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The high antibiotic resistance gene (ARGs) contents in livestock manure pose a potential risk to environment and human health. The heap composting with an ambient temperature and thermophilic composting are two methods for converting livestock manure into fertilizer. This study investigated the variations in ARGs and mobile genetic elements (MGEs) and revealed potential mechanisms for ARGs removal using the two composting methods. The ARGs abundance were enriched by 44-fold in heap composting, among them, the macrolide-resistance genes increased significantly. On the contrary, the ARGs were removed by 92% in thermophilic composting, among them, tetracycline-resistance genes decreased by 97%. The bacterial hosts of ARGs were associated with the variations of ARGs and MGEs. The tetO was correlated with the most diverse bacteria in heap composting, and Bacteroidetes was the major host bacteria. While tetT was correlated with the most diverse bacteria in thermophilic composting, and Proteobacteria was the major host bacteria. Structural equation models showed that the enrichment of ARGs in heap composting was mainly correlated with bacterial communities, whereas, the removal of ARGs in thermophilic composting was directly affect by MGEs. Composting temperature directly affected the variations in ARGs. Higher and lower temperatures significantly decreased and increased, respectively, ARGs and MGEs abundance levels.

Sulfate-reducing bacteria are a group of microorganisms that use sulfate as an electron acceptor. These bacteria are useful in the bioremediation of heavy metal pollution since they can reduce/precipitate metals. Previously, we identified the Alishewanella strain WH16-1 from soil of a copper and iron mine and determined that it can reduce sulfate and chromate and that it was tolerant to many heavy metals. In this study, we investigated the chromate reduction mechanism of strain WH16-1 through Tn5 transposon mutagenesis. A cytochrome bd (cytbd) Tn5 mutant was generated (Δcytbd), and a detail analysis showed that the following: (1) gene cydE (coding for a GbsR-type regulator) was co-transcribed with the two subunits coding genes of the Cytochrome bd complex (Cytbd), namely, cydA and cydB, based on RT-PCR analysis, and similar gene arrangements were also found in other Alteromonadaceae family strains; (2) the chromate resistance level was dramatically decreased and chromate reduction efficiency also decreased in strain Δcytbd compared to the wild-type and a complemented strain (Δcytbd-C); (3) Cytbd could catalyze the decomposition of H2O2 according to the analyses of H2O2 decomposition ability, cellular H2O2 contents, H2O2 inhibition zone, and H2O2 sensitivity tests; (4) surprisingly, chromate was not an inducer of the expression of Cytbd, but sulfate induced expression of Cytbd, and sulfate/sulfide resistance levels were also decreased in the Δcytbd strain; (5) the addition of sulfate enhanced the chromate resistance level and reduction efficiency; (6) Cytbd expression was repressed by CydE and derepressed by sulfate based on an in vivo bacterial one hybrid system and in vitro EMSA tests; and (7) DNA footprinting and short-fragment EMSA tests revealed two binding sites of CydE in its promoter region. All these results showed that Cytbd is negatively regulated by CydE and derepressed by sulfate. In addition, Cytbd contributes to the resistance of sulfate and sulfide, and sulfide could be used as a reductant to reduce chromate. Moreover, Cytbd is essential to decompose H2O2 to decrease cellular oxidative stress. Thus, the regulation and function of Cytbd may explain why sulfate could enhance chromate reduction.

A hypotrichous ciliate, Paracladotricha salina n. g., n. sp., was discovered in hypersaline waters (salinity about 80‰) from Qingdao, China. Its morphology and some major ontogenetic stages were studied and the phylogenetic position was estimated using standard methods. Paracladotricha salina is characterized by a flexible, more or less slender body (size 50–120 × 20–35 μm), a gonostomatid oral apparatus, one short and two long frontoventral rows, four macronuclear nodules, almost completely reduced dorsal kineties 1–3, and a loss of several parts of the ciliature, namely, the slightly shortened ciliary row of the adoral membranelles, the paroral, and the buccal, the postoral and pretransverse ventral, the transverse, and the caudal cirri. The ontogenesis is rather simple: anlage II of both filial products and anlage III of the opisthe originate de novo, while anlagen IV and V are formed within the parental rows. This combination of features requires the establishment of a new genus, Paracladotricha, which is, according to the morphological data, closely related to Schmidingerothrix and Cladotricha. The small-subunit rRNA gene was sequenced, indicating that P. salina is, as also demonstrated by the oral apparatus, a member of the gonostomatids. We provide a first, vague hypothesis about the phylogenetic relationships of the Gonostomatidae, Cladotrichidae, and Schmidingerotrichidae. However, since molecular data of the type species of these higher taxa are lacking, their validity and relationships remain obscure.

A Gram-negative, aerobic, copper-resistant bacterium, designated strain CU4T, was isolated from copper mine soil in Daye, China. Phylogenetic analysis based on 16S rRNA gene sequences showed highest similarity to Sphingobium rhizovicinum CC-FH12-1T (98.4 %), followed by Sphingobium francense Sp+T (97.2 %), Sphingobium japonicum UT26T (97.1 %), Sphingobium abikonense NBRC 16140T (97.0 %), Sphingobium xenophagum DSM 6383T (96.9 %) and Sphingobium yanoikuyae DSM 7462T (95.5 %). The major fatty acids (>5 %) were summed feature 7 (C18 : 1ω7c, C18 : 1ω9t and/or C18 : 1ω12t), summed feature 4 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C14 : 0 2-OH, and the predominant quinone was ubiquinone Q-10. Spermidine was the major polyamine component. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidyldimethylethanolamine and phosphatidylcholine. The genomic DNA G+C content of strain CU4T was 64.9 mol%. Comparison of DNA–DNA hybridization, phenotypic and chemotaxonomic characteristics between strain CU4T and phylogenetically related strains revealed that the new isolate represents a novel species of the genus Sphingobium , for which the name Sphingobium cupriresistens sp. nov. is proposed. The type strain is CU4T ( = KCTC 23865T = CCTCC AB 2011146T). An emended description of the genus Sphingobium is also proposed.

Alishewanella sp. WH16-1 (= CCTCC M201507) is a facultative anaerobic, motile, Gram-negative, rod-shaped bacterium isolated from soil of a copper and iron mine. This strain efficiently reduces chromate (Cr6+) to the much less toxic Cr3+. In addition, it reduces sulfate (SO42−) to S2−. The S2− could react with Cd2+ to generate precipitated CdS. Thus, strain WH16-1 shows a great potential to bioremediate Cr and Cd contaimination. Here we describe the features of this organism, together with the draft genome and comparative genomic results among strain WH16-1 and other Alishewanella strains. The genome comprises 3,488,867 bp, 50.4 % G + C content, 3,132 protein-coding genes and 80 RNA genes. Both putative chromate- and sulfate-reducing genes are identified. Electronic supplementary material The online version of this article (doi:10.1186/s40793-016-0169-3) contains supplementary material, which is available to authorized users.

The systematic position of the scuticociliate, Philaster, has been highly ambiguous owing to a lack of either morphogenetic or molecular information. The small subunit rRNA gene of a new species, Philaster apodigitiformis sp. nov. was isolated from eggs of the puffer fish (Takifugu rubripes), was sequenced, and phylo‐genetic trees were constructed with different methods to assess its position and relationship among the scuticociliates. Results indicate that (1) Philaster apodigitiformis clearly falls into the order Philasterida and it is most closely related to the Uronema‐Paranophrys assemblage, which groups with clusters consisting of families Uronematidae, Parauronematidae, Thyrophilacidae and Entorhipidiidae; (2) the two genera Philaster and Philasterides presently assigned to the family Philaster‐idae are in widely separated clades, indicating that the family is polyphyletic; and (3) the morphological similarity of Philaster and Philasterides is probably an example of evolutionary convergenc...

A population of Kiitricha minuta Xu et al., 2008, a small kiitrichid ciliate, was isolated from a brackish water sample in Jiaozhou Bay, Qingdao, northern China. After comparison of its morphology and infraciliature, it is believed that this morphotype should be assigned to the genus Caryotricha; hence, a new combination is suggested, Caryotricha minuta (Xu et al., 2008) nov. comb. The small-subunit (SSU) rRNA gene sequence was determined in order to elucidate the phylogenetic position of this poorly known, ambiguous genus. The organism can be clearly separated from its congener, Caryotricha convexa Kahl, 1932, by the extremely shortened ventral cirral rows in the posterior ends. Based on the data available, an improved diagnosis is given for the genus: marine Kiitrichidae with prominent buccal field; two highly developed undulating membranes; non-grouped, uniform cirral rows on both ventral and dorsal sides; enlarged transverse cirri present, which are the only differentiated cirri; marginal cirri not present; one short migratory row located posterior to buccal field; structure of dorsal kineties generally in Kiitricha pattern. The sequence of the SSU rRNA gene of C. minuta differs by 13 % from that of Kiitricha marina. Molecular phylogenetic analyses (Bayesian inference, least squares, neighbour joining, maximum parsimony) indicate that Caryotricha, together with Kiitricha, diverges at a deep level from all other spirotrichs. Its branching position is between Phacodiniidia and Licnophoridia. The results strongly support the distinct separation of the Kiitricha-Caryotricha clade, which always branches basal to the Stichotrichia-Hypotrichia-Oligotrichia-Choreotrichia assemblage. These results also confirm the previous hypothesis that the Kiitricha-Caryotricha group, long assumed to be a close relation to the euplotids, represents a taxon at subclass level within the spirotrichs.

The morphology, morphogenesis and small subunit rRNA (SSrRNA) gene sequence of a new marine euplotid ciliate, Diophrys apoligothrix spec. nov., isolated from a sandy beach near Qingdao, north China, were investigated. This organism is characterized as follows: rigid body with a sculptured surface; size in vivo about 60-110 x 40-70microm; adoral zone comprising about 28 membranelles; five frontal, two ventral, five transverse, one left marginal and three caudal cirri; five dorsal kineties with sparsely distributed dikinetids; two ellipsoid macronuclear nodules; marine habitat. Although the main morphogenetic events are similar to those reported in other congeners, three features are noteworthy: (1) the parental adoral zone is retained almost unchanged by the proter except for the outer margin of membranelles in the proximal portion, where the de-differentiation and then reorganization take place in situ in the mid-to-late phases of division; (2) the dorsal kinety anlagen are formed via a two-step mode; (3) the marginal cirrus anlage is formed de novo near the old structure and does not divide. Based on the morphological, morphogenetic and SSrRNA gene sequence data, it was concluded that D. apoligothrix is a well-outlined and distinctive member of the genus Diophrys.

Two insufficiently described marine euplotids, Diophrys irmgard Mansfeld (1923) and Diophrys hystrix Buddenbrock (1920), found in coastal waters near Qingdao, China, were reinvestigated with emphasis on their living morphology and infraciliature. Improved diagnoses and redescriptions are supplied for both organisms. Critical redefinitions of nine morphotypes are presented and the validities of the nominal species are discussed and briefly revised. Following Curds and Wu (1983), and based on data obtained during the present study and a critical review of the literature, five additional nominal species are regarded as junior synonyms of known forms: Diophrys quadricaudatus Agamaliev (1967), D. scutoides Agamaliev (1967), and D. tetramacronucleata Kattar (1970) are synonymized with D. scutum (Dujardin 1841), while D. pentacirratus Alekperov (1984) and D. multicirratus Alekperov (1984) are junior synonyms of D. oligothrix Borror (1965).

Uptake of organic solutes and xenobiotics by mammalian cells is mediated by ATP-independent transporters, and four families of transporters have now been identified. To search for novel organic solute transporters, a liver cDNA library from an evolutionarily primitive marine vertebrate, the little skate Raja erinacea , was screened for taurocholate transport activity by using Xenopus laevis oocytes. In contrast to the organic anion transporters identified to date, a transport activity was identified in this library that required the coexpression of two distinct gene products, termed organic solute transporter α and β (Ostα, Ostβ). Ostα cDNA encodes for a protein of 352 aa and seven putative transmembrane (TM) domains. Ostβ contains 182 aa and has at least one and perhaps two TM domains. There is no significant sequence identity between Ostα and Ostβ, and only low identity with sequences in the databases; however, Ostα bears a resemblance to some G protein-coupled receptors, and Ostβ exhibits 22% amino acid identity with the C-terminal TM and intracellular domains of protocadherin-γ, a cell surface glycoprotein. Xenopus oocytes injected with the cRNA for both Ostα and Ostβ, but not each separately, were able to take up taurocholate, estrone sulfate, digoxin, and prostaglandin E 2 , but not p -aminohippurate or S -dinitrophenyl glutathione. Transport was sodium-independent, saturable, and inhibited by organic anions and steroids, including the major skate bile salt, scymnol sulfate. These results identify an organic anion transporter composed of a putative seven-helix TM protein and an ancillary membrane polypeptide.

The morphology and infraciliature of a hypotrichous ciliate collected from brackish-water biotope (salinity 5 parts per thousand) in South Korea were investigated which indicate this organism should be a new form within the genus Anteholosticha Berger, 2003. Careful morphological comparison and SSU rRNA gene sequence alignment with similar species are performed to support the validity of Anteholosticha pseudomonilata n. sp. The main diagnostic and distinguishing characteristics of the new species include: 1) 8-11 transverse cirri; 2) midventral complex composed of 10-16 pairs of zigzagging midventral cirri, extending posteriorly to slightly ahead of pretransverse cirri; 3) cortical granules colourless and pigment-like, 0.5 mu m across, longitudinally arranged in more or less short rows on whole cortex except along dorsal kineties and cirral rows; and 4) 8-12 macronuclear nodules located left of midline.

The morphology and the small subunit (SSU) rRNA gene sequence of the hypotrich Neobakuella flava n. g., n. sp. from the estuary of the Taehwagang River (Ulsan, South Korea) were investigated. The three frontal cirri, the composition of the midventral complex of cirral pairs and rows, and the simple dorsal kinety pattern of three bipolar kineties assign it to the urostyloid taxon Bakuellidae. The increased number of buccal and parabuccal cirri, the presence of transverse cirri, and more than one left marginal row, as well as the lack of caudal cirri separate Neobakuella n. g. from the other bakuellids. Neobakuella flava n. sp. has many 0.3 μm sized green and/or yellow usually dark-green cortical granules and some sparsely distributed, 2 × 1 μm sized grass green with yellowish shimmer granules. The gene sequence data indicate a close relationship with Diaxonella and a distinct separation from the bakuellid Metaurostylopsis and parabirojimid Parabirojimia. The SSU rRNA gene sequences of four further urostyloids (i.e. Diaxonella pseudorubra, Anteholosticha monilata, Metaurostylopsis struederkypkeae, Pseudourostyla cristata) and two stylonychines (i.e. Sterkiella cavicola, Sterkiella histriomuscorum) from Korea were analyzed. Anteholosticha monilata, type of the genus, is clearly separated from the Holosticha clade, supporting the morphological separation from Holosticha. Sterkiella cavicola, type of Sterkiella, clusters within the stylonychines and is obviously closely related with S. histriomuscorum.

The morphology and infraciliature of the marine hypotrichous ciliate Nothoholosticha fasciola (Kahl, 1932) nov. gen., nov. comb., isolated from mariculture waters near Qingdao, China, are redescribed based on live and protargol-impregnated specimens. Features reported for the first time include the possession of more than 50 macronuclear nodules and details of the infraciliature, i.e. 50–60 adoral membranelles, shortened paroral and endoral membranes, six frontal, one buccal and two to seven transverse cirri, ca. 40 pairs of midventral cirri, ca. 60–120 left and 70–120 right marginal cirri, three dorsal kineties, caudal and frontoterminal cirri absent. In addition, brief details of two stages of cellular reorganization in N. fasciola are supplied and comparisons with some related urostylids based on SS rRNA gene sequence data are reported. The new genus Nothoholosticha is established based primarily on the absence of frontoterminal cirri, which distinctly separates it from similar urostylid genera. Anteholosticha longissima is transferred to Nothoholosticha as N. longissima (Dragesco and Dragesco-Kerneis, 1986) nov. comb. and Holosticha antarctica is transferred to Pseudokeronopsis as P. antarctica (Wilbert and Song, 2008) nov. comb.

The morphology and morphogenesis of a new marine hypotrich ciliate, Apokeronopsis bergeri nov. spec., collected from mussel-farming waters near Qingdao, China, are described from living and protargol-impregnated specimens. This ciliate has characteristics that place it in the family Pseudokeronopsidae, namely, two long rows of frontal cirri (bicorona), which are continuous with the long midventral rows, and a single row of marginal cirri on each side of the body. It shares with its only congener, Apokeronopsis crassa, the long rows of buccal and transverse cirri and the wide spacing between the midventral rows of cirri. These characters separate the genus Apokeronopsis from Pseudokeronopsis, which has a single buccal cirrus, fewer transverse cirri and midventral rows of cirri arranged in a typical zig-zag pattern. A. bergeri differs from A. crassa in its shape, colour and in the numbers of membranelles and transverse cirri. Although morphogenesis in A. bergeri is similar to that of A. crassa in most respects, the mode of formation of the buccal cirri is slightly different. The close relationship of A. bergeri with A. crassa, and the more distant relationship with three Pseudokeronopsis species, is supported by a comparison of the sequences of their ITS1-5.8S-ITS2 rDNA regions.

Leptoamphisiella vermisGruber, 1888 n. g., n. comb. (basionym Epiclintes vermisGruber, 1888) is an extraordinarily large and worm-like marine stichotrichous ciliate. Based on a population isolated recently from coastal waters of Qingdao, China, the living morphology and infraciliature are redescribed and its taxonomic position is defined. Accordingly, a new diagnosis for this species is suggested: large, marine Leptoamphisiella with a conspicuous layer of pellicular alveoli; 400-1000 microm x 40-70 microm in vivo; body band-like, highly flexible; about 40 membranelles; always three frontal and two buccal cirri; 52-80 transverse cirri (TC) extending to the posterior end of the buccal field; 57-79 left midventral and 44-62 right midventral cirri; 62-102 cirri in left and 63-91 cirri in right marginal rows (MR); 9-13 dorsal kineties that extend the full body length; about 100 macronuclear nodules and 5-13 micronuclei. The diagnosis for the new genus is as follows: vermiform Pseudoamphisiellidae with strongly contractile body, differentiated frontal, buccal, and highly developed TC; two remarkably separated midventral rows; one MR on each side of the body; frontoterminal and caudal cirri absent. Leptoamphisiella vermis n. comb. is fixed as the type species of the new genus.