Evidence for Introgressive Hybridization of Captive Markhor (Capra falconeri) with Domestic Goat: Cautions for Reintroduction

Markhors (Capra falconeri) are among the most endangered mammal species, and several conservation measures, including ex situ breeding, are implemented to prevent their extinction. We studied sequence diversity and differentiation of the first hypervariable segment of the mitochondrial DNA control region among C. f. heptneri and C. f. megaceros kept in four zoos in relationship to lineages of other wild and domestic goats, to assess for the first time the level of molecular distinctness and variability among those subspecies, and to check for possible introgression by related Capra taxa, such as domestic goats. Levels of differentiation between some Capra falconeri lineages and modern domestic goats were similar to levels between other wild goat species (i.e., Capra aegagrus, Capra ibex) and domestic goats. Among pure markhor lineages, paraphyly was observed for C. f. heptneri, suggesting occurrence of shared ancestral polymorphism among markhor subspecies and/or ancient or recent gene exchange between subspecies. Interestingly, 35.7% of all studied markhors from three zoos are introgressed by the domestic goat. Furthermore, despite relatively small breeding group sizes, markhors have maintained a relatively high proportion of mtDNA variation within zoo groups. In any case, the existence of markhors introgressed with domestic goat DNA in zoos should be considered when selecting markhors for ex situ breeding programs with the aim of building up a stock for later reintroduction into the wild.     

Genetic diversity of Nubian ibex in comparison to other ibex and domesticated goat species

Capra nubiana is a wild ibex species that is in danger of extinction. This study aimed at assessing the genetic diversity and population structure of Nubian ibex (Capra nubiana, n?=?8) in comparison to Alpine ibex (Capra ibex, n?=?8), Bezoar ibex (Capra aegagrus, n?=?4), and domesticated Taggar goats (Capra aegagrus hircus, n?=?24). All animals were genotyped with the 50K goat SNP chip. Since commercial SNP chips are not designed for wild species, data analysis was done in two ways: (1) using all callable SNPs (33,698) and (2) with a reduced set of SNPs segregating within three out of four populations (662). Using these two sets of SNPs, the observed heterozygosity in Nubian ibex ranged from 0.02 to 0.44, in Alpine ibex from 0.01 to 0.38, and in Bezoar ibex from 0.13 to 0.38, when analyzing 33,698 or 662 SNPs, respectively. In domesticated Taggar goats, the values for the observed heterozygosity using all 33,698 callable SNPs and the reduced set of 662 SNPs were similar (0.40–0.41). Pairwise F_ST values for the differentiation between species ranged from 0.17–0.35 (Bezoar ibex vs. Taggar goats) to 0.47–0.91 (Bezoar vs. Alpine ibex), and was 0.33–0.90 between Bezoar and Nubian ibex, respectively, to the two sets of SNPs. The analysis of molecular variance among all animals revealed that 74–78% can be explained by differences between species, while the residual 22–26% result from differences among individuals, respectively. Cluster analysis of Nei’s genetic distance allowed to detected two distinct clusters comprising Nubian and Alpine ibex on one hand and Taggar goats and Bezoar ibex on the other hand, and clear separation of all four breeds. Principal component (PC) analysis confirmed and further refined the clusters. SNPs that contributed most to PC1 allowed us to identify genomic regions accounting for the distances between species. These regions contain known milk protein genes. The identification of milk protein genes as contributors to the differentiation between species provides insights into the domestication of wild Capra breeds.     

Phylogenetic reconstructions in the genus <Emphasis Type="Italic">Capra</Emphasis> (Bovidae,Artiodactyla) based on the mitochondrial DNA analysis

Mitochondrial genome fragments were examined in all species of the genus Capra (Bovidae, Artiodactyla). Phylogenetic analysis was carried out using 59 cytochrome b gene sequences (392 bp), and 22 sequences of the mtDNA variable fragment (402 bp). In the control region, two unique deletions were revealed. One of the deletions was found only in Capra cylindricornis (17 bp), while another one grouped C. caucasica with C. aegagrus (1 bp). The group of Caucasian wild goats splits into two clades, and furthermore, the sequences of C. caucasica demonstrate remarkable similarity to the sequences of C. aegagrus, while C. cylindricornis seems to have evolved independently for a long period of time. It was demonstrated that C. pyrenaica and C. ibex were extremely close to one another. Capra sibirica formed an outer group relative to the other species, and according to our data, was the most ancient species of the genus. On the contrary, genetic distance separating C. falconeri (the most independent species of the genus related to its morphology) from the other species is small.     

The wild goats Capra aegagrus Erxleben, 1777 of the Mediterranean Sea and the Eastern Atlantic Ocean islands

• 1 Populations of wild goats that can be referred to as phenotypes of the pasang, or Bezoar goat, or wild goat Capra aegagrus Erxleben, 1777, still occur on several of the Mediterranean and Eastern Atlantic islands. Other populations became extinct not many decades ago.
• 2 Fossil evidence for the natural spread of the wild goat to any of these islands has not been found. Originating in the Near East, the region of its natural range and its earliest domestication, the species was introduced by humans onto the Mediterranean islands starting as early as the Pre‐Pottery Neolithic.
• 3 The islands of the Eastern Atlantic were colonized artificially by animals of ‘pre‐Hispanic’ origin. The principal phenotypes expressed by all these populations of goats can be matched with the characteristics of both C. a. aegagrus Erxleben, 1777 (aegagrus phenotype) and C. a. dorcas Reichenow, 1888 (dorcas phenotype).
• 4 Most of these animals currently survive on the islands without being fed by humans, and should be protected.

     

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication

Background

Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics.

Results

We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits.

Conclusion

Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1606-1) contains supplementary material, which is available to authorized users.     

Mitochondrial DNA Reveal that Domestic Goat (Capra hircus) are Genetically Affected by Two Subspecies of Bezoar (Capra aegagurus)

This article describes the complete sequences of the mitochondrial DNA displacement loop (D-loop) region and cytochrome b gene from domestic goats in Laos (Laos native) and wild goat markhor (C. falconeri). The wild goat bezoar (Capra aegagrus) has been considered to be the strongest candidate for the ancestor of the domestic goats (C. hircus); however, there is not sufficient molecular data to verify the hypothesis at present. In phylogenetic analyses, two wild goats, the markhor and the ibex (C. ibex), appeared as an outgroup, while the bezoar was located in a cluster of domestic goats. Mitochondrial haplotypes of Laos natives revealed two distinct major clusters: one was the same as the bezoar, the second, unique to Laos natives. The topology and calibrated levels of sequence divergence suggests that these clusters might represent at least two different subspecies of ancestral bezoars.     

The Origin and Genetic Status of Insular Caprines in the Eastern Mediterranean: A Case Study of Free-Ranging Goats (Capra aegagrus cretica) on Crete

The history and species status of free-ranging goats inhabiting the Eastern Mediterranean islands is discussed with reference to morphometric, archaeological and genetic findings. A case study on the free-ranging goats on Crete (Capra aegagrus cretica) is presented. The phenotype of the Cretan goat resembles that of the wild bezoar goat (C. aegagrus). However, the mitochondrial DNA of cytochrome b and d-loop sequences shows affinity with domestic goats. It has been suggested that the Cretan goat represents a feral animal that was introduced onto the island during the 6th millennium b.c. as a primitive domestic, and has retained the wild morphotype but has undergone significant genetic change. An alternative explanation, and the one that is proposed here, is that the goat was introduced onto the island in wild form and released as a food source. Subsequent introgressions with domestic animals, especially ewes, have influenced its genotype. These conclusions are applicable to other free-living goats and sheep which inhabit islands in the Eastern Mediterranean.     

Polymorphism and nucleotide sequencing of BMPR1B gene in prolific Assam hill goat

Assam hill goat (Capra hircus) is a prolific local goat in India. bone morphogenetic protein receptor (BMPR1B) gene was studied as a candidate gene for the prolificacy of goats. The objective of the present study was to detect the incidence of mutation in the exonic region of BMPR1B gene of Assam hill goat. Total 90 blood samples were collected randomly from different parts of Assam and genomic DNA were extracted using phenol–chloroform method. The quantity and quality of extracted DNA was examined by spectrophotometry and gel electrophoresis, respectively. PCR amplicon showed a product of 140 bp fragment of BMPR1B gene. The purified product upon digestion with AvaII showed monomorphic banding pattern and revealed wild type alleles with AA genotype. Nucleotide sequencing showed one new mutation 773 (G→C) which is found to be unique in Assam hill goat. Construction of tree at nucleotide level generates from the present experiment lies in common cluster which differs from the other breeds of goat. The analysis of polymorphism for BMPR1B in Assam hill goat indicates that the genetic factor responsible for prolificacy or multiple kidding rates is not related to the reported mutated alleles of BMPR1B gene. Therefore, attempts to be made to detect other SNPs for BMPR1B gene or otherwise effort should be made towards other fecundity gene which might be responsible for the prolificacy of Assam hill goat.     

Habitat associations of wild goat in central Iran: implications for conservation

Wild goat (Capra aegagrus) is one of the highly valued but threatened ungulates of Iran. Seasonal habitat use of wild goat was studied from October 2006 to September 2008 in Haftad Gholleh Protected Area, central Iran. We developed averaged logistic regression models based on Akaike Information Criterion weights for each season. The obtained habitat suitability models showed high sensitivity (greater than 88%) for all evaluation datasets. Wild goat habitat use was positively related with steep slopes, areas near rocky substrates and water sources, west-facing slopes and areas far from roads in all seasons. Core zones of protected area covered nearly 70% of suitable habitats for wild goats, predicted by logistic regression models. Northern core zone covered more than 61% of predicted suitable habitats, which should receive more attention in management actions. The southern core zone boundaries should be considered to increase the encompassed suitable habitats. There was a substantial overlap between seasonal suitable habitats with the highest overlap observed between spring and summer and summer and fall.     

Bioremediation potential of Palmaria palmata and Chondrus crispus (Basin Head): effect of nitrate and ammonium ratio as nitrogen source on nutrient removal

Palmaria palmata and Chondrus crispus were grown for 4 weeks in 1-L flasks at 10 °C to evaluate nutrient uptake and their potential application as nutrient biofilters in effluent from finfish culture. For greatest bioremediation benefit within an integrated system, we conclude that a seaweed biofilter using these species should be placed prior to bacterial biofiltration for exposure to greater proportions of ammonium than nitrate, though it is apparent that the productivity of both species is not influenced by the nitrogen source. Five combinations of ammonium– and nitrate–nitrogen were compared, each with a total N concentration of 300 μM (300:0, 270:30, 150:150, 30:270, 0:300). Molar nitrogen/phosphorus ratio was 10:1. The maximum growth rates were 8.9 and 6.0 % per day for P. palmata and C. crispus, respectively. For both species, the total nitrogen uptake was highest at 300 μM ammonium, 4.46 mgN gDW^?1 day^?1 for P. palmata and 3.40 mg?N? g?DW^?1?day^?1 for C. crispus. Over a 24-h period, 23–37 % of the available nitrate and 91–100 % of the available ammonium were taken up by P. palmata. In the same period, C. crispus took up 55–87 % of available nitrate and 89–100 % of ammonium. Tissue N in P. palmata was highest (4.1 %) at 270 and 300 μM ammonium, while the nitrogen source did not have a significant effect on the tissue N of C. crispus (mean of 4.6 %).     

Besprechungen

Book reviewed in this article: Bücher: Haider, U. (1976): Ökologie und Verhalten des Banteng (Bos javanicus) in Java — Eine Feldstudie. Papageorgiou, N. (1979): Population energie relationships of the Agrimi (Capra aegagrus cretica) on Theodorou Island, Greece (Ökologie der kretischen Wildziege auf der Insel Theodorou). Aeschbacher, A. (1978): Das Brunftverhalten des Alpensteinwildes, Capra ibex ibex L. Eine ethologische Beschreibung des Fortpflanzungsverhaltens. Geist, V. (1974): Mountain Sheep. A Study in Behavior and Evolution (Wildschafe. Verhalten und Evolution). Leuthold, W. (1977): African Ungulates. A Comparative Review of their Ethology and Behavioral Ecology (Afrikanische Huftiere. Piatt, D. (1976): Biologie des Alterns.     

Assessing the Role of Livestock in Big Cat Prey Choice Using Spatiotemporal Availability Patterns

Livestock is represented in big cat diets throughout the world. Husbandry approaches aim to reduce depredation, which may influence patterns of prey choice, but whether felids have a preference for livestock or not often remains unclear as most studies ignore livestock availability. We assessed prey choice of the endangered Persian leopard (Panthera pardus saxicolor) in Golestan National Park, Iran, where conflict over livestock depredation occurs. We analyzed leopard diet (77 scats) and assessed wild and domestic prey abundance by line transect sampling (186 km), camera-trapping (2777 camera days), double-observer point-counts (64 scans) and questionnaire surveys (136 respondents). Based on interviews with 18 shepherds, we estimated monthly grazing time outside six villages with 96 conflict cases to obtain a small livestock (domestic sheep and goat) availability coefficient. Using this coefficient, which ranged between 0.40 and 0.63 for different villages, we estimated the numbers of sheep and goats available to leopard depredation. Leopard diet consisted mainly of wild boar (Sus scrofa) (50.2% biomass consumed), but bezoar goat (Capra aegagrus) was the most preferred prey species (I_j = 0.73), whereas sheep and goats were avoided (I_j = -0.54). When absolute sheep and goat numbers (~11250) were used instead of the corrected ones (~6392), avoidance of small livestock appeared to be even stronger (I_j = -0.71). We suggest that future assessments of livestock choice by felids should incorporate such case-specific corrections for spatiotemporal patterns of availability, which may vary with husbandry methods. Such an approach increases our understanding of human-felid conflict dynamics and the role of livestock in felid diets.     

Tobermolite effects on methane removal activity and microbial community of a lab-scale soil biocover

Three identical lab-scale biocovers were packed with an engineered soil (BC 1), tobermolite only (BC 2), and a mixture of the soil and tobermolite (BC 3), and were operated at an inlet load of 338–400 g-CH₄ m^?2 d^?1 and a space velocity of 0.12 h^?1. The methane removal capacity was 293 ± 47 g-CH₄ m^?2 d^?1 in steady state in the BC 3, which was significantly higher than those in the BC 1 and BC 2 (106 ± 24 and 114 ± 48 g-CH₄ m^?2 d^?1, respectively). Quantitative PCR indicated that bacterial and methanotrophic densities (6.62–6.78 × 10⁷ 16S rDNA gene copy number g-dry sample^?1 and 1.37–2.23 × 10⁷ pmoA gene copy number g-dry sample^?1 in the BC 1 and BC 3, respectively) were significantly higher than those in the BC 2. Ribosomal tag pyrosequencing showed that methanotrophs comprised approximately 60 % of the bacterial community in the BC 2 and BC 3, while they only comprised 43 % in the BC 1. The engineered soil favored the growth of total bacteria including methanotrophs, while the presence of tobermolite enhanced the relative abundance of methanotrophs, resulting in an improved habitat for methanotrophs as well as greater methane mitigation performance in the mixture. Moreover, a batch experiment indicated that the soil and tobermolite mixture could display a stable methane oxidation level over wide temperature (20–40 °C, at least 38 μmol g-dry sample^?1 h^?1) and pH (5–8, at least 61 μmol g-dry sample^?1 h^?1) ranges. In conclusion, the soil and tobermolite mixture is promising for methane mitigation.     

A variety of glycolipids in green photosynthetic bacteria

The compositions of glycolipids in the following seven strains of green photosynthetic bacteria were investigated at the molecular level using LC–MS coupled with an evaporative light scattering detector: Chlorobium (Chl.) limicola strains Larsen (30 °C as the optimal cultivation temperature) and DSM245 (30 °C), Chlorobaculum (Cba.) tepidum strain ATCC49652 (45 °C), Cba. parvum strain NCIB8327 (30 °C), Cba. limnaeum strain 1549 (30 °C), Chl. phaeovibrioides DSM269 (30 °C), and Chloroflexus (Cfl.) aurantiacus strain J-10-fl (55 °C). Dependence of the molecular structures of glycolipids including the chain-length of their acyl groups upon bacterial cultivation temperatures was clearly observed. The organisms with their optimal temperatures of 30, 45, and 55 °C dominantly accumulated glycolipids possessing the acyl chains in the range of C₁₅–C₁₆, C₁₆–C₁₇, and C₁₈–C₂₀, respectively. Cba. tepidum with an optimal temperature of 45 °C preferred the insertion of a methylene group to produce finally a C₁₇-cyclopropane chain. Cfl. aurantiacus cultured optimally at 55 °C caused a drastic increase in the chain-length. Notably, the length of such acyl groups corresponded to that of the esterifying chain in the 17-propionate residues of self-aggregative bacteriochlorophylls-c/d/e, indicating stabilization of their supramolecular structures through hydrophobic interactions among those hydrocarbon chains. Based on the detailed compositions of glycolipids, a survival strategy of green photosynthetic bacteria grown in the wide range of temperatures is discussed.     

Behavioral and neuroendocrine response of Brandt's voles,Lasiopodomys brandtii,to odors of different species

Predator odors are nonintrusive natural stressors of high ethological relevance. Behavioral and hormonal responses and changes in the expression of medial hypothalamic c-fos mRNA were examined in Brandt's voles (Lasiopodomys brandtii) after exposure to feces of a domestic cat (Felis catus), weasel (Mustela sibirica), snake (Xenopeltis hainanensis), goat (Capra aegagrus), and distilled water (control). One hundred voles were tested in the defensive withdrawal apparatus. Voles showed an aversion to the predator odors by showing significant high levels of flight-related behaviors, more freezing behavior, and less and higher grooming behavior when they exposed to weasel and cat feces and more vigilant rearing compared to goat and control groups. Adrenocorticotropic hormone and corticosterone serum levels significantly increased when voles were exposed to the predator odors compared to voles exposed to goat and control odors. A significant high c-fos mRNA level indicates a strong predator odor-induced activation of the medial hypothalamus of the tested voles. Our results display significant fear responses of Brandt's voles exposed to predator odors and that they can skillfully differentiate between odors from different species with odors from sympatric predators triggering the highest responses.     

Halomonas zhaodongensis sp. nov., a slightly halophilic bacterium isolated from saline–alkaline soils in Zhaodong, China

A slightly halophilic bacterium (strain NEAU-ST10-25^T) was isolated from saline–alkaline soils in Zhaodong City, Heilongjiang Province, China. The strain is a Gram-negative, aerobic motile rod. It accumulates poly-β-hydroxyalkanoate and produces exopolysaccharide. It produces beige-yellow colonies. Growth occurs at NaCl concentrations (w/v) of 0–15 % (optimum 3 %), at temperatures of 4–60 °C (optimum 35 °C) and at pH 6–12 (optimum pH 9). Its G+C content is 53.8 mol%. Phylogenetic analyses based on the separate 16S rRNA gene and concatenation of the 16S rRNA, gyrB and rpoD genes indicate that it belongs to the genus Halomonas in the class Gammaproteobacteria. The most phylogenetically related species is Halomonas alkaliphila DSM 16354^T, with which strain NEAU-ST10-25^T showed 16S rRNA, gyrB and rpoD gene sequence similarities of 99.2, 82.3 and 88.2 %, respectively. The results of DNA–DNA hybridization assays showed 60.47 ± 0.69 % DNA relatedness between strain NEAU-ST10-25^T and H. alkaliphila DSM 16354^T, 42.43 ± 0.37 % between strain NEAU-ST10-25^T and Halomonas venusta DSM 4743^T and 30.62 ± 0.43 % between strain NEAU-ST10-25^T and Halomonas hydrothermalis DSM 15725^T. The major fatty acids are C_18:1 ω7c (62.3 %), C_16:0 (17.6 %), C_16:1 ω7c/C_16:1 ω6c (7.7 %), C_14:0 (2.9 %), C_12:0 3-OH (2.8 %), C_10:0 (2.1 %) and C_18:1 ω9c (1.6 %) and the predominant respiratory quinone is ubiquinone 9 (Q-9). The proposed name is Halomonas zhaodongensis, NEAU-ST10-25^T (=CGMCC 1.12286^T = DSM 25869^T) being the type strain.     

Rhizobium halotolerans sp. nov., Isolated from Chloroethylenes Contaminated Soil

The strain designated as AB21^T was isolated from chloroethylenes contaminated soil. Cells are gram-negative, aerobic, non-spore-forming, and motile rods. Phylogenetic analysis based on 16S rRNA gene sequence showed that it belonged to the genus Rhizobium, and was closely related to Rhizobium sullae IS 123^T (97.4 %), Rhizobium yanglingense SH 22623^T (97.2 %), Rhizobium gallicum R 602sp^T (97.1 %), Rhizobium alamii GBV 016^T (97.0 %), and Rhizobium monogolense USDA 1844^T (97.0 %). It showed less than 97 % identity with the remaining Rhizobium species. This novel isolate grew optimally at 25–37 °C (optimum, 30 °C) and pH 6–9 (optimum, pH 8.0). It grew in the presence of 0–4 % (w/v) NaCl, tolerating a 4 % (w/v) NaCl. DNA–DNA hybridization experiment shows less than 53 % binding with closely related Rhizobium. Predominant quinone is ubiquinone (Q-10). The major fatty acids were summed feature 8 (composed of C_18:1 ω7c/C_18:1 ω6c), C_19:0 cyclo ω8c, and C_16:0. The G+C molar content is 62.5 mol%. Based on the polyphasic analysis, strain AB21^T is referred to be a novel species of the genus Rhizobium for which the name Rhizobium halotolerans sp. nov. is proposed. The type strain is AB21^T (=KEMC 224-056^T = JCM 17536^T).     

The return of the Iberian wild goat Capra pyrenaica to Portugal: From reintroduction to recolonization

The Iberian wild goat (Capra pyrenaica) is an endemic species of the Iberian Peninsula. Of the four generally accepted subspecies (Capra pyrenaica victoriae, C.p. hispanica, C.p. pyrenaica, C.p. lusitanica) only two subsist (C.p. victoriae, C p. hispanica). The subspecies once found in Portugal, C. p. lusitanica, became extinct in the 19th century. However, the reintroduction of the C. p. victoriae in north-west Spain, led to the natural recolonization of this subspecies into Portugal. Knowledge of the Iberian wild goat in Portugal is still limited, making it difficult to evaluate the major conservation/management needs. To fill this gap, here we describe the historical distribution of the Iberian wild goat in Portugal and summarize the available information on the reintroduction and recolonization process of this species. Additionally, we used line itinerary survey (2011–2012), coupled with Distance Sampling, to estimate current densities, range and population structure of the Iberian wild goat distribution in Portugal. The Iberian wild goat density is 2.78/100 ha (95% CI: 1,72–4,50; CV: 18,36%) and the abundance is of 576 (CI 95%: 356–930; CV: 18,36%). The distribution data shows that the population is divided in three nuclei: 1- Serra do Gerês (13,840 ha); 2–Serra Amarela (1235 ha); 3–Castro Laboreiro (343 ha), in a total area of 15,418 ha. Iberian wild goat population in Portugal has greatly increased in the last years, both in number and distribution range. The demographic data shows a potential for increase in the next years but our current ecological background knowledge still remains limited. Iberian wild goat management will benefit from a long-term project including public awareness, scientific research and management solutions.     

Sphingomonas gimensis sp. nov., a novel Gram-negative bacterium isolated from abandoned lead–zinc ore mine

A novel bacterial strain designated 9PNM-6^T was isolated from an abandoned lead–zinc ore mine site in Meizhou, Guangdong Province, China. The isolate was found to be Gram-negative, rod-shaped, orange-pigmented, strictly aerobic, oxidase- and catalase-positive. Growth occurred at 0–4 % NaCl (w/v, optimum, 0 %), at pH 6.0–8.0 (optimum, pH 7.0) and at 15–32 °C (optimum, 28–30 °C). Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain 9PNM-6^T belongs to the genus Sphingomonas, with the highest sequence similarities with Sphingomonas jejuensis NBRC 107775^T (99.7 %), Sphingomonas koreensis KCTC 2882^T (95.1 %) and Sphingomonas dokdonesis KCTC 12541^T (95.1 %). The chemotaxonomic characteristics of strain 9PNM-6^T were consistent with those of the genus Sphingomonas. The predominant respiratory quinone was identified as ubiquinone Q-10, the major polyamine as sym-homospermidine, and the major cellular fatty acids as C_18:1 ω7c, C_16:0, C_16:1 ω7c and/or C_16:1 ω6c and C_14:0 2-OH. The major polar lipids are sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatideylcholine, an unidentified phospholipid and four unidentified aminolipids. The genomic DNA G+C content of strain 9PNM-6^T was determined to be 69.2 ± 0.6 mol%. Based on comparative analyses of morphological, physiological and chemotaxonomic data, and levels of DNA–DNA relatedness values, strain 9PNM-6^T is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas gimensis sp. nov. (Type strain 9PNM-6^T = GIMCC 1.655^T = CGMCC 1.12671^T = DSM 27569^T) is proposed.     

Response of Antarctic, temperate, and tropical microalgae to temperature stress

The global temperature increase has significant implications on the survival of microalgae which form the basis of all aquatic food webs. The aim of this study was to compare the response of similar taxa of microalgae from the Antarctic (Chlamydomonas UMACC 229, Chlorella UMACC 237, and Navicula glaciei UMACC 231), temperate (Chlamydomonas augustae UMACC 247, Chlorella vulgaris UMACC 248, and Navicula incerta UMACC 249), and tropical (C. augustae UMACC 246, C. vulgaris UMACC 001, and Amphiprora UMACC 239) regions to changing temperature. The Antarctic, temperate, and tropical strains were grown over specific temperature ranges of 4 °C to 30 °C, 4 °C to 32 °C, and 13 °C to 38 °C, respectively. The three Antarctic strains survived at temperatures much higher than their ambient regime. In comparison, the tropical strains are already growing at their upper temperature limits. The three Chlorella strains from different regions are eurythermal, with a large overlap on tolerance ranging from 4 °C to 38 °C. The specific growth rate (μ) of the Antarctic Navicula decreased (<0.34 day^?1) at temperatures above 4 °C, showing it to be sensitive to temperature increase. If further warming of Earth occurs, N. glaciei UMACC 231 is likely to have the most deleterious consequences than the other two Antarctic microalgae studied. The percentage of polyunsaturated fatty acids (PUFA) decreased with increasing temperature in the Antarctic Navicula. As temperature increases, the growth and nutritional value of this commonly occurring diatom in the Antarctic may decrease, with consequences for the aquatic food web. Of the three Chlamydomonas strains, only the Antarctic strain produced predominantly PUFA, especially 16:3 (48.4–57.2 % total fatty acids).