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Consortia of Low-Abundance Bacteria Drive Sulfate Reduction-Dependent Degradation of Fermentation Products in Peat Soil Microcosms

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Consortia of Low-Abundance Bacteria Drive Sulfate Reduction-Dependent Degradation of Fermentation Products in Peat Soil Microcosms Erschienen in: The ISME Journal ; 10 (2016), 10. - S. 2365-2375 https://dx.doi.org/10.1038/ismej.2016.42 The ISME Journal (2016) 10, 2365–2375 OPEN © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms Bela Hausmann1,2, Klaus-Holger Knorr3, Katharina Schreck1, Susannah G Tringe4, Tijana Glavina del Rio4, Alexander Loy1 and Michael Pester1,2 1Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, Vienna, Austria; 2Department of Biology, University of Konstanz, Konstanz, Germany; 3Hydrology Group, Institute of Landscape Ecology, University of Münster, Münster, Germany and 4Joint Genome Institute, US Department of Energy, Walnut Creek, CA, USA Dissimilatory sulfate reduction in peatlands is sustained by a cryptic sulfur cycle and effectively competes with methanogenic degradation pathways. In a series of peat soil microcosms incubated over 50 days, we identified bacterial consortia that responded to small, periodic additions of individual fermentation products (formate, acetate, propionate, lactate or butyrate) in the presence or absence of sulfate. Under sulfate supplementation, net sulfate turnover (ST) steadily increased to 16–174 nmol cm–3 per day and almost completely blocked methanogenesis. 16S rRNA gene and cDNA amplicon sequencing identified microorganisms whose increases in ribosome numbers strongly correlated to ST. Natively abundant (⩾0.1% estimated genome abundance) species-level operational taxonomic units (OTUs) showed no significant response to sulfate. In contrast, low-abundance OTUs responded significantly to sulfate in incubations with propionate, lactate and butyrate. These OTUs included members of recognized sulfate-reducing taxa (Desulfosporosinus, Desulfopila, Desulfomonile, Desulfovibrio) and also members of taxa that are either yet unknown sulfate reducers or metabolic interaction partners thereof. Most responsive OTUs markedly increased their ribosome content but only weakly increased in abundance. Responsive Desulfosporosinus OTUs even maintained a constantly low population size throughout 50 days, which suggests a novel strategy of rare biosphere members to display activity. Interestingly, two OTUs of the non-sulfate-reducing genus Telmatospirillum (Alphapro- teobacteria) showed strongly contrasting preferences towards sulfate in butyrate-amended micro- cosms, corroborating that closely related microorganisms are not necessarily ecologically coherent. We show that diverse consortia of low-abundance microorganisms can perform peat soil sulfate reduction, a process that exerts control on methane production in these climate-relevant ecosystems. The ISME Journal (2016) 10, 2365–2375; doi:10.1038/ismej.2016.42; published online 25 March 2016 Introduction diversity of simultaneously occurring organic carbon degradation pathways is favored by fre- Peatlands currently store about one-third of all quently fluctuating concentrations of electron terrestrial carbon (Limpens et al., 2008), which is acceptors (Schmalenberger et al., 2007; Küsel predicted to be partially released as the greenhouse et al., 2008; Knorr and Blodau, 2009) and donors gases CO and CH because of climate change 2 4 (Schmalenberger et al., 2007; Küsel et al., 2008; (Hodgkins et al., 2014; Schuur et al., 2015). In Wüst et al., 2009). A changing water table that these water-saturated soils, steep gradients in redox – conditions sustain a complex network of biogeo- steadily shifts the oxic anoxic interface (Knorr chemical processes (Limpens et al., 2008), with et al., 2009; Reiche et al., 2009) and complex flow organic matter degradation being carried out by paths of infiltrating and exfiltrating water create different functional guilds of microorganisms. This distinct spatial and temporal patterns (hot spots and hot moments) of various biogeochemical processes, making peatlands very dynamic ecosys- Correspondence: A Loy, Division of Microbial Ecology, tems (Jacks and Norrström, 2004; Knorr et al., 2009; Department of Microbiology and Ecosystem Science, Knorr and Blodau, 2009; Frei et al., 2012). Research Network Chemistry Meets Microbiology, University Below the water table, where anoxic conditions of Vienna, Althanstraße 14, 1090 Vienna, Austria. E-mail: [email protected]. persist, the processes of fermentation and subse- Received 8 September 2015; revised 15 February 2016; accepted quent methanogenesis are competing with energeti- 22 February 2016; published online 25 March 2016 cally more favorable degradation pathways such as Konstanzer Online-Publikations-System (KOPS) URL: http://nbn-resolving.de/urn:nbn:de:bsz:352-0-340633 Sulfate reduction-associated bacteria in peat soil B Hausmann et al 2366 anoxic respiration coupled to nitrate, Fe(III), humic In addition, microorganisms with a specialized meta- matter or sulfate reduction (Loy et al., 2004; Beer bolism often fulfill gatekeeper functions in an ecosys- et al., 2008; Hamberger et al., 2008; Küsel et al., tem while sustaining low-abundance populations 2008; Drake et al., 2009; Keller et al., 2009; Knorr (Lynch and Neufeld, 2015), for example, N2-fixing and Blodau, 2009; Knorr et al., 2009; Reiche et al., microorganisms in the ocean (Großkopf et al., 2012) or 2009; Wüst et al., 2009; Hunger et al., 2011; Pester nitrifiers in wastewater treatment plants (Wang et al., et al., 2012b). The importance of sulfate reduction 2014). The reasons for their constantly low abundance for peatland biogeochemistry is often neglected are not yet resolved but most likely vary between because of the low prevailing sulfate concentrations different taxa and may include a decreased efficiency (μM range). This is contrasted by a highly active but in the competition for resources, predation and viral cryptic sulfur cycle that rapidly reoxidizes reduced attack, or an energy metabolism sustaining little sulfur species and thus sustains sulfate reduction growth (Lynch and Neufeld, 2015). rates that are as high as in sulfate-rich marine surface Recognized SRM are typically members of the rare sediments (Pester et al., 2012b). Here, (bio)geochem- biosphere in peatlands (Loy et al., 2004; Costello and ical sulfur reoxidation can be either coupled to Schmidt, 2006; Dedysh et al., 2006; Kraigher et al., – the reduction of O2 at the oxic anoxic interphase or 2006; Pester et al., 2010; Steger et al., 2011; Tveit to the reduction of Fe(III) (Hansel et al., 2015) and/or et al., 2013). Previous research showed that rare humic matter (Heitmann and Blodau, 2006; Yu peatland Desulfosporosinus spp. have the potential et al., 2015) under completely anoxic conditions. for high cell-specific sulfate reduction rates (Pester As sulfate-reducing microorganisms (SRM) generally et al., 2010) that are at the upper limit of cell-specific outcompete methanogens and syntrophically asso- rates observed for pure cultures (Detmers et al., ciated fermenters (Muyzer and Stams, 2008), they 2001). This provided indirect evidence that rare exert an important intrinsic control function on CH4 biosphere members could contribute substantially production in peatlands (Gauci et al., 2004, 2005; to biogeochemical cycling in peatlands. In the Gauci and Chapman, 2006). same peatland, a high diversity of deep-branching Microbial communities in soils are typically com- lineages of the dsrAB genes (subunit A and B of posed of a large number of species (e.g., Roesch et al., the dissimilatory sulfite reductase) was identified 2007; Serkebaeva et al., 2013). Few of these taxa are previously (Loy et al., 2004; Schmalenberger et al., very or moderately abundant (arbitrarily classified at 2007; Pester et al., 2010; Steger et al., 2011). ⩾ 1% and ⩾ 0.1% relative abundance, respectively). Although dsrAB generally serve as functional marker The remaining majority of species have an individual genes for SRM (Müller et al., 2015), the taxonomic relative abundance of o0.1% and are summarized as identity of these novel lineages and their function the rare biosphere (Pedrós-Alió, 2012; Lynch and with regard to sulfur and carbon metabolism remain Neufeld, 2015). Because of its species richness and unclear (Pester et al., 2012b; Müller et al., 2015). genetic diversity, the rare biosphere functions as Here, we set up controlled incubation experiments a microbial seed bank for the recruitment of dormant supplemented with single substrates and sulfate to cells to become active and numerically dominant simulate sulfate-reducing hot spots and gain insights under favorable environmental conditions. For exam- into the discrepancy between the low abundance of ple, singular disturbance events such as oil spills SRM and the high sulfate reduction rate regularly resulted either in the recruitment of specific taxa observed in peatlands. (Teira et al., 2007) or even widespread changes of the total microbial community (Newton et al., 2013). Furthermore, periodic environmental filtering through Materials and methods seasonal changes led to reoccurring temporal shifts between rare and abundant population sizes in Peat microcosms marine bacterioplankton species (Campbell et al., The acidic peatland Schlöppnerbrunnen II is located 2011; Vergin et al., 2013; Alonso-Sáez et al., 2015). in Germany (50°07′54.8″N, 11°52′51.8″E). Main site Dormant microorganisms may also be introduced to characteristics
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