Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems.

Juan Ling,Siquan Zeng,Weiguo Zhou,Xiancheng Lin,Lijuan Long,Manzoor Ahmad,Junde Dong,Yanying Zhang,Cong Wang,Qingsong Yang,Ying Zhang,Liyun Lin

doi:10.3389/fmicb.2018.00007

Abstract

Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA) and bacteria (AOB), yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA) were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR) assays, targeting the ammonia monooxygenase-subunit (amoA) genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root) at the DNA level (P < 0.05). Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle, particularly nitrification of seagrass meadows in coral reef ecosystems.

Highlights

Many investigations into the effect of ocean acidification (OA) on coral reefs have been conducted (Andersson and Gledhill, 2013), and results indicate that that marine organisms which inhabit the carbonate structures of coral reefs are important and sensitive to OA (Larkum et al, 2006). Albright et al (2016) and Lough (2016) found that changes to pH in the seawater surrounding natural coral reefs in the southern Great Barrier Reef can significantly affect calcification rates, suggesting that OA may already be altering the growth of coral reefs
The first and rate-limiting step of nitrification is performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), both of which are ammonia oxidizers and responsible for converting ammonia to nitrite
The highest Dissolved oxygen (DO) concentration was recorded at AT, and the lowest at site SYT

Summary

Introduction

Many investigations into the effect of ocean acidification (OA) on coral reefs have been conducted (Andersson and Gledhill, 2013), and results indicate that that marine organisms which inhabit the carbonate structures of coral reefs are important and sensitive to OA (Larkum et al, 2006). Albright et al (2016) and Lough (2016) found that changes to pH in the seawater surrounding natural coral reefs in the southern Great Barrier Reef can significantly affect calcification rates, suggesting that OA may already be altering the growth of coral reefs. Seagrass is highly productive and of great ecological importance in the marine environment. It can provide food, nursery and breeding habitats for other marine organisms inhabiting the ecosystem and nutrients for coral reefs. The first and rate-limiting step of nitrification is performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), both of which are ammonia oxidizers and responsible for converting ammonia to nitrite. These microbes have different phylogenetic and physiological features, resulting in significant variations in their abundance, diversity and activity under different environmental conditions. The relative contribution of AOA and AOB to ammonia oxidation is still in debate

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Conclusion