Current Articles

Research Paper
Reconsideration of the taxonomy of the marine ciliate Neobakuella aenigmatica Moon et al., 2019 (Protozoa, Ciliophora, Hypotrichia)
Tengyue Zhang, Jingyi Dong, Ting Cheng, Lili Duan, Chen Shao
2020, 2(2): 97-108. doi: 10.1007/s42995-020-00032-4
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Abstract:
The morphology and divisional morphogenesis in a Chinese population of Neobakuella aenigmatica Moon et al., 2019 are reinvestigated. The body size, number and arrangement of parabuccal cirri and development of nuclear nodules in this population are discussed in comparison with closely related genera. The 18S rRNA gene sequence of the Chinese population is identical to that of a Korean population, supporting a distant relationship between N. aenigmatica and the cluster of N. flava and Apobakuella fusca. We deduce that this may be caused by the differences in the pattern of the parabuccal cirri and the number of parabuccal rows which are important for the phylogeny of Bakuella-like species.
Functional analysis of the methyltransferase SMYD in the single-cell model organism Tetrahymena thermophila
Xiaolu Zhao, Yuan Li, Lili Duan, Xiao Chen, Fengbiao Mao, Mina Juma, Yifan Liu, Weibo Song, Shan Gao
2020, 2(2): 109-122. doi: 10.1007/s42995-019-00025-y
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Abstract:
Lysine methylation of histones and non-histones plays a pivotal role in diverse cellular processes. The SMYD (SET and MYND domain) family methyltransferases can methylate various histone and non-histone substrates in mammalian systems, implicated in HSP90 methylation, myofilament organization, cancer inhibition, and gene transcription regulation. To resolve controversies concerning SMYD's substrates and functions, we studied SMYD1 (TTHERM_00578660), the only homologue of SMYD in the unicellular eukaryote Tetrahymena thermophila. We epitope-tagged SMYD1, and analyzed its localization and interactome. We also characterized ΔSMYD1 cells, focusing on the replication and transcription phenotype. Our results show that: (1) SMYD1 is present in both cytoplasm and transcriptionally active macronucleus and shuttles between cytoplasm and macronucleus, suggesting its potential association with both histone and non-histone substrates; (2) SMYD1 is involved in DNA replication and regulates transcription of metabolism-related genes; (3) HSP90 is a potential substrate for SMYD1 and it may regulate target selection of HSP90, leading to pleiotropic effects in both the cytoplasm and the nucleus.
High-resolution linkage and quantitative trait locus mapping using an interspecifc cross between Argopecten irradians irradians (♀) and A. purpuratus (♂)
Junxia Mao, Qifan Zeng, Zujing Yang, Haoyuan Pan, Lijie Yao, Zhenmin Bao, Chunde Wang, Shi Wang
2020, 2(2): 123-134. doi: 10.1007/s42995-020-00029-z
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Abstract:
The bay scallop and Peruvian scallop are economically important species. Interspecific hybrids of these two scallops outperformed both of their parent species in multiple growth traits but exhibited decreased fertility, which provides good models for the study of heterosis and species divergence. Genetic mapping serves as a chromosomal-level framework to investigate the molecular mechanisms of hybridization and introgression. In this study, high-resolution linkage maps were constructed for the bay and Peruvian scallops with an interspecific hybrid family. The linkage map of the bay scallop covered over 98.9% of the whole genome with 2994 mapped markers and the average marker interval of 0.32 cM. For the Peruvian scallop, 1585 markers were mapped with the average maker interval of 0.51 cM, covering 97.7% of the genome. Both the two linkage maps have 16 linkage groups, corresponding to the haploid chromosome number of the two species. Approximately, 54.5% of markers exhibited significant deviation from the expected Mendelian ratio of segregation, lending insights into the intrinsic incompatibility between the two species. QTLs related to growth and shell coloration were detected, which could explain 13.1% and 74.9% of the phenotypic variance, respectively. This represents important information for further evaluation. These findings are an important addition to the genomic resources for scallop genetic studies, and are especially useful for investigations on genomic incompatibility for hybridization, genome evolution of closely related species, and genetic enhancement programs in aquaculture.
Transcriptomic response to ammonia-N stress in the hepatopancreas of swimming crab Portunus trituberculatus
Lingjun Si, Luqing Pan, Hongdan Wang, Xin Zhang
2020, 2(2): 135-145. doi: 10.1007/s42995-020-00033-3
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Abstract:
The swimming crab Portunus trituberculatus is an important farmed species in China. Ammonia-N represents a major physiological challenge for crab culture and the hepatopancreas plays a major role in physiological adaptation processes. To better understand the molecular mechanism of the crab in response to ammonia-N stress,we performed a transcriptome analysis in the hepatopancreas of P. trituberculatus challenged with ammonia-N stress (5 mg/L),using the high-throughput sequencing technology. In total,52,280 unigenes were obtained from the hepatopancreas of P. trituberculatus,with an average length of 678 bp. Functional categorization and pathways showed some differentially expressed genes were involved in amino acid and nucleobase metabolism,energy metabolism,antioxidation,immune response,reproduction,moulting and material transport. The differential expression patterns of eight randomly selected annotated genes were validated by quantitative real-time PCR (qPCR). Results revealed a substantial number of genes modified by ammonia-N stress and a few significant ammonia acclimation pathways,which will serve as an invaluable resource for revealing the molecular basis of physiological adaptation mechanism in P. trituberculatus.
Effects of latitude gradient and seasonal variation on the community structure and biodiversity of commercially important crustaceans in the Yellow Sea and the northern East China Sea
Qiang Wu, Xiujuan Shan, Xianshi Jin, Yue Jin, Fangqun Dai, Yongqiang Shi, Lisha Gua, Tao Zuo, Jianqiang Sun
2020, 2(2): 146-154. doi: 10.1007/s42995-020-00026-2
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Abstract:
To evaluate the spatio-temporal variations in the community structure and biodiversity of commercially important crustaceans in the Yellow Sea and the northern East China Sea (NECS), the seasonal and regional changes in species composition, biomass structure, biodiversity and distribution of commercially important species were analyzed using bottom trawl survey data during 2014–2015. The results showed that the latitudinal gradient was obvious in species richness, dominant species and biodiversity. The indices of biodiversity increased with the decreasing latitude. When the sampling sites shifted south by one latitudinal degree, Margalef's richness index (D), Pielou's evenness index (J′) and Shannon–Wiener diversity index (H′) increased by 0.10, 0.03 and 0.09, respectively. The biomass proportion of the cold-temperate species represented by Crangon afnis declined with the decreasing latitude, and the warm-temperate species represented by Ovalipes punctatus and Portunus trituberculatus increased. Because of the growth regulation of crustaceans and the fshing moratorium, the biomass of commercially important crustaceans in the Yellow Sea and NECS was highest in October and August, respectively. Salinity had a more signifcant infuence on H′ of commercially important crustaceans than other environmental factors (including zooplankton density, sea bottom temperature and water depth). Overall, the results of this study contribute to a better understanding of community dynamics of crustaceans in the Yellow Sea and NECS, and provide evidence to verify the latitudinal gradient theory in biodiversity.
Three nitrogen-containing metabolites from an algicolous isolate of Trichoderma asperellum
Yinping Song, Fengping Miao, Xiuli Yin, Naiyun Ji
2020, 2(2): 155-160. doi: 10.1007/s42995-020-00030-6
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Abstract:
As one of the most productive species,Trichoderma asperellum,especially isolated from marine algae,has contributed a number of new terpenes and nitrogen-bearing compounds,encouraging our continuous efforts to further explore them. Consequently,three new nitrogen-containing secondary metabolites,including cyclo(L-5-MeO-Pro-L-5-MeO-Pro) (1),5′-acetoxy- deoxycyclonerin B (2),and 5′-acetoxy-deoxycyclonerin D (3) were isolated from the marine alga-derived endophytic fungus Trichoderma asperellum A-YMD-9-2. Their structures and relative configurations were fully elucidated through spectroscopic techniques,mainly including 1D/2D NMR and MS. The absolute configurations of 1 and 2 were ascertained on the basis of X-ray diffraction (Cu Kα radiation) and ECD data,respectively. The isolation of these new nitrogen-bearing compounds adds to the structural diversity of marine algicolous Trichoderma spp.,and they display potent inhibition against some marine phytoplankton species.
Bacteriostatic efect of lipopeptides from Bacillus subtilis N-2 on Pseudomonas putida using soybean meal by solid-state fermentation
Meng Li, Haijin Mou, Qing Kong, Tan Zhang, Xiaodan Fu
2020, 2(2): 172-180. doi: 10.1007/s42995-020-00028-0
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Abstract:
Bacillus subtilis N-2 which was isolated from natto, produced lipopeptides using soybean meal as a substrate. This work aimed to purify, identify, and determine the antibacterial mechanism of lipopeptides produced by B. subtilis N-2. The fermented product obtained by solid-state fermentation was subjected to water extraction, acid precipitation, and methanol extraction. Fractions were separated and collected using a two-step ultrafiltration method and then identified by LC–MS/MS. Mass spectrometry characterization revealed the presence of four variants of iturin A that differed according to the β-amino fatty acid chain from C14 to C17 as well as the amino acid positions. A new lipopeptide (m/z 1070.3) was identified and its structure was different from the previously reported lipopeptides. The lipopeptides were shown to inhibit the growth of an isolate of Pseudomonas putida, a common pathogen in decaying fish, by changing membrane permeability. These results suggest that the lipopeptides from B. subtilis N-2 could be used as a biocontrol agent in aquaculture.
Diversity of culturable heterotrophic bacteria from the Mariana Trench and their ability to degrade macromolecules
Xiuxiu Zhao, Jiwen Liu, Shun Zhou, Yanfen Zheng, Yanhong Wu, Kazuhiro Kogure, Xiao-Hua Zhang
2020, 2(2): 181-193. doi: 10.1007/s42995-020-00027-1
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Abstract:
The Mariana Trench is the deepest location on earth and harbors unique microbial communities as evidenced by 16S rRNA gene amplicon and metagenomic sequencing. Obtaining culturable microorganisms from the Mariana Trench will contribute to a further understanding of hadal biogeochemical processes and act as a unique microbial reservoir with potential applications. Here, 825 bacterial strains, identifed by 16S rRNA gene sequencing, were isolated from 12 water depths (0–10, 400 m) of the Mariana Trench with 2216E and R2A media at 4 ℃ or 28 ℃ on four cruises during 2015–2017. These bacteria belong to four phyla, nine classes, 27 orders, 45 families and 108 genera. Alphaproteobacteria, Gammaproteobacteria, Actinobacteria_c, Bacilli and Flavobacteriia were the most abundant classes, accounting for 37.9%, 33.0%, 11.8%, 8.6% and 8.0% of the total bacterial isolates, respectively. 2216E and R2A media were found to have a better selectivity to Bacilli and Flavobacteriia, respectively. Fifty strains were potential novel bacterial species with a 16S rRNA gene similarity & 98.65%, and a higher percentage of novel strains were obtained from R2A than 2216E medium. Additionally, 301 (150 species) out of 354 strains (178 species) selected from each depth could degrade at least one of the ten kinds of macromolecules tested. These results indicate that there is a high diversity of culturable bacteria in the Mariana Trench and they can produce a variety of extracellular enzymes. Our study provides a valuable resource of microorganisms for investigating their biogeochemical roles in the Mariana Trench and for industrial applications.
Optimization of urease production by Bacillus halodurans PO15: a mangrove bacterium from Poovar mangroves, India
Vinod Kumar Nathan, Jasna Vijayan, Ammini Parvathi
2020, 2(2): 194-202. doi: 10.1007/s42995-020-00031-5
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Abstract:
Mangrove ecosystems are one of the most versatile habitats for microorganisms with a high potential for producing a variety of extracellular hydrolytic enzymes. In this study,bacteria with urease activity,enzymes that catalyze the hydrolysis of urea into carbon dioxide and ammonia,were isolated from mangrove sediments of Poovar (Trivandrum,India). Bacillus halodurans,strain PO15,isolated in this study with high urease (UA) activity (28 U/ml) was subjected to optimization using a Box-Behnken experimental design. Incubation variables included incubation period,pH,inoculation percentage and temperature. Significant factors identified based on the model were incubation period,pH,incubation temperature,and inoculum percentage; variations in these produced a tenfold increase in UA activity (295.80 U/ml). The specific activity of the purified UA enzyme was 62.34 U/mg and was found to be thermostable (active up to 60 ℃). UA of B. halodurans PO15 has potential for microbial-induced biomineralization with a reduction of free Ca2+ to about 82.8%?±?0.17%. The microbial-induced calcium precipitation (MICP) using the UA enzyme will potentially be beneficial in the process of biomineralization as well as for a variety of industrial applications.
Review
The interaction between dietary marine components and intestinal fora
Lin Li, Chang-Hu Xue, Tian-Tian Zhang, Yu-Ming Wang
2020, 2(2): 161-171. doi: 10.1007/s42995-020-00035-1
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Abstract:
The intestine is the natural habitat for a large and dynamic bacterial community,which perform vital metabolic and immune functions that significantly effect the nutritional and health status of the host. The major physiological functions of intestinal flora include metabolic activities that lead to important trophic effects on immune structure and function as well as protection of the colonized host against invasion by transient microbes. The intestinal flora is both a target for nutritional intervention and a factor influencing the biological activity of food compounds acquired orally. Marine environments,as a source of diverse organic compounds,can supply us with a number of beneficial and health-promoting ingredients. This review focuses on the physiological functions of intestinal flora and reciprocal interactions between intestinal flora and dietary marine components including polysaccharides,lipids,protein,taurine,carotenoids,minerals,and polyphenols. This review can serve as a valuable reference regarding the consumption of seafood and marine nutraceuticals.