Bosea psychrotolerans sp. nov., a psychrotrophic alphaproteobacterium isolated from Lake Michigan water.

Three strains of a Gram-stain negative bacterium were isolated from Lake Michigan water. 16S rRNA gene sequence analysis revealed that strain 1131 had sequence similarities to Bosea vaviloviae LMG 28367T, Bosea lathyri LMG 26379T, Bosea lupini LMG 26383T, Bosea eneae CCUG 43111T, Bosea vestrisii CCUG 43114T and Boseamassiliensis CCUG 43117T of 99.8, 99.1, 98.4, 98.4, 98.4 and 98.2 %, respectively. The average nucleotide identity value between strain 1131T and Bosea vaviloviae Vaf-18T was 93.4 % and the DNA relatedness was 38 %. The primary cellular fatty acids of strain 1131T were C16 : 1ω7c and C18 : 1ω7c. The primary polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The major compound in the quinone system was ubiquinone Q-10 and in the polyamine pattern sym-homospermidine was predominant. Additional phenotypic characteristics included growth at 5-35 °C, pH values of pH 5.5-8.0, a salt tolerance range of 0.0-1.2 % (w/v), and production of an unknown water soluble brown pigment. After phenotypic, chemotaxonomic and genomic analyses, this isolate was identified as a novel species for which the name Bosea psychrotolerans is proposed. The type strain is 1131T (NRRL B-65405=LMG 30034).

Reclassification of Deinococcus xibeiensis Wang et al. 2010 as a heterotypic synonym of Deinococcus wulumuqiensis Wang et al. 2010.

Two species of the genus Deinococcus, namely Deinococcus wulumuqiensis Wang et al. 2010 and Deinococcus xibeiensis Wang et al. 2010, were simultaneously proposed and described in the same publication. However, the identical 16S rRNA gene sequence of the two type strains strongly raised the probability of their relatedness at the species level. Thus, the genomic relatedness of the two species of the genus Deinococcus was investigated here to clarify their taxonomic status. The high (99.9 %) average nucleotide identity (ANI) between the genome sequences of the two type strains suggested that the two species are synonymous. Additional phenotypic data including enzymic activities and substrate-utilization profiles showed no pronounced differences between the type strains of the two species. Data from this study demonstrated that the two taxa constitute a single species. According to Rule 42 of the Bacteriological Code, we propose that D. xibeiensis Wang et al. 2010 should be reclassified as a subjective heterotypic synonym of D. wulumuqiensis Wang et al. 2010.

Taeseokella kangwonensis gen. nov., sp. nov., isolated from a freshwater reservoir.

A Gram-stain-negative, non-motile and yellow-pigmented bacterium, designated HME8275T, was isolated from freshwater in Korea. The major fatty acids of strain HME8275T were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and iso-C15 : 0. The only respiratory quinone was MK-7. Polar lipid analysis showed phosphatidylethanolamine, two unidentified aminolipids, two unidentified aminophospholipids and three unidentified polar lipids. The DNA G+C content of strain HME8275T was 37.6 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME8275T formed a lineage within the family Cytophagaceae and was related to Lacihabitans soyangensis HME6675T (92.6 % 16S rRNA gene sequence similarity), Leadbetterella byssophila 4M15T (89.0 %), Fluviimonas pallidilutea TQQ6T (89.7 %) and Emticicia oligotrophica GPTSA100-15T (89.8 %). On the basis of the evidence presented in this study, strain HME8275T represents a novel species of a new genus in the family Cytophagaceae, for which the name Taeseokella kangwonensis, gen. nov., sp. nov. is proposed. The type strain of the type species is HME8275T ( = KACC 16933T = CECT 8198T).

Klebsiella michiganensis sp. nov., a new bacterium isolated from a tooth brush holder.

Isolate W14(T) recovered from a household tooth brush holder was found to be gram-negative, a facultative anaerobic, non-motile, capsulated, and a non-endospore-forming straight rod. Based on phylogenetic analysis with 16S rRNA gene sequence, isolate W14(T) was affiliated to the genus Klebsiella. The closest phylogenetic relative was K. oxytoca with 99 % similarity in the 16S rRNA gene sequence. The major whole-cell fatty acids were C(16:0) (31.23 %), C(18:1ω6c)/C(18:1ω7c) (21.10 %), and C(16:1ω7c)/C(16:1ω6c) (19.05 %). The sequence similarities of isolate W14(T) based on rpoB, gyrA, and gyrB were 97, 98, and 98 % with K. oxytoca, and 97, 93, and 90 % with K. mobilis (=Enterobacter aerogenes), respectively. The ribotyping pattern showed a 0.46 similarity with K. oxytoca ATCC 13182(T) and 0.24 with K. mobilis ATCC 13048(T). The DNA G+C content of isolate W14(T) was 54.6 mol%. The DNA-DNA relatedness was 55.7 % with K. oxytoca ATCC 13182(T). Using the identification technology of MALDI-TOF mass spectrometry, the top matches for this isolate were K. oxytoca ATCC 13182(T) (Match Factor Score 1.998) and K. mobilis (Score 1.797). On the basis of phenotypic, biochemical, chemotaxonomic, and molecular studies, isolate W14(T) could be differentiated from other members of the genus Klebsiella including K. mobilis. Therefore, it is proposed that isolate W14(T) (=ATCC BAA-2403(T)=DSM 25444(T)) should be classified as the type strain of a novel species of the genus Klebsiella, K. michiganensis sp. nov.

Radio Tracking Reveals the Home Range and Activity Patterns of Nutria (Myocastor coypus) in the Macdo Wetland in South Korea.

Nutria (Myocastor coypus) are semi-aquatic rodents that were introduced in South Korea for commercial farming but significantly damaged aquatic ecosystems. Understanding nutria ecological behavior is essential for developing effective control and eradication strategies to mitigate their impacts. Thus, this study aimed to investigate the home range and activity patterns of 24 nutria (12 males and 12 females) in the Macdo wetland in South Korea from 2015-2016 through radio tracking. The average minimum convex polygon home range of the nutria was 0.29 ± 0.55 km2, with a 95% kernel density estimation (KDE) home range of 0.43 ± 0.85 km2 and a 50% KDE home range of 0.05 ± 1.1 km2. The home range of males was larger than that of females; however, the winter home range of females was as large as that of males. The home range also varied seasonally, with the smallest observed in winter. The nutria showed crepuscular and nocturnal activity patterns throughout the year, with no significant difference between sexes. The activities in spring, summer, and autumn showed no significant differences, but the activity in winter was significantly different from that in the other seasons. This study may serve as a basis for developing appropriately timed and scaled management strategies to mitigate the impacts of nutria on ecosystems. In conclusion, several environmental and biological factors contribute to the behavior of nutria in South Korea.

Predicting the Impact of Climate Change on the Habitat Distribution of Parthenium hysterophorus around the World and in South Korea

The global climate change, including increases in temperature and precipitation, may exacerbate the invasion by P. hysterophorus. Here, MaxEnt modeling was performed to predict P. hysterophorus distribution worldwide and in South Korea under the current and future climate global climate changes, including increases in temperature and precipitation. Under the current climate, P. hysterophorus was estimated to occupy 91.26%, 83.26%, and 62.75% of the total land area of Australia, South America, and Oceania, respectively. However, under future climate scenarios, the habitat distribution of P. hysterophorus would show the greatest change in Europe (56.65%) and would extend up to 65°N by 2081-2100 in South Korea, P. hysterophorus currently potentially colonizing 2.24% of the land area, particularly in six administrative divisions. In the future, P. hysterophorus would spread rapidly, colonizing all administrative divisions, except Incheon, by 2081-2100. Additionally, the southern and central regions of South Korea showed greater habitat suitability than the northern region. These findings suggest that future climate change will increase P. hysterophorus distribution both globally and locally. Therefore, effective control and management strategies should be employed around the world and in South Korea to restrict the habitat expansion of P. hysterophorus.

Climate change induced habitat expansion of nutria (Myocastor coypus) in South Korea.

The nutria, (Myocastor coypus), is a semiaquatic rodent native to the subtropical and temperate regions of South America. The species was introduced to South Korea for meat and fur production purposes and a wild population has become established. The species subsequently invaded aquatic ecosystems and destroyed aquatic vegetation and cultivated crops. Thus, it is essential to understand their current distribution and future range expansion for effective control and eradication strategies to reduce the risk of colonization into new regions. In this study, we used niche modeling procedure to identify potentially suitable habitats for M. coypus under current and future predicted climate change using the maximum entropy algorithm. We found that the main habitat area of M. coypus is expected to expand under a warming climate from ~ 4069 km2 in the southern and southeastern regions of South Korea, to the northern border of the country, with estimated ranges of 21,744 km2, 55,859 km2, and 64,937 km2 by 2030, 2050, and 2070, respectively. The findings of the present study assist in identifying the future distribution and potential dispersion routes of M. coypus in South Korea, which is important for informing the government regarding essential management actions plans at regional and local scales.

Site-specific ecological risk assessment of metal-contaminated soils based on the TRIAD approach.

Ecological risk assessment based on scientific data is crucial for understanding causal relationships between chemical pollution and environmental risks. Simultaneously, a balance is required between socioeconomic factors and scientific evidence. The TRIAD approach, which incorporates three lines of evidence (LoE)-chemical (Chem-LoE), ecotoxicological (Ecotox-LoE), and ecological (Eco-LoE)-was applied in five sites of an abandoned mine for site-specific soil ecological risk assessment (SERA). In combination, the three LoEs showed that two sites had extremely high risks, one site had moderate risk, and the other site had low risk. At all sites, Chem-LoE exhibited high-integrated risk values. In Ecotox-LoE and Eco-LoE, some species were not affected despite high metal concentrations in the soil samples collected from the sites, indicating that the bioavailability of metals differed according to the physiochemical properties of the soil medium. This study is significant as multiple analyses were performed considering ecosystem structure to reduce uncertainty in SERA. The results provide information to support effective decision-making risk management to protect the soil ecosystem. Moreover, these findings will be useful in establishing policies and priorities for soil risk management.

A direct contact bioassay using sulfur-oxidizing bacteria (SOB) for toxicity assessment of contaminated field soils.

In this study, 11 low/uncontaminated (including Lufa 2.2) and 9 contaminated field soils with varying geophysical and physicochemical characteristics were evaluated for toxicities based on oxygen consumption of sulfur-oxidizing bacteria (SOB). Oxygen consumption of the low/uncontaminated soils ranged between 7.9 mL and 9.5 mL, while contaminated soils ranged between 0.4 mL and 5.4 mL. Inherent test variability (CVi), variation due to soil natural properties (CVns) and minimal detectable difference (MDD) values ranged 1.2%-3.9%, 3.5%-16.9%, and 2.1%-4.3%, respectively. The toxicity threshold of 20% was established for soil toxicity based maximal tolerable inhibition (MTI). All the contaminated soils were found to be toxic and showed inhibition between 42% and 100% above the 20% threshold value. Increased proportions of clay and slit enhanced the of inhibitory effect of contaminants on SOB by reducing the oxygen consumption. Current study provides a suitable method for the rapid toxicity assessment of contaminated field soils with the advantages of ease of handling and rapidity without employing elutriates and sophisticated equipments and tools.

Assessment of the Spatial Invasion Risk of Intentionally Introduced Alien Plant Species (IIAPS) under Environmental Change in South Korea.

Predicting the regions at risk of invasion from IIAPS is an integral horizon-scanning activity that plays a crucial role in preventing, controlling, and eradicating invasive species. Here, we quantify the spatial distribution area and invasion risk of IIAPS using a species distribution model under different levels of environmental change in South Korea. From the model predictions, the current average spatial extent of the 10 IIAPS is 33,948 km2, and the individual spatial extents are estimated to change by -7% to 150% by 2050 and by -9% to 156% by 2070. The spatial invasion risk assessment shows that, currently, moderate-to-high invasion risk is limited to coastal areas and densely populated metropolitan cities (e.g., Seoul, Busan, and Gwangju), but that the area with this level of risk is expected to spread toward the central and northern regions of the country in the future, covering 86.21% of the total area of the country by 2070. These results demonstrate that the risk of invasion by IIAPS is estimated to enlarge across the whole country under future environmental changes. The modeling system provided in this study may contribute to the initial control and strategic management of IIAPS to maintain the dynamic ecosystems of South Korea.

Intact DNA in ancient permafrost.

Contrary to the generally held notions about microbial survival, the recently published paper by Johnson et al., 'Ancient bacteria show evidence of DNA repair', presents evidence suggesting that non-spore-forming bacteria in ancient samples are apparently alive, as judged by intact DNA, and fare better than spores. The data presented in this work raise intriguing questions about the nature of bacteria in many of the ancient samples reported to date: are they spores, persisters, sessile vegetative cells or do they make up a slow-growing population?

Environmental rRNA inventories miss over half of protistan diversity.

BACKGROUND: The main tool to discover novel microbial eukaryotes is the rRNA approach. This approach has important biases, including PCR discrimination against certain rRNA gene species, which makes molecular inventories skewed relative to the source communities. The degree of this bias has not been quantified, and it remains unclear whether species missed from clone libraries could be recovered by increasing sequencing efforts, or whether they cannot be detected in principle. Here we attempt to discriminate between these possibilities by statistically analysing four protistan inventories obtained using different general eukaryotic PCR primers. RESULTS: We show that each PCR primer set-specific clone library is not a sample from the community diversity but rather from a fraction of this diversity. Therefore, even sequencing such clone libraries to saturation would only recover that fraction, which, according to the parametric models, varies between 17 +/- 4% to 49 +/- 10%, depending on the set of primers. The pooled data is thus qualitatively richer than individual libraries, even if normalized to the same sequencing effort. CONCLUSION: The use of a single pair of primers leads to significant underestimation of the true community richness at all levels of taxonomic hierarchy. The majority of available protistan rRNA gene surveys likely sampled less than half of the target diversity, and might have completely missed the rest. The use of multiple PCR primers reduces this bias but does not necessarily eliminate it.

A novel archaeal group in the phylum Crenarchaeota found unexpectedly in an eukaryotic survey in the Cariaco Basin.

Archaea have been found in many more diverse habitats than previously believed due in part to modern molecular approaches to discovering microbial diversity. We report here an unexpected expansion of the habitat diversity of the Archaea in the Cariaco Basin we found using a primer set designed for 18S eukaryotic rDNA sequence analysis. The results presented here expand the originally identified 9 archaeal clones reported in this environment using bacterial/archaeal primers to 152 archaeal clones: 67 (18 OTU) of these clones were found at a depth of 900 m of station A while 71 (9 OTU) of them were at a depth of between 300 approximately 335 m of station B&C depending upon which location the samples were taken. We used three phylogenetic analysis methods and detected 20 phylotypes belonging to a single previously unreported group distantly related to the Crenarchaeota. Also, we determined that the original nine sequences did not fall into any of the known phyla of the Archaea suggesting that they may represent a novel group within the Kingdom Archaea. Thus, from these two studies, we suggest that Archaea in the Cariaco Basin could be unique; however, further studies using archaeal-specific primers and the design of new primers as well as the systematic use of several different primer combinations may improve the chances of understanding the archeal diversity in the Cariaco Basin.

Cardiopulmonary exercise testing before and one year after mitral valve repair for severe mitral regurgitation.

For the evaluation of efficacy of cardiopulmonary exercise testing, we compared New York Heart Association functional class with peak oxygen consumption rate (VO(2)peak) in 31 patients with severe mitral regurgitation who underwent mitral valve repair surgery. One year later, the VO(2)peak values did not show significant improvement; however, the patients who had more than a mild degree of residual mitral regurgitation (n = 14) after 1 year of surgery had a VO(2)peak value that was significantly decreased (from 22.7 +/- 6.4 to 21.0 +/- 6.3 ml/kg/min, p = 0.04). Patients with a higher preoperative VO(2)peak value (>/=18.5 ml/kg/min) had a significantly better New York Heart Association functional class 1 year after surgery than patients with a lower VO(2)peak value (<18.5 ml/kg/min, p = 0.03).

Monitoring of soil bacterial community and some inoculated bacteria after prescribed fire in microcosm.

The soil bacterial community and some inoculated bacteria were monitored to assess the microbial responses to prescribed fire in their microcosm. An acridine orange direct count of the bacteria in the unburned control soil were maintained at a relatively stable level (2.0 approximately 2.7 x 10(9) cells/g(-1).soil) during the 180 day study period. The number of bacteria in the surface soil was decreased by fire, but was restored after 3 months. Inoculation of some bacteria increased the number of inoculated bacteria several times and these elevated levels lasted several months. The ratios of eubacteria detected by a fluorescent in situ hybridization (FISH) method to direct bacterial count were in the range of 60 approximately 80% during the study period, with the exception of some lower values at the beginning, but there were no definite differences between the burned and unburned soils or the inoculated and uninoculated soils. In the unburned control soil, the ratios of alpha-, beta- and gamma-subgroups of the proteobacteria, Cytophaga-Flavobacterium and other eubacteria groups to that of the entire eubacteria were 13.7, 31.7, 17.1, 16.8 and 20.8%, respectively, at time 0. The overall change on the patterns of the ratios of the 5 subgroups of eubacteria in the uninoculated burned and inoculated soils were similar to those of the unburned control soil, with the exception of some minor variations during the initial period. The proportions of each group of eubacteria became similar in the different microcosms after 6 months, which may indicate the recovery of the original soil microbial community structure after fire or the inoculation of some bacteria. The populations of Azotobacter vinelandii, Bacillus megaterium and Pseudomonas fluorescens, which had been inoculated to enhance the microbial activities, and monitored by FISH method, showed similar changes in the microcosms, and maintained high levels for several months.

Ultralong C100 mycolic acids support the assignment of Segniliparus as a new bacterial genus.

Mycolic acid-producing bacteria isolated from the respiratory tract of human and non-human mammals were recently assigned as a distinct genus, Segniliparus, because they diverge from rhodococci and mycobacteria in genetic and chemical features. Using high accuracy mass spectrometry, we determined the chemical composition of 65 homologous mycolic acids in two Segniliparus species and separately analyzed the three subclasses to measure relative chain length, number and stereochemistry of unsaturations and cyclopropyl groups within each class. Whereas mycobacterial mycolate subclasses are distinguished from one another by R groups on the meromycolate chain, Segniliparus species synthesize solely non-oxygenated α-mycolates with high levels of cis unsaturation. Unexpectedly Segniliparus α-mycolates diverge into three subclasses based on large differences in carbon chain length with one bacterial culture producing mycolates that range from C58 to C100. Both the overall chain length (C100) and the chain length diversity (C42) are larger than previously seen for mycolic acid-producing organisms and provide direct chemical evidence for assignment of Segniliparus as a distinct genus. Yet, electron microscopy shows that the long and diverse mycolates pack into a typical appearing membrane. Therefore, these new and unexpected extremes of mycolic acid chemical structure raise questions about the modes of mycolic acid packing and folding into a membrane.

A comparative lipidomics platform for chemotaxonomic analysis of Mycobacterium tuberculosis.

The lipidic envelope of Mycobacterium tuberculosis promotes virulence in many ways, so we developed a lipidomics platform for a broad survey of cell walls. Here we report two new databases (MycoMass, MycoMap), 30 lipid fine maps, and mass spectrometry datasets that comprise a static lipidome. Further, by rapidly regenerating lipidomic datasets during biological processes, comparative lipidomics provides statistically valid, organism-wide comparisons that broadly assess lipid changes during infection or among clinical strains of mycobacteria. Using stringent data filters, we tracked more than 5,000 molecular features in parallel with few or no false-positive molecular discoveries. The low error rates allowed chemotaxonomic analyses of mycobacteria, which describe the extent of chemical change in each strain and identified particular strain-specific molecules for use as biomarkers.

Polymerase chain reaction primers miss half of rRNA microbial diversity.

The rRNA approach is the principal tool to study microbial diversity, but it has important biases. These include polymerase chain reaction (PCR) primers bias, and relative inefficiency of DNA extraction techniques. Such sources of potential undersampling of microbial diversity are well known, but the scale of the undersampling has not been quantified. Using a marine tidal flat bacterial community as a model, we show that even with unlimited sampling and sequencing effort, a single combination of PCR primers/DNA extraction technique enables theoretical recovery of only half of the richness recoverable with three such combinations. This shows that different combinations of PCR primers/DNA extraction techniques recover in principle different species, as well as higher taxa. The majority of earlier estimates of microbial richness seem to be underestimates. The combined use of multiple PCR primer sets, multiple DNA extraction techniques, and deep community sequencing will minimize the biases and recover substantially more species than prior studies, but we caution that even this--yet to be used--approach may still leave an unknown number of species and higher taxa undetected.

Predicting microbial species richness.

Microorganisms are spectacularly diverse phylogenetically, but available estimates of their species richness are vague and problematic. For example, for comparable environments, the estimated numbers of species range from a few dozen or hundreds to tens of thousands and even half a million. Such estimates provide no baseline information on either local or global microbial species richness. We argue that this uncertainty is due in large part to the way statistical tools are used, if not indeed misused, in biodiversity research. Here we develop a powerful synthetic statistical approach to quantify biodiversity. It provides statistically sound estimates of microbial richness at any level of taxonomic hierarchy. We apply this approach to a large original 16S rRNA dataset on marine bacterial diversity and show that the number of bacterial species in a sample from marine sediments is (2.4 +/- 0.5 SE) x 10(3). We argue that our methodology provides estimates of microbial richness that are reliable and general, have biologically meaningful SEs, and meet other fundamental statistical standards. This approach can be an essential tool in biodiversity research, and the estimates of microbial richness presented here can serve as a baseline in microbial diversity studies.