Hannah K. Marchant

Bio: Hannah K. Marchant is an academic researcher from Max Planck Society. The author has contributed to research in topics: Denitrification & Nitrate. The author has an hindex of 16, co-authored 33 publications receiving 1653 citations. Previous affiliations of Hannah K. Marchant include University of Bremen & University of Plymouth.

The microbial nitrogen-cycling network

Abstract: Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet By far, the largest inventory of freely accessible nitrogen is atmospheric dinitrogen, but most organisms rely on more bioavailable forms of nitrogen, such as ammonium and nitrate, for growth The availability of these substrates depends on diverse nitrogen-transforming reactions that are carried out by complex networks of metabolically versatile microorganisms In this Review, we summarize our current understanding of the microbial nitrogen-cycling network, including novel processes, their underlying biochemical pathways, the involved microorganisms, their environmental importance and industrial applications

Anammox, denitrification and dissimilatory nitrate reduction to ammonium in the East China Sea sediment

Abstract: Benthic nitrogen transformation pathways were investigated in the sediment of the East China Sea (ECS) in June of 2010 using the 15 N isotope pairing technique. Slurry incubations indicated that denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA) as well as intracellular nitrate release occurred in the ECS sediments. These four processes did not exist independently, nitrate release therefore diluted the 15 N labeling fraction of NO 3 − , and a part of the 15 NH 4 + derived from DNRA also formed 30 N 2 via anammox. Therefore, current methods of rate calculations led to over and underestimations of anammox and denitrification respectively. Following the procedure outlined in Thamdrup and Dalsgaard (2002), denitrification rates were slightly underestimated by an average 6% without regard to the effect of nitrate release, while this underestimation could be counteracted by the presence of DNRA. On the contrary, anammox rates calculated from 15 NO 3 − experiment were significantly overestimated by 42% without considering nitrate release. In our study, this overestimation could only be compensated 14% by taking DNRA into consideration. In a parallel experiment amended with 15 NH 4 + + 14 NO 3 − , anammox rates were not significantly influenced by DNRA due to the high background of 15 NH 4 + addition. The significant correlation between potential denitrification rate and sediment organic matter content ( r = 0.68, p 2 was the main pathway, while DNRA was also an important pathway accounting for 20–31% of benthic nitrate reduction in the ECS. Our study demonstrates the complicated interactions among different benthic nitrogen transformations and the importance of considering denitrification, DNRA, anammox and nitrate release together when designing and interpreting future studies.

Denitrifying community in coastal sediments performs aerobic and anaerobic respiration simultaneously

Abstract: Nitrogen (N) input to the coastal oceans has increased considerably because of anthropogenic activities, however, concurrent increases have not occurred in open oceans. It has been suggested that benthic denitrification in sandy coastal sediments is a sink for this N. Sandy sediments are dynamic permeable environments, where electron acceptor and donor concentrations fluctuate over short temporal and spatial scales. The response of denitrifiers to these fluctuations are largely unknown, although previous observations suggest they may denitrify under aerobic conditions. We examined the response of benthic denitrification to fluctuating oxygen concentrations, finding that denitrification not only occurred at high O2 concentrations but was stimulated by frequent switches between oxic and anoxic conditions. Throughout a tidal cycle, in situtranscription of genes for aerobic respiration and denitrification were positively correlated within diverse bacterial classes, regardless of O2 concentrations, indicating that denitrification gene transcription is not strongly regulated by O2 in sandy sediments. This allows microbes to respond rapidly to changing environmental conditions, but also means that denitrification is utilized as an auxiliary respiration under aerobic conditions when imbalances occur in electron donor and acceptor supply. Aerobic denitrification therefore contributes significantly to N-loss in permeable sediments making the process an important sink for anthropogenic N-inputs.

Coupled nitrification–denitrification leads to extensive N loss in subtidal permeable sediments

Abstract: We investigated microbial pathways of nitrogen transformation in highly permeable sediments from the German Bight (South-East North Sea) by incubating sediment cores percolated with 15N-labeled substrates under near in situ conditions. In incubations with added math formula, production of math formula occurred while the sediment was oxic, indicating ammonia oxidation. Similarly, math formula production during math formula incubations indicated nitrite oxidation. Taken together these findings provide direct evidence of high nitrification rates within German Bight sands. The production of 15N-N2 on addition of math formula revealed high denitrification rates within the sediment under oxic and anoxic conditions. Denitrification rates were strongly and positively correlated with oxygen consumption rates, suggesting that denitrification is controlled by organic matter availability. Nitrification and denitrification rates were of the same magnitude and the rapid production of 15N-N2 in incubations with added math formula confirmed close coupling of the two processes. Areal rates of N-transformation were estimated taking advective transport of substrates into account and integrating volumetric rates over modeled oxygen and nitrate penetration depths, these ranged between 22 μmol N m−2 h−1 and 94 μmol N m−2 h−1. Furthermore, results from the 15N-labeling experiments show that these subtidal permeable sediments are, in sharp contrast to common belief, a substantial source of N2O. Our combined results show that nitrification fuels denitrification by providing an additional source of nitrate, and as such masks true N-losses from these highly eutrophic sediments. Given the widespread occurrence of anthropogenically influenced permeable sediments, coupled benthic nitrification–denitrification might have an important but so far neglected role in N-loss from shelf sediments.

Cyanate and urea are substrates for nitrification by Thaumarchaeota in the marine environment.

Abstract: Ammonia-oxidizing archaea of the phylum Thaumarchaeota are among the most abundant marine microorganisms1. These organisms thrive in the oceans despite ammonium being present at low nanomolar concentrations2,3. Some Thaumarchaeota isolates have been shown to utilize urea and cyanate as energy and N sources through intracellular conversion to ammonium4–6. Yet, it is unclear whether patterns observed in culture extend to marine Thaumarchaeota, and whether Thaumarchaeota in the ocean directly utilize urea and cyanate or rely on co-occurring microorganisms to break these substrates down to ammonium. Urea utilization has been reported for marine ammonia-oxidizing communities7–10, but no evidence of cyanate utilization exists for marine ammonia oxidizers. Here, we demonstrate that in the Gulf of Mexico, Thaumarchaeota use urea and cyanate both directly and indirectly as energy and N sources. We observed substantial and linear rates of nitrite production from urea and cyanate additions, which often persisted even when ammonium was added to micromolar concentrations. Furthermore, single-cell analysis revealed that the Thaumarchaeota incorporated ammonium-, urea- and cyanate-derived N at significantly higher rates than most other microorganisms. Yet, no cyanases were detected in thaumarchaeal genomic data from the Gulf of Mexico. Therefore, we tested cyanate utilization in Nitrosopumilus maritimus, which also lacks a canonical cyanase, and showed that cyanate was oxidized to nitrite. Our findings demonstrate that marine Thaumarchaeota can use urea and cyanate as both an energy and N source. On the basis of these results, we hypothesize that urea and cyanate are substrates for ammonia-oxidizing Thaumarchaeota throughout the ocean. Thaumarchaeota isolates are capable of utilizing urea and cyanate for nitrification in vitro. Here, the authors show that this occurs in situ and that Thaumarchaeota are able to use urea and cyanate as an energy and nitrogen source in the marine environment.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Impacts of ocean acidification on marine shelled molluscs

Abstract: Over the next century, elevated quantities of atmospheric CO2 are expected to penetrate into the oceans, causing a reduction in pH (-0.3/-0.4 pH unit in the surface ocean) and in the concentration of carbonate ions (so-called ocean acidification). Of growing concern are the impacts that this will have on marine and estuarine organisms and ecosystems. Marine shelled molluscs, which colonized a large latitudinal gradient and can be found from intertidal to deep-sea habitats, are economically and ecologically important species providing essential

Metagenomic analysis of stressed coral holobionts

Abstract: P>The coral holobiont is the community of metazoans, protists and microbes associated with scleractinian corals. Disruptions in these associations have been correlated with coral disease, but little is known about the series of events involved in the shift from mutualism to pathogenesis. To evaluate structural and functional changes in coral microbial communities, Porites compressa was exposed to four stressors: increased temperature, elevated nutrients, dissolved organic carbon loading and reduced pH. Microbial metagenomic samples were collected and pyrosequenced. Functional gene analysis demonstrated that stressors increased the abundance of microbial genes involved in virulence, stress resistance, sulfur and nitrogen metabolism, motility and chemotaxis, fatty acid and lipid utilization, and secondary metabolism. Relative changes in taxonomy also demonstrated that coral-associated microbiota (Archaea, Bacteria, protists) shifted from a healthy-associated coral community (e.g. Cyanobacteria, Proteobacteria and the zooxanthellae Symbiodinium) to a community (e.g. Bacteriodetes, Fusobacteria and Fungi) of microbes often found on diseased corals. Additionally, low-abundance Vibrio spp. were found to significantly alter microbiome metabolism, suggesting that the contribution of a just a few members of a community can profoundly shift the health status of the coral holobiont.

Predicting the response of molluscs to the impact of ocean acidification.

Abstract: Elevations in atmospheric carbon dioxide (CO2) are anticipated to acidify oceans because of fundamental changes in ocean chemistry created by CO2 absorption from the atmosphere. Over the next century, these elevated concentrations of atmospheric CO2 are expected to result in a reduction of the surface ocean waters from 8.1 to 7.7 units as well as a reduction in carbonate ion (CO32−) concentration. The potential impact that this change in ocean chemistry will have on marine and estuarine organisms and ecosystems is a growing concern for scientists worldwide. While species-specific responses to ocean acidification are widespread across a number of marine taxa, molluscs are one animal phylum with many species which are particularly vulnerable across a number of life-history stages. Molluscs make up the second largest animal phylum on earth with 30,000 species and are a major producer of CaCO3. Molluscs also provide essential ecosystem services including habitat structure and food for benthic organisms (i.e., mussel and oyster beds), purification of water through filtration and are economically valuable. Even sub lethal impacts on molluscs due to climate changed oceans will have serious consequences for global protein sources and marine ecosystems.

Common principles and best practices for engineering microbiomes

Abstract: Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge gaps hinder their efficient use for addressing urgent societal and environmental challenges. We argue that structuring research and technology developments around a design-build-test-learn (DBTL) cycle will advance microbiome engineering and spur new discoveries of the basic scientific principles governing microbiome function. In this Review, we present key elements of an iterative DBTL cycle for microbiome engineering, focusing on generalizable approaches, including top-down and bottom-up design processes, synthetic and self-assembled construction methods, and emerging tools to analyse microbiome function. These approaches can be used to harness microbiomes for broad applications related to medicine, agriculture, energy and the environment. We also discuss key challenges and opportunities of each approach and synthesize them into best practice guidelines for engineering microbiomes. We anticipate that adoption of a DBTL framework will rapidly advance microbiome-based biotechnologies aimed at improving human and animal health, agriculture and enabling the bioeconomy.