Biocementation of Pyrite Tailings Using Microbially Induced Calcite Carbonate Precipitation.

Tailing sand contains a large number of heavy metals and sulfides that are prone to forming acid mine drainage (AMD), which pollutes the surrounding surface environment and groundwater resources and damages the ecological environment. Microbially induced calcium carbonate precipitation (MICP) technology can biocement heavy metals and sulfides in tailing sand and prevent pollution via source control. In this study, through an unconfined compressive strength test, permeability test, and toxic leaching test (TCLP), the curing effect of MICP was investigated in the laboratory and the effect of grouting rounds on curing was also analyzed. In addition, the curing mechanism of MICP was studied by means of Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), X-ray diffraction spectroscopy (XRD), and scanning electron microscopy (SEM). The experimental results showed that MICP could induce calcium carbonate precipitation through relatively complex biochemical and physicochemical reactions to achieve the immobilization of heavy metals and sulfides and significantly reduce the impact of tailing sand on the surrounding environment.

Experimental and theoretical study on the propagation characteristics of stress wave in filled jointed rock mass.

This study is to theoretically and experimentally investigate the propagation of stress waves in the filled joint set. The time-domain recursive method is used to derive the propagation equations in the filled joint set, and the filled joints are further simplified into structural planes without joint thickness. The split-Hopkinson rock bar is modified to simulate P wave propagation normally across the parallel filled joints. The relationship among stress-closure curve, joint specific stiffness, transmission coefficient and loading rate is analyzed. The results show that, for the rock mass with a single joint, both the joint specific stiffness and transmission coefficient of different filling materials increase with loading rate. More serious particle breakage of the filling materials leads to lower joint specific stiffness and transmission coefficient. For the rock mass with two joints, the joint specific stiffness of each joint affects the transmission coefficient of the filled joint set. It is found that our theoretical calculations are basically consistent with the experimental ones, and the joint specific stiffness can well characterize the propagation behavior of stress wave in the filled parallel rock joints.

Phylogenomic evaluation of members above the species level within the phylum Firmicutes based on conserved proteins.

Currently, numerous taxonomic units above species level of the phylum Firmicutes are ambiguously placed in the phylogeny determined by 16S rRNA gene. Here, we evaluated the use of 16S rRNA gene compared with 81 conserved proteins (CPs) or 41 ribosomal proteins (RPs) as phylogenetic markers and applied this to the analysis of the phylum Firmicutes. Results show that the phylogenetic trees constructed are in good agreement with each other; however, the protein-based trees are able to resolve the relationships between several branches where so far only ambiguous classifications are possible. Thus, the phylogeny deduced based on concatenated proteins provides significant basis for re-classifying members in this phylum. It indicates that the genera Coprothermobacter and Thermodesulfobium represent two new phyla; the families Paenibacillaceae and Alicyclobacillaceae should be elevated to order level; and the families Bacillaceae and Thermodesulfobiaceae should be separated to 2 and 3 families respectively. We also suggest that four novel families should be proposed in the orders Clostridiales and Bacillales, and 11 genera should be moved to other existing families different from the current classification status. Moreover, notably, RPs are a well-suited subset of CPs that could be applied to Firmicutes phylogenetic analysis instead of the 16S rRNA gene.

Comparative phylogenies of ribosomal proteins and the 16S rRNA gene at higher ranks of the class Actinobacteria.

The 16S rRNA-based hierarchical system is considered to be the backbone of prokaryote taxonomy at the genus level and above. However, in the class Actinobacteria, the topology of the 16S rRNA-based tree is highly unsteady, and relationships between several families and orders are ambiguous. Recently, phylogenomic information was claimed to provide a more comprehensive understanding of prokaryotic systematics in the genomics era. In this article, a comparative phylogenetic analysis of the class Actinobacteria was carried out using 16S rRNA gene sequences and a set of 46 ribosomal proteins (RPs). Phylogenies based on concatenated RP sequences were generally congruent with 16S rRNA phylogenies, but higher bootstrap values supported the branching orders in the former trees. RP-based trees constructed by the maximum-likelihood and neighbor-joining algorithms provided better-defined phylogenetic relationships within the Actinobacteria and clarified the relationships and positions of several orders, such as Micrococcales and Frankiales. The RP-based phylogeny approach may thus provide a sound basis for assessing the Actinobacteria.

Nocardiopsis valliformis sp. nov., an alkaliphilic actinomycete isolated from alkali lake soil in China.

A strain (HBUM 20028(T)) isolated from alkali lake soil in China was studied by a polyphasic taxonomic approach. The strain produced abundant aerial and substrate mycelia. Long spore chains were borne on the aerial mycelium, and the substrate mycelium was often arranged in a shape like a fence or palisade. The special characteristic of strain HBUM 20028(T) was its abundant growth under alkaline conditions, at pH 8.0-14.0. The cell wall of strain HBUM 20028(T) contained meso-diaminopimelic acid but no diagnostic sugar. Major phospholipids included diphosphatidylglycerol and phosphatidylcholine. The major menaquinones were MK-10(H(2)), MK-10(H(4)) and MK-10(H(6)). The major cellular fatty acids were iso-C(16 : 0) (31.66 %), anteiso-C(17 : 0) (14.85 %) and C(18 : 1)omega9c (14.73 %). All of these characters consistently indicated that strain HBUM 20028(T) belongs to the genus Nocardiopsis. DNA-DNA hybridization between the strain and type strains of related species gave relatedness values far below 70 %. Based on 16S rRNA gene sequence analysis, DNA relatedness and phenotypic characteristics, a novel species with the name Nocardiopsis valliformis sp. nov. is proposed. The type strain is HBUM 20028(T) (=DSM 45023(T) =CGMCC 4.2135(T)).

Nocardiopsis ganjiahuensis sp. nov., isolated from a soil from Ganjiahu, China.

An actinomycete, strain HBUM 20038(T), was isolated from soil from Ganjiahu Natural Reserve in Xinjiang Province, in north-western China, and then characterized using a polyphasic approach. 16S rRNA gene sequence analysis confirmed that strain HBUM 20038(T) was a member of the genus Nocardiopsis, and the morphological and chemotaxonomic characteristics of the strain were also consistent with those of species of Nocardiopsis. DNA-DNA hybridization between the strain and related type strains gave relatedness values far below 70%. These results, together with physiological characteristics, showed that strain HBUM 20038(T) represents a novel species within the genus Nocardiopsis, for which the name Nocardiopsis ganjiahuensis sp. nov. is proposed. The type strain is HBUM 20038(T) (=DSM 45031(T) =CGMCC 4.3500(T)).

Classification of Streptomyces griseus (Krainsky 1914) Waksman and Henrici 1948 and related species and the transfer of 'Microstreptospora cinerea' to the genus Streptomyces as Streptomyces yanii sp. nov.

A soil actinomycete, strain 80-133(T), with the non-validly published name 'Microstreptospora cinerea', was the subject of a polyphasic study designed to clarify its taxonomic status. Comparative 16S rRNA gene sequence studies indicated that the organism belonged to the genus Streptomyces, a result in line with previous chemotaxonomic and morphological data. The strain belonged to the Streptomyces griseus clade, but could be distinguished from representatives of species assigned to this taxon by using DNA-DNA relatedness and phenotypic data. In light of these findings, it is proposed that the organism should be recognized as a novel species of the genus Streptomyces. The name proposed for this taxon is Streptomyces yanii sp. nov., with isolate 80-133(T) (=AS 4.1146(T)=JCM 3331(T)) as the type strain. It was also shown that representative strains of Streptomyces argenteolus, Streptomyces caviscabies, S. griseus and Streptomyces setonii belong to the same genomic species and have key phenotypic properties in common. It is proposed that S. caviscabies and S. setonii should be considered as later heterotypic synonyms of S. griseus and that S. argenteolus AS 4.1693(T) should also be assigned to this taxon.

Actinomadura catellatispora sp. nov. and Actinomadura glauciflava sp. nov., from a sewage ditch and soil in southern China.

Two soil isolates, strains 80-60T and 3.24T, were shown to have chemical and morphological properties consistent with their classification in the genus Actinomadura. The almost complete 16S rDNA sequences generated for the two organisms were aligned with available sequences of representatives of the genus Actinomadura and related taxa. It was apparent from the resultant phylogenetic trees that each of the strains formed a distinct phyletic line within the evolutionary radiation occupied by the genus Actinomadura. The two organisms could also be distinguished from one another and from representatives of all the validly described species of Actinomadura using a set of phenotypic properties. It is proposed that strains 3.24T (=AS 4.1522T =IFO 16341T) and 80-60T (=AS 4.1202T =IFO 14668T =JCM 16161T) be classified in the genus Actinomadura as Actinomadura catellatispora sp. nov. and Actinomadura glauciflava sp. nov., respectively.

Streptomyces beijiangensis sp. nov., a psychrotolerant actinomycete isolated from soil in China.

A psychrotolerant actinomycete, strain YIM6T, was isolated from a soil sample collected from Beijiang in Xinjiang Province, China. Both vegetative and aerial hyphae grew well on various media after 4 weeks. Long spore chains, borne on the aerial mycelium, were straight to flexuous or occasionally Retinaculiaperti and non-motile. The novel isolate grew well at between 8 and 20 degrees C; the lower and upper temperature limits for growth were 0 and 32 degrees C. The cell wall of strain YIM6T contained LL-diaminopimelic acid (A2pm) and traces of meso-A2pm. Whole-cell hydrolysates contained mainly glucose and small amounts of xylose, galactose and arabinose. The predominant menaquinones were MK-9(H6) and MK-9(H8) and phosphatidylethanolamine was the diagnostic phospholipid. The predominant cellular fatty acids were 15:0 anteiso, 16:0 iso and 17:0 cyclo. Phylogenetic analysis indicated that strain YIM6T belongs to the genus Streptomyces. In its morphology, physiological and biochemical characteristics and 16S rDNA sequence, strain YIM6T differed from other members of Streptomyces. Thus, strain YIM6T (= CCTCC 99005T = AS 4.1718T = DSM 41794T) is proposed as the type strain of a novel species, Streptomyces beijiangensis sp. nov.

Proposal to combine the genera Actinobispora and Pseudonocardia in an emended genus Pseudonocardia, and description of Pseudonocardia zijingensis sp. nov..

The 16S rDNA sequences of four strains, i.e. three type strains of Actinobispora and strain 6330T, were determined and compared with those of representatives of the family Pseudonocardiaceae by using two tree-making algorithms. All the validly described species of the genera Actinobispora and Pseudonocardia were consistently recovered as a mixed group in phylogenetic trees, and were distinct from the other genera of the family Pseudonocardiaceae. Strain 6330T formed a distinct phyletic line in the 16S rDNA tree and was most closely associated with the type strain of Actinobispora aurantiaca. The use of specific PCR primers designed for differentiating the genus Pseudonocardia from other genera of the family Pseudonocardiaceae showed that all the Actinobispora species and strain 6330T have the same amplified 640 bp 16S rDNA fragment as members of the genus Pseudonocardia. The DNA-DNA relatedness, chemotaxonomic and phenotypic data also supported classification of these taxa in the genus Pseudonocardia, and distinguished each from the others. On the basis of these observations, it is proposed that the genera Actinobispora and Pseudonocardia be combined in an emended genus Pseudonocardia, and that strain 6330T be classified in the same genus as Pseudonocardia zijingensis sp. nov. The type strain is 6330T (= AS 4.1545T = JCM 11117T).