Adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations: Implications for the relative contributions of different ammonia oxidizers to soil nitrogen cycling

Wang, Jichen; Rhodes, Geoff; He, Ji‐Zheng; Ge, Yuan

doi:10.1016/j.scitotenv.2019.02.427

Cited by 82 publications

(53 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, it was lower than the rice paddy soil and WWTPs (10 11 copies per gram dry sediment) (Pjevac et al ). The abundance of the comammox amoA gene in fertilized soils (Wang et al ) was close to that in the river and lake sediments (Yu et al ). However, it was lower than that in the acidic forest soils (Hu and He ), and the highest abundance value was found in groundwater wells (Pjevac et al ).…”

Section: Discussionmentioning

confidence: 63%

“…The comammox genus found in this study belongs to clade A, indicating comammox clade A may play an important ecological role in the nitrogen cycle of lake sediments in the middle reaches of the Yangtze River. Most of the current research found comammox clade A and clade B co‐existed in rapid gravity sand filter, WWTPs, Vercelli rice rhizosphere, SBR and soil (Palomo et al ; Pjevac et al ; Roots et al ; Wang et al ). However, only comammox clade A was found in our study and in lake sediment, freshwater biofilms and some artificial ecosystems (Pjevac et al ), and only comammox clade B was found in the forest soil (Pjevac et al ).…”

Section: Discussionmentioning

confidence: 99%

“…When applying nutrients to the soil, the relative abundance of comammox Nitrospira clade A increases with the increasing nutrient input gradient, whereas clade B was the opposite. This may be due to the different physiological characteristics between the comammox Nitrospira clades (Wang et al ).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Diversity and abundance of comammox bacteria in the sediments of an urban lake

Xu¹,

Lü

Liu³

et al. 2020

J Appl Microbiol

View full text Add to dashboard Cite

Aims Although comammox have been discovered in a variety of ecosystems, there are few studies in urban lakes. This paper attempted to confirm whether this ammonia‐oxidizing microbe exists in urban lakes and to determine the factors influencing its existence. Methods and Results This study investigated the diversity and abundance of comammox bacteria in sediments of a typical urban lake in China, and their ecological relationship with other ammonia‐oxidizing micro‐organisms. The phylogenetic analysis indicated that comammox clade A existed in the sediment of Lake Donghu, and the comammox bacteria co‐existed with ammonia‐oxidizing archaea (AOA), ammonia‐oxidizing bacteria (AOB) and anaerobic ammonia‐oxidizing (anammox) bacteria in the sediment of this lake. The abundances of the ammonia monooxygenase subunit A (amoA) genes for comammox, AOA, AOB and anammox 16S rRNA were 2·43 × 108, 1·07 × 108, 3·24 × 107 and 3·21 × 1011 copies per gram dry sediment respectively. Moreover, the amoA gene abundance of comammox was positively correlated with that of AOA and AOB. The redundancy analysis showed that the abundance of the comammox amoA gene was negatively correlated with the concentration of main indicators for nitrogen status in both the sediment and the water column, indicating that eutrophication may inhibit the growth of comammox bacteria. Conclusions Comammox bacteria play an important ecological role in the nitrogen cycle of urban lake sediments. Significance and Impact of the Study Our results indicated comammox bacteria were widespread in urban lakes and eutrophication may inhibit their growth.

show abstract

Section: Discussionmentioning

confidence: 63%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Diversity and abundance of comammox bacteria in the sediments of an urban lake

Xu¹,

Lü

Liu³

et al. 2020

J Appl Microbiol

View full text Add to dashboard Cite

show abstract

“…Ten percent and 46% report a positive correlation with only AOA or only AOB, respectively, 11% correlated with neither and 4% and 5% reported a negative correlation with AOA and AOB, respectively. No correlation has yet been observed between PNR and comammox bacteria (Wang et al 2019b;Luchibia et al 2020;Zhang et al, 2020). While these studies suggest that some populations of AOA are using added ammonium, the majority of studies indicate that only ammonia oxidising bacteria (AOB) contribute to PNR, often leading to the conclusion that AOA are not contributing to ammonia oxidation in a soil in situ.…”

Section: Potential Nitrification Rate Does Not Reflect Ammonia Oxidismentioning

confidence: 99%

Use and abuse of potential rates in soil microbiology

Hazard

Prosser

Nicol

2020

Preprint

View full text Add to dashboard Cite

Telephone: +33 (0) 472 18 60 88 25 26 27 28 Running title: Potential rates in microbial ecology 29 Abstract 34Potential rate assays are used in soil microbial ecology to determine the maximum rate of a 35 functional process in environmental samples. They assume that all contributing organisms in a 36 community are active at a maximum rate under one set of 'optimal' incubation conditions. 37Potential rates are then often compared to the abundance of specific taxonomic groups to infer 38 their relative contribution in situ. However, while investigators now recognise that populations 39 within communities are physiologically diverse, they often ignore the consequent suboptimal 40 activity, or even inactivity, of the majority of community members performing that function. 41In this short perspective article, we highlight the underlying conceptual problems associated 42 with potential assays and use potential nitrification rate (PNR) as an example. PNR was 43 originally developed to estimate the size of active ammonia oxidising communities in 44 environmental samples. They are routinely performed in short-term shaken slurry incubations 45 by measuring assumed maximum rates of nitrate or nitrite production under optimal, non-46 substrate-limiting conditions. As with other functional processes, it is now recognised that a 47 broad diversity of organisms contribute to aerobic ammonia oxidation in terrestrial and other 48 habitats, and this diversity represents a substantial range of physiologies, including variation in 49 substrate affinity, ammonia tolerance, cell specific activity and substrate preference. Despite 50 this, PNR is routinely used in an attempt to determine an ecologically relevant measurement of 51 nitrification activity in soil. As with other potential assays, PNR has inherent biases towards 52 particular functional groups and its use in investigating the ecology of ammonia oxidisers in 53 natural systems is severely restricted. 54 55 Main text 56Measurement of the potential rate of microbially mediated soil processes has a long tradition. 57Commonly used examples are measurement of potential nitrification and denitrification rates 58 and substrate-induced respiration. All aim to determine process rate, usually after addition of a 59 relevant substrate, under what are considered to be optimal conditions that enable all organisms 60 capable of performing the process to operate with maximum activity and/or specific growth 61 rate. Potential rate obviously differs from 'actual' process rate, operating under non-optimal 62 environmental conditions, although actual rates are required for most ecological questions. 63Potential process rates may have some value, and have traditionally been used, in the absence 64 of alternatives, to estimate the biomass (or, less justifiably, abundance) of a functional microbial 65 group. However, the assumptions underlying measurement of potential rate are rarely 66 considered, rarely obeyed and even more rarely tested and have been increasingly challenged 67 3 as our underst...

show abstract

“…Notwithstanding the existence of other genetic determinants linked to the N cycle that, as just commented, can occur in soils in the subset of key nitrogen cycle genes (archaeal amoA , eubacterial amoA, nirK, nosZ and nifH ) that we chose to include as suitable proxies for nitrification, denitrification and nitrogen fixation in our analysis was defined based on the following considerations. With respect to the comammox Nitrospira , which was originally discovered upon enriching cultures from material found in a biofilm growing within a steel pipe in deep oil wells [25] subsequent studies had addressed the relevance of such taxa in agricultural contexts [27] and concluded that although the species is present in soils, the dominant contributors of potential nitrification are the classic ammonia oxidizing bacteria and the newly discovered comammox do not play a significant role in these pathways (P < 0.05).…”

Section: Introductionmentioning

confidence: 99%

The distribution of functional N-cycle related genes and nitrogen in soil profiles fertilized with mineral and organic N fertilizer

Zilio

Motta

Tambone

et al. 2020

Preprint

View full text Add to dashboard Cite

17Nitrogen (N) fertilizers applied to agricultural soils result in the release of nitrogen, mainly nitrate 18 (NO 3 -) in addition to nitrous oxide (N 2 O) and ammonia (NH 3 ), into the environment. Nitrogen 19 transformation in soil is a complex process and the soil microbial population can regulate the 20 potential for N mineralization, nitrification and denitrification. Here we show that agricultural soils 21 under standard agricultural N-management are consistently characterized by a high presence of 22 gene copies for some of the key biological activities related to the N-cycle. This led to a strong 23 NO 3reduction (75%) passing from the soil surface kg -1 on average) to 1 24 m deep layer (3.92 ± 4.42 g N-NO 3 kg -1 on average), and ensured low nitrate presence in the 25 deepest layer. Under these circumstances the other soil properties play a minor role in reducing 26 soil nitrate presence in soil. However, with excessive N fertilization, the abundance of bacterial 27 gene copies is not sufficient to explain N leaching in soil and other factors, i.e. soil texture and 28 rainfall, become more important in controlling these aspects. 29 30 31 3 37Agriculture has indeed a major role in this process: the global amount of N used in agriculture has 38 increased from 12 Tg N in 1960 to 104 Tg N in 2010 and the amount of N 2 fixed to NH 4 + by 39 industrial processes and destined for agriculture contributes today to 45% of the total nitrogen 40 fixed annually on the planet [1,3,4]. 41As a consequence of that, the total amount of N brought to the soil today, on a world scale, is more 42 than twice that considered a safe planetary boundary, i.e. a safe operating space for humanity to 43 avoid the risk of ecosystems' deterioration [5][6][7]. Furthermore, an increase in the use of N in the 44 food system by 51% in 2050 has been estimated, with a global increase in the environmental 45 pressure of the food system estimated to be in the range 52%-90%, in the absence of mitigation 46 measures [7,8]. Without emission reductions, global N losses are expected to further increase, 47 reaching in 2050 levels equal to 150% of those of 2010 [9]. 48Nitrogen fertilizers applied to agricultural soils result in the release of N into the environment, 49 both in the atmosphere (NH 3 , N 2 O, N 2 ), and in groundwater (NO 3 -) [10]. In many areas of the 50 world, agriculture has been acknowledged as the single largest source of N (mainly NO 3 -) to 51 environments [11][12][13][14], causing alterations in the carbon cycle, biodiversity reduction, 52 acidification, soil fertility reduction and air pollution [15]. Furthermore, human health problems 53 should be also considered; for example, in recent years many studies reported an increased 54 incidence of colorectal cancer in subjects who regularly drink water with a concentration of nitrate 55 above 8.6 mg L -1 [16,17]. All these problems lead to a social cost that has been estimated to be up 56 to 10 $ kg -1 N [18]. 57Nitrogen in soils can be metabolized and transformed by soil mic...

show abstract

Adaptive responses of comammox Nitrospira and canonical ammonia oxidizers to long-term fertilizations: Implications for the relative contributions of different ammonia oxidizers to soil nitrogen cycling

Cited by 82 publications

References 42 publications

Diversity and abundance of comammox bacteria in the sediments of an urban lake

Diversity and abundance of comammox bacteria in the sediments of an urban lake

Use and abuse of potential rates in soil microbiology

The distribution of functional N-cycle related genes and nitrogen in soil profiles fertilized with mineral and organic N fertilizer

Contact Info

Product

Resources

About