Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis

Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N(2)-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.     

磷酸盐修复重金属污染土壤的研究进展

从研究方法、反应机理以及风险评价等方面综述了磷酸盐修复重金属污染土壤的研究进展,分析和讨论了其中存在的问题和不足,提出了今后加强研究的重点。目前磷酸盐修复重金属污染土壤时,使用的主要研究方法有化学形态提取法、化学平衡形态模型法和光谱及显微镜技术,各个方法都有其优缺点,应该结合使用并探索新方法。磷酸盐稳定重金属的作用机理主要有3个:磷酸盐诱导重金属吸附、磷酸盐和重金属生成沉淀或矿物和磷酸盐表面吸附重金属,但磷酸盐与重金属反应的机理十分复杂,人们尚不完全清楚,因此难以有效区分和评价诱导吸附机理和沉淀机理或其它固定机理,相应地对磷酸盐修复重金属的长期稳定性难以预测。磷酸盐修复重金属污染土壤时由于其较高的施用量可能会造成磷的积聚从而引发一些环境风险,如磷淋失造成水体富营养化,营养失衡造成作物必需的中量和微量元素缺乏以及土壤酸化等。所以应该谨慎选择磷肥种类和用量,最好是水溶性磷肥和难溶性磷肥配合、磷肥与石灰物质等配合施用。今后应着重研究磷酸盐与重金属相互作用的机理区分和评价;关注磷酸盐修复重金属污染土壤时存在的潜在风险,特别是加强植物长期不断吸收磷或其它环境条件变化致使土壤磷素持续减少过程中稳定的重金属溶解性和移动性的研究,磷酸盐修复重金属污染土壤的长期田间实践等。     

Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly

Viruses of the Bacteria and Archaea play important roles in microbial evolution and ecology, and yet viral dynamics in natural systems remain poorly understood. Here, we created de novo assemblies from 6.4 Gbp of metagenomic sequence from eight community viral concentrate samples, collected from 12 h to 3 years apart from hypersaline Lake Tyrrell (LT), Victoria, Australia. Through extensive manual assembly curation, we reconstructed 7 complete and 28 partial novel genomes of viruses and virus-like entities (VLEs, which could be viruses or plasmids). We tracked these 35 populations across the eight samples and found that they are generally stable on the timescale of days and transient on the timescale of years, with some exceptions. Cross-detection of the 35 LT populations in three previously described haloviral metagenomes was limited to a few genes, and most previously sequenced haloviruses were not detected in our samples, though 3 were detected upon reducing our detection threshold from 90% to 75% nucleotide identity. Similar results were obtained when we applied our methods to haloviral metagenomic data previously reported from San Diego, CA: 10 contigs that we assembled from that system exhibited a variety of detection patterns on a timescale of weeks to 1 month but were generally not detected in LT. Our results suggest that most haloviral populations have a limited or, possibly, a temporally variable global distribution. This study provides high-resolution insight into viral biogeography and dynamics and it places "snapshot" viral metagenomes, collected at a single time and location, in context.     

Plant and rhizosphere processes involved in phytoremediation of metal-contaminated soils

This paper reviews the recent advances in understanding of metal removal from contaminated soils, using either hyperaccumulator plants, or high biomass crop species after soil treatment with chelating compounds. Progress has been made at the physiology and molecular level regarding Zn and Ni uptake and translocation in some hyperaccumulators. It is also known that natural hyperaccumulators do not use rhizosphere acidification to enhance their metal uptake. Recently, it has been found that some natural hyperaccumulators proliferate their roots positively in patches of high metal availability. In contrast, non-accumulators actively avoid these areas, and this is one of the mechanisms by which hyperaccumulators absorb more metals when grown in the same soil. However, there are few studies on the exudation and persistence of natural chelating compounds by these plants. It is thought that rhizosphere microorganisms are not important for the hyperaccumulation of metals from soil. Applications of chelates have been shown to induce large accumulations of metals like Pb, U and Au in the shoots of non-hyperaccumulators, by increasing metal solubility and root to shoot translocation. The efficiency of metal uptake does vary with soil properties, and a full understanding of the relative importance of mass flow and diffusion in the presence and absence of artificial chelates is not available. To successfully manipulate and optimise future phytoextraction technologies, it is argued that a fully combined understanding of soil supply and plant uptake is needed.     

Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome

Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus-enriched metagenomes (viromes) isolated from bovine rumen fluid and analysed the resulting data using comparative metagenomics. A high level of diversity was observed with up to 28,000 different viral genotypes obtained from each environment. The majority (~78%) of sequences did not match any previously described virus. Prophages outnumbered lytic phages approximately 2:1 with the most abundant bacteriophage and prophage types being associated with members of the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling based on SEED subsystems revealed an enrichment of sequences with putative functional roles in DNA and protein metabolism, but a surprisingly low proportion of sequences assigned to carbohydrate and amino acid metabolism. We expanded our analysis to include previously described metagenomic data and 14 reference genomes. Clustered regularly interspaced short palindromic repeats (CRISPR) were detected in most of the microbial genomes, suggesting previous interactions between viral and microbial communities.     

丛枝菌根在植物修复重金属污染土壤中的作用

丛枝菌根（Arbuscular mycorrhizae,AM）是自然界中分布最广的一类菌根,AM真菌能与陆地上绝大多数的高等植物共生,常见于包括重金属污染土壤在内的各种生境中。在重金属污染条件下,AM真菌可以减轻重金属对植物的毒害,影响植物对重金属的吸收和转运,在重金属污染土壤的植物修复中显示出极大的应用潜力。重点介绍了AM真菌对植物重金属耐性的影响及其在植物提取和植物稳定中的应用等方面的进展,讨论了未来研究所面临的任务和挑战。     

重金属污染土壤植物修复中的微生物功能研究进展

综述了国内外在重金属污染土壤植物-微生物联合修复领域的研究报道,总结了近5年的研究实例。植物-微生物联合修复体系具有生物固定与生物去除土壤重金属的两种功能,根际微生物可以菌根、内生菌等方式与根系形成联合体,通过增强植物抗性和优化根际环境,促进根系发展,增强植物吸收和向上转运重金属的能力。建立植物-微生物联合修复体系,可充分发挥植物与微生物作用功能的优势,提高污染土壤的修复效率。增强植物修复体系中微生物功能的重点是深入研究根际微生物、根系和介质载体三者之间复合功能,结合污染土壤类型与植物群落配置的特点筛选扩繁高效菌种与菌群。     

Understanding molecular mechanisms for improving phytoremediation of heavy metal-contaminated soils

Heavy metal pollution of soil is a significant environmental problem with a negative potential impact on human health and agriculture. Rhizosphere, as an important interface of soil and plants, plays a significant role in phytoremediation of contaminated soil by heavy metals, in which, microbial populations are known to affect heavy metal mobility and availability to the plant through release of chelating agents, acidification, phosphate solubilization and redox changes, and therefore, have potential to enhance phytoremediation processes. Phytoremediation strategies with appropriate heavy metal-adapted rhizobacteria or mycorrhizas have received more and more attention. In addition, some plants possess a range of potential mechanisms that may be involved in the detoxification of heavy metals, and they manage to survive under metal stresses. High tolerance to heavy metal toxicity could rely either on reduced uptake or increased plant internal sequestration, which is manifested by an interaction between a genotype and its environment.A coordinated network of molecular processes provides plants with multiple metal-detoxifying mechanisms and repair capabilities. The growing application of molecular genetic technologies has led to an increased understanding of mechanisms of heavy metal tolerance/accumulation in plants and, subsequently, many transgenic plants with increased heavy metal resistance, as well as increased uptake of heavy metals, have been developed for the purpose of phytoremediation. This article reviews advantages, possible mechanisms, current status and future direction of phytoremediation for heavy-metal–contaminated soils.     

Comparison of different microbial biomass and activity measurement methods in metal-contaminated soils

The aims of this study were: (1) to compare different microbial methods of detecting the effects of heavy metals on the functioning of the soil ecosystem; and (2) to evaluate the effect of incubation on microbial biomass and microbial activity in soils that were not pre-incubated after sampling in order to determine their suitability for measuring the effects of heavy metals on the soil microbial ecosystem. The microbial biomass methods (included: biomass C, N and ninhydrin-N by fumigation-extraction (FE); substrate-induced respiration (SIR); soil ATP content and microbial activity as evolved CO2-C and arginine ammonification. All were tested in soils from the Woburn Market Garden Experiment. Due to past sludge application the soils contained, Zn, Cu or Ni at around current European Union upper limits and Cd at up to three times the limit. The amount of microbial biomass in metal-contaminated soils was about half of that found in soils from the experiment that received uncontaminated organic manure or inorganic fertilizer. The amount of biomass measured by FE and soil ATP content in incubated soils showed little change over 20 days incubation. However, SIR measurements were statistically affected over the first few days of incubation. The rates of arginine ammonification were higher in this order: farmyard manure (FYM)>inorganic fertilizer>sewage-sludge throughout the incubation. However, the evolved CO2-C rates were not significantly different among the treatments. Discriminant analysis confirmed smaller amounts of biomass in the metal-contaminated soils than in the other treatments. Linked properties, such as relationships between biomass and soil organic matter, or biomass-specific respiration rates, may provide "internal control" which may help overcome problems of establishing suitable control, or comparative measurements, when moving from experimental to natural environments.     

The phylogenetic diversity of thermophilic members of the genus Bacillus as revealed by 16S rDNA analysis

Abstract Sixteen thermophilic strains of the genus Bacillus , representing eight validly described and six invalidly described species, as well as one unassigned strain, were investigated by comparative 16S rDNA analyses and the sequences compared to the existing database for the genera Bacillus and Alicyclobacillus . The majority of strains were found to cluster in two groups represented by B. stearothermophilus and B. pallidus. Bacillus smithii, B. thermocloacae , and B. thermoruber are phylogenetically well separated and cluster within the radiation of mesophilic bacilli. The as yet undescribed taxon 'B. flavothermus' warrants species status. B. schlegelii and B. tusciae group peripherally with members of Alicyclobacillus and may be reclassified when more phenotypic data support their phylogenetic position.     

基于宏基因组学重建来自深海热液喷口的Epsilonproteobacteria基因组及其代谢分析

【背景】非致病性Epsilonproteobacteria广泛存在于全球各种不同的自然环境中,特别是一些极端生境如深海热液喷口,并且经常在微生物群落中作为优势物种被发现。然而,由于现阶段培养技术的限制,仅有为数不多的深海热液Epsilonproteobacteria被分离培养,极大限制了对其生理特征、代谢方式以及生态功能的深入认识。【目的】研究深海热液未培养Epsilonproteobacteria的进化地位、代谢潜能及其在原位生态系统中可能发挥的作用。【方法】基于宏基因组学Binning的方法,从采集自东太平洋海隆深海热液烟囱体样本中构建4个高质量的Epsilonproteobacteria基因组Bin225、Bin51、Bin54和Bin189,并进行了系统发育和代谢途径的分析。【结果】Bin189在系统发育树上相对独立于其他所有已知的Epsilonproteobacteria类群,而其余3个重构基因组都与Nitratiruptor sp. SB155-2具有较近的亲缘关系。在代谢潜能方面,所有的基因组除了都含有sqr硫氧化和rTCA碳固定途径的基因以外,也同时具有脂多糖输出转运子和多种分泌系统。Bin189显示出与其它基因组显著不同的代谢特征,其中还检测到与有机物和氨基酸转运相关的功能基因。而其他的3个基因组均具有完整的反硝化途径的功能基因,其中2个还具有Sox系统、氢化酶和鞭毛移动系统。【结论】Bin189可能是一种新发现的深海热液兼性化能营养型Epsilonproteobacteria,推测其余的3个类群能够利用硫化物和氢气作为能源进行化能自养生长。考虑到它们多样的代谢潜能,这些Epsilonproteobacteria类群很可能在深海热液微生物群落的形成发展和地球化学元素循环中发挥重要作用。     

基于高通量测序的花马盐湖原核微生物及其耐盐基因

【目的】揭示陕北花马盐湖沉积物原核微生物群落组成,并分析其潜在的耐盐功能基因。【方法】构建盐湖沉积物宏基因组16S r RNA文库和fosmid文库,利用Illumina HiSeq高通量测序及生物信息技术分析细菌古菌群落组成和耐盐菌株(5-5)外源宏基因组的潜在耐盐基因。【结果】获得18978条有效的16Sr RNA序列,共5221个OTUs,包括23个门,155个属,其中广古菌门(Euryarchaeota)和变形菌门(Proteobacteria)为优势菌门,盐杆状菌属(Halorhabdus)、盐红菌属(Halorubrum)及假单胞菌属(Pseudomonas)等16个属为优势属,以及嗜盐单胞菌属(Halomonas)、冷弯菌属(Psychroflexus)及不动细菌属(Acinetobacter)等139个属为非优势属。从4126个fosmid文库菌株中筛选出37株耐盐菌株,其中菌株5-5、2E4和2F4对不同浓度的NaCl、CuSO_4、ZnSO_4及CdSO_4具有耐受性,从5-5的外源宏基因组序列中获得61个Unigene,其中12个Unigene的同源基因编码的蛋白质如无机焦磷酸酶、转座酶、亚碲酸钾抗性蛋白及钙调蛋白等广泛参与其他生物的耐盐逆境。【结论】盐湖沉积物中蕴藏着丰富多样的细菌古菌类群以及潜在耐盐功能基因资源。     

Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis

Background

Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathogens detection, many cases are culture-negative, especially in patients who had received long-term antibiotic treatment, and precise diagnosis has therefore become a major challenge in the clinic. Metagenomic sequencing can provide both information on the pathogenic strain and the antibiotic susceptibility profile of patient samples without culturing, offering a powerful method to deal with culture-negative cases.

Methods

To assess the feasibility of a metagenomic approach to detect the causative pathogens in resected valves from IE patients, we employed both next-generation sequencing and Oxford Nanopore Technologies MinION nanopore sequencing for pathogens and antimicrobial resistance detection in seven culture-negative IE patients. Using our in-house developed bioinformatics pipeline, we analyzed the sequencing results generated from both platforms for the direct identification of pathogens from the resected valves of seven clinically culture-negative IE patients according to the modified Duke criteria.

Results

Our results showed both metagenomics methods can be applied for the causative pathogen detection in all IE samples. Moreover, we were able to simultaneously characterize respective antimicrobial resistance features.

Conclusion

Metagenomic methods for IE detection can provide clinicians with valuable information to diagnose and treat IE patients after valve replacement surgery. However, more efforts should be made to optimize protocols for sample processing, sequencing and bioinformatics analysis.

     

Studies on the phosphate potentials of soils

Summary When a sample of Upper Greensand soil was shaken in dilute solutions of calcium chloride containing orthophosphate, microbial activity was sufficiently stimulated to alter the measured value of Schofield's phosphate potential. The effect was more rapid and more marked for air-dried than for field-moist soils. However, the effect on the potential^SP was not significant during the first 2 to 4 hours of shaking a moist sample, and probably not significant during the first 1/2 to 1 hour of shaking an air-dried sample.It was also shown that the changes in the phosphate potential^SP during the first few hours of shaking an untreated field sample are not due to microbial interference. These changes appear to result from the co-existence, in field soils, of micro-volumes of soil of potential^SP higher and lower than the mean for the soil (Part I, and Part III, in preparation).     

Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide- and metal-contaminated subsurface soils

In this study, the immobilization of toxic uranium [U(VI)] mediated by the intrinsic phosphatase activities of naturally occurring bacteria isolated from contaminated subsurface soils was examined. The phosphatase phenotypes of strains belonging to the genera, Arthrobacter, Bacillus and Rahnella, previously isolated from subsurface soils at the US Department of Energy's (DOE) Oak Ridge Field Research Center (ORFRC), were determined. The ORFRC represents a unique, extreme environment consisting of highly acidic soils with co-occurring heavy metals, radionuclides and high nitrate concentrations. Isolates exhibiting phosphatase-positive phenotypes indicative of constitutive phosphatase activity were subsequently tested in U(VI) bioprecipitation assays. When aerobically grown in synthetic groundwater (pH 5.5) amended with 10 mM glycerol-3-phosphate (G3P), phosphatase-positive Bacillus and Rahnella spp. strains Y9-2 and Y9602 liberated sufficient phosphate to precipitate 73% and 95% of total soluble U added as 200 microM uranyl acetate respectively. In contrast, an Arthrobacter sp. X34 exhibiting a phosphatase-negative phenotype did not liberate phosphate from G3P or promote U(VI) precipitation. This study provides the first evidence of U(VI) precipitation via the phosphatase activity of naturally occurring Bacillus and Rahnella spp. isolated from the acidic subsurface at the DOE ORFRC.