The impact of temperature change on the activity and community composition of sulfate-reducing bacteria in arctic versus temperate marine sediments

Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments

Coastal waters such as those found in the Baltic Sea already suffer from anthropogenic related problems including increased algal blooming and hypoxia while ongoing and future climate change will likely worsen these effects. Microbial communities in sediments play a crucial role in the marine energy- and nutrient cycling, and how they are affected by climate change and shape the environment in the future is of great interest. The aims of this study were to investigate potential effects of prolonged warming on microbial community composition and nutrient cycling including sulfate reduction in surface (∼0.5 cm) to deeper sediments (∼ 24 cm). To investigate this, 16S rRNA gene amplicon sequencing was performed, and sulfate concentrations were measured and compared between sediments in a heated bay (which has been used as a cooling water outlet from a nearby nuclear power plant for approximately 50 years) and a nearby but unaffected control bay. The results showed variation in overall microbial diversity according to sediment depth and higher sulfate flux in the heated bay compared to the control bay. A difference in vertical community structure reflected increased relative abundances of sulfur oxidizing- and sulfate reducing bacteria along with a higher proportion of archaea, such as Bathyarchaeota, in the heated compared to the control bay. This was particularly evident closer to the sediment surface, indicating a compression of geochemical zones in the heated bay. These results corroborate findings in previous studies and additionally point to an amplified effect of prolonged warming deeper in the sediment, which could result in elevated concentrations of toxic compounds and greenhouse gases closer to the sediment surface.

Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain)

Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.

Carbon‑sulfur coupling in a seasonally hypoxic, high-sulfate reservoir in SW China: Evidence from stable CS isotopes and sulfate-reducing bacteria

Anthropogenic input of sulfate (SO₄^2-) in reservoirs may enhance bacterial sulfate reduction (BSR) under seasonally hypoxic conditions in the water column. However, factors that control BSR and its coupling to organic carbon (OC) mineralization in seasonally hypoxic reservoirs remain unclear. The present study elucidates the coupling processes by analyzing the concentrations and isotopic composition of dissolved inorganic carbon (DIC) and sulfur (SO₄^2-, sulfide) species, and the microbial community in water of the Aha reservoir, SW China, which has high SO₄^2- concentration due to the inputs from acid mine drainage about twenty years ago. The water column at two sites in July and October revealed significant thermal stratification. In the hypoxic bottom water, the δ¹³C-DIC decreased while the δ³⁴S-SO₄^2- increased, implying organic carbon mineralization due to BSR. The magnitude of S isotope fractionation (Δ³⁴S, obtained from δ³⁴S_sulfate-δ³⁴S_sulfide) during the process of BSR fell in the range of 3.4‰ to 27.0‰ in July and 21.6‰ to 31.8‰ in October, suggesting a change in the community of sulfate-reducing bacteria (SRB). The relatively low water column stability in October compared to that in July weakened the difference of water chemistry and ultimately affected the SRB diversity. The production of DIC (ΔDIC) scaled a strong positive relationship with the Δ³⁴S in July (p < 0.01), indicating that high OC availability favored the survival of incomplete oxidizers of SRB. However, in October, Δ¹³C-DIC was correlated with the Δ³⁴S in the bottom hypoxic water (p < 0.01), implying that newly degraded OC depleted in ¹³C could favor the dominance of complete oxidizers of SRB which caused greater S isotope fractionation. Moreover, the sulfide supplied by BSR might stimulate the reductive dissolution of Fe and Mn oxides (Fe(O)OH and MnO₂). The present study helps to understand the coupling of C and S in seasonally hypoxic reservoirs characterized by high SO₄^2- concentration.

Influence of Temperature and Sulfate Concentration on the Sulfate/Sulfite Reduction Prokaryotic Communities in the Tibetan Hot Springs

The distribution and diversity of sulfate/sulfite reduction prokaryotic (SRP) communities in hot springs from the Quzhuomu and Daggyai Geothermal Zone of Tibetan, China, was reported for the first time. In hot springs that are naturally hyperthermal and anoxic, the sulfur cycle is one of the most active cycles of the elements. The distribution of SRP in response to temperature is of great importance to the understanding of biogeochemical cycling of sulfur in geothermal features. Little is known about the SRP in geothermal zone. In this study, the diversity of SRP was investigated in the sediments from the Daggyai and Quzhuomu geothermal zone using PCR amplification, cloning and sequencing of the dissimilatory sulfite reductase beta subunit gene (dsrB). The abundance of dsrB and 16S rRNA genes, were determined by quantitative polymerase chain reactions. In addition, correlations of the SRP assemblages with environmental factors were analyzed by the aggregated boosted tree (ABT) statistical analysis. The results showed that SRP populations were diverse, but were mainly composed of Desulfobacterales, Desulfovibrionales, Syntrophobacterales, Clostridia and Nitrospirales, and large fraction (25%) of novel sequences have branched groups in the dsrB phylogenetic tree. In Quzhuomu geothermal zone, sulfate-rich hot springs are characterized by thick bacterial mats that are green or red and the SRP populations mainly appear at mid-temperature (50 °C to 70 °C). In low-sulfate hot springs in the Daggyai geothermal zone, although gray or pink streamers are widely formed at 60 °C to 80 °C, they prefer to inhabit in green mat at lower temperature (30 °C to 50 °C). With increasing temperature, the diversity of the dsrB gene at the OTU level (cutoff 97%) decreased, while its relative abundance increased. This result suggests that temperature played an important role in affecting dsrB gene distribution.

Evidence for a Growth Zone for Deep-Subsurface Microbial Clades in Near-Surface Anoxic Sediments

Global marine sediments harbor a large and highly diverse microbial biosphere, but the mechanism by which this biosphere is established during sediment burial is largely unknown. During burial in marine sediments, concentrations of easily metabolized organic compounds and total microbial cell abundance decrease. However, it is unknown whether some microbial clades increase with depth. We show total population increases in 38 microbial families over 3 cm of sediment depth in the upper 7.5 cm of White Oak River (WOR) estuary sediments. Clades that increased with depth were more often associated with one or more of the following: anaerobes, uncultured, or common in deep marine sediments relative to those that decreased. Maximum doubling times (in situ steady-state growth rates could be faster to balance cell decay) were estimated as 2 to 25 years by combining sedimentation rate with either quantitative PCR (qPCR) or the product of the fraction read abundance of 16S rRNA genes and total cell counts (FRAxC). Doubling times were within an order of magnitude of each other in two adjacent cores, as well as in two laboratory enrichments of Cape Lookout Bight (CLB), NC, sediments (average difference of 28% ± 19%). qPCR and FRAxC in sediment cores and laboratory enrichments produced similar doubling times for key deep subsurface uncultured clades Bathyarchaeota (8.7 ± 1.9 years) and Thermoprofundales/MBG-D (4.1 ± 0.7 years). We conclude that common deep subsurface microbial clades experience a narrow zone of growth in shallow sediments, offering an opportunity for selection of long-term subsistence traits after resuspension events.IMPORTANCE Many studies show that the uncultured microbes that dominate global marine sediments do not actually increase in population size as they are buried in marine sediments; rather, they exist in a sort of prolonged torpor for thousands of years. This is because, although studies have shown biomass turnover in these clades, no evidence has ever been found that deeper sediments have larger populations for specific clades than shallower layers. We discovered that they actually do increase population sizes during burial, but only in the upper few centimeters. This suggests that marine sediments may be a vast repository of mostly nongrowing microbes with a thin and relatively rapid area of cell abundance increase in the upper 10 cm, offering a chance for subsurface organisms to undergo natural selection.

The effect of temperature on sulfate release from Pearl River sediments in South China

Sulfate (SO₄^2-) has received attention as means of monitoring water quality and pollution. However, the SO₄^2- content of rivers, lakes, and reservoirs varies significantly by season, so environmental factors such as temperature can affect it. An experiment was conducted with a series of aerobic and anaerobic tanks containing Pearl River sediments and distilled water to assess the release of SO₄^2- from sediments under controlled conditions. "Black-odor river" refers to near anoxic conditions in the water column and foul odors emanating from affected rivers in southeastern China. These river systems typical have sediments containing ammonia (NH₃), hydrogen sulfide (H₂S), and organic sulfide compounds in excess, and precipitates of sulfide (S^2-), with ferrous (Fe²⁺) or manganese (Mn²⁺). SO₄^2- concentration was measured at various depths in pore water and in the water column while controlling temperature and dissolved oxygen (DO) concentrations. Interpolation of study results revealed that SO₄^2- content was highest between temperatures of 20 °C and 25 °C. The relationship between SO₄^2- concentration, which varied with temperature and time, was fit using a linearized Michaelis-Menten function (R² = 0.69). The release of SO₄^2- to the water column was accelerated during the experiment (for temperatures higher than 20 °C), and led to higher SO₄^2- content in the water column than in pore water. The maximum concentration of SO₄^2- within the sediment occurred at a temperature of 20 °C. Comparing aerated and non-aerated tanks at 20 °C, we found that O₂ restricted SO₄^2- content in the water column; DO could, in turn, also be controlled by temperature. Fe²⁺ and Mn²⁺ had a negative correlation with SO₄^2-.

Dynamics of Sulfate-Reducing Bacteria Community Structure in Surface Sediment of a Seasonally Hypoxic Enclosed Bay

We herein report on the dynamics of a sulfate-reducing bacteria (SRB) community structure in the surface sediment of a seasonally hypoxic enclosed bay for two consecutive years (2012 and 2013). The uppermost (0–5 mm) and subsurface (5–10 mm) layers of sediment were examined with a terminal-restriction fragment length polymorphism (T-RFLP) analysis based on the dissimilatory sulfite reductase (dsrA) gene. The SRB community significantly differed between the two sediment layers over the sampling period. This difference was mainly attributed to operational taxonomic units (OTUs) that were unique to either of the sediment layers. However, nearly 70% of total OTUs were shared between the two layers, with a few predominating. Therefore, no significant shift was observed in the SRB community structure under varying dissolved oxygen (DO) conditions in bottom water overlying the sediment surface. An additional analysis of 16S rRNA gene amplicon sequences, conducted for three uppermost sediment samples (July, August, and September in 2012), revealed that Desulfococcus, a member of SRB with high tolerance to oxygen, was the predominant Deltaproteobacteria across the uppermost sediment samples. Based on the predominance of shared OTUs across the SRB community in the sediment (0–10 mm) regardless of bottom-water DO, some SRB that are physiologically tolerant of a wide range of DO conditions may have dominated and masked changes in responsive SRB to DO concentrations. These results suggest that the SRB community structure in the enclosed bay became stable under repeated cycles of seasonal hypoxia, but may be compromised if the severity of hypoxia increases in the future.

Temperature Controls Crystalline Iron Oxide Utilization by Microbial Communities in Methanic Ferruginous Marine Sediment Incubations

Microorganisms can use crystalline iron minerals for iron reduction linked to organic matter degradation or as conduits for direct interspecies electron transfer (mDIET) to syntrophic partners, e.g., methanogens. The environmental conditions that lead either to reduction or conduit use are so far unknown. We investigated microbial community shifts and interactions with crystalline iron minerals (hematite and magnetite) in methanic ferruginous marine sediment incubations during organic matter (glucose) degradation at varying temperatures. Iron reduction rates increased with decreasing temperature from 30°C to 4°C. Both hematite and magnetite facilitated iron reduction at 4°C, demonstrating that microorganisms in the methanic zone of marine sediments can reduce crystalline iron oxides under psychrophilic conditions. Methanogenesis occurred, however, at higher rates with increasing temperature. At 30°C, both hematite and magnetite accelerated methanogenesis onset and maximum process rates. At lower temperatures (10°C and 4°C), hematite could still facilitate methanogenesis but magnetite served more as an electron acceptor for iron reduction than as a conduit. Different temperatures selected for different key microorganisms: at 30°C, members of genus Orenia, Halobacteroidaceae, at 10°C, Photobacterium and the order Clostridiales, and at 4°C Photobacterium and Psychromonas were enriched. Members of the order Desulfuromonadales harboring known dissimilatory iron reducers were also enriched at all temperatures. Our results show that crystalline iron oxides predominant in some natural environments can facilitate electron transfer between microbial communities at psychrophilic temperatures. Furthermore, temperature has a critical role in determining the pathway of crystalline iron oxide utilization in marine sediment shifting from conduction at 30°C to predominantly iron reduction at lower temperatures.

Biodegradation of Crude Oil and Corexit 9500 in Arctic Seawater

The need to understand the biodegradation of oil and chemical dispersants in Arctic marine environments is increasing alongside growth in oil exploration and transport in the region. We chemically quantified biodegradation and abiotic losses of crude oil and Corexit 9500, when present separately, in incubations of Arctic seawater and identified microorganisms potentially involved in biodegradation of these substrates based on shifts in bacterial community structure (16S rRNA genes) and abundance of biodegradation genes (GeoChip 5.0 microarray). Incubations were performed over 28-day time courses using surface seawater collected from near-shore and offshore locations in the Chukchi Sea. Within 28 days, the indigenous microbial community biodegraded 36% (k = 0.010 day^-1) and 41% (k = 0.014 day^-1) of oil and biodegraded 77% and 33% (k = 0.015 day^-1) of the Corexit 9500 component dioctyl sodium sulfosuccinate (DOSS) in respective near-shore and offshore incubations. Non-ionic surfactants (Span 80, Tween 80, and Tween 85) present in Corexit 9500 were non-detectable by 28 days due to a combination of abiotic losses and biodegradation. Microorganisms utilized oil and Corexit 9500 as growth substrates during the incubation, with the Corexit 9500 stimulating more extensive growth than oil within 28 days. Taxa known to include oil-degrading bacteria (e.g., Oleispira, Polaribacter, and Colwellia) and some oil biodegradation genes (e.g., alkB, nagG, and pchCF) increased in relative abundance in response to both oil and Corexit 9500. These results increase our understanding of oil and dispersant biodegradation in the Arctic and suggest that some bacteria may be capable of biodegrading both oil and Corexit 9500.

Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment

Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with 13 C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of 13 C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Sulfide production kinetics and model of stormwater retention ponds

Stormwater retention ponds can play a critical role in mitigating the detrimental effects of urbanization on receiving waters that result from increases in polluted runoff. However, the benthic oxygen demand of stormwater facilities may cause significant hypoxia and trigger the production of hydrogen sulfide (H₂S). This process is not well-documented and further research is needed to characterize benthic processes in stormwater retention ponds in order to improve their design and operation. In this study, sediment oxygen demand (SOD), sediment ammonia release (SAR) and sediment sulfide production (SSP) kinetics were characterized in situ and in the laboratory. In situ SOD and SSP data were utilized to develop a stormwater retention pond water sulfide concentration model which demonstrates strong correlation with sulfide concentrations observed in situ (r = 0.724, N = 91, p < 0.001) and in laboratory experiments (r = 0.691, N = 38, p < 0.001). At 4 °C, in situ rates of SOD, SAR and SSP were higher than those measured in laboratory. Sulfate-reducing bacteria (SRB) represented 4.99% of the bacteria present in the top 30 cm of the pond sediment, with Desulfobulbaceae spp., Desulfobacteraceae spp. and Desulfococcus spp. being the dominant SRB taxa identified.

Vulnerability of macronutrients to the concurrent effects of enhanced temperature and atmospheric pCO2 in representative shelf sea sediment habitats

Fundamental changes in seawater carbonate chemistry and sea surface temperatures associated with the ocean uptake of anthropogenic CO2 are accelerating, but investigations of the susceptibility of biogeochemical processes to the simultaneous occurrence of multiple components of climate change are uncommon. Here, we quantify how concurrent changes in enhanced temperature and atmospheric pCO2, coupled with an associated shift in macrofaunal community structure and behavior (sediment particle reworking and bioirrigation), modify net carbon and nutrient concentrations (NH4-N, NOx-N, PO4-P) in representative shelf sea sediment habitats (mud, sandy-mud, muddy-sand and sand) of the Celtic Sea. We show that net concentrations of organic carbon, nitrogen and phosphate are, irrespective of sediment type, largely unaffected by a simultaneous increase in temperature and atmospheric pCO2. However, our analyses also reveal that a reduction in macrofaunal species richness and total abundance occurs under future environmental conditions, varies across a gradient of cohesive to non-cohesive sediments, and negatively moderates biogeochemical processes, in particular nitrification. Our findings indicate that future environmental conditions are unlikely to have strong direct effects on biogeochemical processes but, particularly in muddy sands, the abundance, activity, composition and functional role of invertebrate communities are likely to be altered in ways that will be sufficient to regulate the function of the microbial community and the availability of nutrients in shelf sea waters.

Similar temperature responses suggest future climate warming will not alter partitioning between denitrification and anammox in temperate marine sediments

Removal of biologically available nitrogen (N) by the microbially mediated processes denitrification and anaerobic ammonium oxidation (anammox) affects ecosystem N availability. Although few studies have examined temperature responses of denitrification and anammox, previous work suggests that denitrification could become more important than anammox in response to climate warming. To test this hypothesis, we determined whether temperature responses of denitrification and anammox differed in shelf and estuarine sediments from coastal Rhode Island over a seasonal cycle. The influence of temperature and organic C availability was further assessed in a 12-week laboratory microcosm experiment. Temperature responses, as characterized by thermal optima (T_opt ) and apparent activation energy (E_a ), were determined by measuring potential rates of denitrification and anammox at 31 discrete temperatures ranging from 3 to 59 °C. With a few exceptions, T_opt and E_a of denitrification and anammox did not differ in Rhode Island sediments over the seasonal cycle. In microcosm sediments, E_a  was somewhat lower for anammox compared to denitrification across all treatments. However, T_opt  did not differ between processes, and neither E_a  nor T_opt  changed with warming or carbon addition. Thus, the two processes behaved similarly in terms of temperature responses, and these responses were not influenced by warming. This led us to reject the hypothesis that anammox is more cold-adapted than denitrification in our study system. Overall, our study suggests that temperature responses of both processes can be accurately modeled for temperate regions in the future using a single set of parameters, which are likely not to change over the next century as a result of predicted climate warming. We further conclude that climate warming will not directly alter the partitioning of N flow through anammox and denitrification.

Application of plow-tillage as an innovative technique for eliminating overwintering cyanobacteria in eutrophic lake sediments

Surface sediment in eutrophic lakes is both a destination and a habitat for overwintering cyanobacteria. The resuspension and recovery of viable, overwintering cyanobacteria from the surface sediment during warm spring weather is usually the primary stage of cyanobacterial blooms (CBs) in shallow eutrophic lakes. Therefore, the elimination of overwintering cyanobacteria in sediment is vital to control CBs. In the present study, sediment plow-tillage (PT) was introduced as an innovative technique for eliminating overwintering cyanobacteria in sediments from Lake Chaohu. Four depths of PT (2, 5, 10, and 15 cm) were tested during the 42-day experiment. The results showed that rapid cell death during the first 0-7 d after PT was accompanied by high oxygen uptake rates. The viable cells in deeper sediment died more quickly and at a higher rate after PT. A PT depth of >10 cm effectively eliminated viable cyanobacteria (with a removal rate of 82.8%) from the sediment and prevented their resuspension. The activity of the viable cyanobacteria also decreased quickly as cyanobacteria were eliminated. It appears that the dark, anoxic environment of the deeper sediment after PT was responsible for the elimination of viable cells. Although high release rates of nitrogen and phosphorus were found to accompany the dying and decomposition of cyanobacteria during days 0-7 of the experiment, greater depth of PT was found to decrease nutrient concentrations in the overlying water. In conclusion, we recommend sediment PT as a new technique for eliminating overwintering algae in sediments. However, the release of nutrients from the sediment and the in situ control of CBs in lakes after PT should be further studied.

Key Factors Influencing Rates of Heterotrophic Sulfate Reduction in Active Seafloor Hydrothermal Massive Sulfide Deposits

Hydrothermal vents are thermally and geochemically dynamic habitats, and the organisms therein are subject to steep gradients in temperature and chemistry. To date, the influence of these environmental dynamics on microbial sulfate reduction has not been well constrained. Here, via multivariate experiments, we evaluate the effects of key environmental variables (temperature, pH, H₂S, SO42−, DOC) on sulfate reduction rates and metabolic energy yields in material recovered from a hydrothermal flange from the Grotto edifice in the Main Endeavor Field, Juan de Fuca Ridge. Sulfate reduction was measured in batch reactions across a range of physico-chemical conditions. Temperature and pH were the strongest stimuli, and maximum sulfate reduction rates were observed at 50°C and pH 6, suggesting that the in situ community of sulfate-reducing organisms in Grotto flanges may be most active in a slightly acidic and moderate thermal/chemical regime. At pH 4, sulfate reduction rates increased with sulfide concentrations most likely due to the mitigation of metal toxicity. While substrate concentrations also influenced sulfate reduction rates, energy-rich conditions muted the effect of metabolic energetics on sulfate reduction rates. We posit that variability in sulfate reduction rates reflect the response of the active microbial consortia to environmental constraints on in situ microbial physiology, toxicity, and the type and extent of energy limitation. These experiments help to constrain models of the spatial contribution of heterotrophic sulfate reduction within the complex gradients inherent to seafloor hydrothermal deposits.

Activity and community structures of sulfate-reducing microorganisms in polar, temperate and tropical marine sediments

Temperature has a fundamental impact on the metabolic rates of microorganisms and strongly influences microbial ecology and biogeochemical cycling in the environment. In this study, we examined the catabolic temperature response of natural communities of sulfate-reducing microorganisms (SRM) in polar, temperate and tropical marine sediments. In short-term sediment incubation experiments with (35)S-sulfate, we demonstrated how the cardinal temperatures for sulfate reduction correlate with mean annual sediment temperatures, indicating specific thermal adaptations of the dominant SRM in each of the investigated ecosystems. The community structure of putative SRM in the sediments, as revealed by pyrosequencing of bacterial 16S rRNA gene amplicons and phylogenetic assignment to known SRM taxa, consistently correlated with in situ temperatures, but not with sediment organic carbon concentrations or C:N ratios of organic matter. Additionally, several species-level SRM phylotypes of the class Deltaproteobacteria tended to co-occur at sites with similar mean annual temperatures, regardless of geographic distance. The observed temperature adaptations of SRM imply that environmental temperature is a major controlling variable for physiological selection and ecological and evolutionary differentiation of microbial communities.

Complex coupled metabolic and prokaryotic community responses to increasing temperatures in anaerobic marine sediments: critical temperatures and substrate changes

The impact of temperature (0-80°C) on anaerobic biogeochemical processes and prokaryotic communities in marine sediments (tidal flat) was investigated in slurries for up to 100 days. Temperature had a non-linear effect on biogeochemistry and prokaryotes with rapid changes over small temperature intervals. Some activities (e.g. methanogenesis) had multiple 'windows' within a large temperature range (∼10 to 80°C). Others, including acetate oxidation, had maximum activities within a temperature zone, which varied with electron acceptor [metal oxide (up to ∼34°C) and sulphate (up to ∼50°C)]. Substrates for sulphate reduction changed from predominantly acetate below, and H2 above, a 43°C critical temperature, along with changes in activation energies and types of sulphate-reducing Bacteria. Above ∼43°C, methylamine metabolism ceased with changes in methanogen types and increased acetate concentrations (>1 mM). Abundances of uncultured Archaea, characteristic of deep marine sediments (e.g. MBGD Euryarchaeota, 'Bathyarchaeota') changed, indicating their possible metabolic activity and temperature range. Bacterial cell numbers were consistently higher than archaeal cells and both decreased above ∼15°C. Substrate addition stimulated activities, widened some activity temperature ranges (methanogenesis) and increased bacterial (×10) more than archaeal cell numbers. Hence, additional organic matter input from climate-related eutrophication may amplify the impact of temperature increases on sedimentary biogeochemistry.

Marine Oil-Degrading Microorganisms and Biodegradation Process of Petroleum Hydrocarbon in Marine Environments: A Review

Due to the toxicity of petroleum compounds, the increasing accidents of marine oil spills/leakages have had a significant impact on our environment. Recently, different remedial techniques for the treatment of marine petroleum pollution have been proposed, such as bioremediation, controlled burning, skimming, and solidifying. (Hedlund and Staley in Int J Syst Evol Microbiol 51:61-66, 2001). This review introduces an important remedial method for marine oil pollution treatment-bioremediation technique-which is considered as a reliable, efficient, cost-effective, and eco-friendly method. First, the necessity of bioremediation for marine oil pollution was discussed. Second, this paper discussed the species of oil-degrading microorganisms, degradation pathways and mechanisms, the degradation rate and reaction model, and the factors affecting the degradation. Last, several suggestions for the further research in the field of marine oil spill bioremediation were proposed.

The negative effects of temperature increase on bacterial respiration are independent of changes in community composition

Temporal changes in environmental conditions and in bacterial community composition (BCC) regulate bacterial processes and ecosystem services. An increase in temperature accelerates bacterial processes in polar or temperate regions, but this relationship has not been documented for the tropics. Here, we tested the interactive effects of changing the BCC and increasing the water temperature on tropical bacterial respiration (BR). The BCC was manipulated through successional changes of the bacterial community in a filtered water sample from a tropical coastal lagoon. Four succession incubation periods (120, 240, 288 and 336 h) and four different water temperatures (23, 28, 33 and 38(o)C) were tested in a full-factorial design microcosm experiment. Both the BCC and the temperature had significant individual, but not interactive, effects on BR. Temperature increasing consistently decreased BR, while there was no clear pattern of successional effects on BR observed. No BCC tested was able to diminish the negative effects of temperature increases on BR. Our results suggest that the effects of an increasing temperature can negatively affect BR, even in tropical ecosystems with different BCC.

Temperature and cyanobacterial bloom biomass influence phosphorous cycling in eutrophic lake sediments

Cyanobacterial blooms frequently occur in freshwater lakes, subsequently, substantial amounts of decaying cyanobacterial bloom biomass (CBB) settles onto the lake sediments where anaerobic mineralization reactions prevail. Coupled Fe/S cycling processes can influence the mobilization of phosphorus (P) in sediments, with high releases often resulting in eutrophication. To better understand eutrophication in Lake Taihu (PRC), we investigated the effects of CBB and temperature on phosphorus cycling in lake sediments. Results indicated that added CBB not only enhanced sedimentary iron reduction, but also resulted in a change from net sulfur oxidation to sulfate reduction, which jointly resulted in a spike of soluble Fe(II) and the formation of FeS/FeS₂. Phosphate release was also enhanced with CBB amendment along with increases in reduced sulfur. Further release of phosphate was associated with increases in incubation temperature. In addition, CBB amendment resulted in a shift in P from the Fe-adsorbed P and the relatively unreactive Residual-P pools to the more reactive Al-adsorbed P, Ca-bound P and organic-P pools. Phosphorus cycling rates increased on addition of CBB and were higher at elevated temperatures, resulting in increased phosphorus release from sediments. These findings suggest that settling of CBB into sediments will likely increase the extent of eutrophication in aquatic environments and these processes will be magnified at higher temperatures.

Diversity and abundance of aromatic catabolic genes in lake sediments in response to temperature change

The abundance and composition of genes involved in the catabolism of aromatic compounds provide important information on the biodegradation potential of organic pollutants and naturally occurring compounds in the environment. We studied catechol 2, 3 dioxygenase (C23O) and benzylsuccinate synthase (bssA) genes coding for key enzymes of aerobic and anaerobic degradation of aromatic compounds in experimental incubations with sediments from two contrasting lakes; humic lake Svarttjärn and eutrophic Vallentunasjön, respectively. Sediment cores from both lakes were incubated continuously for 5 months at constant temperatures ranging from 1.0 to 21.0 °C. The difference in C23O gene composition of the sediment analyzed at the end of the experiment was larger between lakes, than among temperature treatments within each lake. The abundance of C23O gene copies and measured respiration was positively correlated with temperature in Vallentunasjön, whereas putative C23O genes were present in lower concentrations in Svarttjärn sediments. Putative bssA genes were only detected in Svarttjärn. For both lakes, the two catabolic genes were most abundant in the surface sediment. The results emphasize the important role of temperature and nutrient availability in controlling the functional potential of sediment microorganisms and reveal differences between systems with contrasting trophic status. A better understanding of catabolic pathways and enzymes will enable more accurate forecasting of the functional properties of ecosystems under various scenarios of environmental change.

Impacts of shallow geothermal energy production on redox processes and microbial communities

Shallow geothermal systems are increasingly being used to store or harvest thermal energy for heating or cooling purposes. This technology causes temperature perturbations exceeding the natural variations in aquifers, which may impact groundwater quality. Here, we report the results of laboratory experiments on the effect of temperature variations (5-80 °C) on redox processes and associated microbial communities in anoxic unconsolidated subsurface sediments. Both hydrochemical and microbiological data showed that a temperature increase from 11 °C (in situ) to 25 °C caused a shift from iron-reducing to sulfate-reducing and methanogenic conditions. Bioenergetic calculations could explain this shift. A further temperature increase (>45 °C) resulted in the emergence of a thermophilic microbial community specialized in fermentation and sulfate reduction. Two distinct maxima in sulfate reduction rates, of similar orders of magnitude (5 × 10(-10) M s(-1)), were observed at 40 and 70 °C. Thermophilic sulfate reduction, however, had a higher activation energy (100-160 kJ mol(-1)) than mesophilic sulfate reduction (30-60 kJ mol(-1)), which might be due to a trade-off between enzyme stability and activity with thermostable enzymes being less efficient catalysts that require higher activation energies. These results reveal that while sulfate-reducing functionality can withstand a substantial temperature rise, other key biochemical processes appear more temperature sensitive.

Estimation of hydrocarbon biodegradation rates in marine environments: a critical review of the Q10 approach

Offshore oil & gas industry is moving exploration and production activities into Arctic and deep water regions. Governmental regulations require environmental impact assessments before operations to evaluate the possible effects of accidental oil releases. These are often performed by numerical fate models, like the Oil Spill Contingency and Response (OSCAR) model, which has become an industry standard in Norway. In this model, biodegradation rates are adjusted to local conditions by temperature compensation according to a Q10 approach. Q10 is the multiplier by which rates of enzymatic reactions increase at a 10 °C temperature rise. Herein, this Q10 approach implemented in the OSCAR model is investigated based on published data and novel obtained results. Overall, biodegradation rate predictions calculated by temperature compensation are found to be questionable, and choosing one universal Q10 value is considered not feasible. The high variation in Q10 values is herein attributed to indirect effects of temperature.

Naphthalene biodegradation in temperate and arctic marine microcosms

Naphthalene, the smallest polycyclic aromatic hydrocarbon (PAH), is found in abundance in crude oil, its major source in marine environments. PAH removal occurs via biodegradation, a key process determining their fate in the sea. Adequate estimation of PAH biodegradation rates is essential for environmental risk assessment and response planning using numerical models such as the oil spill contingency and response (OSCAR) model. Using naphthalene as a model compound, biodegradation rate, temperature response and bacterial community composition of seawaters from two climatically different areas (North Sea and Arctic Ocean) were studied and compared. Naphthalene degradation was followed by measuring oxygen consumption in closed bottles using the OxiTop(®) system. Microbial communities of untreated and naphthalene exposed samples were analysed by polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing. Three times higher naphthalene degradation rate coefficients were observed in arctic seawater samples compared to temperate, at all incubation temperatures. Rate coefficients at in situ temperatures were however, similar (0.048 day(-1) for temperate and 0.068 day(-1) for arctic). Naphthalene biodegradation rates decreased with similar Q10 ratios (3.3 and 3.5) in both seawaters. Using the temperature compensation method implemented in the OSCAR model, Q10 = 2, biodegradation in arctic seawater was underestimated when calculated from the measured temperate k1 value, showing that temperature difference alone could not predict biodegradation rates adequately. Temperate and arctic untreated seawater communities were different as revealed by pyrosequencing. Geographic origin of seawater affected the community composition of exposed samples.

Abundance, diversity and activity of sulfate-reducing prokaryotes in heavy metal-contaminated sediment from a salt marsh in the Medway Estuary (UK)

We investigated the diversity and activity of sulfate-reducing prokaryotes (SRP) in a 3.5-m sediment core taken from a heavy metal-contaminated site in the Medway Estuary, UK. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene β-subunit (dsrB) and taking into account DNA extraction efficiency. This showed that SRPs were abundant throughout the core with maximum values in the top 50 cm of the sediment core making up 22.4% of the total bacterial community and were 13.6% at 250 cm deep. Gene libraries for dsrA (dissimilatory sulfite reductase α-subunit) were constructed from the heavily contaminated (heavy metals) surface sediment (top 20 cm) and from the less contaminated and sulfate-depleted, deeper zone (250 cm). Certain cloned sequences were similar to dsrA found in members of the Syntrophobacteraceae, Desulfobacteraceae and Desulfovibrionaceae as well as a large fraction (60%) of novel sequences that formed a deep branching dsrA lineage. Phylogenetic analysis of metabolically active SRPs was performed by reverse transcription PCR and single strand conformational polymorphism analysis (RT-PCR-SSCP) of dsrA genes derived from extracted sediment RNA. Subsequent comparative sequence analysis of excised SSCP bands revealed a high transcriptional activity of dsrA belonging to Desulfovibrio species in the surface sediment. These results may suggest that members of the Desulfovibrionaceae are more active than other SRP groups in heavy metal-contaminated surface sediments.

In situ rates of sulfate reduction in response to geochemical perturbations

Rates of in situ microbial sulfate reduction in response to geochemical perturbations were determined using Native Organism Geochemical Experimentation Enclosures (NOGEEs), a new in situ technique developed to facilitate evaluation of controls on microbial reaction rates. NOGEEs function by first trapping a native microbial community in situ and then subjecting it to geochemical perturbations through the introduction of various test solutions. On three occasions, NOGEEs were used at the Norman Landfill research site in Norman, Oklahoma, to evaluate sulfate-reduction rates in wetland sediments impacted by landfill leachate. The initial experiment, in May 2007, consisted of five introductions of a sulfate test solution over 11 d. Each test stimulated sulfate reduction with rates increasing until an apparent maximum was achieved. Two subsequent experiments, conducted in October 2007 and February 2008, evaluated the effects of concentration on sulfate-reduction rates. Results from these experiments showed that faster sulfate-reduction rates were associated with increased sulfate concentrations. Understanding variability in sulfate-reduction rates in response to perturbations may be an important factor in predicting rates of natural attenuation and bioremediation of contaminants in systems not at biogeochemical equilibrium.

Effect of temperature on biogeochemistry of marine organic-enriched systems: implications in a global warming scenario

Coastal biogeochemical cycles are expected to be affected by global warming. By means of a mesocosm experiment, the effect of increased water temperature on the biogeochemical cycles of coastal sediments affected by organic-matter enrichment was tested, focusing on the carbon, sulfur, and iron cycles. Nereis diversicolor was used as a model species to simulate macrofaunal bioirrigation activity in natural sediments. Although bioirrigation rates of N. diversicolor were not temperature dependent, temperature did have a major effect on the sediment metabolism. Under organic-enrichment conditions, the increase in sediment metabolism was greater than expected and occurred through the enhancement of anaerobic metabolic pathway rates, mainly sulfate reduction. There was a twofold increase in sediment metabolism and the accumulation of reduced sulfur. The increase in the benthic metabolism was maintained by the supply of electron acceptors through bioirrigation and as a result of the availability of iron in the sediment. As long as the sediment buffering capacity toward sulfides is not surpassed, an increase in temperature might promote the recovery of organic-enriched sediments by decreasing the time for mineralization of excess organic matter.

Bacterial sulfur cycling shapes microbial communities in surface sediments of an ultramafic hydrothermal vent field

The ultramafic-hosted Logatchev hydrothermal field (LHF) is characterized by vent fluids, which are enriched in dissolved hydrogen and methane compared with fluids from basalt-hosted systems. Thick sediment layers in LHF are partly covered by characteristic white mats. In this study, these sediments were investigated in order to determine biogeochemical processes and key organisms relevant for primary production. Temperature profiling at two mat-covered sites showed a conductive heating of the sediments. Elemental sulfur was detected in the overlying mat and metal-sulfides in the upper sediment layer. Microprofiles revealed an intensive hydrogen sulfide flux from deeper sediment layers. Fluorescence in situ hybridization showed that filamentous and vibrioid, Arcobacter-related Epsilonproteobacteria dominated the overlying mats. This is in contrast to sulfidic sediments in basalt-hosted fields where mats of similar appearance are composed of large sulfur-oxidizing Gammaproteobacteria. Epsilonproteobacteria (7-21%) and Deltaproteobacteria (20-21%) were highly abundant in the surface sediment layer. The physiology of the closest cultivated relatives, revealed by comparative 16S rRNA sequence analysis, was characterized by the capability to metabolize sulfur components. High sulfate reduction rates as well as sulfide depleted in (34)S further confirmed the importance of the biogeochemical sulfur cycle. In contrast, methane was found to be of minor relevance for microbial life in mat-covered surface sediments. Our data indicate that in conductively heated surface sediments microbial sulfur cycling is the driving force for bacterial biomass production although ultramafic-hosted systems are characterized by fluids with high levels of dissolved methane and hydrogen.

Turning up the heat: temperature influences the relative importance of top-down and bottom-up effects

Understanding how communities respond to changes in temperature is a major challenge for community ecology. Temperature influences the relative degree to which top-down and bottom-up forces structure ecological communities. In greenhouse experiments using the aquatic community found in pitcher plants (Sarracenia purpurea), I tested how temperature affected the relative importance of top-down (mosquito predation) and bottom-up (ant carcasses) forces on protozoa and bacteria populations. While bottom-up effects did not vary consistently with temperature, the top-down effects of predators on protozoa increased at higher temperatures. These results suggest that temperature could change the relative importance of top-down and bottom-up effects in ecological communities. Specifically, higher temperature may increase the strength of top-down effects by raising predator metabolic rate and concomitant processes (e.g., activity, foraging, digestion, growth) relative to cooler temperatures. These findings apply broadly to an understanding of trophic interactions in a variable environment and are especially relevant in the context of ongoing climate change.

Temperature-dependent global gene expression in the Antarctic archaeon Methanococcoides burtonii

Methanococcoides burtonii is a member of the Archaea that was isolated from Ace Lake in Antarctica and is a valuable model for studying cold adaptation. Low temperature transcriptional regulation of global gene expression, and the arrangement of transcriptional units in cold-adapted archaea has not been studied. We developed a microarray for determining which genes are expressed in operons, and which are differentially expressed at low (4°C) or high (23°C) temperature. Approximately 55% of genes were found to be arranged in operons that range in length from 2 to 23 genes, and mRNA abundance tended to increase with operon length. Analysing microarray data previously obtained by others for Halobacterium salinarum revealed a similar correlation between operon length and mRNA abundance, suggesting that operons may play a similar role more broadly in the Archaea. More than 500 genes were differentially expressed at levels up to ≈ 24-fold. A notable feature was the upregulation of genes involved in maintaining RNA in a state suitable for translation in the cold. Comparison between microarray experiments and results previously obtained using proteomics indicates that transcriptional regulation (rather than translation) is primarily responsible for controlling gene expression in M. burtonii. In addition, certain genes (e.g. involved in ribosome structure and methanogenesis) appear to be regulated post-transcriptionally. This is one of few experimental studies describing the genome-wide distribution and regulation of operons in archaea.

Seasonal changes in organic matter mineralization in a sublittoral sediment and temperature-driven decoupling of key processes

Seasonal changes in the mineralization of organic compounds in sediments were investigated in temperate, sublittoral zone sediments (Tokyo Bay, Japan). The total mineralization rate and sulfate reduction rate showed large seasonal variations over the year, and although the fluctuations in both rates correlated with temperature, the latter was irregularly high in May. The concentration of organic carbon dissolved in interstitial water was specifically high in April. A culture-based experiment was also conducted under temperatures corresponding to the seasonal changes. In the culture incubated at a temperature corresponding to April (13 °C), hydrolysis and fermentation proceeded, but terminal oxidation was hindered, thereby resulting in acetate accumulation. At a temperature corresponding to May (22 °C), acetate oxidation coupled with sulfate reduction was observed. The temperature-related differences were also reflected in the bacterial community structure in the cultures analyzed by DGGE. In the culture incubated at the lower temperature, sulfate-reducing bacterium of incomplete oxidizer was detected, while sequence found in the culture incubated at the higher temperature was related to complete oxidizers. These results suggest that complete and incomplete-oxidizing sulfate-reducing bacteria act as distinct functional groups, responding to temperature in different ways, particularly in environments characterized by large temperature fluctuations.

Thermophilic anaerobes in Arctic marine sediments induced to mineralize complex organic matter at high temperature

Marine sediments harbour diverse populations of dormant thermophilic bacterial spores that become active in sediment incubation experiments at much higher than in situ temperature. This response was investigated in the presence of natural complex organic matter in sediments of two Arctic fjords, as well as with the addition of freeze-dried Spirulina or individual high-molecular-weight polysaccharides. During 50 degrees C incubation experiments, Arctic thermophiles catalysed extensive mineralization of the organic matter via extracellular enzymatic hydrolysis, fermentation and sulfate reduction. This high temperature-induced food chain mirrors sediment microbial processes occurring at cold in situ temperatures (near 0 degrees C), yet it is catalysed by a completely different set of microorganisms. Using sulfate reduction rates (SRR) as a proxy for organic matter mineralization showed that differences in organic matter reactivity determined the extent of the thermophilic response. Fjord sediments with higher in situ SRR also supported higher SRR at 50 degrees C. Amendment with Spirulina significantly increased volatile fatty acids production and SRR relative to unamended sediment in 50 degrees C incubations. Spirulina amendment also revealed temporally distinct sulfate reduction phases, consistent with 16S rRNA clone library detection of multiple thermophilic Desulfotomaculum spp. enriched at 50 degrees C. Incubations with four different fluorescently labelled polysaccharides at 4 degrees C and 50 degrees C showed that the thermophilic population in Arctic sediments produce a different suite of polymer-hydrolysing enzymes than those used in situ by the cold-adapted microbial community. Over time, dormant marine microorganisms like these are buried in marine sediments and might eventually encounter warmer conditions that favour their activation. Distinct enzymatic capacities for organic polymer degradation could allow specific heterotrophic populations like these to play a role in sustaining microbial metabolism in the deep, warm, marine biosphere.

Effects of freeze-thaw cycles on anaerobic microbial processes in an Arctic intertidal mud flat

Insight into the effects of repeated freezing and thawing on microbial processes in sediments and soils is important for understanding sediment carbon cycling at high latitudes acutely affected by global warming. Microbial responses to repeated freeze-thaw conditions were studied in three complementary experiments using arctic sediment collected from an intertidal flat that is exposed to seasonal freeze-thaw conditions (Ymerbukta, Svalbard, Arctic Ocean). The sediment was subjected to oscillating freeze-thaw incubations, either gradual, from -5 to 4 degrees C, or abrupt, from -20 to 10 degrees C. Concentrations of low-molecular weight carboxylic acids (volatile fatty acids) were measured and sulfate reduction was assessed by measuring (35)S sulfate reduction rates (SRRs). Gradual freeze-thaw incubation decreased microbial activity in the frozen state to 0.25 % of initial levels at 4 degrees C, but activity resumed rapidly reaching >60 % of initial activity in the thawed state. Exposure of sediments to successive large temperature changes (-20 versus 10 degrees C) decreased SRR by 80% of the initial activity, suggesting that a fraction of the bacterial community recovered rapidly from extreme temperature fluctuations. This is supported by 16S rRNA gene-based denaturing gradient gel electrophoresis profiles that revealed persistence of the dominant microbial taxa under repeated freeze-thaw cycles. The fast recovery of the SRRs suggests that carbon mineralization in thawing arctic sediment can resume without delay or substantial growth of microbial populations.