Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems

Zhang, Limei; Duff, Aoife M.; Smith, Cindy J.

doi:10.1111/1462-2920.14238

Cited by 42 publications

(36 citation statements)

References 81 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The dominance of the AOB community by Nitrospira in the present study is consistent with many studies of AOB communities in terrestrial ecosystems ( Figure S2) (Shen et al, 2011;Xiao et al, 2014). The soil pH was neutral in the experimental soils, ranging from 7.12 to 7.37 (Table S1), providing a suitable soil environment for Nitrosopira, especially Nitrosopira cluster 3 (Stephen et al, 1996;Zhang et al, 2018). In addition, the soil NH 4 + content of N-treatments was significantly improved compared to the control treatment, differing from 3.33 mg kg −1 (N0P0) to 28.07 mg kg −1 (N2P3), providing more energy for NH 3 oxidization (Table S1).…”

Section: Integrated Responses Of Ammoniaoxidizer-soil-plant Systemssupporting

confidence: 90%

“…Our findings showed that pH was an important edaphic factor constructing the AOB community (Figure 3). In the soil/sediment interface and in the sediments of two coastal bays, Zhang et al (2018) also found that pH was the key factor determining the abundance of AOB and Nitrosopira preferred in neutral soils surroundings. Taken together, the fact that Nitrosopira were dominant highlighted that neutral pH and higher NH 4 + concentrations promoted the activity of AOB in this steppe grassland.…”

Section: Integrated Responses Of Ammoniaoxidizer-soil-plant Systemsmentioning

confidence: 86%

See 1 more Smart Citation

Responses of ammonia‐oxidizing archaea and bacteria to nitrogen and phosphorus amendments in an alpine steppe

Dong

Che

Jia³

et al. 2019

European J Soil Science

View full text Add to dashboard Cite

With the increasing demands of livestock production, grasslands are under pressure from over‐intensified grazing. Phosphorus (P) and nitrogen (N) fertilization is widely employed to meet the nutrient demands of heavy grazing. Although soil ammonia‐oxidizers play a critical role in determining N dynamics after fertilizer application, their responses to fertilization are still not well understood in steppe grassland systems. Here, the individual and combined effects of N (0, 7.5 and 15 g N m−2 year−1) and P (0, 3.27, 6.55 and 13.09 g P m−2 year−1) applications on soil ammonia‐oxidizers were explored in the Tibetan alpine steppe. Ammonia‐oxidizing archaea (AOA) and bacteria (AOB) abundance and community composition were examined using qPCR, terminal restriction fragment length polymorphism and clone libraries. Results showed that AOB diversity was significantly increased by N fertilization and decreased by P fertilization. The abundance of AOB was significantly increased by N fertilization and its interactive effects with P application. In contrast, AOA community diversity and abundance remained unaffected by either N or P application. The AOB abundance and diversity were affected by the direct effects of N fertilization, as well as its indirect effects of N application through available N and ammonium (NH4+), and further analysis showed that NH4+ and pH were the main factors. The changes to the ammonia‐oxidizing community altered the total N content of plants and the N:P ratio of Gramineae. Plant P properties were influenced by P addition, which also interacted with soil pH and available N to indirectly affect AOB. Overall, AOB exhibited stronger responses to N and P fertilization of alpine steppe grassland than AOA, and appear to play a critical role in plant nutrient absorption under fertilization management. Highlights Effects of N and P application on AOA and AOB communities were evaluated. AOB, not AOA, responded to N or P, and their interaction, and NH4+ and pH were regulators of AOB. N application affected AOB community, resulting in changes to plant nutrient absorption. P addition affected plant tissue stoichiometry, and thus affected AOB community.

show abstract

Section: Integrated Responses Of Ammoniaoxidizer-soil-plant Systemssupporting

confidence: 90%

Section: Integrated Responses Of Ammoniaoxidizer-soil-plant Systemsmentioning

confidence: 86%

Responses of ammonia‐oxidizing archaea and bacteria to nitrogen and phosphorus amendments in an alpine steppe

Dong

Che

Jia³

et al. 2019

European J Soil Science

View full text Add to dashboard Cite

show abstract

“…Surface mud samples (0 to 2 cm) were collected on 11 January 2017 from Rusheen Bay, Ireland (53.2589° N, 9.1203° W) (presence of amoA genes/transcripts previously established (Duff et al ., ; Zhang et al ., ) in sterile 50 ml Eppendorf tubes, flash frozen and stored at −80°C until subsequent use.…”

Section: Methodsmentioning

confidence: 99%

Differential ratio amplicons (R_amp) for the evaluation of RNA integrity extracted from complex environmental samples

Cholet

Ijaz

Smith

2019

Environmental Microbiology

Self Cite

View full text Add to dashboard Cite

Summary Reliability and reproducibility of transcriptomics‐based studies are dependent on RNA integrity. In microbial ecology, microfluidics‐based techniques, such as the Ribosomal Integrity Number (RIN), targeting rRNA are currently the only approaches to evaluate RNA integrity. However, the relationship between rRNA and mRNA integrity is unknown. Here, we present an integrity index, the Ratio Amplicon, R amp , adapted from human clinical studies, to directly monitor mRNA integrity from complex environmental samples. We show, in a suite of experimental degradations of RNA extracted from sediment, that while the RIN generally reflected the degradation status of RNA the R amp mapped mRNA degradation better. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of 16S rRNA , amoA and glnA transcripts. We successfully sequenced transcripts for all three targets even from highly‐degraded RNA samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed for the 16S rRNA transcript profiles. Since both RT‐Q‐PCR and sequencing results were obtained, even from highly degraded samples, we strongly recommend evaluating RNA integrity prior to downstream processing to ensure meaningful results. For this, both the RIN and R amp are useful, with the R amp better evaluating mRNA integrity in this study.

show abstract

“…Surface mud samples (0 to 2 cm) were collected on 11/01/2017 from Rusheen Bay, Ireland (53.2589° N, 9.1203° W) (presence of amoA genes/transcripts previously established [30, 31] in sterile 50ml Eppendorf tubes, flash frozen and stored at -80°C until subsequent use.…”

Section: Methodsmentioning

confidence: 99%

Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples

Cholet

Ijaz

Smith

2018

Preprint

Self Cite

View full text Add to dashboard Cite

26Background 27 Reliability and reproducibility of transcriptomics-based studies are highly dependent on the 28 integrity of RNA. Microfluidics-based techniques based on ribosomal RNA such as the RNA 29 Integrity Number (RIN) are currently the only approaches to evaluate RNA integrity. 30 However, it is not known if ribosomal RNA reflects the integrity of the meaningful part of the 31 sample, the mRNA. Here we test this assumption and present a new integrity index, the Ratio 32 amplicon, R amp , to monitor mRNA integrity based on the differential amplification of long to 33 short RT-Q-PCR amplicons of the glutamine synthetase A (glnA) transcript. 34Results 35 We successfully designed and tested two R amp indexes targeting glnA transcripts. We showed 36 in a suite of experimental degradations of RNA extracted from sediment that while the RIN in 37 general did reflect the degradation status of the RNA well the R amp mapped mRNA 38 degradation better as reflected by changes in Reverse Transcriptase Quantitative PCR (RT-Q-39 PCR) results. Furthermore, we examined the effect of degradation on transcript community 40 structure by amplicon sequencing of the 16S rRNA, amoA and glnA transcript which was 41 successful even form the highly-degraded samples. While RNA degradation changed the 42 community structure of the mRNA profiles, no changes were observed between successively 43 degraded 16S rRNA transcripts profiles. 44 Conclusion 45As demonstrated, transcripts can be quantified and sequenced even from highly degraded 46 samples. Therefore, we strongly recommend that a quality check of RNA is conducted to 47 ensure validity of results. For this both the RIN and R amp are useful, with the R amp better 48 evaluating mRNA integrity in this study. 49 50 3 51 52Background 53 A key question in environmental microbiology is to determine the functioning and activity of 54 microbial communities. While genomic approaches have resulted in an unprecedented 55 understanding of their structure and complexity [1], they do not inform of the actual activity 56 and functioning at a given time. In this case targeting the transcriptome, that is the subset of 57 genes that are actively transcribed at a given time, is more informative. While there can be 58 substantial post translational regulation that may prevent final protein synthesis and/or 59 activity, gene expression is the direct link between the genome and the function it encodes 60 and therefore is a stronger link to activity than DNA approaches alone [2]. As a result 61 transcriptomics based approaches are widely used to assess microbial activity and functioning 62 in the environment [3, 4]. The premise is that that messenger RNA (mRNA) turn-over within 63 cells is rapid, ranging from a few minutes to less than an hour [5]. As such a snap-shot of the 64 transcriptome reflects the cells transcriptional response to its surrounding environment and 65 metabolic needs at a given time. 66A challenge for all transcript-based studies, not least for those from environmental...

show abstract

Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems

Cited by 42 publications

References 81 publications

Responses of ammonia‐oxidizing archaea and bacteria to nitrogen and phosphorus amendments in an alpine steppe

Responses of ammonia‐oxidizing archaea and bacteria to nitrogen and phosphorus amendments in an alpine steppe

Differential ratio amplicons (R_amp) for the evaluation of RNA integrity extracted from complex environmental samples

Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples

Contact Info

Product

Resources

About

Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems

Cited by 42 publications

References 81 publications

Responses of ammonia‐oxidizing archaea and bacteria to nitrogen and phosphorus amendments in an alpine steppe

Responses of ammonia‐oxidizing archaea and bacteria to nitrogen and phosphorus amendments in an alpine steppe

Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples

Differential amplicons for the evaluation of RNA integrity extracted from complex environmental samples

Contact Info

Product

Resources

About

Differential ratio amplicons (R_amp) for the evaluation of RNA integrity extracted from complex environmental samples