DNA- and RNA-SIP Reveal
            <i>Nitrospira</i>
            spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters

Gülay, Arda; Fowler, Jane; Tatari, Karolina; Thamdrup, Bo; Albrechtsen, Hans‐Jørgen; Al‐Soud, Waleed Abu; Sørensen, Søren J.; Smets, Barth F.

doi:10.1128/mbio.01870-19

Cited by 36 publications

(24 citation statements)

References 74 publications

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“…Rapid sand filters (RSF), widely used to produce drinking water from surface-or groundwater, can be a useful model system as they are characterized by stable conditions and active growth primarily driven by the oxidation of ammonia, methane, and other inorganic compounds present at low concentration in the influent water, large populations (~ 10 9 cells/g), significant mixing, continuous but limited immigration from prokaryotes in the influent water, no dispersal between separate sand filters (resulting in allopatric populations), and relatively well defined coupling between chemical and biological processes [5][6][7] . In addition, microbial communities inhabiting these systems have been described and show the dominance of complete ammonia oxidizers (comammox) 8,9 , which are expected to have a relatively simple basic ecology (due to their chemolithoautotrophic metabolism) 10 , yet are poorly studied in terms of what drives their diversity, distribution and evolution.…”

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confidence: 99%

Evolutionary ecology of natural comammoxNitrospirapopulations

Palomo¹,

Dechesne²,

Cordero

et al. 2020

Preprint

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Microbial life on Earth commonly occurs in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during last decades, but most studies of evolutionary dynamics are based on single species in isolation or experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filters as a model to avoid this limitation. In these systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters revealed systematic co-occurrence of at least five comammox Nitrospira species, favoured by low ammonium concentrations. Nitrospira species showed intra-population sequence diversity, although possible clonal expansion was detected in few abundant local comammox populations. Nitrospira populations were separated by gene flow boundaries, suggesting natural and cohesive populations. They showed low homologous recombination and strong purifying selection, the latest process being especially strong in genes essential in energy metabolism. Positive selection was detected on genes related to resistance to foreign DNA and phages. Additionally, we analysed evolutionary processes in populations from different habitats. Interestingly, our results suggest that in comammox Nitrospira these processes are not an intrinsic feature but greatly vary depending on the habitat they inhabit. Compared to other habitats, groundwater fed sand filters impose strong purifying selection and low recombination. Together, this study improves understanding of interactions and evolution of species in the wild, and sheds light on the environmental dependency of evolutionary processes.

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Evolutionary ecology of natural comammoxNitrospirapopulations

Palomo¹,

Dechesne²,

Cordero

et al. 2020

Preprint

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“…In addition, the detection of specific genera performing EET is central in our efforts to isolate pure electro-active cultures and elucidate EET mechanisms. In this study, we first enriched H 2 , S 2 O 3 2-, or CH 4 and NH 4 + oxidizing guilds from a sand filter for groundwater treatment, where we observed a continuous inlet flow of ferrous iron, hydrogen sulfide, methane and ammonium (Gülay et al, 2016(Gülay et al, , 2019. We, then, examined the electrochemical activity and electroactive members of these enrichments with the aim to identify a microbial member of anticipated function performing extracellular electron transfer and to characterize their electron uptake efficiency.…”

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confidence: 99%

Different autotrophic enrichments yield efficient inocula for biocathodic applications

Gülay

Jensen

Sicheritz-Pontén

et al. 2021

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The uptake of extracellular electrons from cathodes by microbes is a recently discovered phenomenon. However, current knowledge on the diversity of microbes accepting extracellular electrons and populating biocathodes is scarce. Research is required to explore the distribution of extracellular electron uptake metabolism in the tree of life across microbial guilds. Here we characterize the electron uptake ability of microbial guilds enriched on H2, S2O32-, or CH4 and NH4+ from the same inoculum taken from a groundwater treatment sand-filter. We hypothesized that functional microbes having dense outer membrane cytochromes in their native pathway, such as pathways of NH4+, CH4, S2O32- and H2, can perform extracellular electron uptake. We aimed of addressing the following questions: (1) Are there any known microbial member of anticipated function performing extracellular electron transfer? (2) How does electron uptake efficiency vary between the different functional guilds? (3) How is the dissipated electron energy distributed across metabolisms? We developed and applied a novel pipeline to identify taxa utilizing direct electron energy and utilizing secondary microbial products. We report the putative direct electron uptake metabolism of types belonging to Methylomonas, UBA6140, and Nitrosomonas. Furthermore, members of Streptococcaceae, Rhizobiaceae, Streptococcus, Brevundimonas, Chryseobacterium, and Pseudomonas are detected as electroactive taxa. Our results reveal novel insights into the diversity, electrochemical activity, and metabolism of taxa performing direct electron uptake.

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“…Further analysis demonstrated that comammox Nitrospira were more abundant than AOB based on amoA gene abundance ( Fowler et al, 2018 ) and had metabolic versatility allowing niche-partitioning among ammonia oxidizers ( Palomo et al, 2018 ). Consequently, ammonia oxidation by comammox Nitrospira was functionally demonstrated by DNA and RNA stable isotope probing ( Gülay et al, 2019 ). Although these culture-independent approaches revealed the occurrence of Nitrospira in oligotrophic environments, little is known about the physiology and genome of a Nitrospira strain from DWTPs.…”

Section: Introductionmentioning

confidence: 99%

Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant

et al. 2020

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Characteristics of Nitrite-Oxidizing Nitrospira genome of strain KM1 was 4,509,223 bp in length and contained 4,318 predicted coding sequences. Average nucleotide identities between strain KM1 and known cultured Nitrospira genome sequences are 76.7-78.4%, suggesting at least specieslevel novelty of the strain in the Nitrospira lineage II. These findings broaden knowledge of the ecophysiological diversity of nitrite-oxidizing Nitrospira.

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DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters

Cited by 36 publications

References 74 publications

Evolutionary ecology of natural comammoxNitrospirapopulations

Evolutionary ecology of natural comammoxNitrospirapopulations

Different autotrophic enrichments yield efficient inocula for biocathodic applications

Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant

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