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The tannic acid (TA)-based modular-assembly strategy has exhibited great prospects for fabricating inorganic–biological hybrid systems recently, albeit the technique is still at the early stage of development. Herein, we investigate this strategy in different aspects, including the material suitability, loading effects, and biocompatibility. The successful functionalization of InP nanoparticles, Bi nanospheres, and g-C3N4 by TA–Fe3+ nanofilm and their subsequent modular assembly onto the yeast surface demonstrated the good versatility of this approach toward the different types of nanomaterials. The proper utilization of TA and nanomaterials in the surface-functionalization step was found to be critical for the material-loading effect, which could also be negatively impacted by the excessive amounts of TA and Fe3+ in the modular-assembly process. The biocompatibility of TA–Fe3+-functionalized nanomaterials to living cells could be optimized via adjusting the relative ratio of TA to nanomaterials during the functionalization. A balance between the material loading and biocompatibility could also be achieved via fine-tuning the TA concentration in the biohybrid studies. The presented deep insight into the TA-based modular-assembly strategy would allow the rational construction of inorganic–biological hybrid systems with a feasible pathway for the development of solar-to-chemical conversion technology, and also for the development of microbe-mediated drug delivery, tumor treatment, and environmental remediation.

We present a full description and analysis of the complete mitochondrial genome of a Pacific Ocean specimen of the coconut crab Birgus latro (Linnaeus, 1767), the largest extant terrestrial arthropod in the world. Our de novo-assembled mitogenome has a massive 16,161 times organelle read coverage, a length of 16,411 bp, contains 22 tDNAs (20 unique), 13 protein-coding genes, two rDNAs, and a putative control region of length 1,381 bp. The control region contains three microsatellites and two pairs of inverted repeats. Contrary to the mitochondrial sentinel gene concept, two-dimensional nucleotide analysis reveals higher GC-content in cox gene families than in nadh gene families. Moreover, cox gene families are more conserved than nadh gene families among the species of Coenobitidae selected for comparison. Secondary structure prediction of the 22 tDNAs shows major deviations from the cloverleaf pattern, which points to a relatively high rate of mutation in these genes. We also present a repertoire of mitochondrial variation between our male Okinawan coconut crab and an Indian Ocean specimen that consists of one insertion, one deletion, 135 SNPs, three MNPs and nine complex polymorphisms. We provide confirmatory evidence that the superfamily Paguroidea, to which the coconut crab belongs, is polyphyletic, that all the protein-coding genes of B. latro are under purifying selection, and that a Pacific versus Indian Ocean coconut crab population divergence occurred during the Pleistocene.

Numerous studies indicated that long non-coding RNAs (lncRNAs) play critical roles in glioma initiation and progression. SNHG25 is a newly identified lncRNA. And the functional role and molecular mechanism of SNHG25 in glioma cells have not been investigated. In this study, we found that SNHG25 was upregulated in glioma cells and tissues. CCK-8, EDU, and colony formation assays demonstrated that SNHG25 knockdown markedly inhibited glioma cell proliferation. In vivo studies showed that SNHG25 knockdown significantly inhibited tumor growth. Further studies indicated that SNHG25 positively regulated MAP2K2 through sponging miR-579-5p. High expression of SNHG25 activated MAPK signaling through MAP2K2. These data suggest that SNHG25 is a potential target and biomarker for glioma.

Heavy metal ions pollution is one of the most dangerous and critical threats to human health and environment. In this work, three different generations of PAMAM dendrimer decorated on magnetic Fe 3 O 4 composites (Fe 3 O 4 @SiO 2 –G1, Fe 3 O 4 @SiO 2 –G3, Fe 3 O 4 @SiO 2 –G5) were fabricated and characterized by FTIR, XRD, TEM, and TGA. The obtained composites were used for Cr(VI) removal. Batch adsorption studies showed that the adsorption reached equilibrium within 60 min, and the optimal pH was 3.0. The result of adsorption kinetics was simulated by the pseudo–second-order model. The adsorption equilibrium isotherm was well fitted with the Langmuir adsorption model. Furthermore, thermodynamics calculations revealed that the adsorption process was endothermic and spontaneous. Importantly, adsorption capacity of Cr(VI) obey the sequence of Fe 3 O 4 @SiO 2 –G1＜Fe 3 O 4 @SiO 2 –G5＜Fe 3 O 4 @SiO 2 –G3, 3 generation of PAMAM (3G) is the optimal for adsorption capacity of Cr(VI). The maximum theoretical Cr(VI) adsorption capacity ( q m ) of Fe 3 O 4 @SiO 2 –G3 was 334.45 mg/g, and removal ration remained above 89.5% after five cycles of adsorption–desorption. Thus, Fe 3 O 4 @SiO 2 –G3 is predicted to be an efficient adsorbent for the adsorption of Cr(VI) from aqueous solution, and the obtained results can help in the generation optimization during fabrication of dendrimer modified adsorbents.

Knowledge graph embedding (KGE) are routinely used to represent entities and their relations in knowledge bases with a quantitative measure, and the triples usually play the role of basic units in KGE learning. Considering that triples are sometimes far from adequate and knowledge graph itself contains a lot of information, this paper employs FCA-based technology to mine the deterministic knowledge from knowledge graph, that is, the formal concept, and attempts to establish the relationship between knowledge graph (KG) and formal concept analysis (FCA). Specically, each set of triples sharing the same head entity are grouped as a graph granule and the concepts of each graph granule are mined. By further exploration, the maximal concepts are integrated into embedding learning to develop a novel KGE model named TransGr for knowledge graph completion. This model learns a matrix for each maximal concept in graph granule as well as a vector for each entity and relation. The performed experiments on link prediction and triple classi cation tasks demonstrate that the proposed TransGr model is effective on the datasets with relatively complete graph granules.

Osmoregulation and osmoconformation are two mechanisms through which aquatic animals adapt to salinity fluctuations. The euryhaline crab Scylla paramamosain, being both an osmoconformer and osmoregulator, is an excellent model organism to investigate salinity adaptation mechanisms in brachyurans. In the present study, we used transcriptomic and proteomic approaches to investigate the response of S. paramamosain to salinity stress. Crabs were transferred from a salinity of 25 ppt to salinities of 5 ppt or 33 ppt for 6 h and 10 days. Data from both approaches revealed that exposure to 5 ppt resulted in upregulation of ion transport and energy metabolism associated genes. Notably, acclimation to low salinity was associated with early changes in gene expression for signal transduction and stress response. In contrast, exposure to 33 ppt resulted in upregulation of genes related to amino acid metabolism, and amino acid transport genes were upregulated only at the early stage of acclimation to this salinity. Our study reveals contrasting mechanisms underlying osmoregulation and osmoconformation within the salinity range of 5–33 ppt in the mud crab, and provides novel candidate genes for osmotic signal transduction, thereby providing insights on understanding the salinity adaptation mechanisms of brachyuran crabs.

Bulk nanobubbles (NBs) that are produced in the hydrodynamic cavitation (HC) process have been widely applied in mineral flotation for more than a decade, while how bulk NBs interact with minerals in the water-solid interface is still unclear. In this study, the adsorption behaviors of bulk NBs generated in the principle of HC on muscovite surfaces in the presence of dodecylamine (DDA) were investigated. The results show that NBs are likely coated with DDA in aqueous solutions. After attaching with muscovite, bulk NBs can adsorb on the mineral surfaces, probably following the three-contact line pinning theory. The adsorption of NBs increases the surface hydrophobicity of minerals, which can be inferred from the larger contact angles and the better flotation performances obtained in the presence of DDA/NBs. In addition, the adsorption of NBs is thought to be able to prevent the adsorption of DDA on the same space of the solid surfaces, which can be confirmed by the results of zeta potential measurements, contact angle measurements and AFM imaging results.

Micro-nanobubbles (MNBs) generated during hydrodynamic cavitation (HC) have been extensively studied in mineral processing field in the past two decades. Many researchers have claimed that MNBs can effectively promote the collection of fine particles in flotation, while studies on MNBs assisted mineral separation are rare. In this study, the role of bulk MNBs in desorbing flotation reagent was investigated, with the aim of illustrating the potential effects of MNBs on minerals separation. The results showed that bulk MNBs could efficiently remove the sodium oleate (NaOl) from diaspore surfaces, reducing the residual concentration of NaOl on solids, which was more significant when the amount of NaOl pre-adsorbed was relatively small. Furthermore, lower residual concentration of NaOl on solids caused by MNBs cleaning made the particles less hydrophobic and flocs more friable. Given that gangue entrapment in flocs was one of the main limits for high-selective flotation, the roles of MNBs in enhancing reagent desorption and associated flocs breakup and reorganization probably contribute to higher separation efficiency of different minerals, which was confirmed by the flotation results of diaspore/kaolinite mixture.

Soil bacteria are very important in biogeochemical cycles and play significant role in soil-borne disease suppression. Although continuous cropping is responsible for soil-borne disease enrichment, its effect on tobacco plant health and how soil bacterial communities change are yet to be elucidated. In this study, soil bacterial communities across tobacco continuous cropping time-series fields were investigated through high-throughput sequencing of 16S ribosomal RNA genes. The results showed that long-term continuous cropping could significantly alter soil microbial communities. Bacterial diversity indices and evenness indices decreased over the monoculture span and obvious variations for community structures across the three time-scale tobacco fields were detected. Compared with the first year, the abundances of Arthrobacter and Lysobacter showed a significant decrease. Besides, the abundance of the pathogen Ralstonia spp. accumulated over the monoculture span and was significantly correlated with tobacco bacterial wilt disease rate. Moreover, Pearson's correlation demonstrated that the abundance of Arthrobacter and Lysobacter, which are considered to be beneficial bacteria had significant negative correlation with tobacco bacterial wilt disease. Therefore, after long-term continuous cropping, tobacco bacterial wilt disease could be ascribed to the alteration of the composition as well as the structure of the soil microbial community.

Rotation is an effective strategy to control crop disease and improve plant health. However, the effects of crop rotation on soil bacterial community composition and structure, and crop health remain unclear. In this study, using 16S rRNA gene sequencing, we explored the soil bacterial communities under four different cropping systems, continuous tobacco cropping (control group), tobacco-maize rotation, tobacco-lily rotation, and tobacco-turnip rotation. Results of detrended correspondence analysis and dissimilarity tests showed that soil bacterial community composition and structure changed significantly among the four groups, such that Acidobacteria and Actinobacteria were more abundant in the maize rotation group (16.6 and 11.5%, respectively) than in the control (8.5 and 7.1%, respectively). Compared with the control group (57.78%), maize and lily were effective rotation crops in controlling tobacco bacterial wilt (about 23.54 and 48.67%). On the other hand, tobacco bacterial wilt rate was increased in the turnip rotation (59.62%) relative to the control. Further study revealed that the abundances of several bacterial populations were directly correlated with tobacco bacterial wilt. For example, Acidobacteria and Actinobacteria were significantly negatively correlated to the tobacco bacterial wilt rate, so they may be probiotic bacteria. Canonical correspondence analysis showed that soil pH and calcium content were key factors in determining soil bacterial communities. In conclusion, our study revealed the composition and structure of bacterial communities under four different cropping systems and may unveil molecular mechanisms for the interactions between soil microorganisms and crop health.

This study used an artificial enrichment microbial consortium to examine the effects of different substrate conditions on microbial diversity, composition, and function (e.g., zinc leaching efficiency) through adding pyrite (SP group), chalcopyrite (SC group), or both (SPC group) in sphalerite bioleaching systems. 16S rRNA gene sequencing analysis showed that microbial community structures and compositions dramatically changed with additions of pyrite or chalcopyrite during the sphalerite bioleaching process. Shannon diversity index showed a significantly increase in the SP (1.460), SC (1.476), and SPC (1.341) groups compared with control (sphalerite group, 0.624) on day 30, meanwhile, zinc leaching efficiencies were enhanced by about 13.4, 2.9, and 13.2%, respectively. Also, additions of pyrite or chalcopyrite could increase electric potential (ORP) and the concentrations of Fe3+ and H+, which were the main factors shaping microbial community structures by Mantel test analysis. Linear regression analysis showed that ORP, Fe3+ concentration, and pH were significantly correlated to zinc leaching efficiency and microbial diversity. In addition, we found that leaching efficiency showed a positive and significant relationship with microbial diversity. In conclusion, our results showed that the complicated substrates could significantly enhance microbial diversity and activity of function.

To observe the clinical parameters and short-term prognosis of Tibetan high-altitude area children with congenital heart disease undergoing surgery and anaesthesia in low-altitude area, and to investigate the perioperative safety of the treatment. Methods: From January, 2016 to December, 2016, 14 children with congenital heart disease who underwent surgery were assigned into 2 groups (n=7 each): the high-altitude area group (X group, children from Tibetan Autonomous Region) and the low-altitude area group (H group, children from Hunan Province). Echocardiography data, perioperative hemodynamic changes, postoperative recovery, complication and perioperative serum N terminal pro B type natriuretic peptide (NT-proBNP) levels were recorded. Results: There were no significant differences in cardiac structure and function between the 2 groups, while the incidence of pulmonary hypertension in the X group was significantly higher than that in the H group (P0.05). There were no significant differences in perioperative hemodynamics between the 2 groups (P0.05), while the duration in ICU in the X group was longer than that in the H group and the serum NT-proBNP level in the X group was higher than that in the H group (P0.05). Conclusion: For children with congenital heart disease in Tibetan high-altitude area, undergoing surgery in low-altitude area contributes to a steady perioperative hemodynamics and helps to increase the perioperative safety. There may be a higher risk of postoperative cardiac dysfunction in Tibetan children than that in low-altitude area.目的：观察高海拔地区先天性心脏病患儿到低海拔地区行先天性心脏病矫治手术的临床指标和短期预后，以探讨其围手术期的安全性。方法：回顾性分析2016年1至12月在中南大学湘雅医院择期行先天性心脏病矫治手术的来自西藏自治区(X组)和湖南省(H组)的患儿各7例。比较两组患儿心脏超声心动图检查指标、围手术期血流动力学、术后恢复与并发症和围手术期氨基末端脑钠肽前体(N terminal pro B type natriuretic peptide，NT-proBNP)水平。结果：心脏超声心动图显示两组患儿心脏结构和心功能无明显差异，X组患儿肺高压的发生率明显高于H组(P0.05)。围手术期血流动力学比较两组之间差异无统计学意义(P0.05)，术后ICU停留时间X组患儿更长(P0.05)。血清NT-proBNP水平X组患儿明显高于H组(P0.05)。结论：高海拔地区的先天性心脏病患儿到低海拔地区行先天性心脏病矫治手术有助于提高围手术期安全性，麻醉手术中血流动力学平稳，但术后心功能不全风险仍高于低海拔地区患儿，术后恢复时间延长。.

Cultivated sesame (Sesamum indicum L.) is an important oil crop because of its high oil content and quality. In order to discover the single nucleotide polymorphisms (SNPs) and insertion/deletions (InDels) in RNA-Seq, we collected a total of 33.47 Gbp of data from three sesame transcriptome datasets. A reference transcriptome covering 267,508 unigenes was constructed. Among the 37,646 transcripts with complete open reading frames, a total of 7,450 SNPs and 362 InDels were found with frequencies of one SNP per 6.66 kb and one InDel per 137 kb, respectively. Most of the SNPs were transition-type with the nucleotide transitions C–T or A–G. A total of 21 InDel types with lengths ranging from 1 to 38 bp were identified, and the short InDels (1–2 bp) were most abundant at a ratio of over 80 %. Furthermore, 4,959 (66.56 %) SNPs were detected in protein-coding regions: 2,899 (58.46 %) were synonymous and 2,060 (41.54 %) were nonsynonymous. All SNPs and InDels detected in this study were bi-allelic. Of the randomly selected 40 SNPs and 40 InDels, 92.5 % of the SNPs and 95.0 % of the InDels exhibited polymorphism according to the PCR-based and Sanger-sequenced results. Furthermore, the efficiencies of the newly developed polymorphic SNP and InDel markers were evaluated among 36 commercial sesame cultivars. More than 90.0 % of the markers displayed the expected polymorphic amplifications. The polymorphism information content values ranged from 0.05 to 0.58 with an average of 0.38. Moreover, all genotypes of the 36 commercial cultivars tested were definitively distinguished by 21 SNPs and 16 InDels. These newly identified molecular markers may provide a foundation for cultivar identification, genetic diversity analysis, qualitative and quantitative trait mapping and marker-assisted selection breeding in sesame.

Background The interaction mechanism between crop and soil microbial communities is a key issue in both agriculture and soil ecology. However, how soil microbial communities respond to crop planting and ultimately affect crop health still remain unclear. In this research, we explored how soil microbial communities shifted during tobacco cultivation under different rotation systems (control, maize rotation, lily rotation and turnip rotation). Results Our analyses showed that soil microbial communities had a general response pattern to tobacco planting, as the abundances of Proteobacteria and Planctomycetes increased while Acidobacteria and Verrucomicrobia decreased during tobacco cultivation, no matter which rotation system was adopted. Notably, tobacco decreased the diversity and co-occurrence of soil microorganisms, but maize rotation might suppress tobacco bacterial wilt by alleviating the decrease in biodiversity and co-occurrence. Molecular ecological network analysis indicated that there was stronger competition between potential disease suppressive (e.g., Acidobacteria) and inducible bacteria (e.g., Chloroflexi) in maize rotation systems. Both soil properties (e.g., pH, Ca content) and microbial communities of tobacco mature period depended on their counterparts of fallow period, and all these factors shaped tobacco disease comprehensively. Conclusions Both soil microbial communities of fallow stage and tobacco selection shaped the communities of tobacco mature stage. And effective rotation crop (maize) could decrease the incidence of tobacco bacterial wilt by alleviating the decrease in diversity and co-occurrences of microbial populations. This study would deepen our understanding about succession mechanism of soil microbial communities during crop cultivation and their relationship with crop health. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0845-x) contains supplementary material, which is available to authorized users.

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

Green manure could improve soil nutrients and crop production, playing a significant role in sustainable agriculture. However, the impacts of green manure on crop health and the roles soil microbial communities play in the process haven’t been clarified clearly yet. In this study, we investigated soil microbial community composition and structure in four tobacco farmlands, which were treated with different green manure (control, ryegrass, pea and rape), using 16S rRNA gene amplicons sequencing. Results showed that green manure had significant impacts on soil properties, microbial communities and tobacco health. First, soil total C, N and Ca content increased significantly in groups treated with green manure than control. Second, soil community diversity was significantly higher in groups treated with green manure. Third, green manure especially ryegrass, decreased tobacco disease (bacterial wilt) rate dramatically, and the process might be mediated by soil microbial communities. On the one hand, several microbial populations were found to be potentially disease inducible or suppressive. For example, the abundances of Dokdonella and Rhodanobacter were positively correlated to tobacco disease rate, while Acidobacteira_Gp4 and Gp6 had negative correlations with tobacco disease. On the other hand, soil microbial communities were shaped by soil properties (e.g., pH, C and N content). In conclusion, our research showed that green manure could increase soil nutrients directly, and further improve tobacco health mediated by soil microorganisms, which may shed light on revealing interactions among soil properties, microorganisms and plants.

The use of green manures in agriculture can provide nutrients, affect soil microbial communities, and be a more sustainable management practice. The activities of soil microbes can effect crop growth, but the extent of this effect on yield remains unclear. We investigated soil bacterial communities and soil properties under four different green manure fertilization regimes (Vicia villosa, common vetch, milk vetch, and radish) and determined the effects of these regimes on maize growth. Milk vetch showed the greatest potential for improving crop productivity and increased maize yield by 31.3 %. This change might be related to changes in soil microbes and soil properties. The entire soil bacterial community and physicochemical properties differed significantly among treatments, and there were significant correlations between soil bacteria, soil properties, and maize yield. In particular, abundance of the phyla Acidobacteria and Verrucomicrobia was positively correlated with maize yield, while Proteobacteria and Chloroflexi were negatively correlated with yield. These data suggest that the variation of maize yield was related to differences in soil bacteria. The results also indicate that soil pH, alkali solution nitrogen, and available potassium were the key environmental factors shaping soil bacterial communities and determining maize yields. Both soil properties and soil microbes might be useful as indicators of soil quality and potential crop yield.

Although the taxonomical/phylogenetic diversity of microbial communities in biological heap leaching systems has been investigated, the diversity of functional genes was still unclear, and, especially, the differentiation and the relationships of diversity and functions of microbial communities in leaching heap (LH) and leaching solution (LS) were also still unclear. In our study, a functional gene array (GeoChip 5.0) was employed to investigate the functional gene diversity, and 16S rRNA gene sequencing was used to explore the taxonomical/phylogenetic diversity of microbial communities in LH and LS subsystems of Dexing copper mine (Jiangxi, China). Detrended correspondence analysis (DCA) showed that both functional gene structure and taxonomical/phylogenetic structure of microbial communities were significantly different between LH and LS. Signal intensities of genes, including genes for sulfur oxidation (e.g., soxB), metal homeostasis (e.g., arsm), carbon fixation (e.g., rubisco), polyphosphate degradation (e.g., ppk), and organic remediation (e.g., hydrocarbons) were significantly higher in LH, while signal intensities of genes for carbon degradation (e.g., amyA), polyphosphate synthesis (e.g., ppx), and sulfur reduction (e.g., dsrA) were significantly higher in LS. Further inspection revealed that microbial communities in LS and LH were dominated by Acidithiobacillus and Leptospirillum. However, rare species were relatively higher abundant in LH. Additionally, diversity index of functional genes was significantly different in LS (9.915 ± 0.074) and LH (9.781 ± 0.165), and the taxonomical/phylogenetic diversity index was also significantly different in LH (4.398 ± 0.508) and LS (3.014 ± 0.707). Functional tests, including sulfur-oxidizing ability, iron-oxidizing ability, and pyrite bioleaching ability, showed that all abilities of microbial communities were significantly stronger in LH than those in LS. Further studies found that most key genes (e.g., soxC and dsrA), rather than functional gene diversity index, were significantly correlated with abilities of microbial communities by linear regression analysis and Pearson correlation tests. In addition, the abilities were significantly correlated with taxonomical/phylogenetic diversity index and some rare species (e.g., Ferrithrix).

This study used an artificial microbial community with four known moderately thermophilic acidophiles (three bacteria including Acidithiobacillus caldus S1, Sulfobacillus thermosulfidooxidans ST and Leptospirillum ferriphilum YSK, and one archaea, Ferroplasma thermophilum L1) to explore the variation of microbial community structure, composition, dynamics and function (e.g., copper extraction efficiency) in chalcopyrite bioleaching (C) systems with additions of pyrite (CP) or sphalerite (CS). The community compositions and dynamics in the solution and on the ore surface were investigated by real-time quantitative PCR (qPCR). The results showed that the addition of pyrite or sphalerite changed the microbial community composition and dynamics dramatically during the chalcopyrite bioleaching process. For example, A. caldus (above 60%) was the dominant species at the initial stage in three groups, and at the middle stage, still dominated C group (above 70%), but it was replaced by L. ferriphilum (above 60%) in CP and CS groups; at the final stage, L. ferriphilum dominated C group, while F. thermophilum dominated CP group on the ore surface. Furthermore, the additions of pyrite or sphalerite both made the increase of redox potential (ORP) and the concentrations of Fe3+ and H+, which would affect the microbial community compositions and copper extraction efficiency. Additionally, pyrite could enhance copper extraction efficiency (e.g., improving around 13.2% on day 6) during chalcopyrite bioleaching; on the contrary, sphalerite restrained it.

Rotation is an effective strategy to control crop disease and improve plant health. However, the effects of crop rotation on soil bacterial community composition and structure, and crop health remain unclear. In this study, using 16S rRNA gene sequencing, we explored the soil bacterial communities under four different cropping systems, continuous tobacco cropping (control group), tobacco-maize rotation, tobacco-lily rotation, and tobacco-turnip rotation. Results of detrended correspondence analysis and dissimilarity tests showed that soil bacterial community composition and structure changed significantly among the four groups, such that Acidobacteria and Actinobacteria were more abundant in the maize rotation group (16.6 and 11.5%, respectively) than in the control (8.5 and 7.1%, respectively). Compared with the control group (57.78%), maize and lily were effective rotation crops in controlling tobacco bacterial wilt (about 23.54 and 48.67%). On the other hand, tobacco bacterial wilt rate was increased in the turnip rotation (59.62%) relative to the control. Further study revealed that the abundances of several bacterial populations were directly correlated with tobacco bacterial wilt. For example, Acidobacteria and Actinobacteria were significantly negatively correlated to the tobacco bacterial wilt rate, so they may be probiotic bacteria. Canonical correspondence analysis showed that soil pH and calcium content were key factors in determining soil bacterial communities. In conclusion, our study revealed the composition and structure of bacterial communities under four different cropping systems and may unveil molecular mechanisms for the interactions between soil microorganisms and crop health.

The microbial communities are important for minerals decomposition in biological heap leaching system. However, the differentiation and relationship of composition and function of microbial communities between leaching heap (LH) and leaching solution (LS) are still unclear. In this study, 16S rRNA gene sequencing was used to assess the microbial communities from the two subsystems in ZiJinShan copper mine (Fujian province, China). Results of PCoA and dissimilarity test showed that microbial communities in LH samples were significantly different from those in LS samples. The dominant genera of LH was Acidithiobacillus (57.2 ∼ 87.9 %), while Leptospirillum (48.6 ∼ 73.7 %) was predominant in LS. Environmental parameters (especially pH) were the major factors to influence the composition and structure of microbial community by analysis of Mantel tests. Results of functional test showed that microbial communities in LH utilized sodium thiosulfate more quickly and utilized ferrous sulfate more slowly than those in LS, which further indicated that the most sulfur-oxidizing processes of bioleaching took place in LH and the most iron-oxidizing processes were in LS. Further study found that microbial communities in LH had stronger pyrite leaching ability, and iron extraction efficiency was significantly positively correlated with Acidithiobacillus (dominated in LH), which suggested that higher abundance ratio of sulfur-oxidizing microbes might in favor of minerals decomposition. Finally, a conceptual model was designed through the above results to better exhibit the sulfur and iron metabolism in bioleaching systems.

Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species. A large proportion of Acidithiobacillus ferrivorans-specific genes were mapped especially to metabolism-related genes, indicating that diverse metabolic pathways might confer an advantage for adaptation to local environmental conditions. Analyses of functional metabolisms revealed the differences of carbon metabolism, nitrogen metabolism, and sulfur metabolism at the species and/or strain level. The findings also showed that Acidithiobacillus spp. harbored specific adaptive mechanisms for thriving under extreme environments. The genus Acidithiobacillus had the genetic potential to resist and metabolize toxic substances such as heavy metals and organic solvents. Comparison across species and/or strains of Acidithiobacillus populations provided a deeper appreciation of metabolic differences and environmental adaptation, as well as highlighting the importance of cellular mechanisms that maintain the basal physiological functions under complex acidic environmental conditions.

Background Metagenomics allows us to acquire the potential resources from both cultivatable and uncultivable microorganisms in the environment. Here, shotgun metagenome sequencing was used to investigate microbial communities from the surface layer of low grade copper tailings that were industrially bioleached at the Dexing Copper Mine, China. A bioinformatics analysis was further performed to elucidate structural and functional properties of the microbial communities in a copper bioleaching heap. Results Taxonomic analysis revealed unexpectedly high microbial biodiversity of this extremely acidic environment, as most sequences were phylogenetically assigned to Proteobacteria, while Euryarchaeota-related sequences occupied little proportion in this system, assuming that Archaea probably played little role in the bioleaching systems. At the genus level, the microbial community in mineral surface-layer was dominated by the sulfur- and iron-oxidizing acidophiles such as Acidithiobacillus-like populations, most of which were A. ferrivorans-like and A. ferrooxidans-like groups. In addition, Caudovirales were the dominant viral type observed in this extremely environment. Functional analysis illustrated that the principal participants related to the key metabolic pathways (carbon fixation, nitrogen metabolism, Fe(II) oxidation and sulfur metabolism) were mainly identified to be Acidithiobacillus-like, Thiobacillus-like and Leptospirillum-like microorganisms, indicating their vital roles. Also, microbial community harbored certain adaptive mechanisms (heavy metal resistance, low pH adaption, organic solvents tolerance and detoxification of hydroxyl radicals) as they performed their functions in the bioleaching system. Conclusion Our study provides several valuable datasets for understanding the microbial community composition and function in the surface-layer of copper bioleaching heap. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0330-4) contains supplementary material, which is available to authorized users.

Key genes encoding enzymes related to heavy metal resistance and low pH tolerance. (DOCX 31 kb)

Summary of metagenome dataset of samples from the surface-layer mine tailings. (DOC 40 kb)

Table S1. Sediment properties and ANOVA analysis among three groups. Table S2. Shannon diversity and Pielou evenness of samples based on sequencing data and Geochip hybridization data respectively. Table S3. Correlation between microbial composition and function. Table S4. (a) Mantel test of sequencing data with environmental attributes at the genus level; (b) Mantel test of GeoChip hybridization data with environmental attributes. (DOCX 41Â kb)

Figure S1. Rarefaction curves of 16r RNA gene sequencing data. Figure S2. Composition and structure of soil microbial communities in each group. Figure S3. Phylogenetic molecular ecological networks (pMEN) of microbial communities in each group, and number of nodes and links of each pMEN. Table S1. Soil properties. Table S2(a). Correlation of microbial populations in abundance between two periods at the phylum level. (b). Correlation of microbial populations in abundance between two periods at the genus level. Table S3. Topological properties of the empirical pMENs of microbial communities in eight groups. Table S4(a). Correlation between abundance of microbial populations and tobacco morbidity at the phylum level. (b). Correlation between abundance of microbial populations and tobacco morbidity at the genus level. Table S5(a). Mantel test of sequencing data with environmental attributes at the phylum level. (b). Mantel test of sequencing data with environmental attributes at the genus level. (DOCX 1100 kb)

Background The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial. Results By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of Geobacter and Fusibacter decreased along contamination gradient (from high to low), while Janthinobacterium and Arthrobacter increased their abundances. Most genes involved in heavy metal resistance (e.g., metc, aoxb and mer) showed higher intensity in sites with higher concentration of heavy metals. Comparing the two shift patterns, there were correlations between them, because functional and phylogenetic β-diversities were significantly correlated, and many heavy metal resistance genes were derived from Geobacter, explaining their high abundance in heavily contaminated sites. However, there was a stronger link between functional composition and environmental drivers, while stochasticity played an important role in formation and succession of phylogenetic composition demonstrated by null model test. Conclusions Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0731-6) contains supplementary material, which is available to authorized users.

Response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. To explore the microbial response to heavy metal contamination (e.g., Cr, Mn, Zn), the composition, structure and functional potential of sedimentary microbial community were investigated by sequencing of 16S rRNA gene amplicons and a functional gene microarray. Analysis of 16S rRNA sequences revealed that the composition and structure of sedimentary microbial communities changed significantly across a gradient of heavy metal contamination and the relative abundances were higher for Firmicutes, Chloroflexi and Crenarchaeota, but lower for Proteobacteria and Actinobacteria in highly contaminated samples. Also, molecular ecological network analysis of sequencing data indicated that their possible interactions might be enhanced in highly contaminated communities. Correspondently, key functional genes involved in metal homeostasis (e.g., chrR, metC, merB), carbon metabolism and organic remediation showed a higher abundance in highly contaminated samples, indicating that bacterial communities in contaminated areas may modulate their energy consumption and organic remediation ability. This study indicated that the sedimentary indigenous microbial community may shift the composition and structure as well as function priority and interaction network to increase their adaptability and/or resistance to environmental contamination.

Background Acidithiobacillus thiooxidans (A. thiooxidans), a chemolithoautotrophic extremophile, is widely used in the industrial recovery of copper (bioleaching or biomining). The organism grows and survives by autotrophically utilizing energy derived from the oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs). However, the lack of genetic manipulation systems has restricted our exploration of its physiology. With the development of high-throughput sequencing technology, the whole genome sequence analysis of A. thiooxidans has allowed preliminary models to be built for genes/enzymes involved in key energy pathways like sulfur oxidation. Results The genome of A. thiooxidans A01 was sequenced and annotated. It contains key sulfur oxidation enzymes involved in the oxidation of elemental sulfur and RISCs, such as sulfur dioxygenase (SDO), sulfide quinone reductase (SQR), thiosulfate:quinone oxidoreductase (TQO), tetrathionate hydrolase (TetH), sulfur oxidizing protein (Sox) system and their associated electron transport components. Also, the sulfur oxygenase reductase (SOR) gene was detected in the draft genome sequence of A. thiooxidans A01, and multiple sequence alignment was performed to explore the function of groups of related protein sequences. In addition, another putative pathway was found in the cytoplasm of A. thiooxidans, which catalyzes sulfite to sulfate as the final product by phosphoadenosine phosphosulfate (PAPS) reductase and adenylylsulfate (APS) kinase. This differs from its closest relative Acidithiobacillus caldus, which is performed by sulfate adenylyltransferase (SAT). Furthermore, real-time quantitative PCR analysis showed that most of sulfur oxidation genes were more strongly expressed in the S0 medium than that in the Na2S2O3 medium at the mid-log phase. Conclusion Sulfur oxidation model of A. thiooxidans A01 has been constructed based on previous studies from other sulfur oxidizing strains and its genome sequence analyses, providing insights into our understanding of its physiology and further analysis of potential functions of key sulfur oxidation genes.