Microbiology

RETRACTED ARTICLE: Phytobacter nematintestini sp. nov., isolated from the intestine of Caenorhabditis elegans and conferring resistance to Bacillus nematocida infection

Thaumarchaeota affiliated with Soil Crenarchaeotic Group are prevalent in the alkaline soil of an alpine grassland in northwestern China Abstract Purpose Thaumarchaeota are key players within the global nitrogen cycle. Investigations of the Thaumarchaeota communities are important for an integrated understanding of nitrogen nutrient cycle in soil ecosystems. Therefore, the objective of this study was to examine the presence and diversity of Thaumarchaeota within an alkaline soil in the Bayinbuluke alpine grassland, China. Methods The community DNAs were directly extracted from soil samples, collected on 15 July 2014, and paired-end V5–V6 amplicons of the 16S rRNA gene were sequenced by Illumina Miseq. Sequencing reads were processed using the Quantitative Insights Into Microbial Ecology (QIIME) v. 1.8.0 pipeline. After quality control, the validated sequence reads were classified into different operational taxonomic units (OTUs) based on a 97% identity level, using the Uclust algorithm to generate stable OTUs. The longest sequence in each cluster was chosen to be the representative sequence, and sequences were annotated using the Silva rRNA database project. Result In the analyzed grassland soil, Thaumarchaeota had a relative abundance of 3.65 to 51.07% of the microbial community (mean = 20.20%), representing the most dominant phylum. The thaumarchaeal community was dominated by the Soil Crenarchaeotic Group (SCG, 34.55 to 99.82%, mean = 95.10%), with specifically low fraction of the ammonia-oxidizing genus Candidatus Nitrososphaera (2.83 to 30.37%, mean = 13.10%) and remaining unclassified genus. Conclusion Our results show Thaumarchaeota affiliated with SCG were prevalent in the alkaline soil of this grassland.

Identification and characterization of ectoine-producing bacteria isolated from Can Gio mangrove soil in Vietnam Abstract Purpose The aim of this study was to characterize high ectoine-producing bacteria obtained from Can Gio mangrove soil samples in Vietnam. Methods Ectoine-producing bacteria were isolated from mangrove soil samples. The selected strains were identified using 16S rDNA sequence analysis, and their biochemical characteristics were also examined. The ability to produce ectoine at different NaCl concentrations and the effect of osmotic downshock solution on ectoine’s release rates and survival rates for the selected bacterial strains were investigated. Results Among more than 200 bacterial colonies isolated from soil samples, two strains exhibiting highest ectoine production (strains D227 and D228) were chosen for further studies. Both strains D227 and D228 were identified as Halomonasspp. and were closely related to Halomonas organivorans, sharing 99.4% 16S rDNA sequence similarity. At 6% (w/v) NaCl concentration, strains D227 and D228 presented the highest cell dry weight (CDW) of 3.85 and 3.55 g/l, respectively. At 18% NaCl concentration, maximum total ectoine (ectoine and hydroxyectoine) production of 16.4 and 18.1 wt% was achieved by strains D227 and D228, respectively. After 30 min of incubation in downshock solution containing 5% NaCl, high bacterial survival rates of 96% and 98%, and ectoines release rates of 61% and 76% were obtained by strains D227 and D228, respectively. Conclusions The accumulation and secretion of ectoine appear to be a typical adaptation strategy of some bacteria to survive under the changing saline conditions of mangrove ecosystem. To the best of our knowledge, this is the first report on ectoine production by halophilic bacteria isolated from mangrove soil. High ectoine-producing bacteria can be found in mangrove forest.

Serial re-pitching: its effect on yeast physiology, fermentation performance, and product quality Abstract Background Serial re-pitching is a term given to a practice whereby yeast harvested at the end of fermentation is re-used in subsequent fermentations. Purpose The purpose of this paper was to review and summarize existing literatures, research data, and case studies to illustrate the effect of re-pitching on the physiology and fermentation performance of brewing yeast and the resulting quality of beer. Methods Data related to biomarkers used to assess yeast physiology and fermentation performance and quality of beer were compared for various articles. Results And comparison of the results was done with caution as many of the studies were conducted using different yeast strains, wort gravity, pitching rate, and other fermentation conditions. Conclusion This study confirms that serial re-pitchings aggravate the effect of pitching rate, wort gravity, cell age, yeast oxygenation, and yeast strain on yeast cell physiology, fermentation performance, and quality of final beer. However, further empirical research at molecular level is crucial.

Archaeal communities in the deep-sea sediments of the South China Sea revealed by Illumina high-throughput sequencing Abstract Purpose Archaea have important roles in global biogeochemical circulation. Although archaeal diversity and their ecological significance in deep-sea environments in the South China Sea (SCS) have been investigated, archaeal communities in deep-sea sediments below 2000 m water depth in the SCS are not well documented. The objective of our work was to investigate archaeal community structure in the four sediments (named as SCS2, SCS5, SCS8, and SCS10) collected from the SCS below 2000 m water depth. Methods Illumina high-throughput sequencing was employed to reveal archaeal community structure. Archaeal communities were evaluated with QIIM software. Result Archaeal communities in the four sediments were dominated by Thaumarchaeota (55%), Bathyarchaeota (24%), Woesearchaeota (6%), Nanohaloarchaeota (4%), and Euryarchaeota (3%). Thaumarchaeota were abundant in the four samples. However, in SCS10, this phylum was almost exclusively represented. We revealed for the first time the presence of Nanohaloarchaeota in SCS2, SCS5, and SCS8. Comparative analysis showed that (1) the archaeal communities varied between the samples and (2) the samples varied between the samples. The detected archaea in each sample are known to be potentially participating in the carbon, nitrogen, and sulfur cycles, and methane metabolism. Conclusion We present a comparative picture of archaeal communities, augmenting the current knowledge on archaeal diversity in deep-sea sediment environments in the SCS.

Alleviation of salt stress response in soybean plants with the endophytic bacterial isolate Curtobacterium sp . SAK1 Abstract Background Salinity has been a major abiotic stressor that reduce the productivity. Previous studies reported that endophytic bacteria produce plant stress response hormones, antioxidants, and enzymes such as ACC deaminase. Augmentation of these metabolites and enzymes by endophytes mitigates the stress effects of salinity and improves plant growth and productivity. Methods Bacterial endophytes were isolated from Artemisia princeps Pamp, and evaluated for indole-3-acetic acid (IAA), abscisic acid (ABA), siderophore, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase production and the ability to solubilize phosphate in the presence of NaCl (100–400 mM). SAK1 was applied to Glycine max cv. Pungsannamul to investigate salinity stress. Results Our results revealed that with an increase in NaCl concentration, the amount of ABA production in SAK1 increased, whereas IAA levels decreased. Bacterial ABA and JA degrade the reactive oxygen species and protect plants against stressors. Gas chromatography-mass spectrometry (GC-MS) analysis detected different gibberellins (GAs) and organic acids in SAK1. Interestingly, SAK1 inoculation significantly increased plant growth attributes under normal and salinity stress conditions, whereas a decrease in endogenous jasmonic acid and ABA content in the plants was recorded under salinity stress. IAA and GAs enhance number of root tips and hence improve nutrients uptake in plants. Polyphenolic oxidase and peroxidase were alleviated by elevated SAK1 in G. max plants under stress. ACC deaminase of SAK1 resulted deamination of ACC, up to 330 nmol α-ketobutyrate mg−1 h−1 which could be a major reason of ethylene reduction promoting plant growth. Conclusion SAK1 relieved salinity stress in plants by producing different phytohormones, antioxidants, and ACC deaminase enzyme. SAK1 could be a new addition in batch of plant stress hormone-regulating endophytic bacteria that mitigates the effects of salt stress and promotes plant growth in G. max.

Cu 2+ regulated sulfonamides resistance gene ( sul ) via reactive oxygen species induced ArcA in a pathogenic Vibrio splendidus Abstract Purpose To detect the sulfonamide resistance of Vibrio splendidus strain Vs, and characterize the factors that regulate the expression of sulfonamide resistance gene sulVs. Methods Minimal inhibitory concentration was measured using growth inhibition method, gene expression was measured using real-time reverse transcriptase PCR, reactive oxygen species (ROS) production under Cu2+ or Cu2+/NAC conditions was measured using an excitation wavelength of 485 nm, and an emission wavelength of 525 nm, and the binding of sulVs promoter and the transcriptional factor ArcA was measured using electrophoretic mobility shift assay (EMSA). Result sulVs gene was cloned and its expression was upregulated to 6.98- and 3.57-fold in the presence of sulfadiazine and sulfamethoxazole, respectively. Moreover, Cu2+ could also upregulate the expression of sulVs to 14.27-fold, the production of ROS to 4.37-fold, and the expressions of antioxidant-related genes and a transcriptional regulator arcA gene. After addition of N-Acetyl-L-cysteine, a ROS inhibitor, the production of ROS decreased to 53.1%, and the expression of arcA gene was also downregulated to 26%. EMSA showed that the purified recombinant ArcA could directly bind to the promoter region of sulVs with specificity. Conclusion V. splendidus strain Vs showed sulfonamide resistance due to sulVs, and Cu2+ could increase the level of ROS followed by ArcA activation as a transcriptional factor to increase the expression of sulVs.

The inhibitory effect of cadmium and/or mercury on soil enzyme activity, basal respiration, and microbial community structure in coal mine–affected agricultural soil Abstract Purpose The Cd and Hg contents in soils can be elevated due to coal mining. To estimate the effects of these two heavy metals on soil enzymes and the key microbial groups, coal mine–affected agricultural soils were cultured for 30 days with Cd and/or Hg. Methods Soil enzyme activities were measured by a colorimetric method, and microbial abundance was assessed according to real-time quantitative PCR analysis of the 16S rRNA and 18S rRNA genes. In addition, the microbial communities were analyzed by Illumina sequencing. Results Heavy metals inhibited soil enzyme activities. For example, both Cd and Hg decreased 25.52–34.89% of the soil catalase activity; the highest level of Hg (30 mg kg−1) decreased 76.50–89.88% of the soil urease activity and 85.60–92.92% of the soil dehydrogenase activity; and the soil acid phosphatase activity significantly decreased by 15.18–32.64% under all the levels of Cd and decreased 17.09–30.32% under the high levels of the Cd–Hg combination (> 3 mg kg−1). In addition, increased Cd levels affected bacterial number more than fungal abundance; however, addition of Hg alone decreased the bacterial number but increased the fungal abundance. Furthermore, the bacterial communities but not fungal communities were altered by heavy metals. A total of 23 highly sensitive genera and 16 highly resistant genera were identified. The sensitive genera were assigned to Actinobacteria, Acidobacteria, Candidate division WS3, Chloroflexi, Gemmatimonadetes, Proteobacteria, and Thermotogae, while the resistant genera were affiliated to Bacteroidetes and Proteobacteria. Conclusion Soils containing the highest level of the combination of Cd and Hg exhibited the lowest soil enzyme activities; bacterial communities were more sensitive to heavy metal contamination than fungi.

AfsR is an important regulatory factor for growth and butenyl-spinosyn biosynthesis of Saccharopolyspora pogona Abstract Purpose To generate a AfsR-like (AfsR-L) overexpression strain Saccharopolyspora pogona-AfsR-L and investigate its effects on the morphology and metabolism of S. pogona. Methods Firstly, we generated the overexpression vector pOJ260-PermE-afsR-L via overlap extension PCR. Then, the recombination strain S. pogona-AfsR-L was constructed via conjugal transfer. To monitor the growth and morphology, mycelia and sporulation were observed. The distinctive proteins and butenyl-spinosyn biosynthesis were investigated by SDS-PAGE, HPLC, and mass spectrometry. And the transcriptional level of afsR-L and other relative functional genes in S. pogona-AfsR-L was analyzed by qRT-PCR. Western blot verified the increased amount of AfsR-L protein in the overexpression strain. Result Growth curve and mycelia observation showed that afsR-L overexpression make the stationary phase of S. pogona-AfsR-L longer than that of wild S. pogona by approximate 3 days. Moreover, S. pogona-AfsR-L exhibited a more obvious white phenotype on the solid medium, which means afsR-L overexpression affects the sporulation ability of S. pogona. HPLC analysis revealed that the peak area of the butenyl-spinosyn yield of S. pogona-AfsR-L was 293.6, while that of S. pogona was 250.9. SDS-PAGE analysis showed that the two strains had different whole protein expression profiles, and the distinctive proteins were further identified by LC-MS/MS identification, which showed the possible control mechanism of afsR-L gene in S. pogona. Conclusion We concluded that AfsR could directly or indirectly positively regulate the biosynthesis of butenyl-spinosyn and affect the growth features of S. pogona. We envisioned that this result can be expanded to other Streptomyces for strain improvement.

A comparison of microeukaryote communities inhabiting sponges and seawater in a Taiwanese coral reef system Abstract Purpose Assess microeukaryote community composition in seawater and sponge samples from Taiwanese coral reefs. Methods In the present study, we used Illumina sequencing to explore the microeukaryote communities of seven biotopes (six sponge species and seawater) sampled in the Penghu archipelago of Taiwan. Result Microeukaryote communities were dominated by Dinoflagellates with Dinophyceae and Syndiniales well represented in all biotopes. Other abundant taxa included metazoa, red and green algae and Radiolaria. The only significant differences were a significantly higher relative abundance of Picobiliphyta and Stramenopiles_X in seawater and Metamonada in the sponge Acanthostylotella cornuta. There was also a significant difference in composition among biotopes with samples from sponges and seawater forming distinct clusters. There was, however, no congruence between prokaryote and microeukaryote community composition. After removing all OTUs < 100 sequences, more than 90% of remaining OTUs representing > 99.5% of sequences were shared between sponge and seawater samples. Conclusion This data in the present study would appear to suggest that marine microeukaryote communities in sponges are largely derived from the surrounding seawater. Abundant OTUs were also related to organisms previously retrieved from seawater. A number of these OTUs though had relatively low sequence similarity to organisms in GenBank suggesting that more research of the microeukaryote communities in the Penghu archipelago may yield novel organisms in this relatively unexplored area.