Whole-Genome Sequence of the Microcystin-Degrading Bacterium Sphingopyxis sp. Strain C-1

This report describes the whole-genome sequence of an alkalitolerant microcystin-degrading bacterium, Sphingopyxis sp. strain C-1, isolated from a lake in China

Characteristics of a Microcystin-Degrading Bacterium under Alkaline Environmental Conditions

The pH of the water associated with toxic blooms of cyanobacteria is typically in the alkaline range; however, previously only microcystin-degrading bacteria growing in neutral pH conditions have been isolated. Therefore, we sought to isolate and characterize an alkali-tolerant microcystin-degrading bacterium from a water bloom using microcystin-LR. Analysis of the 16S rRNA gene sequence revealed that the isolated bacterium belonged to the genus Sphingopyxis, and the strain was named C-1. Sphingopyxis sp. C-1 can grow; at pH 11.0; however, the optimum pH for growth was pH 7.0. The microcystin degradation activity of the bacterium was the greatest between pH 6.52 and pH 8.45 but was also detected at pH 10.0. The mlrA homolog encoding the microcystin-degrading enzyme in the C-1 strain was conserved. We concluded that alkali-tolerant microcystin-degrading bacterium played a key role in triggering the rapid degradation of microcystin, leading to the disappearance of toxic water blooms in aquatic environments

Microcystin degradation in sphingopyxis sp. C-1

The microcystin-degrading gene cluster, mlrA-B-C-D, plaies an important role in the degradation process of hepatotoxic microcystins for several bacterial species. However after microcystin is degraded to linear-microcystin by MlrA, it is still unknown about where and by what it is metabolited. In order to clarify it, we disrupted the mlrB gene and mlrC gene in chromosome of microcystin-degrading bacteria, Sphingopyxis sp. C-1. The cells disrupted mlrB gene and mlrC gene accumulated of microcystin-degradation product, linear-microcystin and tetrapeptide, respectively, whereas the cell free extracts of ?mlrB cells detected Adda and ?mlrC cells accumulated tetrapeptide. Moreover, topology analysis of MlrB using the ß-lactamase gene fusion method insisted MlrB is the peripheral protein binding the inner-membrane. These results insist that MlrB degrades the linear microcystin in the periplasmic space and MlrC degrades tetrapeptide in cytoplasm. Thus, in intact cells, MlrC cannot degrade linear-microcystin as being separated in inner-membrane from linear-microcystin while MlrC is capable of degrading the linear-microcystin in cell-free extract

Severity and Progression Rate of Cerebellar Ataxia in 16q-linked Autosomal Dominant Cerebellar Ataxia (16q-ADCA) in the Endemic Nagano Area of Japan

16q22.1-linked autosomal dominant cerebellar ataxia (16q-ADCA) is a recently defined subtype of ADCA identified by a disease-specific C/T substitution in the 5' untranslated region of the puratrophin-1 gene. In Nagano, the central mountainous district of the main island of Japan, 16q-ADCA and spinocerebellar ataxia type 6 (SCA6) are the most and second most prevalent subtypes of ADCA, respectively. Both subtypes are classified into Harding's ADCA III, but little attention has been given to the differences in the severity and progression rate of cerebellar ataxia between 16q-ADCA and SCA6. We investigated the clinical severity and progression rate of cerebellar ataxia of 16q-ADCA patients using international cooperative ataxia rating scale and scale for the assessment and rating of ataxia and compared them with those of SCA6 patients. The age at onset was much higher in 16q-ADCA patients (60.1 +/- 9.8 years, n = 66) than in SCA6 patients (41.1 +/- 8.7 years, n = 35). Clinical features of 16q-ADCA were basically consistent with pure cerebellar ataxia, as well as in SCA6, but gaze-evoked nystagmus was observed less frequently in 16q-ADCA patients than in SCA6 patients. When compared at almost the same disease duration after onset, the severity of cerebellar ataxia was a little higher, and the progression rate seemed more rapid in 16q-ADCA patients than in SCA6 patients, but the differences were not significant.ArticleCEREBELLUM. 8(1):46-51 (2009)journal articl

Abundance and Diversity of Nitrifying Microorganisms in Marine Recirculating Aquaculture Systems

Recirculating aquaculture systems (RAS) are important for water quality management in aquaculture facilities, and can help resume water consumption. However, information about the community structure of the micro-ecosystem existing in biofilters, especially the participation of the known nitrifying groups (i.e., AOA, AOB, NOB, and comammox Nitrospira), remains to be fully clarified. In this research, we compared the community structures in three RAS systems operated at different temperatures in a marine aquarium, through both amoA-targeted qPCR assay and 16S rRNA-targeted next-generation sequencing. As result, AOA was the primary nitrifier in the biofilters and was typically abundant and diverse in high-temperature samples (ca. 25 °C). NOB’s relative abundance patterns were numerically similar to that of AOA, suggesting a cooperation relationship between AOA and NOB in the marine RAS system. AOB was at a comparable level with AOA in medium-temperature samples (ca. 19 °C), while their abundance sharply decreased in high-temperature samples. The number of observed OTUs of AOA in high-temperature samples was 1.9 and 1.5 times as much as that detected in low (ca. 10 °C) and medium temperature samples respectively, suggesting a much more diverse and predominant occurrence of AOA at high temperatures. Comammox Nitrospira was only detected at a low level in the biofilter samples, suggesting a negligible contribution to the nitrification process in such ammonia-limited, saline biofilms. Although comammox Nitrospira cannot be detected by 16S rRNA-based analysis, the high diversity and abundance of NOB that were detected in high-temperature samples indicated the prospective possibility of the occurrence of complete ammonia oxidation at high temperatures

Abundance and Diversity of Nitrifying Microorganisms in Marine Recirculating Aquaculture Systems

Recirculating aquaculture systems (RAS) are important for water quality management in aquaculture facilities, and can help resume water consumption. However, information about the community structure of the micro-ecosystem existing in biofilters, especially the participation of the known nitrifying groups (i.e., AOA, AOB, NOB, and comammox Nitrospira), remains to be fully clarified. In this research, we compared the community structures in three RAS systems operated at different temperatures in a marine aquarium, through both amoA-targeted qPCR assay and 16S rRNA-targeted next-generation sequencing. As result, AOA was the primary nitrifier in the biofilters and was typically abundant and diverse in high-temperature samples (ca. 25 °C). NOB’s relative abundance patterns were numerically similar to that of AOA, suggesting a cooperation relationship between AOA and NOB in the marine RAS system. AOB was at a comparable level with AOA in medium-temperature samples (ca. 19 °C), while their abundance sharply decreased in high-temperature samples. The number of observed OTUs of AOA in high-temperature samples was 1.9 and 1.5 times as much as that detected in low (ca. 10 °C) and medium temperature samples respectively, suggesting a much more diverse and predominant occurrence of AOA at high temperatures. Comammox Nitrospira was only detected at a low level in the biofilter samples, suggesting a negligible contribution to the nitrification process in such ammonia-limited, saline biofilms. Although comammox Nitrospira cannot be detected by 16S rRNA-based analysis, the high diversity and abundance of NOB that were detected in high-temperature samples indicated the prospective possibility of the occurrence of complete ammonia oxidation at high temperatures

A long-term impact of forest disturbance on spruce seedling regeneration on coarse woody debris

Storm disturbance have huge impacts on subalpine forest ecosystems. However, long-term effects of such disturbance on regeneration of subalpine forests are poorly understood. Picea jezoensis var. hondoensis has limited and discontinuous distributions in subalpine central Japan. Thus, evaluating long-term effects of forest disturbance and their mechanisms have great conservation significance. Picea needs coarse woody debris (CWD) such as logs and stumps for their seedling colonization, and thus their establishment is greatly affected by CWD condition which largely depending on decay activity of decomposer fungal community. Recent studies in Europe found that frequency of occurrence of brown rot fungi, a certain functional group of fungi which decay wood holocellulose without decaying lignin, tends to be increase after forest dieback1), and that CWD decayed by brown rot fungi negatively affects spruce seedling density2). Because the decay process of CWD is known to be several decades long, we hypothesized that the effect of forest disturbance on fungal community and wood decay of CWD, and its negative effect on spruce seedling establishment would be long lasting. To test this hypothesis, we compared fungal communities within CWD and spruce seedling density among forest sites of the three different categories (control old-growth forest, damaged forest with the logs left, and damaged forest with the logs removed) in an old-growth subalpine coniferous forest in Mt. Yastugatake, central Japan. This forest had got a wide-range disturbance by a typhoon in 1959. We surveyed totally 95 logs in 9 sites (5, 2, and 2 sites for the forest categories held in above, respectively). Fungal communities within CWDs were documented using Illumina sequencing. Seedling and epiphytic bryophyte communities were recorded and were analyzed with CWD properties such as wood decay type (white rot, brown rot, and soft rot), pH, moisture, and bryophyte coverage. Illumina sequencing did not show obvious difference in fungal communities among the forest categories. Also, frequencies of the occurrence of wood decay type were not significantly different among the categories. None of these variables had significant association with spruce seedling density. However, experience of the disturbance certainly reduced current spruce seedling density. These results suggested that the forest disturbance do have a long lasting effect on spruces seedling regeneration on CWD, but the effect might not be attributable to their impacts on CWD fungal community and wood decay. 1)Vogel S, Alvarez B, Bassler C Müller J, Thorn S (2017) The Red-belted Bracket (Fomitopsis pinicola) colonizes spruce trees early after bark beetle attack and persists. Fungal Ecology 27:282-288. 2)Bače R, Svoboda M, Pouska V, Janda P, Červenka, J (2012) Natural regeneration in Central-European subalpine spruce forests: Which logs are suitable for seedling recruitment? Forest Ecology and Management 266:254-262.peerReviewe

Whole-genome sequence of the microcystin-degrading bacterium Sphingopyxis sp. strain C-1

This report describes the whole-genome sequence of an alkalitolerant microcystin-degrading bacterium, Sphingopyxis sp. strain C-1, isolated from a lake in China