In vivo growth of Staphylococcus lugdunensis is facilitated by the concerted function of heme and non-heme iron acquisition mechanisms

Staphylococcus lugdunensis has increasingly been recognized as a pathogen that can cause serious infection indicating this bacterium overcomes host nutritional immunity. Despite this, there exists a significant knowledge gap regarding the iron acquisition mechanisms employed by S. lugdunensis, especially during infection of the mammalian host. Here we show that S. lugdunensis can usurp hydroxamate siderophores and staphyloferrin A and B from Staphylococcus aureus. These transport activities all required a functional FhuC ATPase. Moreover, we show that the acquisition of catechol siderophores and catecholamine stress hormones by S. lugdunensis required the presence of the sst-1 transporter-encoding locus, but not the sst-2 locus. Iron-dependent growth in acidic culture conditions necessitated the ferrous iron transport system encoded by feoAB. Heme iron was acquired via expression of the iron-regulated surface determinant (isd) locus. During systemic infection of mice, we demonstrated that while S. lugdunensis does not cause overt illness, it does colonize and proliferate to high numbers in the kidneys. By combining mutations in the various iron acquisition loci (isd, fhuC, sst-1, and feo), we demonstrate that only a strain deficient for all of these systems was attenuated in its ability to proliferate to high numbers in the murine kidney. We propose the concerted action of heme and non-heme iron acquisition systems also enable S. lugdunensis to cause human infection.     

Reduction of iron by extracellular iron reductases: implications for microbial iron acquisition

The extracellular enzymatic reduction of iron by microorganisms has not been appropriately considered. In this study the reduction and release of iron from ferrioxamine were examined using extracellular microbial iron reductases and compared to iron mobilization by chemical reductants, and to chelation by EDTA and desferrioxamine. A flavin semiquinone was formed during the enzymatic reduction of ferrioxamine, which was consistent with the 1 e(-) reduction of iron by an enzyme. The rates for the enzymatic reactions were substantially faster than both the 2 e(-) chemical reductions and the chelation reactions. The rapid rates of the enzymatic reduction reactions demonstrated that these enzymes are capable of accomplishing the extracellular mobilization of iron required by microorganisms. The data suggest that mechanistically there are two phases for the mobilization and transport of iron by those microorganisms that produce both extracellular iron reductases and siderophores, with reduction being the principle pathway.     

Effects of ferrous iron on the performance and microbial community in aerobic granular sludge in relation to nutrient removal

Lab‐scale experiments were conducted to investigate the effects of ferrous iron on nutrient removal performance and variations in the microbial community inside aerobic granular sludge for 408 days. Two reactors were simultaneously operated, one without added ferrous iron (SBR1), and one with 10 mg Fe²⁺ L^?1 of added ferrous iron (SBR2). A total of 1 mg Fe²⁺ L^?1 of added ferrous iron was applied to SBR1 starting from the 191st day to observe the resulting variations in the nutrient removal performance and the microbial community. The results show that ammonia‐oxidizing bacteria (AOB) could not oxidize ammonia due to a lack of iron compounds, but they could survive in the aerobic granular sludge. Limited ferrous iron addition encouraged nitrification. Enhanced biological phosphorus removal (EBPR) from both reactors could not be maintained regardless of the amount of ferrous iron that was applied. EBPR was established in both reactors when the concentration of mixed liquor suspended solid (MLSS) and the percentage of Accumulibacteria increased. A total of 10 mg Fe²⁺ L^?1 of added ferrous iron had a relatively adverse effect on the growth of AOB species compared to 1 mg Fe²⁺ L^?1 of added ferrous iron, but it encouraged the growth of Nitrospira sp. and Accumulibacteria, which requires further study. It could be said that the compact and stable structure of aerobic granular sludge preserved AOB and NOB from Fe‐deficient conditions, and wash‐out during the disintegration period. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:716–725, 2017     

Strigolactones in plant adaptation to abiotic stresses: An emerging avenue of plant research

Phytohormones play central roles in boosting plant tolerance to environmental stresses, which negatively affect plant productivity and threaten future food security. Strigolactones (SLs), a class of carotenoid‐derived phytohormones, were initially discovered as an “ecological signal” for parasitic seed germination and establishment of symbiotic relationship between plants and beneficial microbes. Subsequent characterizations have described their functional roles in various developmental processes, including root development, shoot branching, reproductive development, and leaf senescence. SLs have recently drawn much attention due to their essential roles in the regulation of various physiological and molecular processes during the adaptation of plants to abiotic stresses. Reports suggest that the production of SLs in plants is strictly regulated and dependent on the type of stresses that plants confront at various stages of development. Recently, evidence for crosstalk between SLs and other phytohormones, such as abscisic acid, in responses to abiotic stresses suggests that SLs actively participate within regulatory networks of plant stress adaptation that are governed by phytohormones. Moreover, the prospective roles of SLs in the management of plant growth and development under adverse environmental conditions have been suggested. In this review, we provide a comprehensive discussion pertaining to SL‐mediated plant responses and adaptation to abiotic stresses.     

The role of phytosiderophores in acquisition of iron and other micronutrients in graminaceous species: An ecological approach

Phytosiderophores (PS) are released in graminaceous species (Gramineae) under iron (Fe) and zinc (Zn) deficiency stress and are of great ecological significance for acquisition of Fe and presumably also of Zn. The potential for release of PS is much higher than reported up to now. Rapid microbial degradation during PS collection from nutrient solution-grown plants is the main cause of this underestimation. Due to spatial separation of PS release and microbial activity in the rhizosphere a much slower degradation of PS can be assumed in soil-grown plants. Concentrations of PS up to molar levels have been calculated under non-sterile conditions in the rhizosphere of Fe-deficient barley plants.Besides Fe, PS mobilize also Zn, Mn and Cu. Despite this unspecific mobilization, PS mobilize appreciable amounts of Fe in calcareous soils and are of significance for chlorosis resistance of graminaceous species. In most species the rate of PS release is high enough to satisfy the Fe demand for optimal growth on calcareous soils.In contrast to the chelates ZnPS and MnPS, FePS are preferentially taken up in comparison with other soluble Fe compounds. In addition, the specific uptake system for FePS (translocator) is regulated exclusively by the Fe nutritional status. Therefore, it seems appropriate to retain the term phytosiderophore instead of phytochelate.     

Induction of ferric reductase activity in response to iron deficiency in Arabidopsis

The response to iron deficiency was investigated in 16 ecotypes of Arabidopsis thaliana (L.) Heynh. and in Arabidopsis griffithiana. An increase in root ferric reductase activity was observed under conditions of iron deficiency in these ecotypes and in both species. This observation is consistent with a Strategy I response which is typical for dicot plants. A. griffithiana, however, showed a lower induction of ferric reductase activity in response to iron deficiency than that of the commonly studied A. thaliana Columbia ecotypes.     

Revisiting the Holy Grail: using plant functional traits to understand ecological processes

One of ecology's grand challenges is developing general rules to explain and predict highly complex systems. Understanding and predicting ecological processes from species' traits has been considered a ‘Holy Grail’ in ecology. Plant functional traits are increasingly being used to develop mechanistic models that can predict how ecological communities will respond to abiotic and biotic perturbations and how species will affect ecosystem function and services in a rapidly changing world; however, significant challenges remain. In this review, we highlight recent work and outstanding questions in three areas: (i) selecting relevant traits; (ii) describing intraspecific trait variation and incorporating this variation into models; and (iii) scaling trait data to community‐ and ecosystem‐level processes. Over the past decade, there have been significant advances in the characterization of plant strategies based on traits and trait relationships, and the integration of traits into multivariate indices and models of community and ecosystem function. However, the utility of trait‐based approaches in ecology will benefit from efforts that demonstrate how these traits and indices influence organismal, community, and ecosystem processes across vegetation types, which may be achieved through meta‐analysis and enhancement of trait databases. Additionally, intraspecific trait variation and species interactions need to be incorporated into predictive models using tools such as Bayesian hierarchical modelling. Finally, existing models linking traits to community and ecosystem processes need to be empirically tested for their applicability to be realized.     

黄顶菊对不同入侵地植物群落及土壤微生物群落的影响

为明确不同入侵地植物群落和土壤生态对黄顶菊入侵的反馈机制,选取天津静海(JH)、河北沧州(CZ)、河北衡水(HS)及河南安阳(AY)4个黄顶菊入侵典型区域,研究黄顶菊对不同入侵地植物群落多样性、土壤理化及土壤微生物群落结构的影响,并进一步揭示植物群落、土壤养分和土壤微生物之间的相关关系。结果表明,黄顶菊入侵显著降低了JH、CZ和HS的植物群落多样性指数(P0.05),改变了四个地区的土壤理化性质,显著升高了不同入侵地真菌PLFA的含量、总PLFA的含量、真菌/细菌和革兰氏阴性菌/革兰氏阳性菌(P0.05),降低了土壤微生物的Margalef丰富度指数(P0.05),但均存在地区间差异;RDA和相关分析的结果表明,硝态氮、全氮的含量对植物群落的影响较大,而铵态氮的含量对土壤微生物群落结构的影响较大,除丰富度指数外,植物群落与土壤微生物群落的多样性指数之间存在显著的负相关关系(P0.05)。总之,黄顶菊改变了入侵地植物群落多样性,并且对入侵地土壤理化性质和土壤微生物群落结构产生了显著影响,且存在地区差异。本研究将为更好的理解外来植物的入侵机制及制定相应的防控策略提供理论依据。     

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO₂. Although the stimulating effects of elevated CO₂ (eCO₂) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO₂ conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO₂. PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO₂, and such significant effects of eCO₂ on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO₂. Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO₂. Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO₂ and environmental factors shaping the microbial community structure.     

铁矿物强化厌氧氨氧化效能及其微生物机制研究进展

自然界中的氮循环与铁循环相互交联,参与氮循环的厌氧氨氧化（anaerobic ammonium oxidation,anammox）菌的生长代谢及活性发挥也与铁元素紧密关联。自然界广泛存在的铁矿物因具有运行成本低廉、稳定性好、二次污染小等优势,在污水处理领域得到广泛应用。在厌氧氨氧化脱氮系统中引入适量铁矿物,不仅有助于促进anammox菌和铁还原菌的富集,提高功能基因丰度和相关酶活性,还可能通过影响污泥浓度、血红素c含量、胞外聚合物含量和颗粒化程度,改善污泥性能和提高厌氧氨氧化系统的稳定性。同时,铁矿物具有促进体系多种氮素转化途径（如anammox、铁自养反硝化、铁氨氧化、异化硝酸盐还原成铵和反硝化）相耦合的潜能,可以提高anammox污水处理系统的总氮去除率。本文基于铁矿物在促进污水生物脱氮方面的良好性能及其在anammox系统中的变化,从脱氮效能、污泥特性、微生物特征及酶活性等方面,系统综述了铁矿物对厌氧氨氧化系统的强化作用机制,并从anammox菌对铁矿物的利用及铁元素的摄取角度展望了后续的研究方向,以期为铁矿物强化厌氧氨氧化系统的实际应用提供理论和技术指导。     

Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

Microbes exist in a range of metabolic states (for example, dormant, active and growing) and analysis of ribosomal RNA (rRNA) is frequently employed to identify the ‘active'' fraction of microbes in environmental samples. While rRNA analyses are no longer commonly used to quantify a population''s growth rate in mixed communities, due to rRNA concentration not scaling linearly with growth rate uniformly across taxa, rRNA analyses are still frequently used toward the more conservative goal of identifying populations that are currently active in a mixed community. Yet, evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations. This report highlights the complex and often contradictory relationships between rRNA, growth and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies and non-growth activities. Ways in which rRNA data can be used for useful characterization of microbial assemblages are presented, along with questions to be addressed in future studies.     

Children of Helicobacter pylori-infected dyspeptic mothers are predisposed to H. pylori acquisition with subsequent iron deficiency and growth retardation

BACKGROUND: We tested whether Helicobacter pylori-infected dyspeptic mothers had a higher rate of H. pylori infection in their children, and whether such H. pylori-infected children were predisposed to iron deficiency or growth retardation. MATERIALS AND METHODS: A total of 163 children from 106 dyspeptic mothers (58 with and 48 without H. pylori infection) were enrolled to evaluate body weight, height, hemoglobin, serum ferritin, and H. pylori infection using the 13C-urea breath test. A questionnaire was used to evaluate demographic factors of each child. RESULTS: The rate of H. pylori infection in children with H. pylori-infected dyspeptic mothers was higher than that of children with noninfected mothers (20.5% vs. 5.3%; p<.01, OR: 4.6, 95% CI: 1.5-14.2). The rate of H. pylori infection in children elevated as the number of their H. pylori-infected siblings increased (p<.01). For children below 10 years of age, H. pylori infection was closely related to low serum ferritin and body weight growth (p<.05). CONCLUSION: The children of H. pylori-infected dyspeptic mothers had an increased risk for such infection. The risk further increased once their siblings were infected. H. pylori infection in pre-adolescent children may determine iron deficiency and growth retardation.     

Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops

Seasonal shifts in rhizosphere microbial populations were investigated to follow the influence of plant developmental stage. A field study of indigenous microbial rhizosphere communities was undertaken on pea (Pisum satvium var. quincy), wheat (Triticum aestivum var. pena wawa) and sugar beet (Beta vulgaris var. amythyst). Rhizosphere community diversity and substrate utilization patterns were followed throughout a growing season, by culturing, rRNA gene density gradient gel electrophoresis and BIOLOG. Culturable bacterial and fungal rhizosphere community densities were stable in pea and wheat rhizospheres, with dynamic shifts observed in the sugar beet rhizosphere. Successional shifts in bacterial and fungal diversity as plants mature demonstrated that different plants select and define their own functional rhizosphere communities. Assessment of metabolic activity and resource utilization by bacterial community-level physiological profiling demonstrated greater similarities between different plant species rhizosphere communities at the same than at different developmental stages. Marked temporal shifts in diversity and relative activity were observed in rhizosphere bacterial communities with developmental stage for all plant species studied. Shifts in the diversity of fungal and bacterial communities were more pronounced in maturing pea and sugar beet plants. This detailed study demonstrates that plant species select for specialized microbial communities that change in response to plant growth and plant inputs.     

Response of microbial community structure to the hydrochemical evolution during riverbank filtration: a case study in Shenyang,China

Abstract

Microorganisms are widely involved in the transformation process of physical and chemical properties in the geological and hydrogeological environment. Active participation of microorganisms is important features of the biogeochemical reactions during groundwater exploiting along the riverbank filtration. Hydrodynamic condition has a direct or indirect difference control of the biological effectiveness, chemical activity and mobility of the pollution components, which can affect biogeochemical process. In different biogeochemistry, there will be some exclusive functional bacteria, which is of great significance to understand the biogeochemical mechanism of river water infiltration. This study confirms that there are two main different flow paths from river to the center of the depression cone due to different hydrodynamic conditions and spatial characteristics and scaling effects of redox zonation during riverbank filtration. In different flow paths, the microbial abundance shows obvious spatial heterogeneity. The microbial abundance and species similarity degree of the riverbed and deep flow path sediments has significant correlation. There is a significant correlation between the dominant bacteria and the environmental factors in different hydrodynamic conditions on a spatial scale. This study is the first to reveal the response of microbial community structure to water chemical evolution during riparian filtration. Due to significant positive correlation between the Fe/Mn and As, it brings the potential danger for drinking water.     

Effects of an electric field and zero valent iron on anaerobic treatment of azo dye wastewater and microbial community structures

A zero valent iron (ZVI) bed with a pair of electrodes was packed in an anaerobic reactor aiming at enhancing treatment of azo dye wastewater. The experiments were carried out in three reactors operated in parallel: an electric field enhanced ZVI-anaerobic reactor (R1), a ZVI-anaerobic reactor (R2) and a common anaerobic reactor (R3). R1 presented the highest performance in removal of COD and color. Raising voltage in R1 further improved its performance. Scanning electron microscopy images displayed that the structure of granular sludge from R1 was intact after being fed with the high dye concentration, while that of R3 was broken. Fluorescence in situ hybridization analysis indicated that the abundance of methanogens in R1 was significantly greater than that in the other two reactors. Denaturing gradient gel electrophoresis showed that the coupling of electric field and ZVI increased the diversity of microbial community and especially enhanced bacterial strains responsible for decolorization.     

Soil microbial community structure and enzymatic activity responses to nitrogen management and landscape positions in switchgrass (Panicum virgatum L.)

Switchgrass (Panicum virgatum L.) is usually grown on marginal land for biofuel system, in which nitrogen (N) is an essential management practice, and landscape position is a key topographical factor in impacting the production. However, limited information is available regarding how the N application and landscape positions affect soil microbial communities and enzyme activities under switchgrass. Thus, the specific objective of this study was to evaluate the responses of N rate (high, 112 kg N/ha; medium, 56 kg N/ha; and low, 0 kg N/ha) and landscape positions (shoulder and footslope) on soil biological health under switchgrass field. Data showed that N addition significantly influenced carbon and N fractions. The hot water‐soluble organic carbon (HWC) and nitrogen (HWN) fractions were significantly higher at footslope position than the shoulder position. The amount of total phospholipid fatty acid (PLFA), total bacterial, actinomycetes, gram‐negative and gram‐positive bacteria, total fungi, arbuscular mycorrhizal (AM) fungi, and saprophytes PLFAs were highest with medium and high N rates and footslope position. The N addition increased total PLFAs in N fertilizer treatments, viz. medium (5,946 ng PLFA‐C/g soil) and high N rates (5,871 ng PLFA‐C/g soil). Microbial biomass carbon and nitrogen and enzyme activities (urease, β‐glucosidase, acid phosphatase and arylsulfatase) were significantly enhanced by N fertilization (medium and high N rates) compared to control (low N rates) under footslope position. The urease activity under medium (36.3 µmol N‐NH₄⁺ g^?1 soil hr^?1) and high N rates (31.4 µmol N‐NH₄⁺ g^?1 soil hr^?1) was 42.9% and 23.6% higher than low N rates, respectively. This study suggests that the application of medium N rate in footslope position to switchgrass can enhance the soil biological properties and hence can protect the environment from the excessive use of N fertilizer.     

Novel approach using substrate-mediated radiolabelling of RNA to link metabolic function with the structure of microbial communities

A novel concept was developed applying radioisotope-labelled substrate incorporation into the biomass. The resulting radiolabelled RNA was used both as an indicator of activity and as a template for gaining structural and functional information about a substrate-utilizing microbial community. Sequences of PCR products are separated via cloning or using molecular fingerprinting techniques. Nucleic acids from predominant clones or the whole molecular fingerprinting pattern are transferred to a membrane and hybridized with the radiolabelled sample RNA. Scanning of the hybridized blots for radioactivity indicates the members involved in the utilization of the substrate. This novel 'random walk' approach using radioisotope probing was evaluated in a model community experiment.