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Phylogenetic diversity and ecological niche of ammonia-oxidizing microorganisms 원문보기

  • 저자

    Hong, Jin Kyung

  • 학위수여기관

    HANKUK UNIVERSITY OF FOREIGN STUDIES. GRADUATE SCHOOL

  • 학위구분

    국내박사

  • 학과

    환경학과

  • 지도교수

    Cho, Jae Chang

  • 발행년도

    2014

  • 총페이지

    241 p

  • 키워드

  • 언어

    eng

  • 원문 URL

    http://www.riss.kr/link?id=T13539060&outLink=K  

  • 초록

    Phylogenetic diversity and ecological niche of ammonia-oxidizing microorganisms Chapter-II We observed that Planctomycetes-related sequences deposited in public database formed three monophyletic clusters, each with a group of environmental clones (EC), a group of anammox bacteria (AN), and a group of cultured members of the phylum Planctomycetes (CP). Former two groups, EC and AN, were distinct lineages from the group CP. The inter-group sequence dissimilarity between these three clades was more significant than previously implied by the phylum-level divergence, and each clade was reproducibly monophyletic, suggesting a phylum-level polyphyly of the phylum Planctomycetes. Chapter-III We investigated the phylogenetic diversity of ammonia-oxidizing bacteria (AOB) in Yellow Sea continental shelf sediment by cloning and sequencing of PCR-amplified amoA and 16S rRNA genes. Phylogenetic analysis of the amoA-related clones revealed that the diversity of AOB was extremely low at the study site. The majority (92.7%) of amoA clones obtained belonged to a single cluster, environmental amoA cluster-3, the taxonomic position of which was previously unknown. Phylogenetic analysis on AOB-specific 16S rRNA gene sequences also demonstrated a very low diversity. All of the cloned 16S rRNA gene sequences comprised a single phylotype that belonged to the members of uncultured Nitrosospira cluster-1, suggesting that AOB belonging to the uncultured Nitrosospira cluster-1 could carry amoA sequences of environmental amoA cluster-3. Chapter-IV Based on comparative phylogenetic analysis of 16S rRNA gene sequences deposited in an RDP database, we constructed a local database of thaumarchaeotal 16S rRNA gene sequences and developed a novel PCR primer specific for the archaeal phylum Thaumarchaeota. Among 9,727 quality-filtered (chimeral-checked, size > 1.2 kb) archaeal sequences downloaded from the RDP database, 1,549 thaumarchaeotal sequences were identified and included in our local database. In our study, Thaumarchaeota included archaeal groups MG-I, SAGMCG-I, SCG, FSCG, RC, and HWCG-III, forming a monophyletic group in the phylogenetic tree. Cluster analysis revealed 114 phylotypes for Thaumarchaeota. The majority of the phylotypes (66.7%) belonged to the MG-I and SCG, which together contained most (93.9%) of the thaumarchaeotal sequences in our local database. A phylum-directed primer was designed from a consensus sequence of the phylotype sequences, and the primer's specificity was evaluated for coverage and tolerance both in silico and empirically. The phylum-directed primer, designated THAUM-494, showed >90% coverage for Thaumarchaeota and 95% of the amplified sequences belonged to Thaumarchaeota. The most frequently sampled thaumarchaeotal subgroups in our samples were SCG, MG-I, and SAGMCG-I. To our knowledge, THAUM-494 is the first phylum-level primer for Thaumarchaeota. Furthermore, the high coverage and low tolerance of THAUM-494 will make it a potentially valuable tool in understanding the phylogenetic diversity and ecological niche of Thaumarchaeota. Chapter-V In order to find environmental variables shaping the ecological niche of archaeal phylum Thaumarchaeota in terrestrial environments, we determined the abundance of Thaumarchaeota in various soil samples using real-time PCR targeting 16S rRNA gene sequences. We employed our newly developed primer, THAUM-494, which had higher coverage for Thaumarchaeota and lower tolerance to non-thaumarchaeotal taxa than previous primers. The abundance estimates of Thaumarchaeota were compared with those of Archaea and Bacteria, and the relative abundance estimates (RVs) of Thaumarchaeota (RTHAUM), Archaea (RARCH), and Bacteria (RBACT) were subjected to multivariate statistical analyses. Environmental variables (EVs) included in a series of statistical analyses were soil water content (WC), temperature, pH, and contents of total carbon (TC), total nitrogen (TN), ammonium-nitrogen (NH4+-N), nitrate-nitrogen (NO3--N), total phosphorus (TP), and total sulfur (TS). The copy numbers of thaumarchaeotal 16S rRNA gene sequences ranged from 3.5 ⨉ 104 to 1.8 ⨉ 107 per gram dry soil. Thaumarchaeota comprised 0.1-4.8% (average, 1.4%) of total prokaryotes and was a dominant (average, 58.2%) member of soil Archaea. Redundancy analysis (RDA) showed that a significant (p


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