Methanogenic bacteria in mangrove sediments

The occurrence of methanogenic bacteria in the Kodiakkarai (10° 18 N; 79° 52 E) mangrove sediments, whereAvicennia spp are predominant, was studied. Trimethylamine under N₂:CO₂ (80:20% v/v) was used as the substrate. Most Probable Number (MPN) of methanogenic bacteria was determined for a period of one year from July 1987 to June 1988 with monthly sampling. The methanogenic bacterial populations were found to be at the maximum of 1.1 × 10⁵ MPN gm^–1 of wet sediment during August 1987 and from February to June 1988. The bacterial numbers were found to decrease during October to December 1987 with a minimal value of 3.6 × 10² MPN gm^–1 during December 1987. Environmental factors were correlated with the methanogenic bacterial population.     

Anaerobic oxidation of dimethylsulfide and methanethiol in mangrove sediments is dominated by sulfate-reducing bacteria

The oxidation of dimethylsulfide and methanethiol by sulfate-reducing bacteria (SRB) was investigated in Tanzanian mangrove sediments. The rate of dimethylsulfide and methanethiol accumulation in nonamended sediment slurry (control) incubations was very low while in the presence of the inhibitors tungstate and bromoethanesulfonic acid (BES), the accumulation rates ranged from 0.02–0.34 to 0.2–0.4 nmol g FW sediment⁻¹ h⁻¹, respectively. Degradation rates of methanethiol and dimethylsulfide added were 2–10-fold higher. These results point to a balance of production and degradation. Degradation was inhibited much stronger by tungstate than by BES, which implied that SRB were more important. In addition, a new species of SRB, designated strain SD1, was isolated. The isolate was a short rod able to utilize a narrow range of substrates including dimethylsulfide, methanethiol, pyruvate and butyrate. Strain SD1 oxidized dimethylsulfide and methanethiol to carbon dioxide and hydrogen sulfide with sulfate as the electron acceptor and exhibited a low specific growth rate of 0.010 ± 0.002 h⁻¹, but a high affinity for its substrates. The isolated microorganism could be placed in the genus Desulfosarcina (the most closely related cultured species was Desulfosarcina variabilis , 97% identity). Strain SD1 represents a member of the dimethylsulfide/methanethiol-consuming SRB population in mangrove sediments.     

Biogeochemical cycling of sulfur and iron in sediments of a south-east Asian mangrove,Phuket Island,Thailand

Benthic sulfate reduction and sediment pools of sulfur and iron were examined during January 1992 at 3 stations in the Ao Nam Bor mangrove, Phuket, Thailand. Patterns of sulfate reduction rates (0–53 cm) reflected differences in physical and biological conditions at the 3 stations, and highest rates were found at the vegetated site within the mangrove (Rhizophora apiculata) forest. Due to extended oxidation of mangrove sediments, a large portion of the added³⁵S-label was recovered in the chromium reducible pools (FeS₂ and S⁰) (41–91% of the reduced sulfur). Pyrite was the most important inorganic sulfur component, attaining pool sizes 50–100 times higher than acid volatile pools (FeS). HCl-extractable (0.5 M HCl) iron pools, including Fe(II)_HCl and Fe(III)_HCl, were generally low and Fe(III)_HCl was only present in the upper surface layers (0–5 cm). Maximum concentrations of dissolved Fe²⁺ (35–285 M) occurred just about the depth where dissolved H₂S accumulated. Furthermore Fe²⁺ and H₂S coexisted only where concentrations of both were low. There was an accumulation of organic sulfur in the deep sediment at 2 stations in the inner part of the mangrove. The reoxidation of reduced sulfides was rapid, and storage of sulfur was minor in the upper sediment layers, where factors like bioturbation, the presence of roots, or tidal mixing enhance oxidation processes.Author of correspondence.     

Incidence of heavy metals in the mangrove flora and sediments in Kerala, India

The mangroves of Kerala on the south-west coast of India are fast disappearing due to land reclamation and other anthropogenic disturbances. There are very few ecosystem level studies made in these much threatened biotopes in Kerala. The present study involves the measurement of heavy metals in the mangrove flora and sediments of three mangrove habitats along the Kerala coast. Sampling was carried out for a period of one year at bi-monthly intervals, with concentrations of Fe, Mn, Cu,Zn,Pb and Co analysed using atomic absorption spectrophotometry. An appreciable variation was observed in metal concentrations indifferent mangrove species. Cu, Zn and Pb were found to be in higher concentrations in Avicennia officinalis whereas higher levels of Fe, Mn and Co were observed in the species Barringtonia racemosa. The analysis of heavy metals indicated a high level of metal pollutants such as Fe, Cu, Zn and Pb in the mangrove habitats of Quilon and Veli compared to the relatively uncontaminated areas of Kumarakom. This revised version was published online in August 2006 with corrections to the Cover Date.     

Phylogenetic diversity of nitrogen-fixing bacteria in mangrove sediments assessed by PCR-denaturing gradient gel electrophoresis

Culture-independent PCR–denaturing gradient gel electrophoresis (DGGE) was employed to assess the composition of diazotroph species from the sediments of three mangrove ecosystem sites in Sanya, Hainan Island, China. A strategy of removing humic acids prior to DNA extraction was conducted, then total community DNA was extracted using the soil DNA kit successfully for nifH PCR amplification, which simplified the current procedure and resulted in good DGGE profiles. The results revealed a novel nitrogen-fixing bacterial profile and fundamental diazotrophic biodiversity in mangrove sediments, as reflected by the numerous bands present DGGE patterns. Canonical correspondence analysis (CCA) revealed that the sediments organic carbon concentration and available soil potassium accounted for a significant amount of the variability in the nitrogen-fixing bacterial community composition. The predominant DGGE bands were sequenced, yielding 31 different nifH sequences, which were used in phylogenetic reconstructions. Most sequences were from Proteobacteria, e.g. α, γ, β, δ-subdivisions, and characterized by sequences of members of genera Azotobacter, Desulfuromonas, Sphingomonas, Geobacter, Pseudomonas, Bradyrhizobium and Derxia. These results significantly expand our knowledge of the nitrogen-fixing bacterial diversity of the mangrove environment.     

Seasonal fluctuations in the population of denitrifying and N2-fixing bacteria in an acid soil of a Norway spruce forest

The seasonal fluctuations in the concentration of cultured denitrifying and N₂-fixing bacteria were followed in an ammonium fertilised and a control soil of a Norway spruce forest near Villingen/Black Forest from December 1994 to August 1998. The horizontal distribution of bacteria in three layers was determined by the MPN-method and by molecular probing (colony hybridisation) using specific 0.4–0.7 kb DNA probes for denitrification steps (narG, nirS, nirK and nosZ) and for N₂-fixation (nifH). The data showed that highest bacterial counts and higher numbers of denitrifying and N₂-fixing bacteria were generally detectable in the upper (= 5 cm) soil layer and that their amount decreased with soil depth. The concentration of these cultured bacteria showed seasonal fluctuations with highest numbers in autumn/winter/early spring and with low counts in summer. Denitrifying and N₂-fixing bacteria amounted to less than 10% of the total number of cultured bacteria determined by the MPN-method. Fertilisation with ammonium did not cause a shift in the population of these bacteria. These findings were corroborated by hybridisation experiments with genomic DNA isolated from the different layers. Strongest DNA–DNA hybridisation band intensities were obtained in the upper soil layer and their intensities decreased with soil depth. Soil samples from Villingen assayed in the laboratory produced N₂O (in dependence of nitrate and C₂H₂ added to the vessels) and utilised this gas with higher activities in the assays with the fertilised soil. It is concluded that molecular techniques can successfully be applied for assessing seasonal fluctuations of bacterial populations in soil. Relative abundance of denitrifying and N₂-fixing bacteria can be determined from experiments with DNA isolated from soils. Attempts to transform these results to the total population of soil bacteria on a single cell basis are faced with many uncertainties.     

Growth characteristics of the heterotrophic bacterial population of water and bottom sediments in tanks under different trophic conditions

Treatment of single and double doses of fertilizers had a definite response on the bacterial population of water and bottom sediments in tanks after 7 days (F_2,21 3.61; P < 0.05), but did not cause any significant change after day 32 (F_2,18 1.67; P > 0.05). Although the generation time of water bacteria did not vary much in these treatments of trophic gradients (P > 0.05), there was always a distinct variation (P < 0.01) in the generation time of the bacterial population of bottom sediments. The population size of water bacteria was shown to maintain an inverse relationship with the diurnal variation of temperature (P < 0.05) and dissolved oxygen (P < 0.05) of the water. The changes in the size of the bacterial population of water were positively correlated with the variations of hardness (P < 0.05), chloride (P < 0.05) and ammonia nitrogen (P < 0.05) of water. Although the relationships between the heterotrophic bacterial population and the inorganic phosphate of water was not convincing (P > 0.05), an inverse relationship was established between the bacterial community of bottom sediments and the phosphate content of the water (P < 0.01).     

Effect of temperature on the in vitro reproductive fitness of Pratylenchus coffeae populations from Vietnam

The in vitro reproductive fitness on carrot discs of 10 Pratylenchus coffeae populations collected from different agricultural crops in different agro-ecological regions in Vietnam was studied and compared with the reproductive fitness of a P. coffeae population from Ghana. Few major differences in in vitro reproductive fitness on carrot discs among the 10 P. coffeae populations from Vietnam examined (with the exception of one population originally isolated from the roots of an unidentified ornamental tree and one population originally isolated from banana), and between these populations and the P. coffeae population originally isolated from banana in Ghana were observed. Our observations indicate that although the optimum temperature for reproduction of three P. coffeae populations from Vietnam examined is 25?°C to, at least, 30?°C, these populations are also tolerant to low temperatures (15–20?°C) enabling them to survive the low temperatures which occur during the winter in the northern and central parts of Vietnam.     

Seasonal changes in the microbial population of the water column and sediments of the Ongagawa River,northern Kyushu,Japan

The total viable count, population density of Escherichia coli and coliform bacteria, and nitrogen in the microbiomass (microbiomass-N) in sediments were monitored monthly at 12 points in the Ongagawa River basin from June 2002 to May 2006. The measurement of the sediment microbiomass-N was used for evaluation of the sediment’s microbial population in the river ecosystem. An extraordinarily high population of E. coli was observed during the season when there was stagnant water in the basin, with a high population and an insufficient drain diffusion system, and, thus hydrological water control is indispensable to prevent rapid E. coli growth. Microbiomass-N in sediments showed a negative correlation or independent fluctuation in relation to the bacterial population in the water column of the river. Seasonal changes in extracted nitrogen (N) in river sediments did not show correspondence with microbiomass-N in sediments. The microbiomass-N in sediments changed independently of the bacterial population in the river water, indicating that the high population of bacteria in the water does not lead to a high microbial population in river sediments. Ordination of the microbial parameters by canonical correspondence analysis (CCA) showed that microbiomass-N in sediments was quite different from other parameters. Relatively higher H⁺ (lower pH), PO₄ ³⁻ concentration and dissolved oxygen (DO) were the determinant parameters of higher microbiomass-N in sediments. A relative microbial abundance between the water column and sediments as well as each of the microbial populations in the water column and sediments could be a quantitative parameter for evaluating the biochemical processes of stream water.     

Environmental pH as an important factor for the distribution of urease positive ammonia-oxidizing bacteria

The effect of pH on ureolytic activity of a number of chemolithotrophic ammonia-oxidizing bacteria (AOB) has been studied in context with distribution patterns of these species. The pH-optima for urea-based nitrification were found to differ clearly among the examined species. Pronounced optima ranged between pH 5.0 and 8.0. Urease is an intracytoplasmic enzyme and should therefore be independent of the external pH. Our first results indicated the presence of a pH-dependent uptake system for urea. Simultaneous oxidation of free ammonia, possible only at high pH values, led to a strong intensification of ureolysis. The lag-phase of growth on urea as the sole energy source was clearly prolonged compared to free ammonia. Our results point on the existence of an active, most likely energy-linked urea-uptake system in addition to a possible passive diffusion of urea. The different pH-optima of urea-uptake agree with known distribution patterns of distinct AOB. It might be a reason for the shift of dominant Nitrosospira populations along pH gradients in acid soils as observed by others in molecular analyses of natural AOB populations.     

The occurrence of denitrifying colourless sulphur-oxidising bacteria in marine waters and sediments as shown by the agar shake technique

Abstract The agar shake technique has been tested for the enumeration and isolation of bacteria involved in the anaerobic oxidation of reduced sulphur compounds. High numbers of colony forming units were observed from regions rich in sulphide, and the numbers of these forms were sometimes significantly correlated with the number of sulphate-reducing bacteria. The isolates could oxidise not only thiosulphate but also sulphide in liquid medium at the expense of nitrate. Addition of 1 mM glucose to the medium enhanced the rate and amount of thiosulphate oxidised by many of the isolates. Hence the use of the agar shake technique is recommended for the study of these little known facultatively or even obligately chemolithotrophic bacteria involved in the anaerobic oxidation of reduced inorganic sulphur compounds in the marine and estuarine environment.     

Monomerization alters the dynamics of the lid region in Campylobacter jejuni CstII: an MD simulation study

CstII, a bifunctional (α2,3/8) sialyltransferase from Campylobacter jejuni, is a homotetramer. It has been reported that mutation of the interface residues Phe121 (F121D) or Tyr125 (Y125Q) leads to monomerization and partial loss of enzyme activity, without any change in the secondary or tertiary structures. MD simulations of both tetramer and monomer, with and without bound donor substrate, were performed for the two mutants and WT to understand the reasons for partial loss of activity due to monomerization since the active site is located within each monomer. RMSF values were found to correlate with the crystallographic B-factor values indicating that the simulations are able to capture the flexibility of the molecule effectively. There were no gross changes in either the secondary or tertiary structure of the proteins during MD simulations. However, interface is destabilized by the mutations, and more importantly the flexibility of the lid region (Gly152-Lys190) is affected. The lid region accesses three major conformations named as open, intermediate, and closed conformations. In both Y121Q and F121D mutants, the closed conformation is accessed predominantly. In this conformation, the catalytic base His188 is also displaced. Normal mode analysis also revealed differences in the lid movement in tetramer and monomer. This provides a possible explanation for the partial loss of enzyme activity in both interface mutants. The lid region controls the traffic of substrates and products in and out of the active site, and the dynamics of this region is regulated by tetramerization. Thus, this study provides valuable insights into the role of loop dynamics in enzyme activity of CstII.     

Seasonal and spatial distribution of dissolved and particulate organic carbon and bacteria in the bank of an impounding reservoir on the Enns River, Austria

1. Interstitial bacterial abundance, production and ectoenzyme activity were investigated over an annual cycle in an Austrian river when infiltration of oligotrophic river water into a river-bank was artificially enhanced. These microbial parameters were related to porewater chemistry and the concentration of particulate (POC) and dissolved organic carbon (DOC).
2. Porewater chemistry reflected the hydrodynamic mixing of infiltrating river water with riparian groundwater. Seasonal fluctuations in the microbial parameters resulted mainly from changes in temperature and organic matter supply. Seasonal change in porewater chemistry in the river-bank was detectable laterally only within the first metre of the sediment and decreased rapidly with increasing distance from the sediment–water interface.
3. The DOC concentration decreased only slightly during lateral transport through the aquifer, while total organic carbon (TOC) concentration as well as abundance and activity of interstitial bacteria were reduced by up to one order of magnitude within the top metre of the sediment. Retention of incoming particulate matter structured the lateral distribution pattern of TOC concentration. The POC and not the DOC pool was the main source of carbon for interstitial bacteria and, therefore, the quality of POC determines the distribution of microbial metabolism within the riparian zone.     

Seasonal and inter-stream variations in the population dynamics, growth and secondary production of an algivorous fish (Pseudogastromyzon myersi: Balitoridae) in monsoonal Hong Kong

1. Balitorid loaches are widespread and highly diverse in Asian streams, yet their life history and ecology have received little attention. We investigated seasonal (wet versus dry season) and spatial variation in populations of algivorous Pseudogastromyzon myersi in Hong Kong, and estimated the magnitude of secondary production by this fish in pools in four streams (two shaded and two unshaded) over a 15‐month period. 2. Mean population densities of P. myersi ranged from 6.0 to 23.2 individuals m⁻², constituting more than half (and typically >70%) of benthic fishes censused. Abundance was c. 25% greater in the wet season, when recruitment occurred. Significant density differences among streams were not related to shading conditions and were evident despite small‐scale variations in P. myersi abundance among pools. Mean biomass varied among streams from 0.85 to 3.87 g ash‐free dry weight (AFDW) m⁻². Spatial and seasonal patterns in biomass and density were similar, apart from some minor disparities attributable to differences in mean body size among populations. 3. All four P. myersi populations bred once a year in June and July, and life spans varied from 24 to 26 months. Populations consisted of three cohorts immediately after recruitment but, for most of the study period, only two cohorts were evident. Cohort‐specific growth rates did not differ significantly among streams but, in all streams, younger cohorts had higher cohort‐specific growth rates. 4. Secondary production of P. myersi estimated by the size‐frequency (SF) method was 2.7–11.5 g AFDW m⁻² year⁻¹ and almost twice that calculated by the increment‐summation (IS) method (1.2–6.6 g AFDW m⁻² year⁻¹). Annual P/B ratios were 1.17 – 2.16 year⁻¹ (IS) and 2.73 – 3.22 year⁻¹ (SF). Highest production was recorded in an unshaded stream and the lowest in a shaded stream, but site rankings by production did not otherwise match shading conditions. Wet‐season production was six times greater than dry‐season production, and daily production fell to almost zero during January and February. Cool temperatures (<17 °C) may have limited fish activity and influenced detectability during some dry‐season censuses. Estimates of abundance and annual production by P. myersi are therefore conservative. 5. Comparisons with the literature indicate that the abundance and production of P. myersi in Hong Kong was high relative to other benthic fishes in tropical Asia, or their temperate counterparts in small streams. Manipulative experiments are needed to determine the influence of P. myersi, and algivorous balitorids in general, on periphyton dynamics and energy flow in Asian streams.     

Application of molecular methods for the differentiation of acetic acid bacteria in a red wine fermentation

AIMS: To apply rapid and reliable molecular techniques for typing acetic acid bacteria and studying their population dynamics during wine-making processes. METHODS AND RESULTS: We tested the usefulness of the Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR) and Repetitive Extragenic Palindromic-PCR (REP-PCR) techniques with reference strains of most of the species of acetic acid bacteria. We obtained exclusive patterns for each strain with the ERIC-PCR technique, proving the utility for characterizing below species level. REP-PCR technique was not as adequate for this purpose because some strains yielded identical fingerprint. One hundred twenty isolates from a commercial red wine fermentation were fingerprinted using both techniques. We detected a high degree of strain diversity in the first stage of fermentation that decreased throughout the process. However, several strains and species were dominant in the alcoholic fermentation phases. The identification of different strains or genotypes at the species level was carried out by restriction analysis of the 16S ribosomal DNA gene. Gluconobacter oxydans dominated the fresh must, while Acetobacter aceti was the only isolated species at the end of the process. Gluconacetobacter hansenii and G. liquefaciens were also isolated in significant numbers at the beginning of fermentation. CONCLUSIONS: ERIC-PCR and REP-PCR techniques proved useful for characterizing strains of acetic acid bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY: The availability of molecular techniques for a fast and reliable genotypic characterization should increase our knowledge of the ecology of acetic acid bacteria and determine more accurately their growth behaviour during various stages of vinification.     

Application of the filter plate microbial trap (FPMT), for cultivating thermophilic bacteria from thermal springs in Barguzin area,eastern Baikal,Russia

Hot springs are regarded as treasury of valuable thermophiles. Like other bacteria, thermophiles are not easily cultivated using conventional culture methods. We used an advanced cultivation method, the filter plate microbial trap (FPMT), to isolate bacteria from thermal springs. In total, 184 isolates were obtained from five thermal springs using the FPMT and standard agar plate method, and their 16S rRNA gene sequences were analyzed. FPMT allowed us to obtain a culture collection that was larger, richer, and more novel than that obtained by standard cultivation. Seven novel species were obtained using the FPMT technique, whereas only one was isolated using a standard cultivation. We also found clear differences in the patterns of phylogenetic diversity and physiological properties between isolates from two cultivation methods. The results have encouraged us to apply the FPMT method in other extreme environments and offer further support for fostering the development of new cultivation methods.     

The N-terminal K homology domain of the poly(rC)-binding protein is a major determinant for binding to the poliovirus 5'-untranslated region and acts as an inhibitor of viral translation

The poly(rC)-binding proteins (PCBP1 and PCBP2) are RNA-binding proteins whose RNA recognition motifs are composed of three K homology (KH) domains. These proteins are involved in both the stabilization and translational regulation of several cellular and viral RNAs. PCBP1 and PCBP2 specifically interact with both the 5'-element known as the cloverleaf structure and the large stem-loop IV RNA of the poliovirus 5'-untranslated region. We have found that the first KH domain of PCBP2 (KH1) specifically interacts with the viral RNAs, and together with viral protein 3CD, KH1 forms a high affinity ternary ribonucleoprotein complex with the cloverleaf RNA, resembling the full-length PCBP protein. Furthermore, KH1 acts as a dominant-negative mutant to inhibit translation from a poliovirus reporter gene in both Xenopus laevis oocytes and HeLa cell in vitro translation extracts.