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Variation of bacterial community associated with Phaeodactylum tricornutum in response to different inorganic nitrogen concentrations
SHI Feng, WEI Xiaoxue, FENG Jianfeng, SUN Yingxue, ZHU Lin
2018, 37(12): 118-128. doi: 10.1007/s13131-018-1272-7
Keywords: Phaeodactylum tricornutum, nitrogen concentrations, nitrogen forms, bacterial diversity, community structure, Gammaproteobacteria
Specific bacterial communities interact with phytoplankton in laboratory algal cultures. These communities influence phytoplankton physiology and metabolism by transforming and exchanging phytoplankton-derived organic matter. Functional bacterial groups may participate in various critical nutrients fluxes within these associations, including nitrogen (N) metabolism. However, it is unclear how bacterial communities and the associated algae respond to changes of phycosphere N conditions. This response may have far-reaching implications for global nutrient cycling, algal bloom formation, and ecosystem function. Here, we identified changes in the bacterial communities associated with Phaeodactylum tricornutum when co-cultured with different forms and concentrations of N based on the Illumina HiSeq sequencing of 16S rRNA amplicons. Phylogenetic analysis identified Proteobacteria and Bacteroidetes as the dominant phyla, accounting for 99.5% of all sequences. Importantly, bacterial abundance and community structure were more affected by algal abundance than by the form or concentration of inorganic N. The relative abundance of three gammaproteobacterial genera (Marinobacter, Algiphilus and Methylophaga) markedly increased in N-deficient cultures. Thus, some bacterial groups may play a role in the regulation of N metabolism when co-cultured with P. tricornutum.
The complete genome of hydrocarbon-degrading Pseudoal-teromonas sp. NJ289 and its phylogenetic relationship
LIU Fangming, WANG Yibin, QU Changfeng, ZHENG Zhou, MIAO Jinlai, XU Hua, XIAO Tian
2017, 36(2): 88-93. doi: 10.1007/s13131-017-0979-1
Keywords: Pseudoalteromonas, low temperature, environmental adaptability, sequencing, phylogenetic tree
Genus Pseudoalteromonas belongs to Family Pseudoalteromonadaceae in Gammaproteobacteria. A cold-adapted gram-negative bacterium, hydrocarbon-degrading Pseudoalteromonas sp. NJ289, was isolated from sea-ice of the Antarctica region, and sequenced the whole genome through the next generation sequencing platform. The assembly yielded three contigs representing two chromosomes and one plasmid with the sizes of 3.2 Mb, 636 kb and 1.8 kb, respectively. The G+C contents of genome were 40.83% and included 3 589 ORFs. Functional annotation indicated some potential roles in enzymatic activity and environmental adaptability. This study may help for understanding the population diverse, evolutionary ecology and the microbial interaction.
Phylogenetic diversity of planktonic bacteria in the Chukchi Borderland region in summer
ZENG Yinxin, YU Yong, LI Huirong, HE Jianfeng, LEE Sang H, SUN Kun
2013, 32(6): 66-74. doi: 10.1007/s13131-013-0271-y
Keywords: diversity, planktonic bacteria, 16S rRNA gene clone library, Chukchi Borderland
Planktonic bacteria are abundant in the Chukchi Borderland region. However, little is known about their diversity and the roles of various bacteria in the ocean. Seawater samples were collected from two stations K2S and K4S where sea ice was melting obviously. The analysis of water samples with fluorescence in situ hybridization (FISH) showed that DMSP-degrading bacteria accounted for 13% of the total bacteria at the station K2S. No aerobic anoxygenic phototrophic (AAP) bacteria were detected in both samples. The bacterial communities were characterized by two 16S rRNA gene clone libraries. Sequences fell into four major lineages of the domain Bacteria, including Proteobacteria (Alpha, Beta and Gamma subclasses), Bacteroidetes, Actinobacteria and Firmicutes. No significant difference was found between the two clone libraries. SAR11 and Rhodobacteraceae clades of Alphaproteobacteria and Pseudoalteromonas of Gammaproteobacteria constituted three dominant fractions in the clone libraries. A total of 191 heterotrophic bacterial strains were isolated and 76% showed extracellular proteolytic activity. Phylogenetic analysis reveals that the isolates fell into Gammaproteobacteria,Bacteroidetes, Actinobacteria and Firmicutes. The most common genus in both the bacterial isolates and protease-producing bacteria was Pseudoalteromonas. UniFrac data showed suggestive differences in bacterial communities between the Chukchi Borderland and the northern Bering Sea.
Microbial community structure of Arctic seawater as revealed by pyrosequencing
LI Yang, WANG Zhen, LIN Xuezheng
2016, 35(6): 78-84. doi: 10.1007/s13131-015-0742-4
Keywords: Arctic seawater, pyrosequencing, microbial community
This study aimed to determine the microbial community structure of seawater in (ICE-1) and out (FUBIAO) of the pack ice zone in the Arctic region. Approximate 10 L seawater was filtrated by 0.2 μm Whatman nuclepore filters and the environmental genomic DNA was extracted. We conducted a detailed census of microbial communities by pyrosequencing. Analysis of the microbial community structures indicated that these two samples had high bacterial, archaeal and eukaryotic diversity. Proteobacteria and Bacteroidetes were the two dominant members of the bacterioplankton community in both samples, and their relative abundance were 51.29% and 35.39%, 72.95% and 23.21%, respectively. Euryarchaeota was the most abundant archaeal phylum, and the relative abundance was nearly up to 100% in FUBIAO and 60% in ICE-1. As for the eukaryotes, no_rank_Eukaryota, Arthropoda and no_rank_Metazoa were the most abundant groups in Sample FUBIAO, accounting for 85.29% of the total reads. The relative abundance of the most abundant phylum in Sample ICE-1, no_rank_Eukaryota and no_rank_Metazoa, was up to 90.69% of the total reads. Alphaproteobacteria, Flavobacteria and Gammaproteobacteria were the top three abundant classes in the two samples at the bacterial class level. There were also differences in the top ten abundant bacterial, archaeal and eukaryotic OTUs at the level of 97% similarity between the two samples.
Microbial community structure and nitrogenase gene diversity of sediment from a deep-sea hydrothermal vent field on the Southwest Indian Ridge
Wu Yuehong, Cao Yi, Wang Chunsheng, Wu Min, Aharon Oren, Xu Xuewei
2014, 33(10): 94-104. doi: 10.1007/s13131-014-0544-0
Keywords: deep-sea, hydrothermal vent, microbial diversity, 16S rRNA gene, nifH gene
A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase chain reaction (PCR) amplification of the 16S rRNA and nifH genes. Within the Archaea, the dominant clones were from marine benthic group E (MBGE) and marine group I (MGI) belonging to the phyla Euryarchaeota and Thaumarchaeota, respectively. More than half of the bacterial clones belonged to the Proteobacteria, and most fell within the Gammaproteobacteria. No epsilon Proteobacterial sequence was observed. Additional phyla were detected including the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3 and TM6, confirming their existence in hydrothermal vent environments. The detection of nifH gene suggests that biological nitrogen fixation may occur in the hydrothermal vent field of the Southwest Indian Ridge. Phylogenetic analysis indicated that only Clusters I and III nifH were present. This is consistent with the phylogenetic analysis of the microbial 16S rRNA genes, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.
Isolation, characterization and implications of the bacterial communities associated with established cultures of Chattonella marina (Raphidophyceae) and Skeletonema costatum (Bacillariophyceae)
WANG Jian, WANG Zhaohui, ZHAO Jiangang
2019, 38(1): 128-135. doi: 10.1007/s13131-019-1379-5
Keywords: phycosphere, marine bacteria, Chattonella marina, Skeletonema costatum, Chaetoceros curvisetus, algal growth
Cultivable bacteria coexisting in the cultures of two microalgal species, Chattonella marina (Raphidophyceae) and Skeletonema costatum (diatom, Bacillariophyceae), which have been maintained in the laboratory for several years, were examined in this study. Forty-eight and thirty-four cultivable bacterial strains were isolated from different growth stages of C. marina and S. costatum cultures, respectively. A total of twelve unique bacterial phylotypes were isolated. These bacterial phylotypes belonged to Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Actinobacteria. Alphaproteobacteria predominated in phycospheres of both microalgae, and Rhodobacteraceae was the most common family. Bacterial phylotypes were more diversified in cultures of S. costatum than in those of C. marina. Bacterial concentrations increased remarkably after the late stationary phase of C. marina, which might account for the decline in algal cells. One phylotype of S. costatum-associated bacteria had inhibitory effects on Chaetoceros curvisetus (Bacillariophyceae). However, most bacterial phylotypes from cultures of C. marina showed significant inhibition of the growth of C. curvisetus. The results suggested that bacteria associated with C. marina might have some ecological roles in its competition with diatoms.
Family-level diversity of extracellular proteases of sedimentary bacteria from the South China Sea
Yang Jinyu, Feng Yangyang, Chen Xiulan, Xie Binbin, Zhang Yuzhong, Shi Mei, Zhang Xiying
2019, 38(12): 73-83. doi: 10.1007/s13131-019-1391-9
Keywords: protease-producing bacteria, diversity, extracellular proteases, protease families, N-terminal amino acid sequencing, South China Sea
Protease-producing bacteria and their extracellular proteases are key players in degrading organic nitrogen to drive marine nitrogen cycling and yet knowledge on both of them is still very limited. This study screened protease-producing bacteria from the South China Sea sediments and analyzed the diversity of their extracellular proteases at the family level through N-terminal amino acid sequencing. Results of the 16S rRNA gene sequence analysis showed that all screened protease-producing bacteria belonged to the class Gammaproteobacteria and most of them were affiliated with different genera within the orders Alteromonadales and Vibrionales. The N-terminal amino acid sequence analysis for fourteen extracellular proteases from fourteen screened bacterial strains revealed that all these proteases belonged to the M4 family of metalloproteases or the S8 family of serine proteases. This study presents new details on taxa of marine sedimentary protease-producing bacteria and types of their extracellular proteases, which will help to comprehensively understand the process and mechanism of the microbial enzymatic degradation of marine sedimentary organic nitrogen.
Diversity and distribution of bacterioplankton in the coastal upwelling waters off Hainan Island, China
Fahui Gong, Qixing Ji, Guihao Li, Kedong Yin, Jun Gong
2022, 41(3): 76-85. doi: 10.1007/s13131-021-1807-1  Published:2022-03-01
Keywords: 16S rRNA, bacterioplankton, coastal upwelling, Hainan Island
The diversity, community composition and 16S rRNA gene abundance of bacterioplankton along a transect across an upwelling area off the eastern coast of Hainan Island (the Qiongdong upwelling) were investigated in August of 2016 using high throughput sequencing and quantitative PCR assay of 16S rRNA genes. Compared with the offshore stations, the inner-shelf stations had higher bacterial gene abundance (up to 3 fold) and operational taxonomic unit richness, a result of the influence of upwelled and fresher waters. Overall, a majority of the reads were affiliated with Gammaproteobacteria (11%74%) and Alphaproteobacteria (14%43%). The structure of the bacterial community was significantly affected by salinity, dissolved oxygen, ${\rm{NO}}_3^-$ and ${\rm{NH}}_4^+ $, which also defined the physicochemical features of the upwelled waters. Horizontally, the relative abundances and gene abundances of Rhodobacteraceae, SAR86, Cyanobacteria and Bacteroidetes in eutrophic zone decreased from the inner to outer shelves and slope, whereas Alteromonas, Vibrio and Oceanospirillaceae exhibited an opposite trend. This study stresses the riverine influence on the oceanographic condition and spatial variability of bacterioplankton diversity and distribution in the Qiongdong upwelling.
Characterization of uncultivated magnetotactic bacteria from the sediments of Yuehu Lake, China
DU Haijian, ZHANG Rui, ZHANG Wenyan, XU Cong, CHEN Yiran, PAN Hongmiao, ZHOU Ke, WU Long-fei, XIAO Tian
2017, 36(2): 94-104. doi: 10.1007/s13131-017-0980-8
Keywords: magnetotactic bacteria, magnetosome, biodiversity, Yuehu Lake, intertidal sediments
Marine magnetotactic bacteria were collected from the intertidal sediments of Yuehu Lake (China), where their abundance reached 103-104 ind./cm3. Diverse morphotypes of magnetotactic bacteria were observed, including cocci and oval, vibrio-, spirillum-, rod-, elliptical-, handle- and bar-shaped forms. The magnetococci were the most abundant, and had flagella arranged in parallel within a bundle. The majority of magnetosomes were arranged in one, two or multiple chains, although irregular arrangements were also evident. All the results of high-resolution transmission electron microscopy (HRTEM) analysis show that magnetosome crystals were composed of Fe3O4, and their morphology was specific to particular cell morphotypes. By the 16S rRNA gene sequence analysis, we found fourteen operational taxonomic units (OTUs) which were related to magnetotactic bacteria. Among these, thirteen belonged to the Alphaproteobacteria and one to the Gammaproteobacteria. Compared with known axenic and uncultured marine magnetotactic bacteria, the 16S rRNA gene sequences of most magnetotactic bacteria collected from the Yuehu Lake exhibited sequence identities ranging from 90.1% to 96.2% (<97%). The results indicate that microbial communities containing previously unidentified magnetotactic bacteria occur in the Yuehu Lake.
Geochemical and microbial characters of sediment from the gas hydrate area in the Taixinan Basin, South China Sea
GONG Junli, SUN Xiaoming, LIN Zhiyong, LU Hongfeng, LU Yongjun
2017, 36(9): 52-64. doi: 10.1007/s13131-017-1111-2
Keywords: Geochemistry, Microbial community, 16S rRNA, Gas hydrate, Taixinan Basin, South China Sea
The Taixinan Basin is one of the most potential gas hydrate bearing areas in the South China Sea and abundant gas hydrates have been discovered during expedition in 2013. In this study, geochemical and microbial methods are combinedly used to characterize the sediments from a shallow piston Core DH_CL_11 (gas hydrate free) and a gas hydrate-bearing drilling Core GMGS2-16 in this basin. Geochemical analyses indicate that anaerobic oxidation of methane (AOM) which is speculated to be linked to the ongoing gas hydrate dissociation is taking place in Core DH_CL_11 at deep. For Core GMGS2-16, AOM related to past episodes of methane seepage are suggested to dominate during its diagenetic process; while the relatively enriched δ18O bulk-sediment values indicate that methane involved in AOM might be released from the "episodic dissociation" of gas hydrate. Microbial analyses indicate that the predominant phyla in the bacterial communities are Firmicutes and Proteobacteria (Gammaproteobacteria and Epsilonproteobacteria), while the dominant taxa in the archaeal communities are Marine_Benthic_Group_B (MBGB), Halobacteria, Thermoplasmata, Methanobacteria, Methanomicrobia, Group C3 and MCG. Under parallel experimental operations, comparable dominant members (Firmicutes and MBGB) are found in the piston Core DH_CL_11 and the near surface layer of the long drilling Core GMGS2-16. Moreover, these members have been found predominant in other known gas hydrate bearing cores, and the dominant of MBGB has even been found significantly related to gas hydrate occurrence. Therefore, a high possibility for the existing of gas hydrate underlying Core DH_CL_11 is inferred, which is consistent with the geochemical analyses. In all, combined geochemical and microbiological analyses are more informative in characterizing sediments from gas hydrate-associated areas in the South China Sea.