Soil moisture is a primary driver of comammox Nitrospira abundance in New Zealand soils

Chisholm, Chris; Di, Hong J.; Cameron, K. C.; Podolyan, Andriy; Shah, Anish; Hsu, Lin-Nei; Shen, Jin-Hui

doi:10.1016/j.scitotenv.2022.159961

Cited by 14 publications

(6 citation statements)

References 44 publications

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“…Illumina sequencing of the comammox Nitrospira amoA gene was conducted only on the day-60 samples, based on the qPCR results. Phylogenetic analysis of the comammox Nitrospira amoA gene revealed that only sequences belonging to clade B were found ( Figure 3 ), which is consistent with previous studies on grazed pasture soils ( Hsu et al, 2022 ; Chisholm et al, 2023 ). Beta diversity of clade B sequences was only affected by the application of chlorate (not DCD or the N-inputs), whereas alpha diversity was unaffected by any of the treatments.…”

Section: Discussionsupporting

confidence: 90%

“…Sequences are clustered into Clade B.1, Clade B.2, and reference Nitrospira sequences (belonging to Clade A.1). The tree also includes reference sequences from ( Chisholm et al, 2023 ; Palomo et al, 2022 ; Zhao et al, 2021 ) (in black boxes), and is to scale with pairwise distances indicated on the branches. Nitrosomonas eutropha (accession number APZ84135.1) was used as the outgroup to root the tree.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, comammox Nitrospira can be separated into clade A and clade B based on the phylogeny of the amoA gene, a subunit of AMO. Since their discovery, extensive research has been conducted on the ecology and abundance of comammox Nitrospira in terrestrial ecosystems worldwide ( Shi et al, 2018 ; Zhao et al, 2019 ; Xu et al, 2020 ; Li et al, 2021 ; Sun et al, 2021 ; Wang et al, 2021 ; Hsu et al, 2022 ; Chisholm et al, 2023 ). Some studies suggest that comammox Nitrospira actively contributes to the nitrification process in a nutrient rich environment ( Li et al, 2019 ; Xu et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…However, the comammox Nitrospira community in these ecosystems is dominated by clade A, with clade B typically being undetectable. To date, the comammox Nitrospira community found in New Zealand soils consists almost entirely of clade B ( Hsu et al, 2022 ; Chisholm et al, 2023 ).…”

Section: Introductionmentioning

confidence: 99%

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Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil

Shah,

Hsu,

Chisholm

et al. 2024

Front. Microbiol.

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IntroductionThrough the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study.MethodsThe soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing.Results and DiscussionThe results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities.

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Section: Discussionsupporting

confidence: 90%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil

Shah,

Hsu,

Chisholm

et al. 2024

Front. Microbiol.

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“…The changes in the eutrophic/oligotrophic ratio are related to the selective effects of root exudates on soil microbial communities ( Cappelli et al, 2022 ; Chisholm et al, 2023 ). Under TA, eutrophic bacteria were enriched in FRS (FRS > ARS and BS), while oligotrophic bacteria were enriched in ARS (ARS > FRS and BS; Figures 4A , B ; Supplementary Figure S4 ).…”

Section: Discussionmentioning

confidence: 99%

Hexose/pentose ratio in rhizosphere exudates-mediated soil eutrophic/oligotrophic bacteria regulates the growth pattern of host plant in young apple–aromatic plant intercropping systems

Zhao,

Sun,

Dong

et al. 2024

Front. Microbiol.

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IntroductionThe positive effect of intercropping on host plant growth through plant–soil feedback has been established. However, the mechanisms through which intercropping induces interspecific competition remain unclear.MethodsIn this study, we selected young apple trees for intercropping with two companion plants: medium growth-potential Mentha haplocalyx Briq. (TM) and high growth-potential Ageratum conyzoides L. (TA) and conducted mixed intercropping treatment with both types (TMA) and a control treatment of monocropping apples (CT).ResultsOur findings revealed that TM increased the under-ground biomass of apple trees and TA and TMA decreased the above-ground biomass of apple trees, with the lowest above-ground biomass of apple trees in TA. The above- and under-ground biomass of intercrops in TA and TMA were higher than those in TM, with the highest in TA, suggesting that the interspecific competition was the most pronounced in TA. TA had a detrimental effect on the photosynthesis ability and antioxidant capacity of apple leaves, resulting in a decrease in above-ground apple biomass. Furthermore, TA led to a reduction in organic acids, alcohols, carbohydrates, and hydrocarbons in the apple rhizosphere soil (FRS) compared to those in both soil bulk (BS) and aromatic plant rhizosphere soil (ARS). Notably, TA caused an increase in pentose content and a decrease in the hexose/pentose (C6/C5) ratio in FRS, while ARS exhibited higher hexose content and a higher C6/C5 ratio. The changes in exudates induced by TA favored an increase in taxon members of Actinobacteria while reducing Proteobacteria in FRS compared to that in ARS. This led to a higher eutrophic/oligotrophic bacteria ratio relative to TM.DiscussionThis novel perspective sheds light on how interspecific competition, mediated by root exudates and microbial community feedback, influences plant growth and development.

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Conversion of coastal marsh to aquaculture ponds altered soil ammonia oxidiser community and decreased ammonia oxidation potential

Ye,

Tang,

Lin

et al. 2024

J of Sust Agri & Env

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IntroductionAs a crucial component of the nitrogen cycle, ammonia oxidation in soil can be driven by canonical ammonia‐oxidising archaea (AOA) and bacteria, as well as complete ammonia oxidiser (CMX Nitrospira). Land use change can disrupt and alter the soil microbial community and the nitrogen cycle.Materials & MethodsWe compared the soil ammonia‐oxidising microorganisms and ammonia oxidation potentials in a coastal marsh and nearby reclaimed aquaculture ponds, monthly over a 10‐month period in southeastern China. The abundance of ammonia oxidisers was assessed by real‐time quantitative PCR and the community structure of CMX Nitrospira was evaluated by high‐throughput sequencing.ResultsThe ammonia oxidiser community was dominated by AOA in the marsh (91%) and was made up of similar proportions of AOA and CMX Nitrospira in the aquaculture ponds (46%–47%). The CMX Nitrospira community structure changed significantly between habitat types, mainly driven by opposite change in relative abundance of clade B versus clades A.2 and A.3. Aquaculture reclamation decreased the soil potential ammonia oxidation rate (PAO) by an order of magnitude, and AOA was the only significant predictor of PAO among all ammonia oxidiser groups.ConclusionOur results suggest that aquaculture reclamation from coastal marshes would significantly alter the soil ammonia oxidiser community and decrease ammonia oxidation rate, and CMX Nitrospira appear to play a relative larger role in nitrogen cycling in aquaculture ponds.

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Soil moisture is a primary driver of comammox Nitrospira abundance in New Zealand soils

Cited by 14 publications

References 44 publications

Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil

Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil

Hexose/pentose ratio in rhizosphere exudates-mediated soil eutrophic/oligotrophic bacteria regulates the growth pattern of host plant in young apple–aromatic plant intercropping systems

Conversion of coastal marsh to aquaculture ponds altered soil ammonia oxidiser community and decreased ammonia oxidation potential

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