Effect of introduction of exogenous strain Leptospirillum ferriphilum YSK on functional gene expression,structure,and function of indigenous consortium during pyrite bioleaching

Leptospirillum ferriphilum YSK was added to a native consortium of bioleaching bacteria including Acidithiobacillus caldus,A.thiooxidans,A.ferrooxidans,Sulfobacillus thermosulfidooxidans,Acidiphilium spp.,and Ferroplasma thermophilum cultured in modified 9K medium containing 0.5%(W/V)pyrite.The bioleaching efficiency markedly increased.Changes in community structure and gene expression were monitored with real-time PCR and functional gene arrays.Dynamic changes that varied in different populations in the consortium occurred after the addition of L.ferriphilum YSK,with growth of A.caldus S1,A.thiooxidans A01,Acidiphillum spp.DX1-1 promoted the growth of Ferroplasma L1,inhibited that of S.thermosulfidooxidans ST,and exerted little effect on that of A.ferrooxidans CMS.Genes encoding ADP heptose,phosphoheptose isomerase,glycosyltransferase,biotin carboxylase,and protoheme ferrolyase from L.ferriphilum,acetyl-CoA carboxylase from Acidiphillum spp.,and doxD from A.caldus were up-regulated in 0-20 h.Genes encoding lipid A disaccharide synthase LpxB,glycosyl transferase,and ADP heptose synthase from A.ferrooxidans were up-regulated in 0-8 h and then down-regulated in 8-20 h.Genes encoding ferredoxin oxidoreductase from Ferroplasma sp.were up-regulated in 0-4 h,down-regulated in 4-16 h,and again up-regulated in 16-20 h.CbbS from A.ferrooxidans was down-regulated in 0-20 h.

Geochip-based analysis of microbial functional genes diversity in rutile bio-desilication reactor

Biological desilication process is an effective way to remove silicate from rutile so that high purity rutile could be obtained. However, little is known about the molecular mechanism of this process. In this work, a newly developed rutile bio-desilication reactor was applied to enrich rutile from rough rutile concentrate obtained from Nanzhao rutile mine and a comprehensive high through-put functional gene array(Geo Chip 4.0) was used to analyze the functional gene diversity, structure and metabolic potential of microbial communities in the biological desilication reactor. The results show that TiO2 grade of the rutile concentrate could increase from 78.21% to above 90% and the recovery rate could reach to 96% or more in 8-12 d. The results also show that almost all the key functional genes involved in the geochemical cycling process, totally 4324 and 4983 functional microorganism genes, are detected in the liquid and ore surface, respectively. There are totally 712 and 831 functional genes involved in nitrogen cycling for liquid and ore surface samples, respectively. The relative abundance of functional genes involved in the phosphorus and sulfur cycling is higher in the ore surface than liquid. These results indicate that nitrogen, phosphorus and sulfur cycling are also present in the desiliconization process of rutile. Acetogenesis genes are detected in the liquid and ore surface, which indicates that the desiliconizing process mainly depends on the function of acetic acid and other organic acids. Four silicon transporting genes are also detected in the sample, which proves that the bacteria have the potential to transfer silicon in the molecule level. It is shown that bio-desilication is an effective and environmental-friendly way for enrichment of rough rutile concentrate and presents an overview of functional diversity and structure of desilication microbial communities, which also provides insights into our understanding of metabolic potential in biological desilication reactor ecosystems.

窖水中微生物降解污染物的关键细菌

为探究以氮、磷及有机物污染为主要特征的、窖水中参与污染物降解的关键细菌及它们之间潜在的相关关系,基于16S rRNA的微生物组学截面数据,分析了窖水中细菌群落结构与功能及其与水质因子间的相关性,并通过微生物物种的同现或相关种间作用推断模型,构建了7个微生物菌属间的共现性关联网络.结果表明,窖水中存在具有相对特定生态功能的细菌,进行着诸多活跃的与新陈代谢功能基因相关的代谢活动;窖水微生物类群共现性关联网络中大部分节点的菌属营互利共生类型的生态关系;Lacibacter、Arthrobacter、Candidatus Protochlamydia、Methylocaldum、Sulfuritalea、Mycobacterium、Aquirestis、Rhodobacter、Methylotenera等菌属拥有较高的点度中心度;较强的互作关系发生在Sulfuritalea-Rhodobacter、Azospirillum-Rhodobacter、Methylocaldum-Rhodobacter、Arthrobacter-Rhodobacter、Rhodoplanes-Rhodobacter、Candidatus Protochlamydia-Rhodobacter、Methylotenera-Rhodobacter、Rhodobacter-Aquirestis、Mycobacterium-Rhodobacter、PlanctomycesCandidatus Solibacter、Planctomyces-Legionella、Hymenobacter-Adhaeribacter、Luteolibacter-Crenothrix之间.综合分析节点微生物相关性、点度中心度及菌属间的互作强度,认为Rhodobacter、Methylocaldum、Methylotenera、Acinetobacter、Novosphingobium、Planctomyces、Hymenobacter、Luteolibacter为参与窖水污染物微生物降解的关键细菌,Rhodobacter为关键细菌的代表属.研究结果加深了对窖水中污染物微生物降解机制的认识.

Temporal changes in soil bacterial and archaeal communities with different fertilizers in tea orchards

It is important to understand the effects of temporal changes in microbial communities in the acidic soils of tea orchards with different fertilizers. A field experiment involving organic fertilizer （OF）, chemical fertilizer （CF）, and unfertilized control （CK） treatments was arranged to analyze the temporal changes in the bacterial and archaeal communities at bimonthly intervals based on the 16S ribosomal RNA （rRNA） gene using terminal restriction fragment length polymorphism （T-RFLP） profiling. The abundances of total bacteria, total archaea, and selected functional genes （bacterial and archaeal amoA, bacterial narG, nirK, nirS, and nosZ） were determined by quantitative poly- merase chain reaction （qPCR）. The results indicate that the structures of bacterial and archaeal communities varied significantly with time and fertilization based on changes in the relative abundance of dominant T-RFs. The abundancy of the detected genes changed with time. The total bacteria, total archaea, and archaeal amoA were less abundant in July. The bacterial amoA and denitrifying genes were less abundant in September, except the nirK gene. The OF treatment increased the abundance of the observed genes, while the CF treatment had little influence on them. The soil temperature significantly affected the bacterial and archaeal community structures. The soil moisture was signif- icantly correlated with the abundance of denitrifying genes. Of the soil chemical properties, soil organic carbon was the most important factor and was significantly correlated with the abundance of the detected genes, except the nirK gene. Overall, this study demonstrated the effects of both temporal alteration and organic fertilizer on the structures of mi- crobial communities and the abundance of genes involved in the nitrogen cycle.

Functional genomic analysis of Hawaii marine metagenomes

Using high-throughput sequencing on metagenome to analyze marine microbial community, it is one of current main issues in the field of environmental microbe research. In this paper, we conducted the functional analysis on seven samples of metagenomic data from different depth seawater in Hawaii. The results of gene prediction and function annotation indicate that there are large amounts of potential novel genes of which functions remain unknown at present. Based on the gene annotation, codon usage bias is studied on ribosomal protein-related genes and shows an evident influence by the marine extreme environment. Furthermore, focusing on the marine environmental differences such as light intensity, dissolved oxygen, temperature and pressure among various depths, comparative analysis is carried out on related genes and metabolic pathways. Thus, the understanding as well as new insights into the correlation between marine environment and microbes are proposed at molecular level. Therefore, the studies herein afford a clue to reveal the special living strategies of microbial community from sea surface to deep sea.