Niche separation of comammox Nitrospira and canonical ammonia oxidizers in an acidic subtropical forest soil under long-term nitrogen deposition

Shi, Xiuzhen; Hu, Hang‐Wei; Wang, Jianqing; He, Ji‐Zheng; Zheng, Chengyang; Wan, Xiaohua; Huang, Zhiqun

doi:10.1016/j.soilbio.2018.09.004

Cited by 131 publications

(57 citation statements)

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“…The high abundance of both CAOB amoA clade A and clade B were determined in 300 forest soil samples using the sister primer sets, suggesting they might functionally outcompete the canonical AOA under the oligotrophic soil ecosystems (Hu and He, 2017). However, AOA rather than CAOB were proved to conduct efficient autotrophic nitrification in the forest soil with 13 C labelled CO 2 microcosm experiment (Shi et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

Zhao

Huang

Wang

et al. 2018

Preprint

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1were ubiquitous and unexpectedly abundant in agricultural soils, river sediments, intertidal 3 2 zones, drinking water and wastewater treatment systems. Phylogenetic analysis indicated that 3 3 clade A existed in all the five types of ecosystems, while clade B were only detected in soil and 3 4 sediment samples. Four sub-clusters were further classified within clade A, in which N. 3 5 nitrosa cluster dominated CAOB amoA in activated sludge samples while the new recognized 3 6 soil cluster was the primary constitute in soils. Moreover, the niche specialization between 3 7 different CAOB species and the environmental conditions were supposed to be the primary 3 8 driven force to shape the diversity and community of CAOB. This study provided a strong 3 9 evidence in support of the ubiquities and high abundances of CAOB in various environmental 4 0 ecosystems and highlighted the significance of including CAOB as the new member of AOMs 4 1 to re-evaluate the biogeochemical nitrogen cycle. 4 2 4 3

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Section: Discussionmentioning

confidence: 99%

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

Zhao

Huang

Wang

et al. 2018

Preprint

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“…A recent study reported that nitrification activity in forest and paddy soils when subjected to ammonium limitation is associated with clade B rather than clade A comammox Nitrospira (Wang et al, 2019). Comammox clade B appeared to dominate also in forest soil under increasing nitrogen load and decreasing pH (Shi et al, 2018).…”

Section: Ammonia and Nitrite Metabolismmentioning

confidence: 98%

Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in a Dutch drinking water treatment plant

Poghosyan

Koch

Frank

et al. 2020

Preprint

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Highlights 10• Microbial distribution was mainly influenced by sampling location within the DWTP.• Clade A comammox Nitrospira were the most abundant nitrifying guild in samples from the primary sand filter, while clade B dominated in samples from wall biofilm and the secondary filter.• A novel methanotrophic bacterium affiliated with the Methylophilaceae family comprised 15 the largest bacterial fraction in the primary sand filter. AbstractElevated concentrations of ammonium and methane in groundwater can cause severe problems during drinking water production. To avoid their accumulation, raw water in the Netherlands, and many other countries, is purified by sand filtration. These drinking water filtration systems select 20 for microbial communities that mediate the biodegradation of organic and inorganic compounds.In this study, the active layers and wall biofilm of a Dutch drinking water treatment plant (DWTP) were sampled at different locations along the filtration units of the plant over three years. We used high-throughput sequencing in combination with differential coverage and sequence compositionbased binning to recover 56 near-complete metagenome-assembled genomes (MAGs) with an 25 estimated completion of ≥70% and with ≤10% redundancy. These MAGs were used to characterize the microbial communities involved in the conversion of ammonia and methane. The methanotrophic microbial communities colonizing the wall biofilm (WB) and the granular material of the primary rapid sand filter (P-RSF) were dominated by members of the Methylococcaceae and Methylophilaceae. The abundance of these bacteria drastically decreased in the secondary 30 rapid sand filter (S-RSF) samples. In all samples, complete ammonia-oxidizing (comammox) Nitrospira were the most abundant nitrifying guild. Clade A comammox Nitrospira dominated the P-RSF, while clade B was most abundant in WB and S-RSF, where ammonium concentrations were much lower. In conclusion, the knowledge obtained in this study contributes to understanding the role of microorganisms in the removal of carbon and nitrogen compounds during drinking 35 water production. We furthermore found that drinking water treatment plants represent valuable model systems to study microbial community function and interaction. Methane uptakeMethane-oxidizing capacity was determined for the P-RSF and WB samples collected in 2016. 115For the P-RSF, 2.5, 5, 10, and 20 g of sand material were mixed with 20 ml top water. After settling of the sand, overlaying water samples (20 ml) were transferred into 120 ml serum bottles with Deep aquifer Clay Shallow aquifer Sand and gravel NH 4 + CH 4 Fe H 2 S Mn Groundwater Air supply Air supply WB P-RSF S-RSF Storage and distribution Wall

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“…Available amoA gene sequences suggest two phylogenetic groups (clades A and B) of similar diversity with potential environmental specializations. Currently cultivated representatives belong to clade A (Daims et al, 2015;van Kessel et al, 2015) and while both clades A and B are found in soil, conditions under which comammox bacteria are active in soil have only been demonstrated for clade B (Shi et al, 2018;Wang et al, 2019).…”

Section: Iver S It Y Of Ammonia-oxid Izing Microorg Anis Msmentioning

confidence: 99%

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Prosser

Hink

Gubry‐Rangin

et al. 2019

Global Change Biology

254

157

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Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N 2 O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle.Direct N 2 O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N 2 O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N 2 O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N 2 O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N 2 O emissions.

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Niche separation of comammox Nitrospira and canonical ammonia oxidizers in an acidic subtropical forest soil under long-term nitrogen deposition

Cited by 131 publications

References 50 publications

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set

Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in a Dutch drinking water treatment plant

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

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