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     

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.     

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.     

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.     

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.     

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.     

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.     

Genotypic variation of rice in phosphorus acquisition from iron phosphate: Contributions of root morphology and phosphorus uptake kinetics

To elucidate the contributions of rice root morphology and phosphorus uptake kinetics to P uptake by rice from iron phosphate, a sand culture experiment with either sufficient P supply (control treatment, 10 mg P/l as NaH₂PO₄) or Fe-P as the only source of P (40 mg P/pot as FePO₄ × 4H₂O) and a solution culture experiment supplied with either sufficient P (10 mg P/l) or deficient P (0.5 mg P/l) were conducted. Eight rice cultivars, which differed in P uptake from Fe-P, were investigated. Plant P uptake, root morphology, and P uptake kinetics were determined. There were significant (P < 0.05) genotypic variations in both plant dry weight and P uptake per plant among eight rice (Oryza sativa L.) cultivars when supplied with Fe-P as the P source. The Fe-P treatment significantly (P < 0.05) decreased plant dry weight, P uptake per plant, and P concentration in plant dry matter of all cultivars in comparison with the control plants. In Fe-P treated plants, significant (P < 0.05) genotypic variation was shown in root morphology, including root length, surface area, volume, and number of lateral roots. The P uptake per plant from Fe-P by rice was significantly (P < 0.05) correlated with root surface area and root volume as well as with the number of lateral roots, suggesting that the ability of rice to absorb P from Fe-P was closely related to root morphology. Low P supply in solution significantly increased the I _max (P < 0.05), but significantly decreased the K _M (P < 0.05) for P absorption by all rice cultivars. We supposed that kinetic characteristics of root P uptake could not account for the ability of rice to absorb P from Fe-P. Published in Russian in Fiziologiya Rastenii, 2007, Vol. 54, No. 2, pp. 260–266. The text was submitted by the authors in English.     

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.     

Proteomics analysis of the Francisella tularensis LVS response to iron restriction: induction of the F. tularensis pathogenicity island proteins IglABC

Francisella tularensis is a highly virulent, facultative intracellular pathogen that causes tularemia in humans and animals. Although it is one of the most infectious bacterial pathogens, little is known about its virulence mechanisms. In this study, the response of F. tularensis live vaccine strain to iron depletion, which simulates the environment within the host, was investigated. In order to detect alterations in protein synthesis, metabolic labeling, followed by 2D-PAGE analysis was used. Globally, 141 protein spots were detected whose levels were significantly altered in the iron-restricted medium. About 65% of the spots were successfully identified using mass spectrometric approaches. Importantly, among the proteins produced at an increased level during iron-limited growth, three proteins were found encoded by the igl operon, located in the F. tularensis pathogenicity island I (FPI). Of these, the IglC and IglA proteins were previously reported to be necessary for full virulence of F. tularensis. These results, obtained at the proteome level, support and confirm recently published data showing that the igl operon genes are transcribed in response to iron limitation.     

An assessment of the hypervariable domains of the 16S rRNA genes for their value in determining microbial community diversity: the paradox of traditional ecological indices

Amplicon length heterogeneity PCR (LH-PCR) was investigated for its ability to distinguish between microbial community patterns from the same soil type under different land management practices. Natural sagebrush and irrigated mouldboard-ploughed soils from Idaho were queried as to which hypervariable domains, or combinations of 16S rRNA gene domains, were the best molecular markers. Using standard ecological indices to measure richness, diversity and evenness, the combination of three domains, V1, V3 and V1+V2, or the combined V1 and V3 domains were the markers that could best distinguish the undisturbed natural sagebrush communities from the mouldboard-ploughed microbial communities. Bray-Curtis similarity and multidimensional scaling were found to be better metrics to ordinate and cluster the LH-PCR community profiling data. The use/misuse of traditional ecological indices such as diversity and evenness to study microbial community profiles will remain a major point to consider when performing metagenomic studies.     

How to evaluate the environmental safety of microbial plant protection products: A proposal

Plant protection products with active micro-organisms are allegedly less hazardous to the environment and wildlife than synthetic chemical pesticides. Nevertheless, they need a proper pre-marketing environmental safety evaluation because of their potential toxicity and pathogenicity. Scientific and technical guidance on such a safety evaluation for regulatory purposes is scarce. Therefore, a risk decision tree is proposed to provide such guidance and to discern the acceptable from the unacceptable environmental risks. The decision tree is based on the risk criteria of the European Union. It takes integrally into account the characterisation, identification and efficacy and also emission, exposure, environmental effects and, finally, the environmental risk assessment. Case by case expert judgement remains necessary in view of limited knowledge of microbial ecology, limited experience with regulatory test protocols and taxonomic difficulties in relation to the indigenousness of active micro-organisms. The decision tree offers regulatory guidance on the environmental safety evaluation of microbial plant protection products.     

Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities

Background and Aims

Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover.

Methods

In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities.

Key Results

Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification.

Conclusions

The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils.     

Functional model for catecholase-like activity: Synthesis, structure, spectra, and catalytic activity of iron(III) complexes with substituted-salicylaldimine ligands

Four new mononuclear iron(III) complexes with the substituted-salicylaldimine ligands, [Fe(L¹)(TCC)] (1), [Fe(L²)(TBC)] (2), [Fe(L³)(TBC)] (3) and [Fe(L⁴)(TCC)](CH₃CN) (4) (HL¹ = N′-(5-OH-salicylaldimine)-diethylenetriamine, HL² = (N′-(5-Cl-salicylaldimine)-diethylenetriamine, HL³ N′-(5-Br-salicyl-aldimine)-dipropylenetriamine, HL⁴ = (N′-3,5-Br-salicylaldimine)-dipropylenetriamine, H₂TCC = tetrachlorocatechol, and H₂TBC = tetrabromocatechol), were prepared and characterized by XRD, EPR, and Mössbauer spectroscopy. The coordination sphere of the Fe(III) in complexes 1-4 is a distorted octahedral with N₃O₃ donors set which constructed by the Schiff-base ligands and the catecholate substrates of TBC or TCC. The in situ prepared Fe(III) complexes [Fe(L¹)Cl₂], [Fe(L²)Cl₂], [Fe(L³)(Cl₂)], and [Fe(L⁴)Cl₂] in absence of TBC or TCC show a high catecholase-like activity for the oxidation of 3,5-DTBC to the corresponding quinone 3,5-DTBQ.     

Negative feedback on a perennial crop: Fusarium crown and root rot of asparagus is related to changes in soil microbial community structure

The dynamic equilibrium of an ecosystem is driven by mutual feedback interactions between plants and soil microorganisms. Asparagus exerts a particularly strong influence on its soil environment through abundant production of persistent phenolic acids, which impact selectively soil microorganisms and may be involved in Fusarium crown and root rot (FCRR) of asparagus. In a survey of 50 asparagus plantations of the province of Québec, we found that FCRR was associated with a profound cultivar-specific, reorganization of the soil microbial community, as revealed by phospholipid fatty acid (PLFA) profiling. According to PLFA indicators, microbial biodiversity as well as bacterial and fungal abundance dropped sharply with the onset of FCRR in fields planted with the cultivar Guelph Millenium. This drop was followed by a similar drop in the arbuscular mycorrhizal population. Biodiversity and microbial population size then increased to finally reach a new equilibrium. Discriminant analysis of PLFA profiles obtained from soil samples also indicated a shift in soil microbial community structure associated with FCRR development in fields planted with the cultivar Jersey Giant. Different soil biological conditions, as indicated by microbial biomass C and N and soil enzyme activities, were associated with different cultivars. Preceding crop, manure application, geographical location and tillage depth also influenced the structure of soil microbial communities in asparagus plantations, as determined by PLFA profiling. If higher FCRR incidence is a consequence of the soil microbial community reorganization, means to reduce FCRR incidence in asparagus plantations may be found among practices such as soil organic fertilization, soil tillage and intercropping strategies that would dilute the negative influence of asparagus on the soil microbial community. Finally, FCRR outbreaks were generally promoted by a previous crop of maize. It seems that maize and asparagus host a F. proliferatum teleomorph (Gibberella fujikoroi) of the same mating type.