Biological nitrogen fixation in acidic high-temperature geothermal springs in Yellowstone National Park, Wyoming

The near ubiquitous distribution of nifH genes in sediments sampled from 14 high-temperature (48.0-89.0°C) and acidic (pH 1.90-5.02) geothermal springs in Yellowstone National Park suggested a role for the biological reduction of dinitrogen (N(2)) to ammonia (NH(3)) (e.g. nitrogen fixation or diazotrophy) in these environments. nifH genes from these environments formed three unique phylotypes that were distantly related to acidiphilic, mesophilic diazotrophs. Acetylene reduction assays and (15) N(2) tracer studies in microcosms containing sediments sampled from acidic and high-temperature environments where nifH genes were detected confirmed the potential for biological N(2) reduction in these environments. Rates of acetylene reduction by sediment-associated populations were positively correlated with the concentration of NH(4)(+), suggesting a potential relationship between NH(4)(+) consumption and N(2) fixation activity. Amendment of microcosms with NH(4)(+) resulted in increased lag times in acetylene reduction assays. Manipulation of incubation temperature and pH in acetylene reduction assays indicated that diazotrophic populations are specifically adapted to local conditions. Incubation of sediments in the presence of a N(2) headspace yielded a highly enriched culture containing a single nifH phylotype. This phylotype was detected in all 14 geothermal spring sediments examined and its abundance ranged from ≈ 780 to ≈ 6800 copies (g dry weight sediment)(-1), suggesting that this organism may contribute N to the ecosystems. Collectively, these results for the first time demonstrate thermoacidiphilic N(2) fixation in the natural environment and extend the upper temperature for biological N(2) fixation in terrestrial systems.     

Distinct bacterial communities exist beneath a high Arctic polythermal glacier

Bacterial communities reside in basal ice, sediment, and meltwater in the supra-, sub-, and proglacial environments of John Evans Glacier, Nunavut, Canada. We examined whether the subglacial bacterial community shares common members with the pro- and supraglacial communities, and by inference, whether it could be derived from communities in either of these environments (e.g., by ice overriding proglacial sediments or by in-wash of surface meltwaters). Terminal restriction fragment length polymorphism analysis of bacterial 16S rRNA genes amplified from these environments revealed that the subglacial water, basal ice, and sediment communities were distinct from those detected in supraglacial meltwater and proglacial sediments, with 60 of 142 unique terminal restriction fragments (T-RFs) detected exclusively in subglacial samples and only 8 T-RFs detected in all three environments. Supraglacial waters shared some T-RFs with subglacial water and ice, likely reflecting the seasonal flow of surface meltwater into the subglacial drainage system, whereas supraglacial and proglacial communities shared the fewest T-RFs. Thus, the subglacial community at John Evans Glacier appears to be predominantly autochthonous rather than allochthonous, and it may be adapted to subglacial conditions. Chemical analysis of water and melted ice also revealed differences between the supraglacial and proglacial environments, particularly regarding electrical conductivity and nitrate, sulfate, and dissolved organic carbon concentrations. Whereas the potential exists for common bacterial types to be broadly distributed throughout the glacial system, we have observed distinct bacterial communities in physically and chemically different glacial environments.     

Distinct Bacterial Communities Exist beneath a High Arctic Polythermal Glacier

Bacterial communities reside in basal ice, sediment, and meltwater in the supra-, sub-, and proglacial environments of John Evans Glacier, Nunavut, Canada. We examined whether the subglacial bacterial community shares common members with the pro- and supraglacial communities, and by inference, whether it could be derived from communities in either of these environments (e.g., by ice overriding proglacial sediments or by in-wash of surface meltwaters). Terminal restriction fragment length polymorphism analysis of bacterial 16S rRNA genes amplified from these environments revealed that the subglacial water, basal ice, and sediment communities were distinct from those detected in supraglacial meltwater and proglacial sediments, with 60 of 142 unique terminal restriction fragments (T-RFs) detected exclusively in subglacial samples and only 8 T-RFs detected in all three environments. Supraglacial waters shared some T-RFs with subglacial water and ice, likely reflecting the seasonal flow of surface meltwater into the subglacial drainage system, whereas supraglacial and proglacial communities shared the fewest T-RFs. Thus, the subglacial community at John Evans Glacier appears to be predominantly autochthonous rather than allochthonous, and it may be adapted to subglacial conditions. Chemical analysis of water and melted ice also revealed differences between the supraglacial and proglacial environments, particularly regarding electrical conductivity and nitrate, sulfate, and dissolved organic carbon concentrations. Whereas the potential exists for common bacterial types to be broadly distributed throughout the glacial system, we have observed distinct bacterial communities in physically and chemically different glacial environments.     

Denitrification,Nitrificastion and Nitrogen Fixation in Sublittoral Sediments of the South China Sea

Measurements of denitrification, nitrification and nitrogen fixation rates were made alongside with measuring of chemical and physical properties in sublittoral sediments of the South China Sea near the coast of Vietnam. Studied sediments were suboxic (Eh was positive as a rule), had 0.18–1.5 % of organic carbon, 0.004–0.135 % of total nitrogen and 3-12 % of total iron. The numbers of denitrifying and nitrate-reducing bacteria were as high as millions and hundreds of millions cells per gram wet weight of sediment matter, respectively. The processes of nitrification and denitrification were not spearated spacely. The nitrification was measured in both superficial layer and in a 10-cm sediment column. There were indirect evidences suggesting possibility of anaerobic ammonium oxidation. Denitrification was detectable in the sediments from two sites of sampling; maximal value was 86.2 μmoles N m⁻²h⁻¹. The denitrification potential determined at 1 mM nitrate decreased regularly from the upper to lower layers. Its values in the different sediments ranged from 134 to 532 μmoles N m⁻²h⁻¹. Nitrogen fixation (from 4.8 to 86μmoles N m⁻²h⁻¹) was close to that found in similar sediments in temperate waters in summer, and was not a significant source of nitrogen. It was comparable with diffusion of ammonium from sedimnts.     

Quantification of ammonia-oxidizing bacteria and factors controlling nitrification in salt marsh sediments

To elucidate the geomicrobiological factors controlling nitrification in salt marsh sediments, a comprehensive approach involving sediment geochemistry, process rate measurements, and quantification of the genetic potential for nitrification was applied to three contrasting salt marsh habitats: areas colonized by the tall (TS) or short (SS) form of Spartina alterniflora and unvegetated creek banks (CBs). Nitrification and denitrification potential rates were strongly correlated with one another and with macrofaunal burrow abundance, indicating that coupled nitrification-denitrification was enhanced by macrofaunal burrowing activity. Ammonia monooxygenase (amoA) gene copy numbers were used to estimate the ammonia-oxidizing bacterial population size (5.6 x 10(4) to 1.3 x 10(6) g of wet sediment(-1)), which correlated with nitrification potentials and was 1 order of magnitude higher for TS and CB than for SS. TS and CB sediments also had higher Fe(III) content, higher Fe(III)-to-total reduced sulfur ratios, higher Fe(III) reduction rates, and lower dissolved sulfides than SS sediments. Iron(III) content and reduction rates were positively correlated with nitrification and denitrification potential and amoA gene copy number. Laboratory slurry incubations supported field data, confirming that increased amounts of Fe(III) relieved sulfide inhibition of nitrification. We propose that macrofaunal burrowing and high concentrations of Fe(III) stimulate nitrifying bacterial populations, and thus may increase nitrogen removal through coupled nitrification-denitrification in salt marsh sediments.     

Biogeochemistry of manganese- and iron-rich sediments in Toolik Lake,Alaska

The sediments within Toolik Lake in arctic Alaska are characterized by extremely low rates of organic matter sedimentation and unusually high concentrations of iron and manganese. Pore water and solid phase measurements of iron, manganese, trace metals, carbon, nitrogen, phosphorus, and sulfur are consistent with the hypothesis that the reduction of organic matter by iron and manganese is the most important biogeochemical reaction within the sediment. Very low rates of dissolved oxygen consumption by the sediments result in an oxidizing environment at the sediment-water interface. This results in high retention of upwardly-diffusing iron and manganese and the formation of metal-enriched sediment. Phosphate in sediment pore waters is strongly adsorbed by the metal-enriched phases. Consequently, fluxes of phosphorus from the sediments to overlying waters are very small and contribute to the oligotrophic nature of the Toolik Lake aquatic system. Toolik Lake contains an unusual type of lacustrine sediment, and in many ways the sediments are similar to those found in oligotrophic oceanic environments.     

Spatial variability in nitrification rates and ammonia-oxidizing microbial communities in the agriculturally impacted Elkhorn Slough estuary, California

Ammonia oxidation-the microbial oxidation of ammonia to nitrite and the first step in nitrification-plays a central role in nitrogen cycling in coastal and estuarine systems. Nevertheless, questions remain regarding the connection between this biogeochemical process and the diversity and abundance of the mediating microbial community. In this study, we measured nutrient fluxes and rates of sediment nitrification in conjunction with the diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing betaproteobacteria (β-AOB). Sediments were examined from four sites in Elkhorn Slough, a small agriculturally impacted coastal California estuary that opens into Monterey Bay. Using an intact sediment core flowthrough incubation system, we observed significant correlations among NO(3)(-), NO(2)(-), NH(4)(+), and PO(4)(3+) fluxes, indicating a tight coupling of sediment biogeochemical processes. (15)N-based measurements of nitrification rates revealed higher rates at the less impacted, lower-nutrient sites than at the more heavily impacted, nutrient-rich sites. Quantitative PCR analyses revealed that β-AOB amoA (encoding ammonia monooxygenase subunit A) gene copies outnumbered AOA amoA gene copies by factors ranging from 2- to 236-fold across the four sites. Sites with high nitrification rates primarily contained marine/estuarine Nitrosospira-like bacterial amoA sequences and phylogenetically diverse archaeal amoA sequences. Sites with low nitrification rates were dominated by estuarine Nitrosomonas-like amoA sequences and archaeal amoA sequences similar to those previously described in soils. This is the first report measuring AOA and β-AOB amoA abundance in conjunction with (15)N-based nitrification rates in estuary sediments.     

Abundance and community composition of ammonia-oxidizing archaea and bacteria in two different zones of Lake Taihu

The abundance and community composition of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the surface sediments of 2 different zones (Meiliang Bay and Eastern Lake Taihu) of Lake Taihu were investigated using real-time quantitative polymerase chain reaction and clone libraries. The amoA gene copy numbers in the surface sediment of Meiliang Bay ranged from 4.91?× 10(5) to 8.65?× 10(6) copies/g dry sediment for the archaeal amoA gene and from 3.74?× 10(4) to 3.86?× 10(5) copies/g dry sediment for the bacterial amoA gene, which were significantly higher than those of Eastern Lake Taihu (P?< 0.05). Concentrations of ammonia (NH(4)(+)), total nitrogen, organic matter, and pH of the sediments exhibited significantly negative correlations with the abundance of ammonia-oxidizing archaea or ammonia-oxidizing bacteria (P?< 0.05 or P?< 0.01, respectively). The potential nitrification rates show remarkable correlations with the copy numbers of the archaeal amoA gene. Diversity of the archaeal amoA gene in Eastern Lake Taihu was significantly higher than that of Meiliang Bay, whereas the bacterial amoA gene diversity was comparable for the 2 lake zones. The data obtained in this study would be useful to elucidate the role of ammonia-oxidizing archaea and ammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.     

Comparative analysis of archaeal 16S rRNA and <Emphasis Type="Italic">amoA</Emphasis> genes to estimate the abundance and diversity of ammonia-oxidizing archaea in marine sediments

Considering their abundance and broad distribution, non-extremophilic Crenarchaeota are likely to play important roles in global organic and inorganic matter cycles. The diversity and abundance of archaeal 16S rRNA and putative ammonia monooxygenase alpha-subunit (amoA) genes were comparatively analyzed to study genetic potential for nitrification of ammonia-oxidizing archaea (AOA) in the surface layers (0-1 cm) of four marine sediments of the East Sea, Korea. After analysis of a 16S rRNA gene clone library, we found various archaeal groups that include the crenarchaeotal group (CG) I.1a (54.8%) and CG I.1b (5.8%), both of which are known to harbor ammonia oxidizers. Notably, the 16S rRNA gene of CG I.1b has only previously been observed in terrestrial environments. The 16S rRNA gene sequence data revealed a distinct difference in archaeal community among sites of marine sediments. Most of the obtained amoA sequences were not closely related to those of the clones retrieved from estuarine sediments and marine water columns. Furthermore, clades of unique amoA sequences were likely to cluster according to sampling sites. Using real-time PCR, quantitative analysis of amoA copy numbers showed that the copy numbers of archaeal amoA ranged from 1.1 x 10(7) to 4.9 x 10(7) per gram of sediment and were more numerous than those of bacterial amoA, with ratios ranging from 11 to 28. In conclusion, diverse CG I.1a and CG I.1b AOA inhabit surface layers of marine sediments and AOA, and especially, CG I.1a are more numerous than other ammonia-oxidizing bacteria.     

The effects of sediment desiccation on the potential for nitrification, denitrification, and methanogenesis in an Australian reservoir

Sediments from an Australian reservoir were selected for varying degrees of in situ desiccation (i.e. non-desiccated, partially desiccated and desiccated). Sediment samples were then chemically amended with appropriate electron donors and acceptors to ascertain the effect of sediment desiccation on the potential for nitrification, denitrification, methanogenesis, and the interaction of these processes. There was no detectable nitrification in these sediments yet up to 75% of added nitrate was converted to dinitrogen. Denitrification was predominantly limited by nitrate although there was evidence of carbon co-limitation. None of the nitrogen cycle processes were notably affected by sediment desiccation. There was no flush of mineral nitrogen from desiccated sediments upon rewetting. Methanogenesis did not begin in these sediments until nitrate concentrations fell below 2.25 * 10^-5 M. Methanogenesis was always carbon limited. Methanogens were affected by sediment desiccation but were capable of recovery over time upon rewetting of sediments.     

Characterization of nitrifying, denitrifying, and overall bacterial communities in permeable marine sediments of the northeastern Gulf of Mexico

Sandy or permeable sediment deposits cover the majority of the shallow ocean seafloor, and yet the associated bacterial communities remain poorly described. The objective of this study was to expand the characterization of bacterial community diversity in permeable sediment impacted by advective pore water exchange and to assess effects of spatial, temporal, hydrodynamic, and geochemical gradients. Terminal restriction fragment length polymorphism (TRFLP) was used to analyze nearly 100 sediment samples collected from two northeastern Gulf of Mexico subtidal sites that primarily differed in their hydrodynamic conditions. Communities were described across multiple taxonomic levels using universal bacterial small subunit (SSU) rRNA targets (RNA- and DNA-based) and functional markers for nitrification (amoA) and denitrification (nosZ). Clonal analysis of SSU rRNA targets identified several taxa not previously detected in sandy sediments (i.e., Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Firmicutes). Sequence diversity was high among the overall bacterial and denitrifying communities, with members of the Alphaproteobacteria predominant in both. Diversity of bacterial nitrifiers (amoA) remained comparatively low and did not covary with the other gene targets. TRFLP fingerprinting revealed changes in sequence diversity from the family to species level across sediment depth and study site. The high diversity of facultative denitrifiers was consistent with the high permeability, deeper oxygen penetration, and high rates of aerobic respiration determined in these sediments. The high relative abundance of Gammaproteobacteria in RNA clone libraries suggests that this group may be poised to respond to short-term periodic pulses of growth substrates, and this observation warrants further investigation.     

Arctic sediments (Svalbard): pore water and solid phase distributions of C,N, P and Si

Pore water and solid phase distributions of C, N, P and Si in sediments of the Arctic Ocean (Svalbard area) have been investigated. Concentrations of organic carbon (C_org) in the solid phase of the sediment varied from 1.3 to 2.8% (mean 1.9%), with highest concentrations found at shallow stations south/southwest of Svalbard. Relatively low concentrations were obtained at the deeper stations north/northeast of Svalbard. Atomic carbon to nitrogen ratios in the surface sediment ranged from below 8 to above 10. For some stations, high C/N ratios together with high concentrations of C_org suggest that sedimentary organic matter is mainly of terrigenous origin and not from overall biological activity in the water column. Organic matter reactivity (defined as the total sediment oxygen consumption rate normalized to the organic carbon content of the surface sediment) correlated with water depth at all investigated stations. However, the stations could be divided into two separate groups with different reactivity characteristics, representing the two most dominant hydrographic regimes: the region west of Svalbard mainly influenced by the West Spitsbergen Current, and the area east of Svalbard where Arctic polar water set the environmental conditions. Decreasing sediment reactivity with water depth was confirmed by the partitioning between organic and inorganic carbon of the surface sediment. The ratio between organic and inorganic carbon at the sediment-water interface decreased exponentially with water depth: from indefinite values at shallow stations in the central Barents Sea, to approximately 1 at deep stations north of Svalbard. At stations east of Svalbard there was an inverse linear correlation between the organic matter reactivity (as defined above) and concentration of dissolved organic carbon (DOC) in the pore water. The more reactive the sediment, the less DOC existed in the pore water and the more total carbonate (C_t or ΣCO₂) was present. This observation suggests that DOC produced in reactive sediments is easily metabolizable to CO₂. Sediment accumulation rates of opaline silica ranged from 0.35 to 5.7 μmol SiO₂ m⁻²d⁻¹ (mean 1.3 μmol SiO₂ m⁻²d⁻¹), i.e. almost 300 times lower than rates previously reported for the Ross Sea, Antarctica. Concentrations of ammonium and nitrate in the pore water at the sediment-water interface were related to organic matter input and water depth. In shallow regions with highly reactive organic matter, a pool of ammonium was present in the pore water, while nitrate conoentrations were low. In areas where less reactive organic matter was deposited at the sediment surface, the deeper zone of nitrification caused a build-up of nitrate in the pore water while ammonium was almost depleted. Nitrate penetrated from 1.8 to ≥ 5.8 cm into the investigated sediments. Significantly higher concentrations of “total” dissolved nitrogen (defined as the sum of NO₃, NO₂, NH₄ and urea) in sediment pore water were found west compared to east of Svalbard. The differences in organic matter reactivity, as well as in pore water distribution patterns of “total” dissolved nitrogen between the two areas, probably reflect hydrographic factors (such as ice coverage and production/import of particulate organic material) related to the dominant water mass (Atlantic or Arctic Polar) in each of the two areas. The data presented were collected during the European “Polarstern” Study (Arctic EPOS) sponsored by the European Science Foundation     

The impact of polychaete (Nereis virens Sars) burrows on nitrification and nitrate reduction in estuarine sediments

The influence of Nereis virens Sars burrows on nitrification, denitrification and total nitrate reduction was assessed in poor (0.7% organic matter) and rich (2.0% organic matter) sediment from the estuary, Norsminde Fjord. The experiments were performed as assays of potential activity, since natural conditions proved impossible to simulate in the unpredictable burrow environment. The measurements were made in two microprofiles, extending 15 mm into the sediment from the surface and from the burrow wall lining. Both sediment types showed higher potential nitrification in the wall linings than in the surface sediment. This was positively correlated with the content of silt + clay particles and organic matter (i.e. the mucous lining of burrow walls). An elevated nitrate reduction activity was evident in the oxic layer of surface sediment. No such activity pattern was observed in the burrow walls. Denitrification accounted for 27–53 % of the total nitrate reduction. An empirical relationship between the ratio of predicted oxygen penetration into surface and wall sediment and the contribution of nereid burrows to bulk actual nitrification and nitrate reduction is presented. The burrow contribution to bulk nitrification was, in contrast to bulk nitrate reduction, very sensitive to variable oxygen penetrations. Thus, possible short-time changes in nitrate exchange across the wall lining will apparently be regulated by changes in nitrification activity rather than nitrate reduction activity.     

变性梯度凝胶电泳法研究我国不同土壤氨氧化细菌群落组成及活性

实验选用了我国3种不同土壤研究土壤硝化活性、硝化细菌数量,并使用变性梯度凝胶电泳(DGGE)的方法研究了不同土壤中氨氧化细菌(AOB)区系变化。通过28d的土壤培养实验研究发现,潮土具有最强的硝化势,几乎100%的铵态氮转化为硝态氮;而红壤中的硝化势最弱,只有4.9%的铵态氮转化为硝态氮。对这3种土壤硝化细菌进行计数发现,3种土壤氨氧化菌数量差异显著,而3种土壤亚硝酸氧化菌(NOB)处于一个数量级。采用氨氧化菌功能基因amoA(氨单加氧酶ammoniamonooxygenase)特异PCR结合DGGE的方法对土壤氨氧化菌区系进行分析。红壤有4个氨氧化菌种属,与潮土和黄泥土没有共同的氨氧化菌种属。4个种属中两个是与潮土和黄泥土亲源性比较远的,特有的氨氧化菌种属,这两个种属与已知的Nitrosospira属的cluster3bz97838和Nitrosospira属的cluster3aAF353263亲源性比较近。潮土有5个氨氧化菌种属,潮土与黄泥土有两个共同的氨氧化菌种属,这两个种属中的一个是潮土和黄泥土特有的,与其他氨氧化菌种属亲源性比较远的氨氧化菌种属,这个种属与已知的Nitrosospira属的cluster3bZ97849亲源性比较近。黄泥土有4个氨氧化菌种属,除了与潮土共有的一个种属是两种土壤特有的氨氧化菌种属外,黄泥土还有一个与其他氨氧化菌种属亲源性比较远的,黄泥土特有的种属,与Nitrosospira属的cluster3aAF353263亲源性很近。3种土壤中分离到的硝化细菌表现出不同的硝化能力。实验结果表明,以amoA基因为目标的PCR-DGGE是比以16SrDNA为目标的PCR-DGGE更有效的研究氨氧化菌种群的方法;3种土壤的氨氧化菌种群差异显著,尤其是红壤的氨氧化菌种群与另外两种土壤差异明显,这种差异可能与红壤的低pH条件对氨氧化菌种群的长期选择有关;3种土壤中的硝化活性与土壤中的硝化细菌数量没有显著相关,可能由于3种土壤差异显著的土壤环境对硝化活性的影响造成。因此在对不同土壤硝化细菌进行研究时不仅需要对硝化细菌数量进行研究,还需要研究不同土壤中硝化细菌的种属及不同土壤环境条件对硝化细菌硝化活性的影响。     

Nitrogen-fixing phylotypes of Chesapeake Bay and Neuse River estuary sediments

Sediments often exhibit low rates of nitrogen fixation, despite the presence of elevated concentrations of inorganic nitrogen. The organisms that potentially fix nitrogen in sediments have not previously been identified. Amplification of nifH genes with degenerate primers was used to assess the diversity of diazotrophs in two distinct sediment systems, anoxic muds of Chesapeake Bay and shallow surficial sediments of the Neuse River. Phylogenetic analysis revealed that sequences obtained from mid-Chesapeake Bay, which receive high organic loading and are highly reducing, clustered closely with each other and with known anaerobic microorganisms, suggesting a low abundance of aerobic or facultative diazotrophs in these sediments. Sulfate reduction dominates in the surface, but methanogenesis becomes more important with depth. A thin (<1 cm) oxidized layer is present only in the spring. No archaeal nifH sequences were obtained from Chesapeake Bay. Sequences of nifH amplified from surficial sediments of the Neuse River were distant from Chesapeake Bay sequences and included nif phylotypes related to sequences previously reported from marine mats and the Spartina rhizosphere. Differences in environmental site characteristics appear to select for different types of sediment diazotrophs, which is reflected in the phylogenetic composition of amplified nifH sequences.     

Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments

Nitrate is an important nutrient and electron acceptor for microorganisms, having a key role in nitrogen (N) cycling and electron transfer in anoxic sediments. High-nitrate inputs into sediments could have a significant effect on N cycling and its associated microbial processes. However, few studies have been focused on the effect of nitrate addition on the functional diversity, composition, structure and dynamics of sediment microbial communities in contaminated aquatic ecosystems with persistent organic pollutants (POPs). Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants including polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons (PAHs), before and after nitrate injection using a comprehensive functional gene array (GeoChip 4.0). Our results showed that the sediment microbial community functional composition and structure were markedly altered, and that functional genes involved in N-, carbon (C)-, sulfur (S)-and phosphorus (P)- cycling processes were highly enriched after nitrate injection, especially those microorganisms with diverse metabolic capabilities, leading to potential in situ bioremediation of the contaminated sediment, such as PBDE and PAH reduction/degradation. This study provides new insights into our understanding of sediment microbial community responses to nitrate addition, suggesting that indigenous microorganisms could be successfully stimulated for in situ bioremediation of POPs in contaminated sediments with nitrate addition.     

Microbial community structure and ecology of subglacial sediments in two polythermal Svalbard glaciers characterized by epifluorescence microscopy and PLFA

Biological and physico-chemical characteristics of subglacial sediments were studied in Svalbard. Sediment from close proglacial and supraglacial environments was used for a comparison. Viable bacteria, cyanobacteria and microalgae were detected in subglacial sediments from two polythermal glaciers using epifluorescence microscopy and phospholipid fatty acid (PLFA) analyses. The subglacial samples were generally of higher pH values, coarser texture and lower water content, organic matter, organic carbon, and nitrogen compared to proglacial and supraglacial sediments). Bacterial counts of 1.6 × 10⁷ cells mg^{− 1} OM (organic matter) were found. Cyanobacteria and algae were also of low abundance [4.2 cells mg^{− 1} DW (dry weight)]. Cyanobacteria comprised the major proportion of the autophotothrophic assemblages of subglacial soils. Deglaciated soils were similar to subglacial sediment in physico-chemical properties and microbial structure and numbers, unlike soil from vegetated sites or cryoconite sediment. In subglacial and deglaciated soil, relatively low diversity of microorganisms and low substrate availability was detected by PLFA analyses. Good accordance in microbial community structure assessments between epifluorescence microscopy and PLFA analyses was found. Our results suggest that the subglacial microbial populations can be divided into two groups: autochthonous microorganims (chemoheterotrophic bacteria) and allochthonous that retain the ability to proliferate and give rise to active population when conditions become favorable. Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Experimental measurement of sediment nitrification and denitrification in Hamilton Harbour,Canada

This research examines the role of sediment nitrification and denitrification in the nitrogen cycle of Hamilton Harbour. The Harbour is subject to large ammonia and carbon loadings from a waste-water treatment plant and from steel industries. Spring ammonia concentrations rapidly decrease from 4.5 to 0.5 mg 1⁻¹, while spring nitrate concentrations increase from 1 to 2 mg l⁻¹, by mid-summer. A three-layer sediment model was developed. The first layer is aerobic; in it, oxidation of organics and nitrification occurs. The second layer is for denitrification, and the third layer is for anaerobic processes. Ammonia sources for nitrification include diffusion from the water column, sources associated with the oxidation of organics, sources from denitrification and from anaerobic processes. Diffusion of oxygen, ammonia and nitrate across the sediment-water interface occurs. Temperature effects are modelled using the Arrhenius concept. A combination of zero-order kinetics for nitrate or ammonia consumption with diffusion results in a half-order reaction, with respect to the water column loss rate to sediments. From experimental measurement, the rate of nitrification is 200 mg N 1⁻¹ sediment per day, while that of denitrification is 85 mg N 1–1 sediment per day at 20 °C. The Arrhenius activation energy is estimated as 15 000 cal/ mole-K and 17 000 cal/ mole-K for nitrification and denitrification, respectively, between 10 °C and 20 °C. Calculations of the flux of ammonia with the sediments, using the biofilm model, compare favourably with experimental observations. The ammonia flux from the water column is estimated to account for 20% of the observed decrease in water column stocks of ammonia, while the nitrate flux from the water column is estimated to account for 25% of the total nitrogen produced by the sediments.     

Activities of benthic nitrifiers in streams and their role in oxygen consumption

The in situ rates of oxygen consumption by benthic nitrifiers were estimated at 11 study sites in 4 streams. Two methods were used: an in situ respiration chamber method and a method involving conversion of nitrifying potential measurements to in situ rates. Estimates of benthic nitrogenous oxygen consumption (BNOC) rate ranged from 0–380 mmol of O₂ m^–2·day^–1, and BNOC contributed between 0–85% of the total benthic oxygen consumption rate. The activity of nitrifiers residing in the sediments was influenced by O₂ availability, temperature, pH, and substrate. Depending upon site, nitrification could approximate either first-order or zero-order kinetics with respect to ammonium concentration. The source of ammonium for benthic nitrifiers could be either totally from within the sediment or totally from the overlying water. Nitrate produced in the sediments could flux to the water above or be lost within the sediment. The sediments could act as a source (positive flux) or sink (negative flux) for both ammonium (–185 mmol·m^–2·day^–1 to +195 mmol·m^–2·day^–1) and nitrate (–135 mmol·m^–2·day^–1 to +185 mmol·m^–2·day^–1).This study provides evidence to suggest that measurements of down-stream mass flow changes in inorganic nitrogen forms may give poor estimates of in situ rates of nitrification in flowing waters.