Nitrate removal microbiology in woodchip bioreactors: A case-study with full-scale bioreactors treating aquaculture effluents

Aalto, Sanni L.; Suurnäkki, Suvi; Ahnen, Mathis von; Siljanen, Henri; Pedersen, Palle; Tiirola, Marja

doi:10.1016/j.scitotenv.2020.138093

Cited by 44 publications

(26 citation statements)

References 41 publications

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“…To detect the changes in N cycling-relevant microbial community structure with permafrost thaw and post-thaw succession, we studied the relative abundances of the key N cycling genes using a captured metagenomic tool. The method has been validated and tested for overall performance and specificity of the probes used for sequence capture 45 , and it has been successfully applied for studying N cycling genes in bioreactors treating aquaculture effluents 71 . This method is designed for targeting and sequencing the organisms carrying the key N cycling genes involved in the following processes: N 2 fixation ( nifH ), nitrification ( amoA ), NO 3 − reduction ( narG, napA ), denitrification ( nir ( nirK + nirS ) , norB, nosZ ), dissimilatory nitrate reduction to ammonium (DNRA) ( nrfA ) and anammox ( hdhA ) using gene-specific probes following the NimbleGen SeqCap EZ protocol by Roche NimbleGen, Inc. A detailed description of the method can be found in Supplementary Note 1 .…”

Section: Methodsmentioning

confidence: 99%

Thawing Yedoma permafrost is a neglected nitrous oxide source

et al. 2021

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In contrast to the well-recognized permafrost carbon (C) feedback to climate change, the fate of permafrost nitrogen (N) after thaw is poorly understood. According to mounting evidence, part of the N liberated from permafrost may be released to the atmosphere as the strong greenhouse gas (GHG) nitrous oxide (N2O). Here, we report post-thaw N2O release from late Pleistocene permafrost deposits called Yedoma, which store a substantial part of permafrost C and N and are highly vulnerable to thaw. While freshly thawed, unvegetated Yedoma in disturbed areas emit little N2O, emissions increase within few years after stabilization, drying and revegetation with grasses to high rates (548 (133–6286) μg N m−2 day−1; median with (range)), exceeding by 1–2 orders of magnitude the typical rates from permafrost-affected soils. Using targeted metagenomics of key N cycling genes, we link the increase in in situ N2O emissions with structural changes of the microbial community responsible for N cycling. Our results highlight the importance of extra N availability from thawing Yedoma permafrost, causing a positive climate feedback from the Arctic in the form of N2O emissions.

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Section: Methodsmentioning

confidence: 99%

Thawing Yedoma permafrost is a neglected nitrous oxide source

et al. 2021

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“…In brief, gene fragments of CH 4 ‐producing archaea ( mcrA , coding for the methyl‐coenzyme M reductase) were searched with H mmer (hidden Markov model search of gene structures) from the published SRA database (NCBI), and phylogenetics of them were analyzed against obtained cultured and candidate divisions of functional genes. Second, we utilized a novel ‘probe‐targeted capture’ method (Aalto et al ., 2020; Siljanen et al ., 2021) to analyze genes related to CH 4 cycling from Norway spruce needles collected from eastern Finland (Kuopio). The same method was used recently for the detection of N‐cycling microbes in plant biomass (Aalto et al ., 2020).…”

Section: Current Understanding Of the Methane Production In Treesmentioning

confidence: 99%

“…Second, we utilized a novel ‘probe‐targeted capture’ method (Aalto et al ., 2020; Siljanen et al ., 2021) to analyze genes related to CH 4 cycling from Norway spruce needles collected from eastern Finland (Kuopio). The same method was used recently for the detection of N‐cycling microbes in plant biomass (Aalto et al ., 2020). Here, capture reaction was carried out with 12 190 unique probes, which were designed based on the currently known mcrA gene diversity in the public databases (Siljanen et al ., 2021).…”

Section: Current Understanding Of the Methane Production In Treesmentioning

confidence: 99%

“…First, the SRA database was searched for methanotrophic functional genes pmoA and mmoX , coding for the particulate and soluble forms of methane monooxygenase (MMO), respectively. Second, the same genes were targeted with the capture enrichment approach (Aalto et al ., 2020) to detect methanotrophs in spruce shoots, which were first incubated to enhance the detection of CH 4 ‐cycling microbes (as described in the section Methanogenic microbes in canopies of coniferous trees; Dunfield et al ., 2003; Dedysh et al ., 2005). Capture reaction included 640 unique probes for mmoX and 19 900 probes for pmoA (Siljanen et al ., 2021).…”

Section: Methane Consumption Within Tree Stems and Canopies: An Unrecognized Methane Sink?mentioning

confidence: 99%

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New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing

Putkinen

Siljanen

Laihonen³

et al. 2021

New Phytologist

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Methane (CH 4 ) exchange in tree stems and canopies and the processes involved are among the least understood components of the global CH 4 cycle. Recent studies have focused on quantifying tree stems as sources of CH 4 and understanding abiotic CH 4 emissions in plant canopies, with the role of microbial in situ CH 4 formation receiving less attention. Moreover, despite initial reports revealing CH 4 consumption, studies have not adequately evaluated the potential of microbial CH 4 oxidation within trees. In this paper, we discuss the current level of understanding on these processes. Further, we demonstrate the potential of novel metagenomic tools in revealing the involvement of microbes in the CH 4 exchange of plants, and particularly in boreal trees. We detected CH 4 -producing methanogens and novel monooxygenases, potentially involved in CH 4 consumption, in coniferous plants. In addition, our field flux measurements from Norway spruce (Picea abies) canopies demonstrate both net CH 4 emissions and uptake, giving further evidence that both production and consumption are relevant to the net CH 4 exchange. Our findings, together with the emerging diversity of novel CH 4 -producing microbial groups, strongly suggest microbial analyses should be integrated in the studies aiming to reveal the processes and drivers behind plant CH 4 exchange.

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“…This was in agreement with field measurements of dissolved and gaseous N 2 O fluxes from the three mature woodchip bioreactors, which showed a mean N 2 O-N emission factor of 0.6% of NO 3 -N removal (Audet et al, 2021). In studies of lab-scale woodchip bioreactors, ratios of nir/nosZ were initially high (> 10), but decreased after 6 months (Hellman et al, 2021), which supported that the genetic potential for N 2 O reduction develops toward generally low emissions from denitrifying bioreactors (Aalto et al, 2020).…”

Section: Functional Groupsmentioning

confidence: 79%

Microbiome Structure and Function in Woodchip Bioreactors for Nitrate Removal in Agricultural Drainage Water

et al. 2021

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Woodchip bioreactors are increasingly used to remove nitrate (NO3–) from agricultural drainage water in order to protect aquatic ecosystems from excess nitrogen. Nitrate removal in woodchip bioreactors is based on microbial processes, but the microbiomes and their role in bioreactor efficiency are generally poorly characterized. Using metagenomic analyses, we characterized the microbiomes from 3 full-scale bioreactors in Denmark, which had been operating for 4–7 years. The microbiomes were dominated by Proteobacteria and especially the genus Pseudomonas, which is consistent with heterotrophic denitrification as the main pathway of NO3– reduction. This was supported by functional gene analyses, showing the presence of the full suite of denitrification genes from NO3– reductases to nitrous oxide reductases. Genes encoding for dissimilatory NO3– reduction to ammonium were found only in minor proportions. In addition to NO3– reducers, the bioreactors harbored distinct functional groups, such as lignocellulose degrading fungi and bacteria, dissimilatory sulfate reducers and methanogens. Further, all bioreactors harbored genera of heterotrophic iron reducers and anaerobic iron oxidizers (Acidovorax) indicating a potential for iron-mediated denitrification. Ecological indices of species diversity showed high similarity between the bioreactors and between the different positions along the flow path, indicating that the woodchip resource niche was important in shaping the microbiome. This trait may be favorable for the development of common microbiological strategies to increase the NO3– removal from agricultural drainage water.

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Nitrate removal microbiology in woodchip bioreactors: A case-study with full-scale bioreactors treating aquaculture effluents

Cited by 44 publications

References 41 publications

Thawing Yedoma permafrost is a neglected nitrous oxide source

Thawing Yedoma permafrost is a neglected nitrous oxide source

New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing

Microbiome Structure and Function in Woodchip Bioreactors for Nitrate Removal in Agricultural Drainage Water

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