜酸乳杆菌(L.acidophilus)和德氏乳杆菌(L.delbrueckii)是微生物肥料生产中常用的乳酸菌,它们表型特征相似,若采用传统方法鉴定则费时费力,为准确、快速地鉴定这些种,建立种特异PCR方法。【方法】利用NCBI中Primer-BLAST(引物设计和特异性检验工具),以GenBank数据库中上述菌种的recA和gyrB为靶基因,设计和筛选种特异性引物从而建立相应特异PCR鉴定方法。【结果】经过乳杆菌属(Lactobacillus)、乳球菌属(Lactococcus)、片球菌属(Pediococcus)、芽孢杆菌属(Bacillus)、类芽孢杆菌属(Paenibacillus)、短芽孢杆菌属(Brevibacillus)和假单胞菌属(Pseudomonas)7个属24个种共40株标准菌株的实验验证,4个目标种分别扩增出唯一的目的产物,而其他种均无目的扩增产物。采用建立的4种特异PCR方法对产品中分离的16株乳杆菌进行鉴定,结果与16S rDNA序列分析、Biolog鉴定结果一致。【结论】建立的特异PCR鉴定方法均具有较高的种内通用性和种间特异性,可快速、准确的用于微生物制剂中植物乳杆菌、德氏乳杆菌、鼠李糖乳杆菌、嗜酸乳杆菌的检测和鉴定,具有较好的应用前景。     

Use of two 16S DNA targeted oligonucleotides as PCR primers for the specific detection of Salmonella in foods

A 16S DNA targeted polymerase chain reaction (PCR) method specific for the detection of Salmonella isolates with various serotypes was developed. The primers used for such a PCR method were 16SF1 and 16SIII. 16SF1 is the reverse and complementary strand of 16SI which has been shown to be able to hybridize with Salmonella and Citrobacter spp. 16III on the other hand, is able to hybridize with Klebsiella and Serratia spp. in addition to Salmonella. Although 16SF1 and 16SIII were not specific to Salmonella only, when they were used as PCR primers, only the Salmonella isolates could be specifically detected. The interference from Citrobacter, Klebsiella and Serratia spp. could be prevented. None of the other non- Salmonella isolates including strains of the family of Enterobacteriaceae closely related to Salmonella would generate the false-positive reaction. When this PCR system was used for the detection of Salmonella cells artificially contaminated in food samples, results obtained were satisfactory. A detection limit of N × 10⁰ cells per assay could be obtained.     

Antigenic diversity of cytochromes c3 from the anaerobic,sulfate-reducing bacteria,Desulfovibrio

An indirect enzyme-linked immunoadsorption assay (ELISA) was developed for cytochrome c₃ using antisera to the cytochromes fromDesulfovibrio africanus Benghazi, Desulfovibrio vulgaris Hildenborough andDesulfovibrio salexigens British Guiana. The ELISA system was used to test for cross-reactions between these antisera and the heterologous antigens. In contrast to previous experiments using the Ouchterlony technique, all of the cytochromes c₃ tested exhibited some degree of cross-reaction. Considerable variation was seen in cross-reactions for cytochromes c₃ from differing strains ofD. desulfuricans. This observation raises questions about the taxonomic relatedness of these strains. No cross-reaction was seen with eukaryotic cytochrome c or withD. vulgaris cytochrome c₅₅₃. The data demonstrate that cytochrome c₃ is capable of undergoing nonprecipitating cross-reactions, and thus may not be as immunologically unique as was once thought.Abbreviations ELISA Enzyme-linked immunoadsorption assay     

DsrB gene-based DGGE for community and diversity surveys of sulfate-reducing bacteria

A denaturing gradient gel electrophoresis (DGGE) method was developed to assess the diversity of dsrB (dissimilatory sulfite reductase beta-subunit)-genes in sulfate-reducing communities. For this purpose a PCR primer pair was optimized for the amplification of a approximately 350 bp dsrB gene fragment that after DGGE gel electrophoresis enabled us to discriminate between dsrB genes of different SRB-subgroups,-genera and -species. The dsrB-DGGE method revealed considerable genetic diversity when applied to DNA extracts obtained from aquifer samples that were derived from monitoring wells of an in situ metal precipitation (ISMP) pilot project conducted at the site of a non-ferrous industry or from environmental heavy metal contaminated samples. The sequences of the excised and sequenced DGGE bands represented dsrB genes of different SRB-subgroups,-genera and -species, thus confirming the broad applicability of the PCR primer pair. Linking the results of the physico-chemical follow-up of the field and lab experiments to the dsrB-DGGE data will provide a better understanding of the contribution of the SRB populations to the ongoing ISMP processes.     

Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces

16S rRNA gene-targeted group-specific primers were designed and validated for specific detection and quantification of the Clostridium leptum subgroup and the Atopobium cluster. To monitor the predominant bacteria in human feces by real-time PCR, we used these specific primers together with four sets of group-specific primers for the Clostridium coccoides group, the Bacteroides fragilis group, Bifidobacterium, and Prevotella developed in a previous study (T. Matsuki, K. Watanabe, J. Fujimoto, Y. Miyamoto, T. Takada, K. Matsumoto, H. Oyaizu, and R. Tanaka, Appl. Environ. Microbiol. 68:5445-5451, 2002). Examination of DNA extracted from the feces of 46 healthy adults showed that the C. coccoides group was present in the greatest numbers (log10 10.3 +/- 0.3 cells per g [wet weight] [average +/- standard deviation]), followed by the C. leptum subgroup (log10 9.9 +/- 0.7 cells per g [wet weight]), the B. fragilis group (log10 9.9 +/- 0.3 cells per g [wet weight]), Bifidobacterium (log10 9.4 +/- 0.7 cells per g [wet weight]), and the Atopobium cluster (log10 9.3 +/- 0.7 cells per g [wet weight]). These five bacterial groups were detected in all 46 volunteers. Prevotella was found in only 46% of the subjects at a level of log10 9.7 +/- 0.8 cells per g (wet weight). Examination of changes in the population and the composition of the intestinal flora for six healthy adults over an 8-month period revealed that the composition of the flora of each volunteer remained stable throughout the test period.     

Oxygenic Photosynthesis and Respiratory Activity in Microbial Mats of the Ebro Delta, Spain, by Oxygen Exchange Method

Photosynthetic and respiratory activities at low light intensities (300 μE m⁻² s⁻¹) in the microbial mats of the Ebro Delta were measured by the oxygen exchange method in the laboratory. The response to H₂S concentration, a significant factor in the dynamics of that ecosystem, was assessed. Total photosynthesis reached 23.78–28.17 μg O₂ cm⁻² h⁻¹. Photosynthetic activity was not significantly different at the two temperatures tested. Respiratory activity reached a consumption of 6.95–8.56 μg O₂ cm⁻² h⁻¹ at 25°C and 11.42–11.70 μg O₂ cm⁻² h⁻¹ at 35°C. The Q₁₀ value for respiration was 1.37–1.64. Oxygen production in Microcoleus chthonoplastes, the most abundant cyanobacterium in those microbial mats, was highly resistant to sulfide inhibition. Concentrations less than 0.02 mM sulfide did not affect the rate of photosynthesis. Concentrations up to 0.1 mM sulfide caused different degrees of partially reversible inhibition, with a maximum of 67% at 0.78 mM sulfide. Primary production (g C assimilated/m²/year) in those microbial mats was also assessed and compared with data from other ecosystems. Received: 24 October 1997 / Accepted: 18 December 1997     

Activity and diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer

Microbial sulfate reduction is an important metabolic activity in petroleum hydrocarbon (PHC)-contaminated aquifers. We quantified carbon source-enhanced microbial SO(4)(2-) reduction in a PHC-contaminated aquifer by using single-well push-pull tests and related the consumption of sulfate and added carbon sources to the presence of certain genera of sulfate-reducing bacteria (SRB). We also used molecular methods to assess suspended SRB diversity. In four consecutive tests, we injected anoxic test solutions (1,000 liters) containing bromide as a conservative tracer, sulfate, and either propionate, butyrate, lactate, or acetate as reactants into an existing monitoring well. After an initial incubation period, 1,000 liters of test solution-groundwater mixture was extracted from the same well. Average total test duration was 71 h. We measured concentrations of bromide, sulfate, and carbon sources in native groundwater as well as in injection and extraction phase samples and characterized the SRB population by using fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Enhanced sulfate reduction concomitant with carbon source degradation was observed in all tests. Computed first-order rate coefficients ranged from 0.19 to 0.32 day(-1) for sulfate reduction and from 0.13 to 0.60 day(-1) for carbon source degradation. Sulfur isotope fractionation in unconsumed sulfate indicated that sulfate reduction was microbially mediated. Enhancement of sulfate reduction due to carbon source additions in all tests and variability of rate coefficients suggested the presence of specific SRB genera and a high diversity of SRB. We confirmed this by using FISH and DGGE. A large fraction of suspended bacteria hybridized with SRB-targeting probes SRB385 plus SRB385-Db (11 to 24% of total cells). FISH results showed that the activity of these bacteria was enhanced by addition of sulfate and carbon sources during push-pull tests. However, DGGE profiles indicated that the bacterial community structure of the dominant species did not change during the tests. Thus, the combination of push-pull tests with molecular methods provided valuable insights into microbial processes, activities, and diversity in the sulfate-reducing zone of a PHC-contaminated aquifer.     

Physiological Status and Community Composition of Microbial Mats of the Ebro Delta, Spain, by Signature Lipid Biomarkers

Abstract Physiological status of microbial mats of the Ebro Delta (Tarragona, Spain) based on the extraction of lipids considered ``signature lipid biomarkers' (SLB) from the cell membranes and walls of microorganisms has been analyzed. Data from a day–night cycle show significant differences in viable cells countings (PLFA cells counts) ranging from 1.5 × 10¹⁰ to 5.0 × 10¹⁰ cells g⁻¹ of sediment. Minimum values were observed at 18:00 and 6:00, when physicochemical conditions change drastically. The diversity of the microbial community was assessed by GC/MS analysis of phospholipid fatty acids (PLFA). The ratio of PLFA, representative of Gram-negative bacteria, comprises 47.8% of the total PLFA of the microbial mat community. The remaining PLFA was representative of Gram-positive (10.0%), anaerobic (5.7%), and eukaryotic microorganisms (5.7%), and other common lipids. Two different approaches were used as a comparative study to assess the physiological status of the microbial mats. Two parameters (cyclopropane fatty acids/ω7c monoenoic fatty acids, and measurement of the trans/cis monoenoic PLFA ratio) showed a minimum at midnight, suggesting the highest microbial activity. Higher values were observed at 18:00 and 6:00, coinciding with lower PLFA cell counts. Received: 14 May 1999; Accepted: 6 September 1999; Online Publication: 24 March 2000     

Distribution, diversity, and activity of sulfate-reducing bacteria in the water column in Gek-Gel Lake, Azerbaijan

The distribution and activity of sulfate-reducing bacteria (SRB) in the water column of the alpine meromictic Gek-Gel lake were studied. Apart from traditional microbiological methods based on cultivation and on measuring the process rates with radioactive labels, in situ fluorescent hybridization (FISH) was used, which enables identification and quantification without cultivating organisms. The peak rate of sulfate reduction, 0.486 microg S/(l day), was found in the chemocline at 33 m. The peak SRB number of 2.5 x 106 cells/ml, as determined by the end-point dilutions method on selective media, was found at the same depth. The phylogenetic position of the SRB, as determined by FISH, revealed the predominance of the Desulfovibrio spp., Desulfobulbus spp., and Desulfoarculus spp./Desulfomonile spp. groups. The numbers of spore-forming Desulfotomaculum spp. increased with depth. The low measured rates of sulfate reduction accompanied with high SRB numbers and the predominance of the groups capable of reducing a wide range of substrates permit us to propose utilization of electron acceptors other than sulfate as the main activity of the SRB in the water column.     

Distribution, diversity, and activity of sulfate-reducing bacteria in the water column in Gek-Gel lake, Azerbaijan

The distribution and activity of sulfate-reducing bacteria (SRB) in the water column of the alpine meromictic Gek-Gel lake were studied. Apart from traditional microbiological methods based on cultivation and on measuring the process rates with radioactive labels, in situ fluorescent hybridization (FISH) was used, which enables identification and quantification without cultivating organisms. The peak rate of sulfate reduction, 0.486 μg S 1⁻¹ day⁻¹, was found in the chemocline at 33 m. The peak SRB number of 2.5×10⁶ cells/ml, as determined by the most probable number method on selective media, was found at the same depth. The phylogenetic affiliation of the SRB, as determined by FISH, revealed the predominance of the Desulfovibrio spp., Desulfobulbus spp., and Desulfoarculus spp./Desulfomonile spp. groups. The numbers of spore-forming Desulfotomaculum spp. increased with depth. The low measured rates of sulfate reduction accompanied by high SRB numbers and the predominance of the groups capable of reducing a wide range of substrates permit us to assume utilization of electron acceptors other than sulfate as the main activity of the SRB in the water column. Original Russian Text ? O.V. Karnachuk, N.V. Pimenov, S.K. Yusupov, Yu.A. Frank, Ya.A. Puhakka, M.V. Ivanov, 2006, published in Mikrobiologiya, 2006, Vol. 75, No. 1, pp. 101–109.