Bioturbation: Impact on the Marine Nitrogen Cycle

Enzymology and Ecology of the Nitrogen Cycle 315

Bioturbation: impact on the marine nitrogen cycle

Bonnie Laverock*†1, Jack A. Gilbert*, Karen Tait*, A. Mark Osborn† and Steve Widdicombe* *Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, U.K., and †Department of Animal and Plant Sciences, The University of Shefﬁeld, Western Bank, Shefﬁeld S10 2TN, U.K.

Abstract Sediments play a key role in the marine nitrogen cycle and can act either as a source or a sink of biologically available (fixed) nitrogen. This cycling is driven by a number of microbial remineralization reactions, many of which occur across the oxic/anoxic interface near the sediment surface. The presence and activity of large burrowing macrofauna (bioturbators) in the sediment can significantly affect these microbial processes by altering the physicochemical properties of the sediment. For example, the building and irrigation of burrows by bioturbators introduces fresh oxygenated water into deeper sediment layers and allows the exchange of solutes between the sediment and water column. Burrows can effectively extend the oxic/anoxic interface into deeper sediment layers, thus providing a unique environment for nitrogen-cycling microbial communities. Recent studies have shown that the abundance and diversity of micro-organisms can be far greater in burrow wall sediment than in the surrounding surface or subsurface sediment; meanwhile, bioturbated sediment supports higher rates of coupled nitrification–denitrification reactions and increased fluxes of ammonium to the water column. In the present paper we discuss the potential for bioturbation to significantly affect marine nitrogen cycling, as well as the molecular techniques used to study microbial nitrogen cycling communities and directions for future study.

Nitrogen cycling in marine sediments nitrate via nitrification. This occurs within the oxic zone Microbially driven cycling of nitrogen (Figure 1) in the comprising a few millimetres at the sediment/water interface world’s oceans is a key process regulating biological (Figure 1). These oxidized compounds are then either released productivity. Sediments play a fundamental role in recycling to the water column or used to fuel reductive processes such as fixed nitrogen to the water column: it is estimated that denitrification. Thus nitrification performs several important up to 80% of the nitrogen needed by primary producers functions, linking (i) the oxic and anoxic reactions within the in shallow shelf seas is provided by benthic (sea floor) nitrogen cycle, (ii) the production of new compounds to the remineralization reactions [1]. Conversely, marine sediments loss of fixed nitrogen, and (iii) the decomposition of organic also represent an important sink for fixed nitrogen via matter to the release of nutrients from the sediment [2,3,6]. the burial of organic matter; and by either the reduction For this reason, the oxic/anoxic interface occurring at the of nitrate into N2 or N2O via denitrification; and/or the sediment surface is of particular importance in the marine conversion of nitrite and ammonium into N2 via anaerobic nitrogen cycle [3]. ammonium oxidation (anammox) [2,3]. According to current nitrogen budgets, benthic processes account for two-thirds Investigating the marine nitrogen cycle of the total marine conversion of fixed nitrogen into N2: − − Despite its obvious importance, our understanding of the 300 Tg·year 1 of a total 450 Tg·year 1 [4]. Sediments are marine nitrogen cycle is far from complete. In particular, our therefore a key site for marine nitrogen cycling, because they knowledge concerning the identity, distribution and function provide a largely anoxic environment in which anaerobic of the key microbial organisms involved is rapidly evolving. reduction reactions, such as denitrification, can take place, For example, the recent discoveries of both anaerobic often within a few millimetres of the sediment/water interface ammonium oxidation (anammox) and of archaea as key [3]. Sediments also provide a large repository for sinking drivers of ammonia oxidation have sparked considerable organic matter from the water column, with the fate of research effort into the distribution and importance of these this organic matter, once it reaches the sea floor, being processes in the marine realm. These discoveries have been dependent upon the compartmentalization of the different reviewed extensively elsewhere [7–9]. However, controversy remineralization processes occurring within the sediment [5]. remains over the comparative importance of denitrification Once nitrogen within organic matter is remineralized through and anammox, especially within the oxygen minimum ammonification, ammonium is then oxidized to nitrite and zones of the world’s oceans [10]. Much of this research has relied on the application of genetic markers to study Key words: bioturbation, microbial community structure, nitrogen cycle, nutrient ﬂux, the micro-organisms responsible for the different nitrogen oxic/anoxic interface. Abbreviation used: SRB, sulfate-reducing bacteria. cycling processes (Table 1) combined with isotope-pairing 1 To whom correspsondence should be addressed (email [email protected]). techniques [11] to study rates of nitrification, denitrification

Biochem. Soc. Trans. (2011) 39, 315–320; doi:10.1042/BST0390315 C The Authors Journal compilation C 2011 Biochemical Society 316 Biochemical Society Transactions (2011) Volume 39, part 1

Figure 1 The marine nitrogen cycle occurring across oxic/anoxic interfaces Unshaded boxes indicate organic nitrogen. PON, particulate organic nitrogen. DON, dissolved organic nitrogen. Shaded boxes indicate dissolved inorganic nitrogen. Processes: A, nitrogen fixation; B, ammonification; C, ammonia oxidation; D, nitrite oxidation (C+D = nitrification); E, nitrate reduction; F, nitrite reduction (E+F = denitrification); G, dissimilatory reduction of nitrite to ammonium (DNRA); H, anaerobic ammonium oxidation (anammox). Broken arrows indicate fluxes in/out of sediment porewater; continunous arrows indicate microbial remineralization reactions. Arrowhead sizes across the

sediment/water interface reﬂect the predominant ﬂux direction in coastal sediments. NO (Nitric oxide) and N2O (nitrous oxide) are intermediate products of both ammonia oxidation (C) and nitrite reduction (F).

and anammox. These, combined with the advent of high- means that they have the potential to have an impact throughput sequencing technologies, are allowing us to on a substantial proportion of the world’s shallow shelf explore more fully the marine nitrogen cycle in order to marine habitats via their bioturbating activities. It has long address many of the current knowledge gaps. been known that the macrofaunal burrow environment can support different physicochemical properties from those experienced in both the sediment surface and the surrounding Bioturbation: an introduction ambient sediment [32,33]. In particular, the burrow may Macrofauna living in or on marine sediments can significantly be frequently or intermittently ventilated by its inhabitant, alter both the physical structure and chemical composition thereby introducing fresh oxygenated water into the burrow; of the sediment through their burrowing and irrigation allowing greater solute exchange and an extension of activities. For this reason, they have long been considered the oxic/anoxic interface into deeper sediment [5,34]. For ‘ecosystem engineers’ [21], and their presence can create example, it is estimated that the presence of thalassinidean unique microniches for sediment micro-organisms to inhabit shrimp burrows can increase the sediment surface area by up [22–24]. To date, most bioturbation studies have concentrated to nine times [35]. Additionally, it is thought that the physical on burrowers such as polychaete worms and crustaceans (e.g. mixing of sediment during burrow building and maintenance [25–29]). However, bioturbation may be carried out by other activities can contribute to increased biodiversity of both benthic macrofauna, including molluscs and echinoderms, meiofaunal [36] and microbial communities [29,37]. as well as pelagic bottom-feeders such as walrus, fish and stingrays, and meiofaunal communities such as larvae and nematode worms [30]. Microbial community structure within Infaunal tubes and burrows are semi-permanent or sediment burrows permanent structures that differ in size, appearance and The layer of sediment, organic matter and biopolymers that composition according to the mode of life and habits of make up the burrow wall has the potential to affect the benthic the inhabitant. A previous study has calculated the global nitrogen cycle. First, bacterial abundance and activity can be volume of bioturbated sediment to be >20 700 km3 (based 10-fold higher in the macrofaunal burrow wall compared with on an estimated ocean surface area of 360 million km2) [31]; surrounding sediment [27,32]. Secondly, the composition clearly, the sheer abundance of these ‘ecosystem engineers’ of the microbial communities inhabiting burrow walls can

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Table 1 Genetic markers for nitrogen-cycling processes showing genes for which probes or PCR primers have been developed Based on data taken from [12] (and references therein). AOB, ammonia-oxidizing bacteria.

Micro-organisms Transformation Gene(s) Protein (principally) responsible Reference(s)

N2 fixation nifHDK Nitrogenase Diazotrophs Nitrite assimilation nirB Nitrite reductase – Nitrate assimilation narB, nasA Assimilatory nitrate reductase Nitrate reduction and narG (membrane bound) napA (periplasmic) Nitrate reductase Genes are widespread across [13] denitrification nirS, nirK Nitrite reductase Bacteria, Archaea and norB Nitric oxide reductase Eukarya nosZ Nitrous oxide reductase Dissimilatory nitrate nrf (nrfA) Nitrite reductase Bacteroides spp., [13,14] reduction to Planctomycetales and ammonia (DNRA) Proteobacteria Ammonia oxidation amo (amoA) Ammonia Nitrosomonas, Nitrospira, [15–17] mono-oxygenase (AOB in the β-Proteobacteria subgroup) and Thaumarchaeota (Archaea) Nitrite oxidation nxrB Nitrite oxidoreductase Nitrobacter and Nitrospira [18] Anammox ?hao? (also found within groups of nitrifiers) Hydroxylamine Planctomycetes [19,20] Planctomycete-specific 16S genes oxidoreductase

also be significantly different from those in the surrounding bioturbation. Burrow walls effectively act as an extension sediment, in terms of both their structure and diversity of the oxic surface of the sediment, which has particular [28,29,38]. More specifically, Satoh et al. [39] found that relevance to nitrification–denitrification reactions coupled the ammonia-oxidizing and nitrite-oxidizing communities across the oxic/anoxic interface [41]. Fluxes of O2, in the burrow walls of a polychaete worm were similar total CO2 and dissolved inorganic nitrogen across the to those in surface sediment and the abundance of gene sediment/water interface have been observed to increase by markers for these functional guilds was much higher in the 2.5–3.5 times in bioturbated sediment relative to control non- burrow wall than in the bulk sediment. However, it should bioturbated sediment [5,26,42]. The concentration profiles be noted that the exact effects of bioturbation on microbial for ammonium, nitrite and nitrate are linked with changes community structure may be dependent upon the individual in oxygen concentration. Nedwell and Walker [43] showed burrow builder. For example, the burrows of specific nereidid that the presence of amphipods in Antarctic sediments + worms [40], thalassinidean shrimp [27] and fiddler crabs doubled the production of NH4 by direct release or [28] were found to be more similar to the surrounding stimulation of vertical transport processes, and Aller and subsurface (anoxic) sediment than to surface sediment in Aller [44] demonstrated that the net remineralization rate for + terms of microbial community structure. Conversely, the NH4 increases as the efficiency of solute exchange with the burrows of some polychaete worms [38] and thalassinidean overlying water increases. Meanwhile, several studies have shrimp [28,29] were found to contain microbial communities shown that bioturbation activity increases denitrification by more similar to those in the oxygenated surface sediment than up to 400% [26,45,46]. However, this is not simply a direct those in subsurface ambient sediment. It is therefore probable consequence of macrofaunal bioturbation, rather the result that the individual burrowing and irrigation behaviours of of environmental alterations which affect microbially driven different macrofaunal burrowers contribute to creating a biogeochemical processes. For instance, Howe et al. [26] physicochemical environment that may in itself be unique, noted that most of the increase in denitrification stimulated by but more similar to either the surface or subsurface sediment, the presence of burrowing shrimp was fuelled by nitrification depending on the burrow inhabitant [23,32]. occurring within the burrow walls, suggesting that it is the elevated rates of nitrifying bacteria utilizing the increased + Inﬂuence of bioturbation on nutrient fluxes of O2 and NH4 , rather than the direct supply of − ﬂuxes and nitrogen cycling rates NO3 , that is the driving factor. It is generally accepted Nutrient flux rates depend on many factors, including the that the most important role of bioturbation in stimulating type of sediment substrate and the mode and extent of remineralization reactions, such as denitrification, is the

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introduction of oxygen into subsurface sediments which activity is enhanced within the unique burrow environment. can stimulate the decay of organic matter by a factor of Several studies (as cited previously) have also shown that ten [23]. microbial diversity and abundance may be greater in The impact of bioturbation on microbial activity is burrow walls, which may also contain a different microbial complicated further by the existence of microniches within community from that of the surrounding sediment. However, sediment systems and within the burrow wall in particular it is important now to investigate more deeply the taxonomy [28]. The burrow can be viewed as a unique environment and functional diversity of burrow communities, specifically which experiences fluctuations in its biogeochemistry as in relation to the abundance and activity of key nitrogen a result of the irrigation, burrow building and burrow cycling genes. maintenance behaviours of its inhabitant; this may indeed Sampling marine sediments is challenging, especially when lead to unique communities of micro-organisms inhabiting it is important to retain as much as possible the in situ the burrow wall [23]. Burrow walls are therefore not biogeochemical conditions of the sediment. Many studies geochemically uniform structures, and often exhibit patterns have sampled in situ infaunal burrows, mostly at periods of zonation and heterogeneity [5]. For example, nitrogen when they are exposed by low tides (e.g. [28]). Some have also fixation is normally assumed to be unimportant in burrows used mesocosms to investigate the burrow in the laboratory because of the high levels of oxygen and ammonium, both environment (e.g. [29]), whereas others have used ‘mimic’ of which inhibit the activity of the nitrogenase enzyme. burrow structures in the laboratory (e.g. [51]). All of these However, Bertics et al. [24] observed far greater levels of techniques have their attendant benefits and drawbacks, and nitrogenase activity in sediments that were heavily populated often the choice will be down to logistical questions as by burrowing ghost shrimp. This activity was apparently well as knowledge of which technique will allow the most linked to the presence of nifH genes (Table 1) in SRB effective sampling for the analyses to be done. However, it (sulfate-reducing bacteria), suggesting that the SRB were able is important to note that mesocosm studies will inevitably to exploit anoxic microniches within the shrimp burrows, differ from those conducted in situ [23,52], and, where and contribute to increased benthic nitrogen fixation and possible, it is essential to take into account the changes in sulfate reduction. The authors suggest that in benthic nitrogen macrofaunal and microbial activity that occur with season, cycling models, bioturbated sediments could be a source temperature, salinity, sediment type and organic loading, of fixed nitrogen as well as a loss term due to stimulated and to compare any laboratory results with relevant in situ denitrification [24]. data. A greater understanding of the occurrence and activity of Finally, given the clear relationship between bioturbating these microbial microniches could significantly change our activity and microbial nutrient cycling, it would be beneficial understanding of the effects of bioturbation on the marine to consider the factors that may affect this relationship. nitrogen cycle. This may be particularly important when In particular, it is known that many bioturbators may be we consider that the changes in sediment biogeochemistry physiologically and/or behaviourally sensitive to environ- and microbial diversity brought about by bioturbation may mental changes such as increasing seawater temperature have indirect effects on the nitrogen cycle via changes to the and decreasing pH (e.g. [53–55]). In addition, it seems that anaerobic respiration pathways that occur in sediments. For there is increasing eutrophication within coastal waters from example, any increase in sulfate reduction is likely to have industrial and agricultural run-off [4], and an expansion an inhibitive effect on both nitrification and denitrification of the world’s oceans’ oxygen minimum zones, which are in the burrow [47]. Meanwhile, it appears that within themselves important sites for pelagic denitrification and fiddler crab burrows in salt marsh sediments, iron-reducing anammox [56]. Considering the relatively rapid changes that bacteria may out-compete SRB [48]. This repartitioning are occurring within our oceans, a key question should be of remineralization reactions could be important because what knock-on effects these changes will have on macrofaunal the inhibitory effects of sulfide on nitrification may be bioturbator behaviour, and hence on the essential functioning ameliorated by increased amounts of iron(III) present of nitrogen cycling micro-organisms in the sediment. in the burrow wall, which rapidly scavenges sulfide from the environment [23,49]. The spatial overlap of respiration Funding processes, including denitrification, sulfate reduction and iron reduction, may therefore be encouraged by the presence B.L. acknowledges funding from a Natural Environment Research of burrow microniches [23,24,50]. Council (NERC) algorithm Ph.D. Studentship [NE/F008864/1] and from the NERC-funded programme Oceans 2025 (Theme 3: Coastal Challenges and future directions and Shelf Processes). We are still at the beginning of our understanding of how bioturbating macro-organisms interact with the sediment and its microbial communities, and the effects this interaction has on important biogeochemical cycles in the marine References 1 Dale, A.W. and Prego, R. (2002) Physico-biogeochemical controls on realm. It is clear from the numerous studies on nutrient benthic-pelagic coupling of nutrient ﬂuxes and recycling in a coastal flux measurements and biogeochemical rates that microbial upwelling system. Mar. Ecol. Prog. Ser. 235, 15–28

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2 Herbert, R.A. (1999) Nitrogen cycling in coastal marine ecosystems. 25 Kristensen, E. (1984) Effect of natural concentrations on nutrient FEMS Microb. Rev. 23, 563–590 exchange between a polychaete burrow in estuarine sediment and the 3 Thamdrup, B. and Dalsgaard, T. (2008) Nitrogen cycling in sediments. In overlying water. J. Exp. Mar. Biol. Ecol. 75, 171–190 Microbial ecology of the oceans, 2nd edn (Kirchmann, D.L., ed.), 26 Howe, R.L., Rees, A.P. and Widdicombe, S. (2004) The impact of two pp. 527–569, John Wiley & Sons, Hoboken species of bioturbating shrimp (Callianassa subterranea and Upogebia 4 Codispoti, L.A. (2007) An oceanic fixed nitrogen sink exceeding 400 Tg deltaura) on sediment denitrification. J. Mar. Biol. Assoc. U.K. 84, − 1 Na vs the concept of homeostasis in the fixed-nitrogen inventory. 629–632 Biogeosciences 4, 233–253 27 Papaspyrou, S., Gregersen, T., Cox, R.P., Thessalou-Legaki, M. and 5 Kristensen, E. (2000) Organic matter diagenesis at the oxic/anoxic Kristensen, E. (2005) Sediment properties and bacterial community in interface in coastal marine sediments, with emphasis on the role of burrows of the ghost shrimp Pestarella tyrrhena (Decapoda: burrowing animals. Hydrobiologia 426,1–24 Thalassinidea). Aquat. Microb. Ecol. 38, 181–190 6 Canfield, D.E., Kristensen, E. and Thamdrup, D. (2005) Aquatic Geomicrobiology, Elsevier Academic Press, London 28 Bertics, V.J. and Ziebis, W. (2009) Biodiversity of benthic microbial 7 Jetten, M.S.M., Cirpus, I., Kartal, B., van Niftrik, L., van de Pas-Schoonen, communities in bioturbated coastal sediments is controlled by K.T., Sliekers, O., Van Der Star, W., Schmid, M., van de Vossenburg, J., geochemical microniches. ISME J. 3, 1269–1285 Schmidt, I. et al. (2005) 1994–2004: 10 years of research on the 29 Laverock, B., Smith, C.J., Tait, K., Osborn, A.M., Widdicombe, S. and anaerobic oxidation of ammonium. Biochem. Soc. Trans. 33, 119–123 Gilbert, J.A. (2010) Bioturbating shrimp alter the structure and diversity 8 Francis, C.A., Beman, J.M. and Kuypers, M.M.M. (2007) New processes of bacterial communities in coastal marine sediments. ISME J. 4, and players in the nitrogen cycle: the microbial ecology of anaerobic and 1531–1544 archaeal ammonia oxidation. ISME J. 1, 19–27 30 Meysman, J.J.R., Middelburg, J.J. and Heip, C.H.R. (2006) Bioturbation: a 9 Ward, B.B., Capone, D.G. and Zehr, J.P. (2007) What’s new in the fresh look at Darwin’s last idea. Trends Ecol. Evol. 21, 688–695 nitrogen cycle? Oceanography 20, 101–109 31 Teal, L.R., Bulling, M.T., Parker, E.R. and Solan, M. (2008) Global patterns 10 Ward, B.B., Devol, A.H., Rich, J.J., Chang, B.X., Bulow, S.E., Naik, H., of bioturbation intensity and mixed depth of marine soft sediments. Pratihary, A. and Jayakumar, A. (2009) Denitrification as the dominant Aquat. Biol. 2, 207–218 nitrogen loss process in the Arabian Sea. Nature 461, 78–82 32 Bird, F.L., Boon, P.I. and Nichols, P.D. (2000) Physicochemical and 11 Nielsen, L.P. (1992) Denitrification in sediment determined from microbial properties of burrows of the deposit-feeding thalassinidean nitrogen isotope pairing. FEMS Microb. Ecol. 86, 357–362 ghost shrimp Biffarius arenosus (Decapoda: Callianassidae) Estuar. Coast. 12 Zehr, J.P. and Ward, B.B. (2002) Nitrogen cycling in the ocean: new Shelf Sci. 51, 279–291 perspectives on processes and paradigms. Appl. Env. Microb. 68, 33 Furukawa, Y. (2001) Biogeochemical consequences of macrofauna 1015–1024 13 Smith, C.J., Nedwell, D.B., Dong, L.F. and Osborn, A.M. (2007) Diversity burrow ventilation. Geochem. Trans. 11, 83–91 and abundance of nitrate reductase genes (narG and napA), nitrite 34 Forster, S. and Graf, G. (1995) Impact of irrigation on oxygen flux into reductase (nirS and nrfA), and their transcripts in estuarine sediments. the sediment: intermittent pumping by Callianassa subterranea and Appl. Environ. Microbiol. 73, 3612–3622 “piston-pumping” by Lanice conchilega.Mar.Biol.123, 335–346 14 Mohan, S.B., Schmid, M., Jetten, M. and Cole, J. (2004) Detection and 35 Griffis, R.B. and Suchanek, T.H. (1991) A model of burrow architecture widespread distribution of the nrfA gene encoding nitrite reduction to and trophic modes in thalassinidean shrimp (Decapoda: Thalassinidea). ammonia, a short circuit in the biological nitrogen cycle that competes Mar. Ecol. Prog. Ser. 79, 171–183 with denitrification. FEMS Microb. Ecol. 49, 433–443 36 Widdicombe, S., Austen, M.C., Kendall, M.A., Warwick, R.M. and Jones, 15 Francis, C.A., O’Mullan, G.D. and Ward, B.B. (2003) Diversity of ammonia M.B. (2000) Bioturbation as a mechanism for setting and maintaining monooxygenase (amoA) genes across environmental gradients in levels of diversity in subtidal macrobenthic communities. Hydrobiologia Chesapeake Bay sediments. Geobiology 1, 129–140 440, 369–377 16 Francis, C.A., Roberts, K.J., Beman, J.M., Santoro, A.E. and Oakley, B.B. 37 Parnell, J.J., Crowl, T.A., Weimer, B.C. and Pfrender, M.E. (2009) (2005) Ubiquity and diversity of ammonia-oxidising archaea in water Biodiversity in microbial communities: system scale patterns and columns and sediments of the ocean. Proc. Natl. Acad. Sci. U.S.A. 102, mechanisms. Mol. Ecol. 18, 1455–1462 14683–14688 38 Steward, C.C., Nold, S.C., Ringelberg, D.B., White, D.C. and Lovell, C.R. 17 Wuchter, C., Abbas, B., Coolen, M.J.L., Herfort, L., van Bleijswijk, J., (1996) Microbial biomass and community structures in the burrows of Timmers, P., Strous, M., Teira, E., Herndl, G.J., Middelburg, J.J. et al. bromophenol producing and non-producing marine worms and (2006) Archaeal nitrification in the ocean. Proc. Natl. Acad. Sci. U.S.A. 103, 12317–12322 surrounding sediments. Mar. Ecol. Prog. Ser. 133, 149–165 18 Vanparys, B., Spieck, E., Heylen, K., Wittebolle, L., Geets, J., Boon, N. and 39 Satoh, H., Nakamura, Y. and Okabe, S. (2007) Influences of infaunal de Vos, P. (2007) The phylogeny of the genus Nitrobacter based on burrows on the community structure and activity of ammonia-oxidizing comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene bacteria in intertidal sediments. Appl. Environ. Microbiol. 73, 1341–1348 sequence analysis. Syst. Appl. Microbiol. 30, 297–308 40 Lucas, F.S., Bertru, G. and Hofle, ¨ M.G. (2003) Characterization of 19 Penton, C.R., Devol, A.H. and Tiedje, J.M. (2006) Molecular evidence for free-living and attached bacteria in sediments colonized by Hediste the broad distribution of anaerobic ammonium-oxidizing bacteria in diversicolor.Aquat.Microb.Ecol.32, 165–174 freshwater and marine sediments. Appl. Env. Microbiol. 72, 6829–6832 41 Aller, R.C. (2001) Transport and reactions in the bioirrigated zone. In The 20 Rich, J.J., Dale, O.R., Song, B. and Ward, B.B. (2008) Anaerobic Benthic Boundary Layer: Transport Processes and Biogeochemistry ammonium oxidation (anammox) in Chesapeake Bay sediments. Microb. (Boudreau, B.P. and Jørgensen, B.B., eds), pp. 269–301, Oxford Ecol. 55, 311–320 University Press, Oxford 21 Jones, C.G., Lawton, J.H. and Shachak, M. (1994) Organisms as 42 Tuominen, L., Makel ¨ a, ¨ K., Lehtonen, K.K., Haahti, H., Hietanen, S. and ecosystem engineers. Oikos 69, 373–386 Kuparinen, J. (1999) Nutrient fluxes, porewater profiles and 22 Fenchel, T. (1996) Worm burrows and oxic microniches in marine denitrification in sediment influenced by algal sedimentation and sediments. 1. Spatial and temporal scales. Mar. Biol. 127, 289–295 bioturbation by Monoporeia affinis. Estuar. Coast. Shelf Sci. 49, 83–97 23 Kristensen, E. and Kostka, J.E. (2005) Macrofaunal burrows and irrigation 43 Nedwell, D.B. and Walker, T.R. (1995) Sediment-water fluxes of in marine sediment: microbiological and biogeochemical interactions. In nutrients in an Antarctic coastal environment: influence of bioturbation. Coastal and Estuarine Studies: Interactions between Macro- and Microorganisms in Marine Sediments (Kristensen, E., Haese, R.R and Polar Biol. 15, 57–64 Kostka, J.E., eds), pp. 125–157, American Geophyiscal Union, 44 Aller, R.C. and Aller, J.Y. (1998) The effect of biogenic irrigation intensity Washington, DC and solute exchange on diagenetic reaction rates in marine sediments. J. 24 Bertics, V.J., Sohm, J.A., Treude1, T., Chow, C.-E.T., Capone, D.G., Mar. Res. 56, 905–936 Fuhrman, J.A. and Ziebis, W. (2010) Burrowing deeper into benthic 45 Gilbert, F., Stora, G. and Bonin, P. (1998) Influence of bioturbation on nitrogen cycling: the impact of bioturbation on nitrogen fixation coupled denitrification activity in Mediterranean coastal sediments: an in situ to sulfate reduction. Mar. Ecol. Prog. Ser. 409,1–15 experimental approach. Mar. Ecol. Prog. Ser. 163, 99–107

C The Authors Journal compilation C 2011 Biochemical Society 320 Biochemical Society Transactions (2011) Volume 39, part 1

46 Webb, A.P. and Eyre, B.D. (2004) Effect of natural populations of 52 Papaspyrou, S., Kristensen, E. and Christensen, B. (2007) Arenicola burrowing thalassinidean shrimp on sediment irrigation, benthic marina (Polychaeta) and organic matter mineralisation in sandy marine metabolism, nutrient fluxes and denitrification. Mar. Ecol. Prog. Ser. 268, sediments: in situ and microcosm comparison. Estuar. Coast. Shelf Sci. 205–220 72, 213–222 47 Joye, S.S. and Hollibaugh, J.T. (1995) Influence of sulfide inhibition of 53 Widdicombe, S. and Needham, H.R. (2007) Impact of CO2-induced nitrification on nitrogen regeneration in sediments. Science 270, seawater acidification on the burrowing activity of Nereis virens and 623–625 sediment nutrient flux. Mar. Ecol. Prog. Ser. 341, 111–122 48 Gribsholt, B., Gundersen, J.K., Roy, H. and Jørgensen, B.B. (2003) Impact 54 Dashfield, S.L., Sommerfield, P.J., Widdicombe, S., Austen, M. and of fiddler crabs and plant roots on sediment biogeochemistry in a Nimmo, M. (2008) Impacts of ocean acidification and burrowing urchins Georgia saltmarsh. Mar. Ecol. Prog. Ser. 259, 237–251 on within-sediment pH profiles and subtidal nematode communities. J. 49 Dollhopf, S.L., Hyun, J.-H., Smith, A.C., Adams, H.J., O’Brien, S. and Kostka, Exp. Mar. Biol. Ecol. 365, 46–52 J.E. (2005) Quantification of ammonia-oxidizing bacteria and factors 55 Wood, H.L., Spicer, J.I. and Widdicombe, S. (2008) Ocean acidification controlling nitrification in salt marsh sediments. Appl. Environ. Microbiol. may increase calcification rates, but at a cost. Proc. R. Soc. London Ser. B 71, 240–246 275, 1767–1773 50 Postma, D. and Jakobsen, R. (1996) Redox zonation-equilibrium 56 Stramma, L., Johnson, G.C., Sptrinall, J. and Mohrholz, V. (2008) 2 − constraints on the Fe(III)/SO4 reduction interface. Geochim. Expanding oxygen-minimum zones in the tropical oceans. Science 320, Cosmochim. Acta 60, 3169–3175 655–658 51 Marinelli, R.L., Lovell, C.R., Wakeham, S.G., Ringelberg, D.B. and White, D.C. (2002) Experimental investigation of the control of bacterial community composition in macrofaunal burrows. Mar. Ecol. Prog. Ser. Received 29 October 2010 235,1–13 doi:10.1042/BST0390315

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