Acidithiobacillus acidisediminis sp. nov., an acidophilic sulphur-oxidizing chemolithotroph isolated from acid mine drainage sediment.

Strain S30A2T, isolated from the acid mine drainage sediment of Mengzi Copper Mine, Yunnan, is proposed to represent a novel species of the sulphur-oxidizing genus Acidithiobacillus. Cells were Gram-stain-negative, non-endospore forming, highly motile with one or two monopolar flagella and rod-shaped. The strain was mesophilic, growing at 30-50 °C (optimum, 38 °C), acidophilic, growing at pH 2.0-4.5 (optimum, pH 2.5), and tolerant of 0-4 % (w/v; 684 mol l-1) NaCl. The 16S rRNA gene-based sequence analysis showed that strain S30A2T belongs to the genus Acidithiobacillus and shows the largest similarity of 96.6 % to the type strain Acidithiobacillus caldus KUT. The genomic DNA G+C content of strain S30A2T was 59.25 mol%. The average nucleotide identity ANIb and ANIm values between strain S30A2T and A. caldus KUT were 70.95 and 89.78 %, respectively and the digital DNA-DNA hybridization value was 24.9 %. Strain S30A2T was strictly aerobic and could utilize elementary sulphur and tetrathionate to support chemolithotrophic growth. The major cellular fatty acid of S30A2T was C19 : 1ω7c. The respiratory quinones were ubiquinone-8 and ubiquinone-7. Based upon its phylogenetic, genetic, phenotypic, physiologic and chemotaxonomic characteristics, strain S30A2T is considered to represent a novel species of the genus Acidithiobacillus, for which the name Acidithiobacillus acidisediminis sp. nov. is proposed. The type strain is S30A2T (=CGMCC 1.17059T=KCTC 72580T).

Xiashengella succiniciproducens gen. nov., sp. nov., a succinate-producing bacterium isolated from an anaerobic digestion tank in the family Marinilabiliaceae of the order Bacteroidales.

A strictly anaerobic, motile bacterium, designated as strain Ai-910T, was isolated from the sludge of an anaerobic digestion tank in China. Cells were Gram-stain-negative rods. Optimal growth was observed at 38 °C (growth range 25-42 °C), pH 8.5 (growth range 5.5-10.5), and under a NaCl concentration of 0.06% (w/v) (range 0-2.0%). Major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The respiratory quinone was MK-7. Using xylose as the growth substrate, succinate was produced as the fermentation product. Phylogenetic analysis based on the 16 S rRNA gene sequences indicated that strain Ai-910T formed a distinct phylogenetic lineage that reflects a new genus in the family Marinilabiliaceae, sharing high similarities to Alkaliflexus imshenetskii Z-7010T (92.78%), Alkalitalea saponilacus SC/BZ-SP2T (92.51%), and Geofilum rubicundum JAM-BA0501T (92.36%). Genomic similarity (average nucleotide identity and digital DNA-DNA hybridization) values between strain Ai-910T and its phylogenetic neighbors were below 65.27 and 16.90%, respectively, indicating that strain Ai-910T represented a novel species. The average amino acid identity between strain Ai-910T and other related members of the family Marinilabiliaceae were below 69.41%, supporting that strain Ai-910T was a member of a new genus within the family Marinilabiliaceae. Phylogenetic, genomic, and phenotypic analysis revealed that strain Ai-910T was distinguished from other phylogenetic relatives within the family Marinilabiliaceae. The genome size was 3.10 Mbp, and the DNA G + C content of the isolate was 42.8 mol%. Collectively, differences of the phenotypic and phylogenetic features of strain Ai-910T from its close relatives suggest that strain Ai-910T represented a novel species in a new genus of the family Marinilabiliaceae, for which the name Xiashengella succiniciproducens gen. nov., sp. nov. was proposed. The type strain of Xiashengella succiniciproducens is Ai-910T (= CGMCC 1.17893T = KCTC 25,304T).

Responses of microbial community to geochemical parameters on vertical depth in bioheap system of low-grade copper sulfide.

Monitoring of the microbial community in bioleaching system is essential for control process parameters and enhance the leaching efficiency. Due to the difficulty of sampling, microbial distribution, community succession and bioleaching activity along the vertical depth of bioleaching heaps remain unresolved. This study investigated the geochemical parameters and microbial community structure along a depth profile in a bioleaching heap and leachate. 80 ore samples at different heap depths and 9 leaching solution samples from three bioheaps of Zijin Copper Mine were collected. Microbial composition, mineral types and geochemical parameters of these samples were analyzed by 16S rRNA high-throughput sequencing and a series of chemical measurement technologies. The results revealed that the pH, Cu, Fe and the total sulfur contents were the major factors shaping the composition of the microbial communities in the bioleaching system. The extent of mineral oxidation increased as the sample depth increases, followed by the increasing of sulfur oxidizers. The abundance of sulfur and iron oxidizers including members of Acidithiobacillus, Sulfobacillus and Acidiferrobacter were significantly higher in the leaching heap than in the leaching solution, meanwhile, they showed strong positive interactions with other members within the same genera and iron oxidizer Leptospirillum and Ferroplasma. Besides, Acidithiobacillus negatively interacted with heterotrophs such as Sphingobium, Exiguobacterium, Brevundimonas and so on. On the contrast, members of Leptospirillum and unclassified Archaea were significantly abundant in the leaching solution and revealed strong interactions with members of Thermoplasmatales. The main conclusion of this study, especially the leaching potential of microorganisms prevailing in bioheaps and their relationships with geochemical factors, provides theoretical guidance for future process design such as the control of processing parameters and microbial community in heap leaching.

Alicyclobacillus curvatus sp. nov. and Alicyclobacillus mengziensis sp. nov., two acidophilic bacteria isolated from acid mine drainage.

Two acidophilic strains, designated as ALEF1T and S30H14T, were isolated from acid mine drainage sediment. Cells of both strains were Gram-stain-positive, aerobic, endospore-forming rods. Strains ALEF1T and S30H14T were acidophilic and mesophilic, the former grew at 20-40 °C (optimum, 30 °C) and pH 2.5-4.5 (optimum, pH 3.5), while the latter grew at 20-45 °C (optimum, 30 °C) and pH 2.0-5.5 (optimum, pH 4.5). The 16S rRNA gene-based sequence analysis revealed that strains ALEF1T and S30H14T belonged to the genus Alicyclobacillus, and were phylogenetically close to Alicyclobacillus ferrooxydans TC-34T with 97.1 and 97.4% similarity, respectively. The similarity between the two novel strains was 98.6 %. The average nucleotide identity value between the genome sequences of ALEF1T and S30H14T was 79.5 %, and that between each of the two isolates and A. ferrooxydans TC-34T were 72.0 and 74.3 %. In addition, the digital DNA-DNA hybridization value between ALEF1T and S30H14T was 24.9 %, between strain ALEF1T and A. ferrooxydans TC-34T was 21.7 %, and between S30H14T and A. ferrooxydans TC-34T was 26.3 %, far below the interspecies threshold. Both strains could utilize diverse carbon sources for heterotrophic growth; strain ALEF1T could utilize ferrous iron as the energy source for autotrophic growth. Menaquinone 7 was the only quinone detected in either strain. Both strains contained anteiso-C15 : 0 and anteiso-C17 : 0, while ω-alicyclic fatty acids were not detected. Based on their phylogenetic positions, as well as phenotypic and genomic data, it is considered that strains ALEF1T and S30H14T represent two novel species within the genus Alicyclobacillus, for which the names Alicyclobacillus curvatus sp. nov. (type strain ALEF1T=CGMCC 1.17055T=KCTC 43124T) and Alicyclobacillus mengziensis sp. nov. (S30H14T=CGMCC 1.17050T=KCTC 43125T) are proposed.

Key Factors Governing Microbial Community in Extremely Acidic Mine Drainage (pH <3).

The microbial community of acid mine drainage (AMD) fascinates researchers by their adaption and roles in shaping the environment. Molecular surveys have recently helped to enhance the understanding of the distribution, adaption strategy, and ecological function of microbial communities in extreme AMD environments. However, the interactions between the environment and microbial community of extremely acidic AMD (pH <3) from different mining areas kept unanswered questions. Here, we measured physicochemical parameters and profiled the microbial community of AMD collected from four mining areas with different mineral types to provide a better understanding of biogeochemical processes within the extremely acidic water environment. The prominent physicochemical differences across the four mining areas were in SO4 2-, metal ions, and temperature, and distinct microbial diversity and community assemblages were also discovered in these areas. Mg2+ and SO4 2- were the predominant factors determining the microbial structure and prevalence of dominant taxa in AMD. Leptospirillum, Ferroplasma, and Acidithiobacillus were abundant but showed different occurrence patterns in AMD from different mining areas. More diverse communities and functional redundancy were identified in AMD of polymetallic mining areas compared with AMD of copper mining areas. Functional prediction revealed iron, sulfur, nitrogen, and carbon metabolisms driven by microorganisms were significantly correlated with Mg2+ and SO4 2-, Ca2+, temperature, and Fe2+, which distinguish microbial communities of copper mine AMD from that of polymetallic mine AMD. In summary, microbial diversity, composition, and metabolic potential were mainly shaped by Mg2+ and SO4 2- concentrations of AMD, suggesting that the substrate concentrations may contribute to the distinct microbiological profiles of AMD from different mining areas. These findings highlight the microbial community structure in extremely acidic AMD forming by types of minerals and the interactions of physicochemical parameters and microbiology, providing more clues of the microbial ecological function and adaptation mechanisms in the extremely acidic environment.

Responses of soil microbiome to steel corrosion.

The process of microbiologically influenced corrosion (MIC) in soils has received widespread attention. Herein, long-term outdoor soil burial experiments were conducted to elucidate the community composition and functional interaction of soil microorganisms associated with metal corrosion. The results indicated that iron-oxidizing (e.g., Gallionella), nitrifying (e.g., Nitrospira), and denitrifying (e.g., Hydrogenophaga) microorganisms were significantly enriched in response to metal corrosion and were positively correlated with the metal mass loss. Corrosion process may promote the preferential growth of the abundant microbes. The functional annotation revealed that the metabolic processes of nitrogen cycling and electron transfer pathways were strengthened, and also that the corrosion of metals in soil was closely associated with the biogeochemical cycling of iron and nitrogen elements and extracellular electron transfer. Niche disturbance of microbial communities induced by the buried metals facilitated the synergetic effect of the major MIC participants. The co-occurrence network analysis suggested possible niche correlations among corrosion related bioindicators.

Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera.

Members of the genus Metallosphaera are widely found in sulfur-rich and metal-laden environments, but their physiological and ecological roles remain poorly understood. Here, we sequenced Metallosphaera tengchongensis Ric-A, a strain isolated from the Tengchong hot spring in Yunnan Province, China, and performed a comparative genome analysis with other Metallosphaera genomes. The genome of M. tengchongensis had an average nucleotide identity (ANI) of approximately 70% to that of Metallosphaera cuprina. Genes sqr, tth, sir, tqo, hdr, tst, soe, and sdo associated with sulfur oxidation, and gene clusters fox and cbs involved in iron oxidation existed in all Metallosphaera genomes. However, the adenosine-5'-phosphosulfate (APS) pathway was only detected in Metallosphaera sedula and Metallosphaera yellowstonensis, and several subunits of fox cluster were lost in M. cuprina. The complete 3-hydroxypropionate/4-hydroxybutyrate cycle and dicarboxylate/4-hydroxybutyrate cycle involved in carbon fixation were found in all Metallosphaera genomes. A large number of gene family gain events occurred in M. yellowstonensis and M. sedula, whereas gene family loss events occurred frequently in M. cuprina. Pervasive strong purifying selection was found acting on the gene families of Metallosphaera, of which transcription-related genes underwent the strongest purifying selection. In contrast, genes related to prophages, transposons, and defense mechanisms were under weaker purifying pressure. Taken together, this study expands knowledge of the genomic traits of Metallosphaera species and sheds light on their evolution.