Unexpected population distribution in a microbial mat community: sulfate-reducing bacteria localized to the highly oxic chemocline in contrast to a eukaryotic preference for anoxia.

The distribution and abundance of sulfate-reducing bacteria (SRB) and eukaryotes within the upper 4 mm of a hypersaline cyanobacterial mat community were characterized at high resolution with group-specific hybridization probes to quantify 16S rRNA extracted from 100-microm depth intervals. This revealed a preferential localization of SRB within the region defined by the oxygen chemocline. Among the different groups of SRB quantified, including members of the provisional families "Desulfovibrionaceae" and "Desulfobacteriaceae," Desulfonema-like populations dominated and accounted for up to 30% of total rRNA extracted from certain depth intervals of the chemocline. These data suggest that recognized genera of SRB are not necessarily restricted by high levels of oxygen in this mat community and the possibility of significant sulfur cycling within the chemocline. In marked contrast, eukaryotic populations in this community demonstrated a preference for regions of anoxia.     

Anaerobic degradation of naphthalene by a pure culture of a novel type of marine sulphate-reducing bacterium

Incubation of marine sediment in anoxic, sulphate-rich medium in the presence of naphthalene resulted in the enrichment of sulphate-reducing bacteria. Pure cultures with short, oval cells (1.3 by 1.3–1.9 μm) were isolated that grew with naphthalene as the only organic carbon source and electron donor for sulphate reduction to sulphide. One strain, NaphS2, was characterized. It affiliated with completely oxidizing sulphate-reducing bacteria of the δ-subclass of the Proteobacteria, as revealed by 16S rRNA sequence analysis. 2-Naphthoate, benzoate, pyruvate and acetate were used in addition to naphthalene. Quantification of substrate consumption, sulphide formation and formed cell mass revealed that naphthalene was completely oxidized with sulphate as the electron acceptor.     

Biogeochemistry of microbial mats under Precambrian environmental conditions: a modelling study

Microbial mats have arguably been the most important ecosystem on Earth over its 3.5 Gyr inhabitation. Mats have persisted as consortia for billions of years and occupy some of Earth's most hostile environments. With rare exceptions (e.g. microbial mats developed on geothermal springs at Yellowstone National Park, USA), today's mats do not exist under conditions analogous to Precambrian habitats with substantially lower oxygen and sulphate concentrations. This study uses a numerical model of a microbial mat to investigate how mat composition in the past might have differed from modern mats. We present a numerical model of mat biogeochemistry that simulates the growth of cyanobacteria (CYA), colourless sulphur bacteria (CSB), and purple sulphur bacteria (PSB), with sulphate‐reducing bacteria (SRB) and heterotrophic bacteria represented by parameterized sulphate reduction rates and heterotrophic consumption rates, respectively. Variations in the availability of light, oxygen, sulphide, and sulphate at the upper boundary of the mat are the driving forces in the model. Mats with remarkably similar biomass and chemical profiles develop in models under oxygen boundary conditions ranging from 2.5 × 10^?13 to 0.25 mm and sulphate boundary concentrations ranging from 0.29 to 29 mm , designed to simulate various environments from Archean to modern. The modelled mats show little sensitivity to oxygen boundary conditions because, independent of the overlying oxygen concentrations, cyanobacterial photosynthesis creates similar O₂ concentrations of 0.45–0.65 mm in the upper reaches of the mat during the photoperiod. Varying sulphate boundary conditions have more effect on the biological composition of the mat. Sulphide generated from sulphate reduction controls the magnitude and distribution of the PSB population, and plays a part in the distribution of CSB. CSB are the most sensitive species to environmental change, varying with oxygen and sulphide.     

Inorganic carbon fixation by sulfate-reducing bacteria in the Black Sea water column

The Black Sea is the largest anoxic water basin on Earth and its stratified water column comprises an upper oxic, middle suboxic and a lower permanently anoxic, sulfidic zone. The abundance of sulfate-reducing bacteria (SRB) in water samples was determined by quantifying the copy number of the dsrA gene coding for the alpha subunit of the dissimilatory (bi)sulfite reductase using real-time polymerase chain reaction. The dsrA gene was detected throughout the whole suboxic and anoxic zones. The maximum dsrA copy numbers were 5 x 10(2) and 6.3 x 10(2) copies ml(-1) at 95 m in the suboxic and at 150 m in the upper anoxic zone, respectively. The proportion of SRB to total Bacteria was 0.1% in the oxic, 0.8-1.9% in the suboxic and 1.2-4.7% in the anoxic zone. A phylogenetic analysis of 16S rDNA clones showed that most clones from the anoxic zone formed a coherent cluster within the Desulfonema-Desulfosarcina group. A similar depth profile as for dsrA copy numbers was obtained for the concentration of non-isoprenoidal dialkyl glycerol diethers (DGDs), which are most likely SRB-specific lipid biomarkers. Three different DGDs were found to be major components of the total lipid fractions from the anoxic zone. The DGDs were depleted in (13)C relative to the delta(13)C values of dissolved CO(2) (delta(13)C(CO2)) by 14-19 per thousand. Their delta(13)C values [delta(13)C(DGD(II-III))] co-varied with depth showing the least (13)C-depleted values in the top of the sulfidic, anoxic zone and the most (13)C-depleted values in the deep anoxic waters at 1500 m. This co-variation provides evidence for CO(2) incorporation by the DGD(II-III)-producing SRB, while the 1:2 relationship between delta(13)C(CO2) and delta(13)C(DGD(II-III)) indicates the use of an additional organic carbon source.     

Ecology of the bacteria of the sulphur cycle with special reference to anoxic-oxic interface environments

H2S is produced as a main end-product of anaerobic mineralization in anoxic, sulphate-rich environments by a diverse population of sulphate-reducing bacteria. The sulphate reducers can carry out an almost complete oxidation of detrital organic matter to CO2. The H2S consequently becomes an important electron carrier from the anoxic to the oxic world. Thiobacilli and other colourless sulphur bacteria have the potential to oxidize the H2S at the oxic-anoxic interface in sediments or stratified waters, but their role is still poorly understood. A comparison of sulphide oxidation processes in the chemoclines of the Black Sea, the Solar Lake and in A beggiatoa mat indicated that depth scales and retention times of coexisting O2 and H2S regulate the bacterial involvement in the sulphide oxidation. The H2S specialists, Beggiatoa and Thiovulum, are optimally adapted to compete with the autocatalytic oxidation of H2S by O2. Microelectrode measurements show retention times of O2-H2S in the bacterial mats or veils of less than 1 s. In photic chemoclines of stratified waters or sulfureta, the phototrophic sulphur bacteria or cyanobacteria interact with the sulphide oxidation at the O2-H2S interface. Short cycles between H2S and intermediate oxidation products, So or S2O2 3-, are created. The bacteria of the sulfuretum are highly adapted to the diurnal rhythm of light, O2 and H2S.     

Dimethyl sulphide and methanethiol formation in microbial mats: potential pathways for biogenic signatures

Mechanisms of dimethyl sulphide (DMS) and methanethiol (MT) production and consumption were determined in moderately hypersaline mats, Guerrero Negro, Mexico. Biological pathways regulated the net flux of DMS and MT as revealed by increases in flux resulting from decreased salinity, increased temperature and the removal of oxygen. Dimethylsulphoniopropionate (DMSP) was not present in these microbial mats and DMS and MT are probably formed by the reaction of photosynthetically produced low-molecular weight organic carbon and biogenic hydrogen sulphide derived from sulphate reduction. These observations provide an alternative to the notion that DMSP or S-containing amino acids are the dominant precursors of DMS in intertidal sediment systems. The major sink for DMS in the microbial mats was biological consumption, whereas photochemical oxidation to dimethylsulphoxide was the major sink for DMS in the overlying water column. Diel flux measurements demonstrated that significantly more DMS is released from the system during the night than during the day. The major consumers of DMS in the presence of oxygen were monooxygenase-utilizing bacteria, whereas under anoxic conditions, DMS was predominantly consumed by sulphate-reducing bacteria and methanethiol was consumed by methanogenic bacteria. Aerobic and anaerobic consumption rates of DMS were nearly identical. Mass balance estimates suggest that the consumption in the water column is likely to be smaller than net the flux from the mats. Volatile organic sulphur compounds are thus indicators of high rates of carbon fixation and sulphate reduction in these laminated sediment ecosystems, and atmospheric sulphur can be generated as a biogenic signature of the microbial mat community.     

Bacterial oxidation of sulphide under denitrifying conditions

Anoxic H2S oxidation under denitrifying conditions produced sulphur and sulphate in almost equal proportions by an isolated Thiobacillus denitrificans. Under nitrate reducing conditions the rate of sulphide oxidation was approximately 0.9 g sulphide/g biomass h. Nitrate was reduced to nitrite and accumulated during sulphide oxidation. Above 100 mg nitrite/l, the sulphide oxidation rate declined and at 500 mg/l it was totally arrested. The optimum pH for the anoxic sulphide oxidation was around 7.5. Concentrations of sulphate 1500 mg/l and acetate 400 mg/l had no effect on anoxic sulphide oxidation.     

Unexpected Population Distribution in a Microbial Mat Community: Sulfate-Reducing Bacteria Localized to the Highly Oxic Chemocline in Contrast to a Eukaryotic Preference for Anoxia

The distribution and abundance of sulfate-reducing bacteria (SRB) and eukaryotes within the upper 4 mm of a hypersaline cyanobacterial mat community were characterized at high resolution with group-specific hybridization probes to quantify 16S rRNA extracted from 100-μm depth intervals. This revealed a preferential localization of SRB within the region defined by the oxygen chemocline. Among the different groups of SRB quantified, including members of the provisional families “Desulfovibrionaceae” and “Desulfobacteriaceae,” Desulfonema-like populations dominated and accounted for up to 30% of total rRNA extracted from certain depth intervals of the chemocline. These data suggest that recognized genera of SRB are not necessarily restricted by high levels of oxygen in this mat community and the possibility of significant sulfur cycling within the chemocline. In marked contrast, eukaryotic populations in this community demonstrated a preference for regions of anoxia.     

In situ analysis of oxygen consumption and diffusive transport in high‐temperature acidic iron‐oxide microbial mats

The role of dissolved oxygen as a principal electron acceptor for microbial metabolism was investigated within Fe(III)‐oxide microbial mats that form in acidic geothermal springs of Yellowstone National Park (USA). Specific goals of the study were to measure and model dissolved oxygen profiles within high‐temperature (65–75°C) acidic (pH = 2.7–3.8) Fe(III)‐oxide microbial mats, and correlate the abundance of aerobic, iron‐oxidizing Metallosphaera yellowstonensis organisms and mRNA gene expression levels to Fe(II)‐oxidizing habitats shown to consume oxygen. In situ oxygen microprofiles were obtained perpendicular to the direction of convective flow across the aqueous phase/Fe(III)‐oxide microbial mat interface using oxygen microsensors. Dissolved oxygen concentrations dropped from ～ 50–60 μM in the bulk‐fluid/mat surface to below detection (< 0.3 μM) at a depth of ～ 700 μm (～ 10% of the total mat depth). Net areal oxygen fluxes into the microbial mats were estimated to range from 1.4–1.6 × 10^?4 μmol cm^?2 s^?1. Dimensionless parameters were used to model dissolved oxygen profiles and establish that mass transfer rates limit the oxygen consumption. A zone of higher dissolved oxygen at the mat surface promotes Fe(III)‐oxide biomineralization, which was supported using molecular analysis of Metallosphaera yellowstonensis 16S rRNA gene copy numbers and mRNA expression of haem Cu oxidases (FoxA) associated with Fe(II)‐oxidation.     

Optimization of sulphur production in a biotechnological sulphide-removing reactor

A new biotechnological process for sulphide removal is proposed. The principle of this process is that sulphide is converted into elemental sulphur, which can be removed by sedimentation. In this article, investigations on the optimization of the sulphur production are reported. It seems that less than 10% sulphate is produced at low oxygen concentration, when the sulphide concentration in the reactor exceeds 10 mg/L. At sulphide concentrations higher than 20 mg/L only 5% of the incoming sulphide is converted to sulphate even at high oxygen concentrations. An immobilized biomass on recticulated polyurethane produced more sulphate than a free cell suspension at the same oxygen and sulphide concentration.     

Population structure and physiological changes within a hot spring microbial mat community following disturbance.

The influence of disturbance on a hot spring cyanobacterial mat community was investigated by physically removing the top 3.0 mm, which included the entire cyanobacterial layer. Changes in 16S rRNA-defined populations were monitored by denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments. Some previously absent cyanobacterial populations colonized the disturbed areas, while some populations which were present before the disturbance remained absent for up to 40 days. Changes in physiological activity were measured by oxygen microelectrode analyses and by 14CO2 incorporation into cyanobacterial molecular components. These investigations indicated substantial differences between the disturbed and undisturbed mats, including an unexplained light-induced oxygen consumption in the freshly exposed mat, increased carbon partitioning by phototrophs into growth-related macromolecules, bimodal vertical photosynthesis profiles, and delayed recovery of respiration relative to photosynthesis.     

In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area

Anaerobic oxidation of methane (AOM) and sulphate reduction were examined in sediment samples from a marine gas hydrate area (Hydrate Ridge, NE Pacific). The sediment contained high numbers of microbial consortia consisting of organisms that affiliate with methanogenic archaea and with sulphate-reducing bacteria. Sediment samples incubated under strictly anoxic conditions in defined mineral medium (salinity as in seawater) produced sulphide from sulphate if methane was added as the sole organic substrate. No sulphide production occurred in control experiments without methane. Methane-dependent sulphide production was fastest between 4 degree C and 16 degree C, the average rate with 0.1 MPa (approximately 1 atm) methane being 2.5 micro mol sulphide day(-1) and (g dry mass sediment)(-1). An increase of the methane pressure to 1.1 MPa (approximately 11 atm) resulted in a four to fivefold increase of the sulphide production rate. Quantitative measurements using a special anoxic incubation device without gas phase revealed continuous consumption of dissolved methane (from initially 3.2 to 0.7 mM) with simultaneous production of sulphide at a molar ratio of nearly 1:1. To test the response of the indigenous community to possible intermediates of AOM, molecular hydrogen, formate, acetate or methanol were added in the absence of methane; however, sulphide production from sulphate with any of these compounds was much slower than with methane. In the presence of methane, such additions neither stimulated nor inhibited sulphate reduction. Hence, the experiments did not provide evidence for one of these compounds acting as a free extracellular intermediate (intercellular shuttle) during AOM by the presently investigated consortia.     

Characterization of functional bacterial groups in a hypersaline microbial mat community (Salins-de-Giraud, Camargue, France)

A photosynthetic microbial mat was investigated in a large pond of a Mediterranean saltern (Salins-de-Giraud, Camargue, France) having water salinity from 70 per thousand to 150 per thousand (w/v). Analysis of characteristic biomarkers (e.g., major microbial fatty acids, hydrocarbons, alcohols and alkenones) revealed that cyanobacteria were the major component of the pond, in addition to diatoms and other algae. Functional bacterial groups involved in the sulfur cycle could be correlated to these biomarkers, i.e. sulfate-reducing, sulfur-oxidizing and anoxygenic phototrophic bacteria. In the first 0.5 mm of the mat, a high rate of photosynthesis showed the activity of oxygenic phototrophs in the surface layer. Ten different cyanobacterial populations were detected with confocal laser scanning microscopy: six filamentous species, with Microcoleus chthonoplastes and Halomicronema excentricum as dominant (73% of total counts); and four unicellular types affiliated to Microcystis, Chroococcus, Gloeocapsa, and Synechocystis (27% of total counts). Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments confirmed the presence of Microcoleus, Oscillatoria, and Leptolyngbya strains (Halomicronema was not detected here) and revealed additional presence of Phormidium, Pleurocapsa and Calotrix types. Spectral scalar irradiance measurements did not reveal a particular zonation of cyanobacteria, purple or green bacteria in the first millimeter of the mat. Terminal-restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA gene fragments of bacteria depicted the community composition and a fine-scale depth-distribution of at least five different populations of anoxygenic phototrophs and at least three types of sulfate-reducing bacteria along the microgradients of oxygen and light inside the microbial mat.     

Near-surface mixing and pronounced deep-water stratification in a compartmentalised, human-disturbed atoll lagoon system

Palmyra Atoll has four partially isolated lagoons up to 50 m in depth, each with complex and variable bottom topographies. Measurements of depth, temperature, salinity, turbidity and dissolved oxygen (DO) revealed a well-mixed shallow surface layer (0–10 m depth) and below that pronounced stratification of DO in the absence of a pycnocline. Turbidity increased in a step-like manner at ~25 m depth, at the oxycline. For all deep sections of the lagoon (>30 m), DO declined uniformly to 0% saturation. As determined from filtration, mass of particulates was independent of depth. Surface mixing and deep-water stratification are both stable at different temporal scales, including day versus night, daily, weekly and annually. We suggest that lagoon circulation is represented by a shallow, westward-moving surface layer of well-to-partially mixed water with high DO and low turbidity, underlain by a relatively static and temporally stable layer with low to zero DO and elevated turbidity. This is the first report of such conditions within a deep lagoon system, and only the second report of anoxic conditions in any such system. In deep-water, stable euxinic conditions reflect bottom topography, with dysoxic and anoxic water being constrained within silled basins. The occurrence and depth of large volumes of sediment-laden and dysoxic/anoxic water need to be considered in management proposals designed to increase water flow through the lagoon. These novel water column conditions most probably arose as a consequence of military construction work, consistent with published reports of profound changes to the atoll during 1940–1945. If so, they highlight the need to better understand the possible consequences of cutting channels and modification of lagoon flow at many atolls across the central Pacific Ocean.     

Denaturing gradient gel electrophoresis used to monitor the enrichment culture of aerobic chemoorganotrophic bacteria from a hot spring cyanobacterial mat.

Previous studies investigating microbial diversity in the Octopus Spring cyanobacterial mat community (Yellowstone National Park) have shown a discrepancy between bacterial populations observed by molecular retrieval and cultivation techniques. To investigate how selective enrichment culture techniques affect species composition, we used denaturing gradient gel electrophoresis (DGGE) separation of PCR-amplified 16S rRNA gene fragments to monitor the populations contained within enrichment cultures of aerobic chemoorganotrophic bacteria from the ca. 50 degrees C region of the mat community. By varying the degree of dilution of the inoculum, medium composition, and enrichment conditions and duration and by analyzing the cultures by DGGE, we detected 14 unique 16S rRNA sequence types. These corresponded to alpha-, beta-, gamma-, and delta-proteobacteria, Thermus relatives, and gram-positive bacteria with high G + C ratio and, at the highest inoculum dilutions, Chloroflexus aurantiacus relatives, which were estimated to still be approximately 300 times less abundant than cells of the mat primary producer, Synechococcus spp. Only three of these populations were previously cultivated on solidified medium after similar enrichment. Only two of these population have 16S rRNA sequences which were previously cloned directly from the mat. These results reveal a diversity of bacterial populations in enrichment culture which were not detected by either molecular retrieval or strain purification techniques.     

Mixing patterns in Amazon lakes

The diel mixing patterns of two small floodplain lakes, Lago Jacaretinga in the Amazon drainage, and Lago Cristalino in the Rio Negro system, were investigated during both the high-water and low-water states of the Amazon River hydrograph. Measurements included temperature, oxygen, ammonia, phosphate, and chlorophyll. In both lakes thermal stratification developed during the day and was eroded at night. During the low-water period when the lakes were shallow, nocturnal circulation extended to the lake bottom, whereas when the lakes were deeper (greater than about 5 m), circulation did not reach the bottom and an anoxic hypolimnion developed. During the low-water period, percent of oxygen concentrations were relatively high but always less than saturation. Low oxygen concentrations were observed during the high-water period. At all times nocturnal mixing supplied a significant amount of oxygen to the lake ecosystems. Nighttime upward mixing of recycled nitrogen and phosphorus also appeared to be important nutrient sources for algal productivity.     

Reaction of estuarine ecosystems to effluent from pulp and paper industry

A major problem associated with the discharge of pulp or paper-mill effluent into shallow estuarine ecosystems, such as the upper L'Etang in Canada or the Don in Scotland, is the development of anoxic conditions in water column and sediment. The effluent modifies the balance, within the ecosystem, between the supply of, and demand for, oxygen. The lignosulphonate component of pulpmill effluent blocks the transmission of light energy to photosynthetic green plants. The oxygen demand is increased by the microbial degration of the additional organic matter in water and sediment. The addition of cellulosic pulp fibre to the sediment also results in an increase in the concentration of their metabolic by-product, sulphide. The oxidation of sulphide exerts an additional oxygen demand on the system, which is an important factor in the development and maintenance of anoxic conditions. It is suggested that temperature is an important factor in controlling the release of sulphide from the sediment into the overlying water and in modifying the toxicity of sulphide towards the bacterial populations and, therefore, the capacity of the ecosystem to cope with the effluent.     

Sulphate reduction and sulphur cycling in lake sediments: a review

1. The concentration of sulphate is low in lakes and sulphur cycling has often been neglected in studies of organic matter diagenesis in lake sediments. The cycling of sulphur is, however, both spatially and temporally dynamic and strongly influences many biogeochemical reactions in sediments, such as the binding of phosphorus. This review examines the control of sulphate reduction and sulphur cycling in sediments of lakes with different trophic status. 2. The factors that control the rate of sulphate reduction have not been identified with certainty in the various environments because many factors are involved, e.g. oxygen and sulphate concentrations, temperature and organic matter availability. 3. Sulphate reduction is less significant under oligotrophic conditions, where mineralization is dominated by oxic decomposition. The supply of organic matter may not be sufficient to support sulphate reduction in the anoxic parts of sediments and, also, sulphate availability may control the rate as the concentration is generally low in oligotrophic lakes. 4. There is a potential for significant sulphate reduction in eutrophic lakes, as both the availability of organic matter and sulphate concentration are often higher than in oligotrophic lakes. Sulphate is rapidly depleted with sediment depth, however, and methanogenesis is generally the most important process in overall carbon mineralization. Sulphate reduction is generally low in acidic lakes because of low sulphate availability and reduced microbial activity. 5. It is still unclear which of the forms of sulphur deposits are the most important and under which conditions burial occurs. Sulphur deposition is controlled by the rate of sulphate reduction and reoxidation. Reoxidation of sulphides occurs rapidly through several pathways, both under oxic and anoxic conditions. Only a few studies have been able to examine the importance of reoxidation, but it is hypothesized that most of the reoxidation takes place under anoxic conditions and that disproportionation is often involved. The presence of sulphide oxidizing bacteria, benthic fauna and rooted macrophytes may substantially enhance oxic reoxidation. Deposition of sulphur is generally higher in eutrophic than in oligotrophic lakes because of a number of factors: a higher rate of sulphate reduction, enhanced sedimentation of organic sulphur and less reoxidation as a result of reduced penetration of oxygen into the sediments, a lack of faunal activity and rooted macrophytes.