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Environmental Microbiology 8, 684-696.Pdf Blackwell Science, LtdOxford, UKEMIEnvironmental Microbiology 1462-2912© 2005 The Authors; Journal compilation © 2005 Society for Applied Microbiology and Blackwell Publishing Ltd ?? 200584684696ArticleOriginalA-mo nia oxidizers in a freshwater–marine estuarine gradientT. E. Freitag, L. Chang and J. I. Prosser Environmental Microbiology (2006) 8(4), 684–696 doi:10.1111/j.1462-2920.2005.00947.x Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater–marine gradient Thomas E. Freitag, Lisa Chang and James I. Prosser* nas cryotolerans and to the nitrite oxidizer Nitrospira School of Biological Sciences, University of Aberdeen, marina. No sequence with similarity to the Nitrosos- Cruickshank Building, St Machar Drive, Aberdeen AB24 pira cluster 1 clade was recovered during SIP analy- 3UU, UK. sis. The potential role of Nitrosospira cluster 1 in autotrophic ammonia oxidation therefore remains uncertain. Summary To determine whether the distribution of estuarine Introduction ammonia-oxidizing bacteria (AOB) was influenced by salinity, the community structure of betaproteo- The intertidal areas in coastal zones include some of the bacterial ammonia oxidizers (AOB) was characterized most productive marine ecosystems and are thus vital as along a salinity gradient in sediments of the Ythan breeding and feeding grounds for many species of birds, estuary, on the east coast of Scotland, UK, by dena- fish and crustaceans. These areas are under threat from turant gradient gel electrophoresis (DGGE), cloning anthropogenic activities, through land reclamation, fisher- and sequencing of 16S rRNA gene fragments. Ammo- ies and in particular through eutrophication caused by nia-oxidizing bacteria communities at sampling sites nutrient input through terrestrial runoff of nitrogen. Estua- with strongest marine influence were dominated by rine intertidal systems are especially vulnerable because Nitrosospira cluster 1-like sequences and those with the river catchments in areas of intensive farming can strongest freshwater influence were dominated by result in the transport of highly enriched nutrients (Raf- Nitrosomonas oligotropha-like sequences. Nitroso- faelli, 1999). The low species diversity of brackish-water monas sp. Nm143 was the prevailing sequence type estuarine ecosystems (Remane and Schlieper, 1971; in communities at intermediate brackish sites. Diver- Attrill, 2002) may additionally enhance effects of elevated sity indices of AOB communities were similar at nutrient levels and promote growth of antagonistic phy- marine- and freshwater-influenced sites and did not toplankton or macroalgal species, resulting in low- indicate lower species diversity at intermediate brack- diversity, high-density ecosystems. Nitrification, the con- ish sites. The presence of sequences highly similar to version of ammonia to nitrate via nitrite, is central to the the halophilic Nitrosomonas marina and the freshwa- global cycling of nitrogen and, when linked to anoxic envi- – ter strain Nitrosomonas oligotropha at identical sam- ronments, where NO3 can serve as alternative electron pling sites indicates that AOB communities in the acceptor for denitrification, is a major regulating factor estuary are adapted to a range of salinities, while alleviating eutrophication processes (Kemp et al., 1990; individual strains may be active at different salinities. Rysgaard et al., 1994). However, nitrification processes Ammonia-oxidizing bacteria communities that were depend on the availability of free dissolved oxygen and dominated by Nitrosospira cluster 1 sequence types, may be totally eliminated if hypoxia occurs through for which no cultured representative exists, were sub- eutrophication (Kemp et al., 1990). 13 – jected to stable isotope probing (SIP) with C-HCO3 , The first, usually rate-limiting oxidation step in nitrifica- to label the nucleic acids of active autotrophic nitrifi- tion, is carried out by ammonia-oxidizing bacteria (AOB), ers. Analysis of 13C-associated 16S rRNA gene which can also reduce nitrite to nitric oxide (NO) and fragments, following CsCl density centrifugation, by nitrous oxide (N2O) at low oxygen tension. Ammonia- cloning and DGGE indicated sequences highly similar oxidizing bacteria consist of three evolutionary distant to the AOB Nitrosomonas sp. Nm143 and Nitrosomo- groups, two of which belong to the class Proteobacteria (Head et al., 1993; Koops et al., 2003). One group forms a deep branch within the Gammaproteobacteria and com- Received 20 June, 2005; accepted 27 September, 2005. *For corre- spondence. E-mail [email protected]; Tel. (+44) 1224 273254; prises only three recognized, closely related marine Fax (+44) 1224 272703. Nitrosococcus species. The second group, which includes © 2005 The Authors Journal compilation © 2005 Society for Applied Microbiology and Blackwell Publishing Ltd Ammonia oxidizers in a freshwater–marine estuarine gradient 685 the majority of cultured strains, forms a monophyletic estuarine environment, the Ythan estuary, for which data group within the Betaproteobacteria and consists of two on seasonal and spatial distributions of salinity, hydrogra- genera, Nitrosomonas and Nitrosospira. The third group, phy, nutrients and flushing times are available (Balls et al., belonging to the order Planctomycetales, is associated 1995; Gillibrand and Balls, 1998; Raffaelli et al., 1999). with the Anammox process and its importance in marine Ammonia-oxidizing bacteria communities were analysed systems has been suggested, particularly for oxic–anoxic by amplification of 16S rRNA gene fragments from envi- interfaces (Jetten et al., 2003). Molecular studies of AOB ronmental DNA and subsequent analysis by denaturing communities in freshwater and estuarine systems suggest gradient gel electrophoresis (DGGE), cloning, sequencing the dominance of betaproteobacterial AOB (Caffrey et al., and phylogenetic analysis. These techniques were com- 2003). Laboratory isolates of freshwater and marine bined with stable isotope probing (SIP; Radajewski et al., betaproteobacterial AOB laboratory isolates (Koops and 2000; Lueders et al., 2004) to characterize the active AOB Pommerening-Röser, 2001), and AOB 16S rRNA gene community. Application of SIP to determine AOB activity sequences from freshwater and estuarine environments involves incubation of environmental samples with 13C- 12 13 (Speksnijder et al., 1998; de Bie et al., 2001; Caffrey labelled CO2 and fractionation of extracted C- and C- et al., 2003) fall predominantly within Nitrosomonas lin- labelled nucleic acids. Molecular analysis of labelled and eages. In marine systems, prevalent sequence types are unlabelled nucleic acids characterizes active and inactive associated with the Nitrosomonas eutropha lineage (Phil- community members, respectively, and thereby provides lips et al., 1999) or belong to the Nitrosomonas cluster 5 a more reliable measure of links between community or Nitrosospira cluster 1 clone groups, for which no cul- structure and ecosystem function. tured representative has yet been isolated (McCaig et al., 1999; Hollibaugh et al., 2002; Freitag and Prosser, 2003; 2004). Results Salt requirement is a major ecophysiological parameter 16S rRNA gene analysis of environmental AOB in determining the niche specialization of many bacteria. communities Characterization of both laboratory isolates (Koops and Pommerening-Röser, 2001; Koops et al., 2003) and clone Denaturing gradient gel electrophoresis analysis of the libraries (Stephen et al., 1996) suggests that the influence CTO189f-CTO654r 16S rRNA gene polymerase chain of salt concentration is a distinguishing feature within both reaction (PCR) products nested with 357f-GC-518r, span- Nitrosomonas and Nitrosospira lineages. This suggests ning the hypervariable V3 region only, produced almost that patterns of diversity, community composition and identical patterns for replicate samples from each sam- activity of different sequence types of AOB will differ in pling site, demonstrating more than 30 clearly distinguish- estuaries in response to salinity gradients. The aim of this able sequence types (Fig. 1A). Denaturing gradient gel study was to test this hypothesis in a well-characterized electrophoresis migration patterns varied significantly A Ma ri ne Freshwater B Salinity 28 16 11 10 0 1 Eb 2 freshwater ig o. ig o. 3 4 9 Ea ol ol 5 Nm ma r. / r. Nm ma Db 5 5 Da Cl Cl 10 Cb 6 11 brackish 143 Ca 7 B Nm b Ba 1 12 A b marine Cl 8 13 Aa p Ns 14 15 CL 1 CL 2 A B C D E Sa mpli ng lo cati on s Fig. 1. Analysis of betaproteobacterial ammonia oxidizer communities in Ythan estuary sediments at sampling locations indicated in Fig. 5, with salinities ranging from close to seawater (A) to freshwater (E). Betaproteobacterial AOB-like 16S rRNA gene sequences were amplified from extracted DNA using CTO189f and CTO654r PCR primers, nested with 357f-GC and 518r. Closest BLAST matches of clone sequences shown in lanes CL1 and CL2 (marked by arrows) are shown in Table 2. A. Denaturant gradient gel electrophoresis analysis of amplification products. B. UPGMA dendrogram assessing the similarity of DGGE profiles illustrated in (A). Salinities (‰) according to Gillibrand and Balls (1998), calculated from conductivity measurements. © 2005 The Authors Journal compilation © 2005 Society for Applied Microbiology and Blackwell Publishing Ltd, Environmental Microbiology, 8, 684–696 686 T. E. Freitag, L. Chang and J. I. Prosser Table 1. Diversity indices obtained for DGGE migration
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