Abstract
Ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) oxidize ammonia to nitrite, and therefore play essential roles in nitrification and global nitrogen cycling. To better understand the population structure and the distribution of AOA and AOB in the deep Eastern Indian Ocean (EIO), nine surface sediment samples (>3,300 m depth) were collected during the inter-monsoon Spring 2013. One sediment sample from the South China Sea (SCS; 2,510 m) was also included for comparison. The community composition, species richness, and diversity were characterized by clone libraries (total 1,238 clones), and higher diversity of archaeal amoA genes than bacterial amoA genes was observed in all analyzed samples. Real time qPCR analysis also demonstrated higher abundances (gene copy numbers) of archaeal amoA genes than bacterial amoA genes, and the ratios of AOA/AOB ranged from 1.42 to 8.49 among sites. In addition, unique and distinct clades were found in both reconstructed AOA and AOB phylogeny, suggesting the presence of niche-specific ammonia-oxidizing microorganisms in the EIO. The distribution pattern of both archaeal and bacterial amoA genes revealed by NMDS (non-metric multidimensional scaling) showed a distinct geographic separation of the sample from the SCS and most of the samples from the EIO following nitrogen gradients. Higher abundance and diversity of archaeal amoA genes indicated that AOA may play a more important role than AOB in the deep Indian Ocean. Environmental parameters shaping the distribution pattern of AOA were different from that of AOB, indicating distinct metabolic characteristics and/or adaptation mechanisms between AOA and AOB in the EIO, especially in deep-sea environments.
Highlights
Nitrification is an integrative component in the nitrogen cycle, which includes oxidization of ammonia to nitrite by ammoniaoxidizing Bacteria (AOB) and ammonia-oxidizing Archaea (AOA), and nitrite is further oxidized to nitrate by nitriteoxidizing Bacteria (NOB)
The highest concentration of [NO−2 + NO−3 ] reached 0.0045 mg/L in sample I207, which was located at the Bay of Bengal (BOB), while the lowest concentration of [NO−2 + NO−3 ] was 0.002 mg/L in samples I704 and I503, which was close to the equator and the Eastern Boundary of the Eastern Indian Ocean (EIO)
It is characterized by extreme conditions including high pressure, low temperature, lack of light etc., and it harbors taxonomically and metabolically diverse microorganisms (D’Hondt et al, 2004; Inagaki et al, 2006; Kallmeyer et al, 2012)
Summary
Nitrification is an integrative component in the nitrogen cycle, which includes oxidization of ammonia to nitrite by ammoniaoxidizing Bacteria (AOB) and ammonia-oxidizing Archaea (AOA), and nitrite is further oxidized to nitrate by nitriteoxidizing Bacteria (NOB). The chemolithotrophic AOB are placed taxonomically in the beta- and the gamma-subdivision of Proteobacteria, and their natural population/distribution has been widely investigated by molecular tools, such as using the 16S rRNA gene sequences (Stephen et al, 1996, 1998; Kowalchuk et al, 2000) and the genes encoding ammonia monooxygenase (amoA; Bothe et al, 2000; Purkhold et al, 2000). In order to better understand their roles in global nitrogen cycling, it is critical to characterize the abundance, diversity, and distribution of AOA and AOB in natural environments
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