The distribution and activity of sulphate reducing bacteria in estuarine and coastal marine sediments

Sulphate-reducing bacteria (SRB) play a vital role both the carbon and sulphur cycles and thus are extremely important components of the global microbial community. However, it is clear that the ecology, the distribution and activity of different SRB groups is poorly understood. Probing of rRNA suggests that different sediments have distinctly different patterns of SRB with complex factors controlling the activity of these organisms. The linking of community structure and function using sediment slurry microcosms suggests that certain groups of SRB, e.g., Desulfobacter and Desulfobulbus, can be linked to the use of specific substrates in situ. However, it is still unclear what environmental substrates are utilised by the majority of known SRBs. The work to date has greatly enhanced our understanding of the ecology of these organisms and is beginning to suggest patterns in their distribution and activity that may be relevant to understanding microbial ecology in general. This revised version was published online in August 2006 with corrections to the Cover Date.     

Characterization of sulphate-reducing bacterial populations within marine and estuarine sediments with different rates of sulphate reduction

Viable counts of sulphate-reducing bacteria, able to use a range of different growth substrates were determined in sediments from two Sea Lochs (Etive and Eil) and an estuarine site (Tay), in Scotland. The composition of the sulphate-reducing bacterial population, in terms of substrate utilization, broadly corresponded to the in situ substrates for sulphate reduction and concentration of substrates at each site. Addition of acetate, lactate, propionate, butyrate, hydrogen and glutamate/serine (20 mM) to replicate slurries from each site resulted in stimulation of the corresponding population of sulphate-reducing bacteria and the in situ rates of sulphate reduction. The metabolism of the added substrates and changes in bacterial phospholipid fatty acids (PLFA) were quantified. With the exception of acetate and hydrogen, added substrates were incompletely oxidised, producing a mixture of further substrates, which predominantly were sequentially oxidised, and resulted in the stimulation of a mixed population of sulphate-reducing bacteria. There were significant changes in the PLFA of slurries with added substrate compared to controls. Acetate was completely removed at all sites and the small increase in even chain PLFA together with the absence of stimulation of any other biomarker, indicated that acetate was oxidised by sulphate-reducing bacteria distinctly different from those using other substrates. A biomarker for Desulfobacter, 10 Methyl 16:0, was not stimulated in any of the acetate slurries or in slurries where acetate was produced. Biomarkers for the propionate utilizing Desulfobulbus sp (17:1w6, 15:1w6) were always stimulated in propionate slurries and also in lactate slurries, where partial lactate fermentation produced propionate and acetate. In lactate and glutamate / serine slurries from the Tay estuary and lactate and hydrogen slurries from Loch Etive the biomarker for Desulfovibrio sp (i17:1w7) as well as those for Desulfobulbus were stimulated. This provides direct evidence for the significance of Desulfovibrio sp. within sediment slurries and demonstrates the competitive interaction between members of this genus and Desulfobulbus sp. for lactate, hydrogen and amino acid metabolism. At the estuarine site, sulphate reduction was limited at higher sulphate concentrations (about 3.5 mM) than the Sea Loch sites (<2 mM) and this had a significant effect on propionate and butyrate metabolism, as well as on methane production. These results demonstrate that although the sulphate-reducing bacterial population at each site could metabolise identical substrates, the types of sulphate-reducing bacteria involved and their sulphate thresholds were characteristically different.     

海洋沉积物中铁还原细菌组成及异化铁还原与产氢性质分析

【背景】一些铁还原细菌具有异化铁还原与产氢的能力,该类细菌在环境污染修复的同时能够解决能源问题。【目的】从海洋沉积物中富集获得异化铁还原菌群,明确混合菌群组成、异化铁还原及产氢性质。获得海洋沉积物中异化铁还原混合菌群组成,分析菌群异化铁还原和产氢性质。【方法】利用高通量测序技术分析异化铁还原菌群的优势菌组成,在此基础上,分析异化铁还原混合菌群在不同电子供体培养条件下异化铁还原能力和产氢性质。【结果】高通量数据表明,在不溶性氢氧化铁为电子受体和葡萄糖为电子供体厌氧培养条件下,混合菌群的优势菌属主要是梭菌(Clostridium),属于发酵型异化铁还原细菌。混合菌群能够利用电子供体蔗糖、葡萄糖以及丙酮酸钠进行异化铁还原及发酵产氢。葡萄糖为电子供体时,菌群累积产生Fe(Ⅱ)浓度和产氢量最高,分别是59.34±6.73 mg/L和629.70±11.42 mL/L。【结论】异化铁还原混合菌群同时具有异化铁还原和产氢能力,拓宽了发酵型异化铁还原细菌的种质资源,探索异化铁还原细菌在生物能源方面的应用。     

Bacterial abundance in relation to surface area and organic content of marine sediments

Based on direct measurements on surface sediments collected from an intertidal salt marsh, a positive relationship was demonstrated between bacterial abundance and specific surface area of sediment. While this relationship has been postulated previously, this is the first direct confirmation that it holds over a wide range of sediment types. A laboratory experiment was conducted to determine the effects of specific surface area, distribution of surface area, and organic loading on bacterial colonization. Model sediments included angular silica particles, kaolin, and spherical glass beads, used singly or in mixtures. Organic loading resulted in substantial enhancement of bacterial colonization. Distribution of surface area controlled by textural, shape, and sorting, had a complex effect, with glass bead sediments generally supporting better colonization than silica particles or kaolin. The effect of specific surface area was noted only in restricted comparisons of similarly shaped glass beads.     

Bicarbonate-dependent production and methanogenic consumption of acetate in anoxic paddy soil

Abstract Acetate turnover was measured in slurries of anoxic methanogenic paddy soil after addition of carrier-free [2-¹⁴C]-acetate. Acetate concentrations stayed fairly constant for about 1–2 days indicating steady state between production and consumption reactions. Depending on the experiment, acetate concentrations were between 100 and 3000 μM. Turnover rates were determined from the logarithmic decrease of [2-¹⁴C]-acetate or from the accumulation of acetate in the presence of chloroform resulting in similar values, i.e. 12–13 nmol h⁻¹g⁻¹d.w. soil at 17°C and 36–88 nmol h⁻¹g⁻¹d.w. at 30°C. Acetate consumption was completely inhibited by chloroform. The respiratory index (RI) was < 0.27. Hence, acetate was apparently consumed by methanogenic bacteria. About 80–90% of the CH₄ produced originated from the methyl group of acetate. The role of homoacetogenesis for acetate production was studied by measuring the incorporation of radioactive bicarbonate into acetate. In different experiments, CO₂ incorporation accounted for fractions of 1–60% of the acetate produced, about 10% being the most likely value for steady-state conditions. The fraction increased at high H₂ concentrations and decreased at high acetate concentrations. The rate of H₂ production that was required for chemolithotrophic acetate production from CO₂ was two orders of magnitude higher than the actually measured rate. Hence, most of the CO₂ incorporation into acetate was caused by electron donors other than H₂ (e.g., carbohydrates) and/or by exchange reactions.     

Uptake and turnover of acetate in hypersaline environments

Abstract: Acetate uptake and turnover rates were determined for the heterotrophic community in hypersaline environments (saltern crystallizer ponds, the Dead Sea) dominated by halpphilic Archaea. Acetate was formed from glycerol, which is potentially the major available carbon source for natural communities of halophilic Archaea. Values of [ K _t+ S _n] (the sum of the substrate affinity and the substrate concentration present in situ) for acetate measured in saltern crystallizer ponds were around 4.5–11.5 μM, while in the Dead Sea during a Dunaliella bloom values up to 12.8 μM were found. Maximal theoretical rates ( V _max) of acetate uptake in saltern crystallizer ponds were 12–56 nmol l⁻¹ h⁻¹, with estimated turnover times for acetate ( T _t) between 127–730 h at 35°C. V _max values measured in the Dead Sea were between 0.8 and 12.8 nmol l⁻¹ h⁻¹, with turnover times in the range of 320–2190 h. V _max values for acetate were much lower than those for glycerol. Comparisons with pure cultures of halophilic Archaea grown under different conditions showed that the natural communities were not adapted for preferential use of acetate. Both in natural brines and in pure cultures of halophilic Archaea, acetate incorporation rates rapidly decreased above the optimum pH value, probably since acetate enters the cell only in its unionized form. The low affinity for acetate, together with low potential utilization rates result in the long acetate turnover times, which explains the accumulation of acetate observed when low concentrations of glycerol are supplied as a nutrient to natural communities of halophilic Archaea.     

Sulfide-induced dissimilatory nitrate reduction to ammonia in anaerobic freshwater sediments

Abstract: Different reduced sulfur compounds (H₂S, FeS, S₂O₃²⁻) were tested as electron donors for dissimilatory nitrate reduction in nitrate-amended sediment slurries. Only in the free sulfide-enriched slurries was nitrate appreciably reduced to ammonia (     ), with concomitant oxidation of sulfide to S⁰ (     ). The initial concentration of free sulfide appears as a factor determining the type of nitrate reduction. At extremely low concentrations of free S²⁻ (metal sulfides) nitrate was reduced via denitrification whereas at higher S²⁻ concentrations, dissimilatory nitrate reduction to ammonia (DNRA) and incomplete denitrification to gaseous nitrogen oxides took place. Sulfide inhibition of NO- and N₂O- reductases is proposed as being responsible for the driving part of the electron flow from S²⁻ to NH₄⁺.     

Measure of microbial turnover of carbon in anoxic freshwater sediments: cautionary comments

Small sediment cores were used to determine the turnover of a range of carbon substrates, particularly volatile fatty acids, by bentic bacteria. Volatile fatty acids were determined using an HPLC sytem in cojunction with a conductivity detector. At the low eluent strength used 1 μM acetate was detected with ease. Small cores were used in an attempt to maintain the natural partial pressure of hydrogen, an important factor in the control of anerobic metabolism of fatty acids. Although this is preferable to the disturbance of the sediment which occurs if it is resuspended a a slurry, problems are encountered at low substrate concentrations. The time taken for the added substrate to equilibrate in both radial and vertical planes may result in turnover times which vary with the incubation time used. Reduction of the qunatity of added substrate and increased replication may improve the accuracy of the estimates obtained, but more serious consideration must be given to the availability of the substrates to the benthic bacteria.     

Protein turnover in relation to maintenance metabolism at low photon flux in two marine microalgae

Acclimation to very low photon fluxes involves adjusting a suite of physiological characteristics that collectively elicit a physiological response. Facilitating such changes is pro‐tein turnover. Dunaliella tertiolecta (Butcher) and Phaeodactylum tricornutum (Bohlin) were grown in turbidostats at a range of photon fluxes between 2 and 300 µmol photons m^?2 s^?1. The kinetics of pulse‐chase labelling of the protein with ³H showed that (1) two protein pools were present, one of which turned‐over rapidly (hours), and a second which turned over more slowly (days); and (2) protein turnover rates were slower in P. tricornutum than in D. tertiolecta. Phaeodactylum tricornutum had a lower maintenance coefficient for protein turnover than D. tertiolecta, and correspondingly a smaller proportion of its respiratory demands (30%) were associated with protein turnover than in D. tertiolecta (36%). There appears to be a correlation between lower metabolic activity, requiring lower protein concentrations, and an associated decreased cost of maintenance processes in P. tricornutum compared to D. tertiolecta. Differences between protein turnover rates and maintenance metabolic costs may be one of the photo‐acclimation strategies that determine which photon niches microalgae can successfully exploit.     

Evidence for the biological turnover of thiols in anoxic marine sediments

The concentrations of methanethiol (MSH) and 3-mercaptopropionate (3-MPA) increased for a period of up to 24 h in fresh slurries of anoxic Biscayne Bay sediments. Other endogenous thiols such as glutathione (GSH) deceased immediately after slurry preparation or were not detectable at all. The maximum concentrations reached by 3-MPA and MSH were sometimes as high as 1 M, but were usually in the 100 to 300 nM range. After the initial increases, the concentrations of these thiols decreased rapidly to nearly constant levels of 20 nM for MSH and < 1nM for 3-MPA. In pre-incubated slurries, which had constant levels of thiols, the addition of microbial inhibitors including tungstate, molybdate, chloroform, and a mixture of chloramphenicol plus tetracycline caused MSH and 3-MPA to accumulate steadily. In the presence of inhibitors, accumulation rates of MSH ranged from 18 to 730 nM · d^-1 and those of 3-MPA ranged from 0 to 185 nM · d^-1. Tungstate and chloroform generally gave the highest accumulation rates, while molybdate gave the lowest, possibly due to its complexation with sulfhydryl compounds. BES (2-Bromoethanesulfonate) was also tested for its effects, but no 3-MPA and only trace amounts (19 nM · d^-1) of MSH accumulated with this treatment. However, additions of BES (10 mM) to sulfidic sediments caused significant (8 M · d^-1) production of 2-mercaptoethanesulfonate (HS-CoM). Formation of HS-CoM was abiotic and was due to sulfide attack on the bromine atom in BES. The accumulations of 3-MPA and MSH in the presence of several different microbial inhibitors, suggests that these thiols may turn over in anoxic sediments. The relatively low concentrations of thiols observed in pore water profiles may be due to continuous microbial removal of these compounds. Much larger amounts of thiols were associated with sediment particles than present in the pore water. Evidence is presented which suggests that bound thiols may be exchangeable with the porewater, and therefore potentially available for microbial consumption.     

Comparative study of enrichment methods for the isolation of autotrophic nitrifying bacteria from soil, estuarine and marine sediments

Abstract A comparative study has been undertaken to determine the efficiency of methods for the enrichment and isolation of autotrophic nitrifying bacteria from soils and estuarine and marine sediments. Chemostat enrichments proved to be the most efficient means of isolating autotrophic NH⁺₄ oxidisers whereas NO⁻₂ oxidising bacteria were never successfully enriched by this method. In contrast, gel enrichment and traditional batch culture enrichments of nitrifying bacteria were comparatively time consuming procedures and the degree of enrichment obtained for NH⁺₄ oxidising bacteria never approached that obtained with continuous culture enrichments. Gel enrichments, however, because they have continuous physicochemical gradients provide qualitative advantages in that morphologically distinct types of nitrifying bacteria can be isolated from the same gel.     

The effect of long-term nitrate treatment on SRB activity,corrosion rate and bacterial community composition in offshore water injection systems

Biogenic production of hydrogen sulphide (H₂S) is a problem for the oil industry as it leads to corrosion and reservoir souring. Continuous injection of a low nitrate concentration (0.25–0.33 mM) replaced glutaraldehyde as corrosion and souring control at the Veslefrikk and Gullfaks oil field (North Sea) in 1999. The response to nitrate treatment was a rapid reduction in number and activity of sulphate-reducing bacteria (SRB) in the water injection system biofilm at both fields. The present long-term study shows that SRB activity has remained low at ≤0.3 and ≤0.9 μg H₂S/cm²/day at Veslefrikk and Gullfaks respectively, during the 7–8 years with continuous nitrate injection. At Veslefrikk, 16S rRNA gene based community analysis by PCR–DGGE showed that bacteria affiliated to nitrate-reducing sulphide-oxidizing Sulfurimonas (NR–SOB) formed major populations at the injection well head throughout the treatment period. Downstream of deaerator the presence of Sulfurimonas like bacteria was less pronounced, and were no longer observed 40 months into the treatment period. The biofilm community during nitrate treatment was highly diverse and relative stable for long periods of time. At the Gullfaks field, a reduction in corrosion of up to 40% was observed after switch to nitrate treatment. The present study show that nitrate injection may provide a stable long-term inhibition of SRB in sea water injection systems, and that corrosion may be significantly reduced when compared to traditional biocide treatment.     

Bioremediation of organic and metal contaminants with dissimilatory metal reduction

PCR fingerprinting offers a practical molecular means to quickly and reliably differentiate bacteria for microbial products screening. A combination of low resolution and high resolution PCR fingerprinting provides a hirarchical system which allows the discrimination of bacteria at species and subspecies level within 7 h. DNA was extracted from cells by incubating them in water at 95°C for 30 min. A sample of 1 l of the cell-free aqueous extract then was used as a source of template DNA in the PCR. The PCR products were separated by electrophoresis on an acrylamide gel and visualized by ethidium bromide staining. The band patterns generated for each different culture were unique, reproducible, and independent of cultivation conditions. Band patterns may be compared visually or by using imaging and pattern matching software. In our laboratory, bacteria such as actinomycetes, Gram-negative and Gram-positive soil eubacteria, and photosynthetic non-sulfur bacteria have been differentiated using PCR fingerprinting.     

Mechanisms of acetate formation and acetate activation in halophilic archaea

The halophilic archaea Halococcus (Hc.) saccharolyticus, Haloferax (Hf.) volcanii, and Halorubrum (Hr.) saccharovorum were found to generate acetate during growth on glucose and to utilize acetate as a growth substrate. The mechanisms of acetate formation from acetyl-CoA and of acetate activation to acetyl-CoA were studied. Hc. saccharolyticus, exponentially growing on complex medium with glucose, formed acetate and contained ADP-forming acetyl-CoA synthetase (ADP-ACS) rather than acetate kinase and phosphate acetyltransferase or AMP-forming acetyl-CoA synthetase. In the stationary phase, the excreted acetate was completely consumed, and cells contained AMP-forming acetyl-CoA synthetase (AMP-ACS) and a significantly reduced ADP-ACS activity. Hc. saccharolyticus, grown on acetate as carbon and energy source, contained only AMP-ACS rather than ADP-ACS or acetate kinase. Cell suspensions of Hc. saccharolyticus metabolized acetate only when they contained AMP-ACS activity, i.e., when they were obtained after growth on acetate or from the stationary phase after growth on glucose. Suspensions of exponential glucose-grown cells, containing only ADP-ACS but not AMP-ACS, did not consume acetate. Similar results were obtained for the phylogenetic distantly related halophilic archaea Hf. volcanii and Hf. saccharovorum. We conclude that, in halophilic archaea, the formation of acetate from acetyl-CoA is catalyzed by ADP-ACS, whereas the activation of acetate to acetyl-CoA is mediated by an inducible AMP-ACS.Abbreviations. Hc. Halococcus - Hf. Haloferax - Hr. Halorubrum - Hb. Halobacterium An erratum to this article can be found at     

Biological invasions drive size increases in marine and estuarine invertebrates

Ecologists have long been fascinated by the morphological changes that species frequently undergo when introduced into new regions. In this study an unusual pattern of size change associated with the invasion of 19 species of marine and estuarine invertebrates is reported. The results show that the majority of species are significantly larger in the introduced range compared with the native range with little evidence for any decrease in size following invasion. This invasion‐driven increase in body size sharply contrasts with the pattern observed in many other taxa including plants, mammals and lizards, where invaders frequently exhibit post‐invasion decreases and increases in size. These size changes were not influenced by differences in latitude, sample size or length of time since invasion. Although several mechanisms, may explain the results, none have been demonstrated.     

Ommatidial structure in relation to turnover of photoreceptor membrane in the locust

Summary In the compound eye of the locust, Locusta, the cross-sectional area of the rhabdoms increases at dusk by 4.7-fold due to the rapid assembly of new microvillar membrane, and decreases at dawn by a corresponding amount as a result of pinocytotic shedding from the microvilli. The rhabdoms at night have more and longer photoreceptor microvilli than rhabdoms during the day. The orientations of the six rhabdomeres that comprise the distal rhabdom also change. The density of intramembrane particles on the P-face of the microvillar membrane, putatively representing mostly rhodopsin molecules, or aggregates thereof, does not change.An alteration in the size of the ommatidial field-stop, produced by the primary pigment cells, is concomitant with the change in rhabdom size. At night the increase in size of the field-stop must widen the angular acceptance of a rhabdom, increasing the capture of photons from an extended field. Conversely, during the day, when photons are more abundant, its decrease must narrow the acceptance angle, increasing angular resolution. Because of the presence of this field-stop, the optics of the ommatidium would not be greatly affected if the rhabdom were to remain always at its night size. It is argued, therefore, that the variable-size rhabdom must have resulted from some demand other than that of light/dark adaptation.Changes in size and organisation of the rhabdoms in response to various light regimes indicate that: (1) Rapid shedding of photoreceptor membrane is induced by the onset of light, but shedding also occurs slowly in darkness during the day. (2) Microvillar assembly is initiated by the onset of darkness, but also occurs at the normal time of dusk without a change in ambient lighting, provided there has been some light during the day. Therefore, both shedding and assembly of microvillar membrane are affected by the state of illumination, but also appear to be under some endogenous control.