Rivers are an important global sink for excess bioavailable nitrogen: they convert approximately 4 40% of terrestrial N-runoff per year (~47 Tg) to biologically unavailable N 2 gas and return it to 5 the atmosphere. 1 Currently, riverine N 2 production is conceptualised and modelled as 6 denitrification. [2][3][4] The contribution of anaerobic ammonium oxidation (or anammox), an alternate 7 pathway of N 2 production important in marine environments, is not well understood. 5,6 Here we 8 use in situ and laboratory measurements of anammox activity using 15 N tracers and molecular 9 analyses of microbial communities to evaluate anammox in clay, sand, and chalk-dominated rates. In spite of requiring anoxic conditions, anammox, most likely coupled to partial 14 nitrification, contributed up to 58% of in situ N 2 production in oxic, permeable riverbeds.. In 15 contrast, denitrification dominated in low permeability clay-bed rivers, where anammox 16 contributes roughly 7% to the production of N 2 gas. We conclude that anammox can represent an 17 important nitrogen loss pathway in permeable river sediments. and increases a river's capacity to attenuate nitrogen. 49Much of what is known about anammox in the environment comes from estuaries and 50 coastal seas where anammox varies in response to sediment reactivity. The relative 51 contribution of anammox to marine N 2 production (ra) decreases with proximity to the shore 52 as supply of carbon stimulates denitrification over anammox. 12,13 Extrapolating this trend 53 further inshore suggested anammox activity would be insignificant in estuaries but anammox 54 potential actually increased. 14,15 In both estuaries and coastal seas, however, anammox is 55 important in low permeability sediments (ra <1 to 11 %) 9,16 , where oxygen penetration is 56 restricted 12,15 and it is these muddy sediments that the few studies of riverine anammox have 57 occurred. 5,6 In addition, anammox is widespread in marine sediments but the affiliated 64Using a combination of in situ and laboratory-based 15 N tracer techniques 12,18 and molecular 65 assays we characterised both the anammox community and its activity within rivers from 66 clay, sand and chalk-dominated sub-catchments under summer, base flow conditions (Table 67 S1). For rivers in which in situ measurements were performed we indexed catchment 68 permeability by calculating the base-flow index (BFI , Table S2), the proportion of river flow 69 4 derived from deep groundwater sources. In clay catchments, low soil permeability leads to 70 routing of rainfall overland or through shallow, more permeable soils into the river (low BFI). 71Whilst in chalk or sand catchments, the higher soil permeability allows infiltrated water to 72 percolate deeper into the aquifer and follow much longer flow paths to towards the river 73 (high BFI). 74We began by characterising the anammox hzo functional gene that encodes hydrazine 75 oxidoreductase which catalyses the oxidation of hydrazine to N 2 . The hzo gene was detected 76 in all sediment...

Naphthenic acids (NAs) occur naturally in oil sands and enter the environment through natural and anthropogenic processes. NAs comprise toxic carboxylic acids that are difficult to degrade. Information on NA biodegradation mechanisms is limited, and there are no studies on alkyl branched aromatic alkanoic acid biodegradation, despite their contribution to NA toxicity and recalcitrance. Increased alkyl side chain branching has been proposed to explain NA recalcitrance. Using soil enrichments, we examined the biodegradation of four aromatic alkanoic acid isomers that differed in alkyl side chain branching: (4 0 -n-butylphenyl)-4-butanoic acid (n-BPBA, least branched); (4 0 -iso-butylphenyl)-4-butanoic acid (iso-BPBA); (4 0 -sec-butylphenyl)-4-butanoic acid (sec-BPBA) and (4 0 -tert-butylphenyl)-4-butanoic acid (tert-BPBA, most branched). n-BPBA was completely metabolized within 49 days. Mass spectral analysis confirmed that the more branched isomers iso-, sec-and tert-BPBA were transformed to their butylphenylethanoic acid (BPEA) counterparts at 14 days. The BPEA metabolites were generally less toxic than BPBAs as determined by Microtox assay. n-BPEA was further transformed to a diacid, showing that carboxylation of the alkyl side chain occurred. In each case, biodegradation of the carboxyl side chain proceeded through betaoxidation, which depended on the degree of alkyl side chain branching, and a BPBA degradation pathway is proposed. Comparison of 16S rRNA gene sequences at days 0 and 49 showed an increase and high abundance at day 49 of Pseudomonas (sec-BPBA), Burkholderia (n-, iso-, tert-BPBA) and Sphingomonas (n-, sec-BPBA).

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bNitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 mol N grams dry weight [gdw] ؊1 day ؊1 in June, increasing to 37.4 mol N gdw ؊1 day ؊1 in January). At the estuary head, the nitrification potential was 4.3 mol N gdw ؊1 day ؊1 in June, increasing to 11.7 mol N gdw ؊1 day ؊1 in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification. N itrification is central to the global nitrogen cycle, coupling ammonia production from mineralization of organic matter with denitrification. In estuaries, discharge of domestic and industrial waste as well as runoff from mineral fertilizers and nitrogen fixation may contribute to ammonium enrichment. Ammonia oxidation is considered to be the rate-limiting step of nitrification and is catalyzed by ammonia monooxygenase (AMO), which is encoded by the amoA gene. It was previously considered that autotrophic ammonia oxidation is carried out solely by ammonia-oxidizing bacteria (AOB). However, the discovery of a marine archaeon belonging to the thaumarchaea which also oxidizes ammonia showed that this is not the case (1, 2). Ammonia-oxidizing archaea (AOA) belonging to the phylum Thaumarchaeota (AOA) are widely distributed in terrestrial and aquatic environments (2, 3) and thus may be more important contributors to nitrification than was previously considered. While previous studies of marine sediments showed different patterns of either AOA or AOB dominance, in estuarine environments where gradients of salinity and ammonia concentrations occur, there may be a differential selection for ammonia-oxidizer populations along these gradients (4-9). It has been previously suggested that AOA are significant in estuarine nitrogen cycling (6) and that AOA were more abundant than ...

Acropora and Porites corals are important reef builders in the Indo-Pacific and Caribbean. Bacteria associated with mucus produced by Porites spp. and Acropora spp. from Caribbean (Punta Maroma, Mexico) and Indo-Pacific (Hoga and Sampela, Indonesia) reefs were determined. Analysis of pyrosequencing libraries showed that bacterial communities from Caribbean corals were significantly more diverse (H=, 3.18 to 4.25) than their Indonesian counterparts (H=, 2.54 to 3.25). Dominant taxa were Gammaproteobacteria, Alphaproteobacteria, Firmicutes, and Cyanobacteria, which varied in relative abundance between coral genera and region. Distinct coral host-specific communities were also found; for example, Clostridiales were dominant on Acropora spp. ). This is also the first report describing geographically distinct Psychrobacter spp. associated with coral mucus. In addition, the predominance of Clostridiales associated with Acropora spp. provided additional evidence for coral host-specific microorganisms.

The rapid expansion of the oil sands industry has seen a concomitant expansion of the production of associated waste containing toxic naphthenic acids (NAs). Bioremediation of such waste is thus an important goal, but the mechanisms of biodegradation are still poorly understood, despite recent advances. Many oil sands NAs are resistant to biodegradation, and alkyl side chain branching has been invoked as an explanation. To investigate this hypothesis we examined the biotransformation by a sedimentary bacterial community of novel, synthetic, surrogate NAs (butylcyclohexylbutanoic acids (BCHBAs)) with variously branched butyl side chains (n- through t-) and unbranched alkanoate groups, plus one (4-(4'-isobutylcyclohexyl)pentanoic acid (iso-BCHPA)), with both branched butyl and branched alkanoate chains. Sediment microbial populations were inoculated into media containing the individual surrogate NAs, and gas chromatography-mass spectrometry (GC-MS) was used to determine the extent of biotransformation. Biotransformation decreased as NA side chain branching increased. For example, over 97% of the n-BCHBA with the nonbranched alkyl side chain was transformed in 30 days compared to the tert-BCHBA with the most highly branched side chain where only 2.5% was transformed. Both the iso-BCHBA and sec-BCHBA had intermediate transformation rates with about 77% and 47% transformed respectively after 30 days. The metabolites were identified as butylcyclohexylethanoic acids in each case, indicating beta-oxidation of the alkanoate substituents. The iso-BCHPA with both chains branched was resistant to degradation. The results are thus consistent with earlier hypotheses for the resistance of oil sands NAs. Identification of bacteria capable of oxidizing such branched alkyl chains-or of attacking the cyclic rings of NAs, may be important if bioremediation of oil sands NAs is to be achieved.

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Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases.