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

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.

Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites

“…The identified Thaumarchaeota were mainly composed of Group C3, Marine Group I (formerly referred to as Marine Group 1.1a), and Soil Crenarchaeotic Group (formerly Marine Group 1.1b) in this study (). The last two classes are important ammonium-oxidizing archaea (AOA) [51], which presented much lower proportions in vegetated sediments that could be linked to lower NH 4 + concentrations in the sediments [10, 52]. The high affinity of seagrass roots for NH 4 + may allow seagrasses to outcompete sediment AOA for NH 4 + [53].…”

The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator

“…The main microbial groups found associated with the belowground seagrass compartment are those involved in the sulfur and/or nitrogen cycles [26,28,29,32,89,91,95,[97][98][99]180], like Gamma-, Alpha-, Delta-and Epsilon-Proteobacteria. Members of these classes are able to produce antimicrobial compounds, such as those belonging to the Vibrionaceae family (Gammaproteobacteria) [181] or Actinobacteriaceae (Gammaproteobacteria) [112,182] and may potentially affect the microbial community compositions [31,112].…”

Spatial and Species Variations of Bacterial Community Structure and Putative Function in Seagrass Rhizosphere Sediment

“…Samples of seagrass rhizosphere sediment were collected in triplicate for each sample, and 24 samples in total were obtained. Sediment collection and physic-chemical property measurements were performed, according to Ling et al [ 23 ]. Environmental parameters, e.g., pH, salinity, and DO, were simultaneously measured in situ.…”

“…However, there was rare information about the taxonomic and phylogenetic composition in the coral reef ecosystems’ seagrass rhizosphere [ 23 ]. Therefore, we conducted this study to answer the following questions in the coral reef ecosystem: (1) are there significant spatial and species variations in the diversity and composition in the seagrass rhizosphere bacterial communities?…”