• Journal of Microbiology and Biotechnology
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• v.27 no.1
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• pp.130-140
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• 2017

It is vital to understand the changing characteristics of interphase microbial communities and interspecies synergism during the fermentation of Chinese liquors. In this study, microbial communities in the three indispensable phases (pit mud, zaopei, and huangshui) of Luzhou-flavored liquor manufacturing pits and their shifts during cellars use were first investigated by polyphasic culture-independent approaches. The archaeal and eubacterial communities in the three phases were quantitatively assessed by combined phospholipid ether lipids/phospholipid fatty acid analysis and fluorescence in situ hybridization. In addition, qualitative information regarding the microbial community was analyzed by PCR-denaturing gradient gel electrophoresis. Results suggested that the interphase microbial community profiles were quite different, and the proportions of specific microbial groups evolved gradually. Anaerobic bacteria and gram-positive bacteria were dominant and their numbers were higher in pit mud ($10^9$ cells/g) than in huangshui ($10^7$ cells/ml) and zaopei ($10^7$ cells/g). Hydrogenotrophic methanogenic archaea were the dominant archaea, and their proportions were virtually unchanged in pit mud (around 65%), whereas they first increased and then decreased in zaopei (59%-82%-47%) and increased with pit age in huangshui (82%-92%). Interactions between microbial communities, especially between eubacteria and methanogens, played a key role in the formation of favorable niches for liquor fermentation. Furthermore, daqu (an essential saccharifying and fermentative agent) and metabolic regulation parameters greatly affected the microbial community.

• ALGAE
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• v.21 no.4
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• pp.349-375
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• 2006

The application of modern ecological, ultrastructural and molecular methods, aided by the cultivation of numerous cyanobacterial morphotypes, has substantially changed our knowledge of these organisms. It has led to major advances in cyanobacterial taxonomy and criteria for their phylogenetic classification. Molecular data provide basic criteria for cyanobacterial taxonomy; however, a correct phylogenetic system cannot be constructed without combining genetic data with knowledge from the previous 150 years research of cyanobacterial diversity. Thus, studies of morphological variation in nature, and modern morphological, ultrastructural, ecophysiological and biochemical characters need to be combined in a “polyphasic” approach. Taxonomic concepts for generic and infrageneric ranks are re-evaluated in light of combined phenotypic and molecular criteria. Despite their usefulness in experimental studies, the limitations of using strains from culture collections for systematic and nomenclatural purposes is highlighted. The need for a continual revision of strain identification and proper nomenclatural practice associated with either the bacteriological or botanical codes is emphasized. Recent advances in taxonomy are highlighted in the context of prospects for understanding cyanobacterial diversity from natural habitats, and the evolutionary and adaptational processes that cyanobacteria undergo.

• ALGAE
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• v.37 no.1
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• pp.1-14
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• 2022

Cyanobacteria are distributed worldwide, and many new cyanobacterial species are discovered in tropical region. The Nostoc-like genus Amazonocrinis has been separated from the genus Nostoc based on polyphasic methods. However, species diversity within this genus remains poorly understood systematically because only one species (Amazonocrinis nigriterrae) has been described. In this study, two novel strains (NUACC02 and NUACC03) were isolated from moist rice field soil in Thailand. These two strains were characterized using a polyphasic approach, based on morphology, 16S rRNA phylogenetic analysis, internal transcribed spacer secondary structure and ecology. Phylogenetic analyses based on 16S rRNA gene sequences confirmed that the two novel strains formed a monophyletic clade related to the genus Amazonocrinis and were distant from the type species A. nigriterrae. The 16S rRNA gene sequence similarity (<98.1%) between novel strains and all other closely related taxa including the Amazonocrinis members exceeded the cutoff for species delimitation in bacteriology, reinforcing the presence of a new Amazonocrinis species. Furthermore, the novel strains possessed unique phenotypic characteristics such as the presence of the sheath, necridia-like cells, larger cell dimension and akinete cell arrangement in long-chains and the singularity of D1-D1', Box-B, V2, and V3 secondary structures that distinguished them from other Amazonocrinis members. Considering all the results, we described our two strains as Amazonocrinis thailandica sp. nov. in accordance with the International Code of Nomenclature for Algae, Fungi and Plants.

• ALGAE
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• v.38 no.2
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• pp.93-110
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• 2023

Progress in phylogenomic analysis has led to a considerable re-evaluation of former cyanobacterial system, with many new taxa being established at different nomenclatural levels. The family Geminocystaceae is among cyanobacterial taxa recently described on the basis of polyphasic approach. Within this family, there are six genera: Geminocystis, Cyanobacterium, Geminobacterium, Annamia, Picocyanobacterium, and Microcrocis. The genus Geminocystis previously encompassed two species: G. herdmanii and G. papuanica. Herein, a new species G. urbisnovae was proposed under the provision of the International Code of Nomenclature for algae, fungi, and plants (ICN). Polyphasic analysis was performed for five strains from the CALU culture collection (St. Petersburg State University, Russian Federation), and they were assigned to the genus Geminocystis in accordance with high 16S rRNA gene similarity to existing species, as well as because of proximity to these species on the phylogenetic trees reconstructed with RaxML and Bayes methods. Plausibility of their assignment to a separate species of the genus Geminocystis was substantiated with smaller cell size; stenohaline freshwater ecotype; capability to complementary chromatic adaptation of second type (CA2); distinct 16S rRNA gene clustering; sequences and folding of D1-D1' and B box domains of the 16S-23S internal transcribed spacer region. The second objective pursued by this communication was to provide a survey of the family Geminocystaceae. The overall assessment was that, despite attention of many researchers, this cyanobacterial family has been understudied and, especially in the case of the crucially important genus Cyanobacterium, taxonomically problematic.

• ALGAE
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• v.35 no.1
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• pp.1-15
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• 2020

Two strains isolated from a subtropical region in China, were morphologically identified as a Nostoc-like species, but its taxonomic identity was unknown. In this study, these two strains were taxonomically and phylogenetically characterized based on polyphasic approach combining morphological and genetic characteristics. Though both were virtually indistinguishable from Nostoc in field and cultured material, these two strains were phylogenetically distinct from Nostoc based on 16S rRNA phylogeny. The 16S-23S internal transcribed spacer rRNA secondary structure of these strains showed the unique pattern of D1-D1', Box-B, and V3 helix, which distinguished them from other Nostoc-like heterocytous genera. A unique cluster separated from Nostoc sensu stricto supports the establishment of Violetonostoc gen. nov. with the type species as Violetonostoc minutum sp. nov.

• Journal of Microbiology
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• v.37 no.2
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• pp.66-72
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• 1999

Mycolic acid-containing actinomycetes associated with extensive foaming in the aeration basin of the activated sludge process were isolated and analyzed by phenotypical, chemotaxonomical and phylogenetic methods. Whole cell sugar patterns of two isolates were pattern A. The nearly complete sequences of the 16S rRNA genes (rDNAs) of the isolates were determined and compared by using several tree-making algorithms. With polyphasic methods, strain SCNU1 was identified as Gordona sputi, and strain SCNU5 assigned to the genus Tsukamurella. The presence of opportunistic pathogens of chronic lung infections within foams can cause public health problems and render waste-treatment processes inefficient.

• Korean Journal of Medicinal Crop Science
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• v.28 no.1
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• pp.1-8
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• 2020

Background: This study was conducted to investigate the effects of NaCl concentration on the photosynthetic parameters, chlorophyll fluorescence and growth characteristics of Crepidiastrum sonchifolium. Methods and Results: As treatments, we subjected C. sonchifolium plants to four different concentrations of NaCl (0, 50, 100 and 200 mM). We found that the photosynthetic parameters maximum photosynthesis rate (P_{N max}), net apparent quantum yield (Φ), maximum carboxylation rate (V_cmax), and maximum electron transport rate (J_max) were significantly reduced at an NaCl concentration greater than 100 mM. In contrast, there was an increase in water-use efficiency with increasing NaCl concentration, although in terms of growth performances, leaf dry weight, root dry weight, stem length, and total dry weight all decreased with increasing NaCl concentration. Furthermore, leakage of electrolytes, as a consequence of cell membrane damage, clearly increased in response to an increase in NaCl concentration. Analysis of the polyphasic elevation of chlorophyll a fluorescence transients (OKJIP) revealed marked decrease in flux ratios (Φ_PO, Ψ_O and Φ_EO) and the PI_abs, performance index in response to treatment with 200 mM NaCl, thereby reflectings the relatively reduced state of photosystem II. This increase in fluorescence could be due to a reduction in electron transport beyond Q^-_A. We thus found that the photosynthetic parameters, chlorophyll fluorescence and growth characteristics of C. sonchifolium significantly increased in response to treatment with 200 mM NaCl. Conclusions: Collectively, the findings of this study indicate that C. sonchifolium shows relatively low sensitivity to NaCl stress, although photosynthetic activity was markedly reduced in plants exposed to 200 mM NaCl.

• The Plant Pathology Journal
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• v.34 no.1
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• pp.1-10
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• 2018

A previously unreported bacterial disease on chili pepper (Capsicum annuum L.) seedlings affecting as many as 4% of seedlings was observed in greenhouses in Chihuahua, Mexico (Delicias and Meoqui counties). Initial lesions appeared as irregular small spots on leaves and brown necrosis at margins tips were observed. Later, the spots became necrotic with a chlorotic halo. Advanced disease was associated with defoliation. A Gram negative, rod-shaped bacterium was isolated from diseased chili pepper seedlings. Three inoculation methods revealed that isolated strains produce foliage symptoms, similar to those observed in naturally infected seedlings. Pathogenic strains that caused symptoms in inoculated seedlings were re-isolated and identified to fulfill koch's postulate. Polyphasic approaches for identification including biochemical assays (API 20E and 50CH), carbon source utilization profiling (Biolog) and 16S rDNA, hsp60 and rpoB sequence analysis were done. Enterobacter cloacae was identified as the causal agent of this outbreak on chili pepper seedlings.

• Journal of Microbiology and Biotechnology
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• v.12 no.4
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• pp.635-642
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• 2002

To effectively investigate the identification and distribution of the lactic acid bacteria in Kimchi, polyphasic methods, including a PCR, SDS-PAGE of the whole-cell proteins, and 16S rRNA gene sequence analysis, were used. In various types of Kimchi fermented at 20$\^{C}$, the isolate KHU-31 was found to be the predominant lactic acid bacteria. This isolate was identified as Lactobacillus sake KHU-31, based on SDS-PAGE of the whole-cell proteins and a 165 rRNA gene sequence analysis, which provided accurate and specific results. Accordingly, the approach used in the current study demonstrated that Lactobacillus sake KHU-31, together with Leuconostoc mesenteroides, were the most predominant lactic acid bacteria in all types of Kimchi in the middle stage of fermentation at 20$\^{C}$.

• Sleep Medicine and Psychophysiology
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• v.17 no.2
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• pp.75-84
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• 2010

The cyclic alternating pattern (CAP) is a periodic EEG activity in NREM sleep, characterized by sequences of transient electrocortical events that are distinct from background EEG activities. A CAP cycle consists of two periodic EEG features, phase A and subsequent phase B whose durations are 2-60 s. At least two consecutive CAP cycles are required to define a CAP sequence. The CAP phase A is a phasic EEG event, such as delta bursts, vertex sharp transients, K-complex sequences, polyphasic bursts, K-alpha, intermittent alpha, and arousals. Phase B is repetitive periods of background EEG activity. The absence of CAP more than 60 seconds or an isolated phase A is classified as non-CAP. Phase A activities can be classified into three subtypes (A1, A2, and A3), based on the amounts of high-voltage slow waves (EEG synchrony) and low-amplitude fast rhythms (EEG desynchrony). CAP rate, the percentage of CAP durations in NREM sleep is considered to be a physiologic marker of the NREM sleep instability. In insomnia, the frequent discrepancy between self-reports and polysomnographic findings could be attributed to subtle abnormalities in the sleep tracing, which are overlooked by the conventional scoring methods. The conventional scoring scheme has superiority in analysis of macrostructure of sleep but shows limited power in finding arousals and transient EEG events that are major component of microstructure of sleep. But, it has recently been found that a significant correlation exists between CAP rate and the subjective estimates of the sleep quality in insomniacs and sleep-improving treatments often reduce the amount of CAP. Thus, the extension of conventional sleep measures with the new CAP variables, which appear to be the more sensitive to sleep disturbance, may improve our knowledge on the diagnosis and management of insomnia.