The Irr and RirA proteins participate in a complex regulatory circuit and act in concert to modulate bacterioferritin expression in Ensifer meliloti 1021

In this work we found that the bfr gene of the rhizobial species Ensifer meliloti, encoding a bacterioferritin iron storage protein, is involved in iron homeostasis and the oxidative stress response. This gene is located downstream of and overlapping the smc03787 open reading frame (ORF). No well-predicted RirA or Irr boxes were found in the region immediately upstream of the bfr gene although two presumptive RirA boxes and one presumptive Irr box were present in the putative promoter of smc03787. We demonstrate that bfr gene expression is enhanced under iron-sufficient conditions and that Irr and RirA modulate this expression. The pattern of bfr gene expression as well as the response to Irr and RirA is inversely correlated to that of smc03787. Moreover, our results suggest that the small RNA SmelC759 participates in RirA- and Irr-mediated regulation of bfr expression and that additional unknown factors are involved in iron-dependent regulation.Fil: Costa, Daniela. Instituto de Investigaciones Biológicas "Clemente Estable"; UruguayFil: Amarelle, Vanesa. Instituto de Investigaciones Biológicas "Clemente Estable"; UruguayFil: Valverde, Claudio Fabián. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: O`Brian, Mark R.. State University of New York; Estados UnidosFil: Fabiano, Elena. Instituto de Investigaciones Biológicas "Clemente Estable"; Urugua

Mechanisms and Regulation of Iron Homeostasis in the Rhizobia

Rhizobia are soil bacteria belonging to different genera whose most conspicuous characteristic is the ability to establish a symbiotic association with legumes and carry out nitrogen fixation. The success of these organisms in the rhizosphere or within the host plant involves the ability to sense the environment to assess the availability of nutrients, and to optimize cellular systems for their acquisition. Iron in natural habitats is mostly inaccessible due to low solubility, and microorganisms must compete for this limited nutrient. In addition to their agricultural and economic importance, rhizobia are model organisms that have given new insights into related, but less tractable animal pathogens. In particular, genetic control of iron homeostasis in the rhizobia and other a-Proteobacteria has moved away from the Fur paradigm to an iron sensing mechanism responding to the metal indirectly. Moreover, utilization of heme as an iron source is not unique to animal pathogens, and the rhizobial strategy reveals some interesting novel features. This chapter reviews advances in our understanding of iron metabolism in rhizobia.Agencia Nacional de Investigación e Innovació

Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing.

UNLABELLED: The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination of in vivo high-density mariner Tn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) in H. seropedicae SmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth of H. seropedicae SmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential in H. seropedicae SmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of the H. seropedicae endophytic lifestyle. IMPORTANCE: A focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyte Herbaspirillum seropedicae SmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms of H. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria.This work was funded by an EMBO ASTF 425-2014 short-term fellowship awarded to FR and conducted in the laboratory of AJG. SPWdV and AB were funded by BBSRC grant BB/K004514/1.This is the author accepted manuscript. The final version is available from the American Society for Microbiology at http://dx.doi.org/10.1128/AEM.02281-16

Battery- and Petrol-Powered Chainsaws: An Investigation of Productivity in Conifer Thinning

In recent years, battery technology has been greatly improved and some types of battery chainsaws are currently comparable with light-type petrol machines, suggesting their possible introduction into forest operations. In this context, the aim of this study was to test and compare the performance, in a Douglas-fir thinning, of two chainsaws similar in terms of weight and power, the Stihl MS 220 CB battery-powered saw and the Stihl MS 201 CM petrol-powered saw, measuring the working times and calculating the productivities. The results showed that, within a working day (about 6 h gross time), an average of 15 trees of 0.56 m3 was felled in each area. No statistically significant differences between the two chainsaws were found in terms of gross and net productivity; and the same result was obtained when focusing the analysis only on operations conducted using the chainsaws. Moreover, the average battery charge duration was 1.04 h, while the full tank duration for the petrol model was 1.12 h. In conclusion, our study demonstrates that, on the basis of their performance, battery chainsaws can be introduced into thinning operations, but a solution is needed to manage batteries in the forest, since the actual need is for 7–8 charges per workday

Draft genome sequence of Cupriavidus UYMMa02A, a novel beta-rhizobium species

We present the draft genome of Cupriavidus UYMMa02A, a rhizobium strain isolated from root nodules of Mimosa magentea. The assembly has approximately 8.1 million bp with an average G+C of 64.1%. Symbiotic and metal-resistance genes were identified. The study of this genome will contribute to the understanding of rhizobial evolution

Comparing the Productivity of the Latest Models of Li-Ion Battery and Petrol Chainsaws in a Conifer Clear-Cut Site

The recent technological development of batteries has allowed the production of powerful tools that are also used in forestry operations. For this reason, this study aimed to compare the performance of two latest chainsaw models in a conifer clear-cut. The examined chainsaws, the battery-powered Stihl MSA 300 and the petrol-powered MS 261 C-M, have comparable power and weight. The overall working times were recorded and then gross, net and felling/processing productivities were quantified. Our findings reported that in a working day (7.4 h gross time), each chainsaw felled and processed an average of 20 trees of 0.64 m3 with an average diameter at breast height of 28 cm. Considering the net productivity, no statistically significant differences were recorded between the two chainsaws. Investigating the productivities on operations conducted using the chainsaws, the battery chainsaw showed a lower average tree-processing productivity than that recorded for the petrol chainsaw. On average, the battery duration was 0.88 h, while the petrol tank duration was 0.97 h. Our study shows that battery chainsaws have great potential in forestry operations; however, considering the actual need for 8 charges per standard workday, optimizing battery management is an important objective for future work

Impacts of wood extraction on soil: assessing rutting and soil compaction caused by skidding and forwarding by means of traditional and innovative methods

Intensive forestry operations may cause soil compaction, plastic soil disturbances and rutting, which are responsible for undesirable effects on soils, vegetation and water bodies. Despite the numerous studies aimed to identify the main factors affecting soil damages, it still remains unclear whether wood extraction methods and driving direction (uphill or downhill) may affect the impacts of forest machines. This research analyses soil compaction and soil penetration resistance as well as rutting from forwarding and skidding using the same farm tractor in up- and downhill wood extraction. Rutting was estimated by 3D soil reconstruction derived by portable laser scanning (PLS) and close-range photogrammetry using structure for motion (SfM). Our findings showed that the direction of extraction did not affect soil damage severity during forwarding on a 25% slope. On the contrary, in order to reduce soil compaction, downhill skidding is preferable to uphill skidding. The results showed that the pressure on the ground caused by vehicles can be distributed horizontally, thus affecting also the soil between the wheel tracks. The soil bulk density inside the tracks after 10 forwarding passes increased by 40% and with 23% between the wheel tracks. The soil displacement in skidding trails (7.36 m(3) per 100 m of trail) was significantly higher than in forwarding (1.68 m(3) per 100 m of trail). The rutting estimation showed no significant difference between the PLS and SfM methods, even comparing the two digital surface models (DSMs) obtained, even if photogrammetry was preferred for technical and practical reasons

Construction and screening of a functional metagenomic library to identify novel enzymes produced by Antarctic bacteria

A metagenomic fosmid library of approximately 52 000 clones was constructed to identify functional genes encoding cold-adapted enzymes. Metagenomic DNA was extracted from a sample of glacial meltwater, collected on the Antarctic Peninsula during the ANTARKOS XXIX Expedition during the austral summer of 2012–2013. Each clone contained an insert of about 35–40 kb, so the library represented almost 2 Gb of genetic information from metagenomic DNA. Activity-driven screening was used to detect the cold-adapted functions expressed by the library. Fifty lipase/esterase and two cellulase-producing clones were isolated, and two clones able to grow on Avicel® as the sole carbon source. Interestingly, three clones formed a brown precipitate in the presence of manganese (II). Accumulation of manganese oxides was determined with a leucoberbelin blue assay, indicating that these three clones had manganese-oxidizing activity. To the best of our knowledge, this is the first report of a manganese oxidase activity detected with a functional metagenomic strategy

Identification of Antarctic culturable bacteria able to produce diverse enzymes of potential biotechnological interest

It is estimated that more than three quarters of the Earth’s biosphere is in perennially cold environments. Despite the extreme environmental conditions of desiccation and freezing, microbes can colonize these habitats through the adaptation of metabolic functions and the synthesis of structurally adapted enzymes. Enzymes within psychrophilic microbes exhibit high specific activity at low and moderate temperature, with low thermostability. In this study we used a classic microbiological approach to isolate Antarctic bacteria with cellulolytic, lipolytic, and ligninolytic activities. From 15 different environmental samples, we generated a collection of approximately 800 bacterial isolates that could grow on R2A or Marine medium at 4°C. This collection was then screened for the presence of the three types of activity at 4°C. We found that 47.7% of the isolates displayed lipolytic activity, 10.2% had cellulase/xylanase activity, and 7.7% showed guaiacol oxidase activity. Of these, 10% displayed two different types of activity, while 0.25% displayed all three types of activity. Our results indicate that cold environments represent outstanding resources for bioprospecting and the study of enzymatic adaptation