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Fe(II)-oxidizing bacteria (FeOB) are important catalysts for iron cycling in iron-rich marine, groundwater, and freshwater environments. However, few studies have reported the distribution and diversity of these bacteria in flooded paddy soils. This study investigates the microbial structure and diversity of microaerophilic Fe(II)-oxidizing bacteria (mFeOB) and their possible role in Fe(II) oxidation in iron-rich paddy soils. Using enrichment experiments that employed serial transfers, the changes in microaerophilic microbial community were examined via 16S rRNA gene high-throughput sequencing. During enrichments, the Fe(II) oxidation rate decreased as transfers increased, and the maximum rate of Fe(II) oxidation was observed in the first transfer (0.197 mM day−1). Results from X-ray diffraction of minerals and scanning electron microscopy of the cell-mineral aggregates revealed that cell surfaces in all transfers were partly covered with amorphous iron oxide formed by FeOB. After four transfers, the phyla of Proteobacteria had a dominant presence that reached up to 95%. Compared with the original soil, the relative abundances of Cupriavidus, Massilia, Pseudomonas, Ralstonia, Sphingomonas, and Variovorax increased in FeS gradient tubes and became dominant genera after transfers. Cupriavidus, Pseudomonas, and Ralstonia have been identified as FeOB previously. Furthermore, the structure of the microbial community tended to be stable as transfers increased, indicating that other bacterial species might perform important roles in Fe(II) oxidation. These results suggest the potential involvement of mFeOB and these other microorganisms in the Fe(II)-oxidizing process of soils. It will be helpful for future studies to consider their role in related biogeochemical processes, such as transformation of organic matters and heavy metals.

Catechol 1,2-dioxygenases catalyze catechol ring-opening, a critical step in the degradation of aromatic compounds.

12 páginas, 1 figura, 1 tabla, Phaseolus vulgaris L. (common bean) is a legume indigenous to American countries currently cultivated in all continents, which is nodulated by diferent rhizobial species and symbiovars. Most of species able to nodulate this legume worldwide belong to the genus Rhizobium, followed by those belonging to the genera Ensifer (formerly Sinorhizobium) and Pararhizo bium (formerly Rhizobium) and minority by species of the genus Bradyrhizobium. All these genera belong to the phylum alpha-Proteobacteria, but the nodulation of P. vulgaris has also been reported for some species belonging to Paraburkholderia and Cupriavidus from the beta-Proteobacteria. Several species nodulating P. vulgaris were originally isolated from nodules of this legume in American countries and are linked to the symbiovars phaseoli and tropici, which are currently present in other continents probably because they were spread in their soils together with the P. vulgaris seeds. In addition, this legume can be nodulated by species and symbiovars originally isolated from nodules of other legumes due its high promiscuity, a concept currently related with the ability of a legume to be nodulated by several symbiovars rather than by several species. In this article we review the species and symbiovars able to nodulate P. vulgaris in diferent countries and continents and the challenges on the study of the P. vulgaris endosymbionts diversity in those countries where they have not been studied yet, that will allow to select highly efective rhizobial strains in order to guarantee the success of P. vulgaris inoculation, This review article was funded under the fnancial project STDF1268 from the Academy of Scientifc Research and Technology Applications, Cairo, Egypt. Special thanks should be given by authors to the reviewers who gave important notes that contributed signifcantly to strength our manuscript.

Phenol and ammonia in wastewater pose a serious threat to ecosystems and human health. However, the currently limited studies on single bacterium simultaneously removing phenol and nitrogen pollution have not fully elucidated the relevant metabolic mechanisms. The differences in proteomic profile after supplementing with phenol and ammonia for 6 and 24 h, respectively, were evaluated to explore the metabolic characteristics and adaptive mechanism of Cupriavidus oxalaticus T2 during the simultaneous removal process of phenol and nitrogen. Results revealed that a new potential phenol para-degradation pathway appeared in T2. Phenol induced changes in nitrogen metabolism, resulting in increased denitrification and decreased synthesis of glutamate from ammonia at 6 h. In addition, phenol exposure enhanced the expression of cytochrome oxidases with high oxygen affinity and increased ATP synthesis. The increase in chemotaxis and flagellar assembly was conducive to the uptake and utilization of phenol. The synthesis of lipoic acid and biotin was also promoted to resist phenol toxicity. Moreover, phenol triggered cellular stress response, thereby leading to the upregulation of anti-stress proteins, such as universal stress protein, iron‑sulfur cluster protein, and chaperones. This study contributes to revealing the metabolic characteristics and adaptive mechanism of T2 during simultaneous nitrogen and phenol removal. Significance Phenol and ammonia often co-exist in wastewater, causing serious environmental problems. The information on the metabolic mechanism of simultaneously removing these two pollutants by bacteria is insufficient at present. Moreover, phenol is toxic to microbial and causes cells damage. Therefore, exploring the response mechanism of bacteria to phenol stress is conducive to understand their tolerance mechanism to aromatic compounds. In this study, the metabolic characteristics and adaptive mechanism of C. oxalaticus T2 during the simultaneous removal of phenol and nitrogen process were evaluated by comparing the proteome profiles at different stages. The results revealed the degradation pathways of phenol and nitrogen by strain T2. A variety of phenol response mechanisms were determined, including enhanced energy production, improved cell motility, increased the synthesis of lipoic acid and biotin, and combined action of multiple anti-stress proteins. This study is potentially useful to future phenol and nitrogen co-pollution bioremediation strategies and provides insight into the phenolic compound resistance mechanism in bacteria.

A Gram-stain negative, strictly aerobic, mesophilic bacterial strain, designated strain S23T, was isolated from pond-side soil of an artificial pond in South Korea. Cells were observed to be peritrichously flagellated short rods showing positive oxidase and catalase activities. Growth of strain S23T was observed at 15–37 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 7.0–8.0) and 0–2% (w/v) NaCl (optimum, 0–0.5%). The major respiratory quinone was identified as ubiquinone-8 and the major fatty acids were identified as C16:0, cyclo-C17:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The G + C content of the genomic DNA was determined to be 65.1 mol%. Phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid were detected as the major polar lipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain S23T formed a phyletic lineage with Cupriavidus necator N-1T within the genus Cupriavidus. Strain S23T is closely related to C. necator N-1T (99.2%), Cupriavidus basilensis DSM 11853T (98.8%), Cupriavidus alkaliphilus ASC-732T (98.8%) and Cupriavidus numazuensis TE26T (98.7%), based on 16S rRNA gene sequence similarities. However, the DNA–DNA relatedness values between strain S23T and the closely related type strains were less than 46%. On the basis of phenotypic, chemotaxonomic and molecular properties, strain S23T represents a novel species of the genus Cupriavidus, for which the name Cupriavidus lacunae sp. nov. is proposed. The type strain is S23T (KACC 19624T = JCM 32674T).

Cupriavidus sp. L7L, a newly isolated wild-type soil bacterium, was found to synthesize polyhydroxyalkanoate (PHA) terpolymers from levulinic acid (LA), a top bio-based platform chemical, as the sole carbon source. NMR spectra showed that the terpolymers consisted mainly of 3-hydroxybutyrate (3HB), 3-hydroxyvalerate (3HV), and a small amount (2.1–4.8 mol%) of 4-hydroxyvalerate (4HV). The combination of monomers together with high molecular weights improved markedly the thermal and mechanical properties of the terpolymers. Increasing cultivation temperature of Cupriavidus sp. L7L increased the proportions of 3HB and decreased the proportions of 3HV. A fed-batch fermentation using LA as the sole carbon source without pH control produced a biomass of 15.8 dry weight g L−1 that contained 81 dry weight% of a terpolymer P(3HB-co-33.7 mol% 3HV-co-2.1 mol% 4HV), equaling a productivity of 0.213 g PHA L−1 h−1. The terpolymer showed a melting point of 92 °C and elongation at break of 630%, compared to 84.6 °C and 462%, respectively, for the copolymer P(3HB-co-35.9 mol% 3HV) that contained no 4HV. This study showed that Cupriavidus sp. L7L exhibited a great potential for producing PHA polymers with excellent mechanical property that could be modulated by cultivation temperature when cultivated exclusively in LA.

Irawati W, Yuwono T, Ompusunggu NP. 2018. Growth characteristics and copper accumulation of bacterial consortium Acinetobacter sp. and Cupriavidus sp. isolated from a wastewater treatment plant. Biodiversitas 19: 1884-1890. Pollutant treatments are part of the human calling, as the crown of creation, to subdue, preserve, and cultivate the earth in bringing goodness for all creatures. Bioremediation of copper using indigenous bacteria is well known as the best water treatment for polluted environment recovery. Acinetobacter sp. and Cupriavidus sp. are indigenous bacteria isolated from industrial sewage in Indonesia. Bioremediation in environment is a process involving community of bacterial consortium for heavy metal or any other polluting materials accumulation. The purposes of this research were: (i) to characterize growth of Acinetobacter sp. and Cupriavidus sp. consortia in sewage medium, enrichment medium, and medium supplemented with copper, (ii) to establish the potency of bacterial consortia to accumulate copper. The growth of bacteria was observed based on cell turbidity using spectrophotometer at wavelength of 600 nm. Cells pellet was destructed by nitric acid at 100oC and copper concentration was analyzed by atomic absorption spectrophotometer as copper accumulation value. The results showed that the growth of bacterial consortia in medium containing copper was better than that of single bacterium. The best bacterial consortium was the mixture of Acinetobacter sp. IrC1 and Acinetobacter sp. IrC2. The use of sewage as cultivation medium decreased bacterial growth by up to 25% but still resulted in the same level of logarithmic phase in enrichment medium. The highest accumulation capability was of a consortium of Acinetobacter sp. IrC1 and Acinetobacter sp. IrC2 at a level of 6.45 g/mg copper/g cells dry weight, suggesting that 5.09% of copper were accumulated by cells. It was concluded that the best composition of consortia in growth and copper accumulation capability was the mixture of Acinetobacter sp. IrC1 and Acinetobacter sp. IrC2. These results may be due to the fact that both bacteria belong to the same genus that allowed them for synergistic interactions.

Long carbon chain alkanediols are used in the production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)], however these substrates possess high toxicity towards bacterial cells. This study demonstrated the effective utilisation of a long carbon chain alkanediol, namely 1,8-octanediol, to enhance the yield and production of a copolymer with a high molecular weight of over 1000 kDa, which is desirable for novel applications in medical and biopharmaceuticals. The increased PHA content (47–61 wt%) and concentration (1.7–4.5 g/L) was achieved by additional feeding of a combination of C4 substrates at C/N 10, with 1,8-octanediol + γ-butyrolactone producing P(3HB-co-22 mol% 4HB) with a high molecular weight (1060 kDa) and elongation at break of 970%. The DO-stat feeding strategy of C/N 10 has shown an increment of PHA concentration for both carbon combination, 0.45–4.27 g/L and 0.32–3.36 g/L for 1,8-octanediol + sodium 4-hydroxybutyrate (4HB-Na) and 1,8-octanediol + γ-butyrolactone, but with a slight reduction on molecular weight and mechanical strength. Nonetheless, further study revealed that a nitrogen-absence feeding strategy could retain the high molecular weight and elongation at break of the copolymer, and simultaneously improving the overall P(3HB-co-4HB) production.

Investigation of the diverse evolutionary developed mechanisms enabling bacteria to maintain homeostasis and to be resistant to lead is crucial for the discovery of novel strategies for isolation of this highly toxic metal and its subsequent elimination from contaminated environments. The metalloregulatory protein

The objective of the study was to isolate microorganism that can produce growth hormone, fix atmospheric nitrogen, and solubilize inorganic phosphate that may be used for enhancing the growth of banana in marginal land. A total of 25 bacteria associated with banana that belonged to six genera were isolated from namely Acinetobacter , Enterobacter , Pantoea , Klebsiella , Rhizobium , and Cupriavidus genera. Gammaproteobacteria is the dominant class, followed by Betaproteobacteria and Alphaproteobacteria . All isolates were screened for multiple plant growth promoting traits which may play a role in banana growth, namely fixing nitrogen, solubilizing phosphate, and producing Indole Acetic Acid (IAA). Twenty-two isolates were capable to fix nitrogen, 21 isolates can solubilize insoluble phosphate, and 15 isolates produced IAA dependent of L-Tryptophan presence. Despite most of the bacteria isolates exhibited one plant growth-promoting activities, Enterobacter and Klebsiella genera showed three of plant growth promoting bacteria traits.

portuguesInhame, macaxeira e batata-doce sao vegetais importantes no Nordeste brasileiro, uma vez que esses tuberculos sao ricos em amido. Os Polihidroxialcanoatos (PHAs) sao polimeros biodegradaveis produzidos a partir de amido e utilizados na producao de plasticos. O objetivo deste trabalho foi isolar e identificar bacterias com potencial aplicacao biotecnologica para producao de polihidroxialcanoatos a partir da rizosfera e superficie de tuberas de inhame, macaxeira e batata-doce. A coleta das culturas bacterianas ocorreu por meio da retirada do solo da rizosfera e da superficie das tuberas. Apos diluicoes seriadas e semeio do solo em meio de cultura, bacterias com caracteristicas morfologicas distintas foram selecionadas para analise atraves do PCR de colonia. Das 214 bacterias analisadas, 11 amostras foram positivas para o gene phaC, fator fundamental para sintese de PHA. Nove bacterias apresentaram resultado satisfatorio para producao de grânulos de PHAs apos coloracao de Sudan Black. Dentre as bacterias positivas no PCR e Sudan Black, oito foram identificadas por sequenciamento ao nivel de genero ou especie, como: Pseudomonas, Bacillus, Agrobacterium, Stenotrophomonas, Cupriavidus e Microvirga flocculans, sendo esta ultima descrita pela primeira vez na literatura como produtora de PHA. A aplicacao de PCR de colonia com coloracao por Sudan Black mostrou-se eficiente e rapida para a selecao de bacterias potencialmente produtoras de PHAs a partir de amostras de solo. EnglishYam, sweet potatoes and cassava are important cultures in northeastern Brazil once these tubercles are full of starch. Polyhydroxyalkanoates are biodegradable polymers made ​​from starch used in the production of plastics. The objective of this work was isolate and identify bacterial communities with potential biotechnological applications from rhizosphere and surface soil of yam, cassava and sweet potatoes tubers. The bacterial cultures collection occurred through the removal of rhizosphere and surface soil from the tubers. After serial dilutions and soil sowing in culture medium, bacteria with distinct morphological characteristics were selected for analysis by colony PCR. Of the 214 bacteria analyzed, 11 samples were positive for phaC gene, a key factor for PHA synthesis. Nine bacteria showed satisfactory results for the production of PHAs granules after staining with Sudan Black. Among the bacteria positive in PCR and Sudan Black, eight were identified by sequencing to genus or species, such as: Pseudomonas, Bacillus, Agrobacterium, Stenotrophomonas, Cupriavidus e Microvirga flocculans. Microvirga flocculans was described first time in the literature as producing PHA. The application of colony PCR with Sudan Black staining was efficient and rapid selection of bacteria potentially producing PHAs from soil samples.

Earlier research on the biogeochemical factors affecting natural attenuation in coal-tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field-based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single-cell imaging and shotgun metagenomics now provide cultivation-independent tools for their study. We tracked carbon from (13)C-labeled naphthalene through microbial populations in contaminated surface sediments over six days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant-based trophic web. Contaminant-exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome-assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.

Acrylamide is neurotoxic, genotoxic, teratogenic and carcinogenic. Its widespread use in various industrial processes leads to environmental contamination. Acrylamidase produced by certain bacteria degrade acrylamide to acrylic acid and ammonia. The present study details the isolation and identification of soil bacterium which could degrade acrylamide. Among the 18 acrylamide-degrading isolates tested, isolate ICTDB921 demonstrated superior acrylamide degradation which was confirmed by HPLC, FTIR and GC-MS. The partial 16S rRNA sequencing confirmed the isolate to be Cupriavidus oxalaticus ICTDB921, which showed highest growth at 60 mM acrylamide, neutral pH and 30 °C. The kinetic model predictions were consistent with experimental results. The acrylamidase from this isolate showed potency at pH (6–8) and temperatures (30–60 °C), with reasonable pH (6–8) and thermal stability (upto 60 °C). The enzyme was stable against most metal ions and amino acids, and also degraded other aliphatic amides, demonstrating its potential in remediation of acrylamide from the environment and food systems.

The ability to harness cellular redox processes for abiotic synthesis might allow the preparation of engineered hybrid living systems. Towards this goal we describe a new bacteria-mediated iron-catalysed reversible deactivation radical polymerisation (RDRP), with a range of metal-chelating agents and monomers that can be used under ambient conditions with a bacterial redox initiation step to generate polymers. Cupriavidus metallidurans, Escherichia coli, and Clostridium sporogenes species were chosen for their redox enzyme systems and evaluated for their ability to induce polymer formation. Parameters including cell and catalyst concentration, initiator species, and monomer type were investigated. Water-soluble synthetic polymers were produced in the presence of the bacteria with full preservation of cell viability. This method provides a means by which bacterial redox systems can be exploited to generate "unnatural" polymers in the presence of "host" cells, thus setting up the possibility of making natural-synthetic hybrid structures and conjugates.

Nitrobenzene, nitrotoluenes and nitrobenzoic acid are toxic and mutagenic. Their removal from the environment is necessary to avoid health and environmental damage. In this study, Cupriavidus strain a3 was found to utilize 2-nitrotoluene (2NT), 3-nitrotoluene (3NT), 4-nitrotoluene (4NT), nitrobenzene (NB) and 2-nitrobenzoic acid (2NBA) as carbon and nitrogen source, resulting in their detoxification. The metabolism involved reductive transformation of nitroaromatics to the corresponding amines followed by cleavage of amino group to release ammonia. Cell free extract showed nitroreductase activity in the range of 310-389 units/mg. NB was reduced to form benzamine and 4-aminophenol, 2NT was reduced to 2-aminotoluene, whereas 2NBA was reduced to form 2-aminobenzoic acid. Similarly, 3NT was metabolized to 3-aminotoluene and 2-amino-4-methylphenol, while 4NT was reduced to 4-nitrosotoluene and 4-aminotoluene. Cytotoxicity and apoptosis assays using Jurkat cell line, and Ames test were used to evaluate the detoxification of nitroaromatics during biodegradation. Biodegradation with Cupriavidus resulted in 2.6-11 fold increase in cell viability, 1.3-2.3 fold reduction in apoptosis, 1.6-55 fold reduction in caspase-3 activation, and complete disappearance of mutagenic activity. In soil microcosm, bioaugmentation with Cupriavidus resulted in 16-59% degradation of various nitroaromatics, as against14% degradation without bioaugmentation. Thus, the present study reflects promising capability of Cupriavidus strain a3 in degradation and detoxification of multiple nitroaromatics.

Phosphorus (P) deficiency is an important factor that limits the agricultural production potential in acidic soils. The bacterial phoC gene encodes non-specific acid phosphatase (ACP), which participates in the mineralization of soil organic P and is therefore important for the improvement of soil P availability. However, the function and community population of phoC-harboring bacteria and their driving factors in acidic soil remain largely unknown. For this study, 51 soil samples and 207 plant samples were collected from four locations in the acidic soil region of southern China. Quantitative PCR and high-throughput sequencing were employed to analyze abundance and community composition of phoC-harboring bacteria. The results showed that soil P availability was the important nutrient element limiting the growth of both plants and soil bacteria. Soil ACP activity was clearly higher than alkaline phosphatase, indicating the important effect of phoC-harboring bacteria in acidic soils. ACP activity and phoC gene abundance showed a significant positive correlation, and both were closely related to soil available P, total carbon, and total nitrogen. The dominant genera of phoC-harboring bacteria involved Cupriavidus, Stenotrophomonas, and Xanthomonas. Compared to land-use pattern, sampling location, and soil parent material, soil property played a more important role in affecting phoC-harboring bacterial community structure, where N-related variables including soil NO 3 - -N, NH 4 + -N, and C/N ratio appeared to be the main factors. These findings suggest that phoC-harboring bacteria should provide an important contribution to soil P availability in acidic soil, and its function and community composition were strongly associated with soil nutrients.

Organophosphorus insecticides (OPs) have been widely used to control agricultural pests, which has raised concerns about OP residues in crops and the environment. In this study, we investigated the degradation kinetics and pathways of 8 OPs by

Dynamic changes in power generation and electrochemical properties were compared between the control microbial fuel cells (C-MFC) and an oxytetracycline (OTC)-treated MFC (O-MFC) on days 84, 139, 174, 224, 295, 307 and 353. The results showed that a high concentration of OTC (>5 mg·L−1) could inhibit microbial activity and result in a decline of voltage output and power density compared with the same C-MFC. However, with the prolongation of incubation time, the inhibitory effect was gradually weakened. Electrochemical analyses demonstrated that long-term OTC acclimation reduced the ohmic and polarisation resistance of the anode, which was conducive to the recovery of electrochemical performance. More than 99% of 10 mg·L−1 OTC could be removed within 48 h, and the antibacterial activity of the MFC effluent on Escherichia coli DH5α was conclusively eliminated. High-throughput sequencing analysis revealed that the diversity and richness of the microbial community decreased significantly after long-term OTC enrichment. Acinetobacter, Petrimonas, Spirochaetaceae and Delftia were enriched and played a dominant role in C-MFC stability and power generation. The promotion by Cupriavidus, Geobacter and Stenotrophomonas in simultaneous OTC degradation and bioelectricity generation in the O-MFC was demonstrated.

Chlorpyrifos was one of the most widely used organophosphorus insecticides and the neurotoxicity and genotoxicity of chlorpyrifos to mammals, aquatic organisms and other non-target organisms have caused much public concern. Cupriavidus nantongensis X1T, a type of strain of the genus Cupriavidus, is capable of efficiently degrading 200 mg/L of chlorpyrifos within 48 h. This is ~100 fold faster than Enterobacter B-14, a well-studied chlorpyrifos-degrading bacterial strain. Strain X1T can tolerate high concentrations (500 mg/L) of chlorpyrifos over a wide range of temperatures (30&ndash, 42 &deg, C) and pH values (5&ndash, 9). RT-qPCR analysis showed that the organophosphorus hydrolase (OpdB) in strain X1T was an inducible enzyme, and the crude enzyme isolated in vitro could still maintain 75% degradation activity. Strain X1T can simultaneously degrade chlorpyrifos and its main hydrolysate 3,5,6-trichloro-2-pyridinol. TCP could be further metabolized through stepwise oxidative dechlorination and further opening of the benzene ring to be completely degraded by the tricarboxylic acid cycle. The results provide a potential means for the remediation of chlorpyrifos- contaminated soil and water.

A genetic linkage between a conserved gene cluster (Nit1C) and the ability of bacteria to utilize cyanide as the sole nitrogen source was demonstrated for nine different bacterial species. These included three strains whose cyanide nutritional ability has formerly been documented (Pseudomonas fluorescens Pf11764, Pseudomonas putida BCN3 and Klebsiella pneumoniae BCN33), and six not previously known to have this ability [Burkholderia (Paraburkholderia) xenovorans LB400, Paraburkholderia phymatum STM815, Paraburkholderia phytofirmans PsJN, Cupriavidus (Ralstonia) eutropha H16, Gluconoacetobacter diazotrophicus PA1 5 and Methylobacterium extorquens AM1]. For all bacteria, growth on or exposure to cyanide led to the induction of the canonical nitrilase (NitC) linked to the gene cluster, and in the case of Pf11764 in particular, transcript levels of cluster genes (nitBCDEFGH) were raised, and a nitC knock-out mutant failed to grow. Further studies demonstrated that the highly conserved nitB gene product was also significantly elevated. Collectively, these findings provide strong evidence for a genetic linkage between Nit1C and bacterial growth on cyanide, supporting use of the term cyanotrophy in describing what may represent a new nutritional paradigm in microbiology. A broader search of Nit1C genes in presently available genomes revealed its presence in 270 different bacteria, all contained within the domain Bacteria, including Gram-positive Firmicutes and Actinobacteria, and Gram-negative Proteobacteria and Cyanobacteria. Absence of the cluster in the Archaea is congruent with events that may have led to the inception of Nit1C occurring coincidentally with the first appearance of cyanogenic species on Earth, dating back 400-500 million years.

3-Hydroxyanthranilate 3,4-dioxygenase (HAO) is an iron-dependent protein that activates O(2) and inserts both oxygen atoms into 3-hydroxyanthranilate (3-HAA). An intriguing question is how HAO can rapidly bind O(2), even though local O(2) concentrations and diffusion rates are relatively low. Here, a close inspection of the HAO structures revealed that substrate- and inhibitor-bound structures exhibit a closed conformation with three hydrophobic loop regions moving toward the catalytic iron center, whereas the ligand-free structure is open. We hypothesized that these loop movements enhance O(2) binding to the binary complex of HAO and 3-HAA. We found that the carboxyl end of 3-HAA triggers changes in two loop regions and that the third loop movement appears to be driven by an H-bond interaction between Asn(27) and Ile(142). Mutational analyses revealed that N27A, I142A, and I142P variants cannot form a closed conformation, and steady-state kinetic assays indicated that these variants have a substantially higher K(m) for O(2) than WT HAO. This observation suggested enhanced hydrophobicity at the iron center resulting from the concerted loop movements after the binding of the primary substrate, which is hydrophilic. Given that O(2) is nonpolar, the increased hydrophobicity at the iron center of the binary complex appears to be essential for rapid O(2) binding and activation, explaining the reason for the 3-HAA–induced loop movements. Because substrate binding-induced open-to-closed conformational changes are common, the results reported here may help further our understanding of how oxygen is enriched in nonheme iron-dependent dioxygenases.

Engineering of plant rhizosphere with beneficial plant growth promoting (PGP) bacteria offers a great promise for sustainable crop productivity. In this context, 49 rhizospheric/endophytic bacterial isolates were purified using N-free medium, screened in vitro for PGP characteristics and evaluated for their beneficial effects on the early growth of maize (Zea mays L.). The biodiversity of isolated bacteria was analyzed by amplified ribosomal DNA restriction analysis (ARDRA) using four restriction enzymes. Out of the 49 isolates, 7 produced high levels (32.1–82.8 μg mL−1) of indole-3-acetic acid (IAA); 11 had potential phosphate solubilizing abilities (101–163 μg mL−1), while significant acetylene reduction activities (100–1800 nmole C2H4 mg−1 protein h−1) were observed in 12 isolates. Five ribogroups (A-E) were identified using ARDRA. The 16S rRNA-sequence analysis of bacterial representatives from different ribogroups revealed that, 89% of isolates belonged to phylum Proteobacteria, while 11% of them were assigned into phylum Bacteroidetes. Phylum Proteobacteria included Achromobacter, Agrobacterium, Bordetella, Cupriavidus, Ochrobactrum, Pseudoxanthomonas and Stenotrophomonas genera. While, phylum Bacteroidetes was represented by Chryseobacterium and Flavobacterium genera. Under greenhouse conditions, all the selected isolates significantly increased shoot and root fresh and dry biomass of maize plants, compared to the non-inoculated control. Inoculation with Chryseobacterium sp. NGB-29 and Flavobacterium sp. NGB-31 showed the highest beneficial effects on plant growth parameters that were tentatively associated with the high efficiency of these isolates to fix nitrogen and produce high amounts of IAA. The study indicates the potential use of these isolates for production of maize biofertilizers under field conditions. Keywords: Isolation, PGPR, Zea mays, Diversity, IAA, N2- fixation, P- solubilization, Plant inoculation, Plant biomass production

The present study investigates physicochemical, mechanical, and biological properties of polyhydroxyalkanoate (PHA) copolymers containing 4-hydroxybutyrate (4HB) synthesized in Cupriavidus eutrophus B10646 culture. In poly(3-hydroxybutyrate/4-hydroxybutyrate) [P(3HB/4HB)] bipolymers, 4HB varied between 10.4 and 75.0 mol%; in poly(3-hydroxybutyrate/3-hydroxyvalerate/4-hydroxybutyrate) terpolymers, 4HB constituted 28.7–55.6 mol%; and in poly(3-hydroxybutyrate/3-hydroxyvalerate/4-hydroxybutyrate/3-hydroxyhexanoate) quaterpolymers, 4HB varied between 9.3 and 13.3 mol%. The degree of crystallinity of P(3HB/4HB) copolymers decreased consistently with an increase in 4HB content, reaching 38%. The incorporation of 3-hydroxyvalerate and 3-hydroxyhexanoate into copolymers enhanced that effect. The effect of 4HB monomer units on temperature properties of copolymers was exhibited as lowering of the melting temperature and crystallization temperature, which improved the processing-related properties of the copolymers. All copolymers containing 4HB showed enhanced elongation at break compared to poly(3-hydroxybutyrate). Polymer films prepared from PHAs with different chemical composition had similar microstructure and porosity and had no toxic effect on mouse fibroblast NIH 3 T3 cells, proving their high biocompatibility.

The valorization of lignocellulose encounters both opportunities and challenges as the lignocellulose is an abundant and intrinsically heterogeneous natural source. However, the successful design of an integrated process for complete carbon utilization of lignocellulose is limited. A classic base-catalyzed pretreatment strategy and a natural Cupriavidus strain with the capacity of lignin degradation and polyhydroxyalkanoates (PHAs) biosynthesis were selected to establish a fundamental and functional module necessary to enable a new platform for lignocellulose pretreatment and waste carbon conversion. The in situ bioconversion was first introduced to the pretreatment. Specifically, selectively cleaving insensitive C–C bonds (e.g., β-5) of lignin via a “washing” mechanism, Cupriavidus basilensis B-8 promoted the digestibility of the rice straw to realize almost complete carbohydrate conversion, yielding 984.2 mg g–1 of reducing sugar when combined with alkaline pretreatment. A demonstrated concentration of ...

This paper presents a whole-cell biosensor that operates in conjunction with a smartphone-based fluorescence diagnostic system on a paper device to monitor the concentration of gold ions in human urine. The heavy metal-tolerant bacteria Cupriavidus metallidurans was genetically engineered for use as a chassis in a red fluorescent protein (RFP)-based microbial sensor. The biosensor is highly sensitive to gold ions, with a detection limit of 110 nM. The proposed smartphone-based analysis system provides a user-friendly approach to design tools of personal health monitoring for reporting the presence of gold ions in human urine.

Several rhizobial strains possess the ability to modulate leguminous plants ethylene levels by producing the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase. While the effect of ACC deaminase has been studied in several rhizobia belonging to the Alphaproteobacteria class, not much is understood about its impact in the nodulation abilities of rhizobia belonging to the Betaproteobacteria class, which are common symbionts of Mimosa species. In this work, we report the impact of ACC deaminase production by the Betaproteobacterium, Cupriavidus taiwanensis STM894, and its role in the nodulation of Mimosa pudica. C. taiwanensis STM894 was studied following its transformation with the plasmid pRKACC, containing an ACC deaminase gene. The expression of the exogenous ACC deaminase led to increased nodulation and M. pudica growth promotion by C. taiwanensis STM894. These results indicate that ACC deaminase plays an important role in modulating ethylene levels that inhibit the nodulation process induced by both rhizobia belonging to the Alpha and Betaproteobacteria class.

To assess the physiology and low temperature adaptability of the key players of nitrification and denitrification, denitrifying bacteria were isolated and characterized from the selected paddy fields. Bacterial strains belonging to Cupriavidus and Ochrobactrum sp. were explored through the selective screening of heterotrophic nitrifying and aerobic denitrifying bacteria. The direct implication of nitrate removal in the natural sample was estimated by taking the nitrate supplemented soil as well as the enriched culture. A more prominent cold-adaptive bacterium was identified as Cupriavidus sp. PDN31. The utilization of ammonium, nitrate, and nitrite and the presence of nitrous oxide reductase (nosZ) gene, catalyses the first step of the denitrification conferred its heterotrophic nitrification and aerobic denitrification ability. The ammonium, nitrate, and nitrite removal efficiency of PDN31 was found to be 92.1%, 93.5%, and 99.8%, respectively. The functional traits, evaluated from metabolizing va...

d -Amino acids are important building blocks for various compounds, such as pharmaceuticals and agrochemicals. A more cost-effective enzymatic method for d -amino acid production is needed in the industry. We improved a one-pot enzymatic method for d -amino acid production by the dynamic kinetic resolution of N-succinyl amino acids using two enzymes: d -succinylase (DSA) from Cupriavidus sp. P4-10-C, which hydrolyzes N-succinyl- d -amino acids enantioselectively to their corresponding d -amino acid, and N-succinyl amino acid racemase (NSAR, EC.4.2.1.113) from Geobacillus stearothermophilus NCA1503. In this study, DSA and NSAR were purified and their properties were investigated. The optimum temperature of DSA was 50°C and it was stable up to 55°C. The optimum pH of DSA and NSAR was around 7.5. In d -phenylalanine production, the optical purity of product was improved to 91.6% ee from the examination about enzyme concentration. Moreover, 100 mM N-succinyl- dl -tryptophan was converted to d -tryptophan at 81.8% yield with 94.7% ee. This enzymatic method could be useful for the industrial production of various d -amino acids.

The tfdA gene encodes α-ketoglutarate-dependent dioxygenase, which catalyzes the first step of the 2,4-dichlorophenoxyacetic acid (2,4-D) degradation pathway. The entire range of 2,4-D-degrading bacteria is divided into three groups based on their phylogeny, physiological and biochemical features, and isolation source. Each of these groups has its own version of the tfdA gene. The first group is the most studied and consists of fast-growing copiotrophic β- and γ-Proteobacteria isolated from anthropogenic habitats. The bacteria of this group possess the canonical sequence of this gene. Within this group, tfdA forms at least three classes (I, II, and III) of highly homologous gene families. The tfdA gene of Cupriavidus necator JMP134 was recognized as a Class I type. Class II consists of tfdA sequences belonging only to the genus Burkholderia of β-Proteobacteria, whereas Class III includes tfdA sequences belonging to the genera Delftia, Cupriavidus, Variovorax, Achromobacter, Comamonas, Rhodoferax, Halomonas, and Pseudomonas of β- and γ-Proteobacteria. The similarity of full-length nucleotide sequences between Class I and other classes was about 77–78%, and that between Class II and Class III was 93%. The second and third groups of 2,4-D-degrading bacteria are closely related to the genera Sphingomonas and Bradyrhizobium, which belong to α-Proteobacteria. tfdA-Like genes were identified only in four Sphingomonas spp. This fact and their phylogenetically distinct position make it possible to suggest that these genes evolved independently from each other through vertical gene transfer. The tfdAα gene was identified in the third group of bacteria of the genus Bradyrhizobium, which are both able and unable to degrade 2,4-D. Nevertheless, 2,4-D-degrading bacteria of the genera Bradyrhizobium and Sphingomonas have cad genes, which initiate the first step of the chlorophenoxyacetic acid degradation pathway. Based on the data on tfdAα localization in bacteria isolated from pristine ecosystems, a theory has been proposed that the tfdAα gene is ancestral for tfdA. Horizontal transfer and further adaptation to anthropogenic habitats probably led to the emergence of tfdA. However, tfdA and tfdAα may have diverged from a common ancestor, because they show a high similarity (51–57%) and separate distribution in the β-Proteobacteria, γ-Proteobacteria, and α-Proteobacteria, respectively.

Seasonal variations and land use responses of nirS-type denitrifying bacterial communities were investigated in a cultivated black soil (0–20 cm) in Northeast China with different fertilization treatments [no fertilizer (NoF), chemical fertilizer (CF) and CF plus manure (CFM)] and in a neighbouring plot of natural restoration (NR) using qPCR and Illumina Miseq sequencing. The NR plot was revegetated naturally with grasses without human disturbance since 1985. In general, the abundance of nirS-type denitrifying bacteria did not change significantly between NR and NoF across all sampling times, but fertilization increased the abundance of the nirS gene, except for samples collected in October. Aromatoleum, Rhodanobacter, Cupriavidus, Bradyrhizobium, unclassified genus of Proteobacteria, Magnetospirillum and unclassified genus of Rhodocyclaceae were the main denitrifiers in this study, accounting for 65.6–78.2% of the total nirS sequences. Rhodanobacter and unclassified genus of Rhodocyclaceae were significantly (P

Eukaryotic and archaeal proteasomes are paradigms for self-compartmentalizing proteases. To a large extent, their function requires interplay with hexameric ATPases associated with diverse cellular activities (AAA+) that act as substrate unfoldases. Bacteria have various types of self-compartmentalizing proteases; in addition to the proteasome itself, these include the proteasome homolog HslV, which functions together with the AAA+ HslU; the ClpP protease with its partner AAA+ ClpX; and Anbu, a recently characterized ancestral proteasome variant. Previous bioinformatic analysis has revealed a novel bacterial member of the proteasome family Betaproteobacteria proteasome homolog (BPH). Using cluster analysis, we here affirmed that BPH evolutionarily descends from HslV. Crystal structures of the Thiobacillus denitrificans and Cupriavidus metallidurans BPHs disclosed a homo-oligomeric double-ring architecture in which the active sites face the interior of the cylinder. Using small-angle X-ray scattering (SAXS) and electron microscopy averaging, we found that BPH forms tetradecamers in solution, unlike the dodecamers seen in HslV. Although the highly acidic inner surface of BPH was in striking contrast to the cavity characteristics of the proteasome and HslV, a classical proteasomal reaction mechanism could be inferred from the covalent binding of the proteasome-specific inhibitor epoxomicin to BPH. A ligand-bound structure implied that the elongated BPH inner pore loop may be involved in substrate recognition. The apparent lack of a partner unfoldase and other unique features, such as Ser replacing Thr as the catalytic residue in certain BPH subfamilies, suggest a proteolytic function for BPH distinct from those of known bacterial self-compartmentalizing proteases.

Over the last century, contamination of polycyclic aromatic hydrocarbons (PAHs) has risen tremendously due to the intensified industrial activities like petrochemical, pharmaceutical, insecticides and fertilizers applications. PAHs are a group of organic pollutants with adverse effects on both humans and the environment. These PAHs are widely distributed in various ecosystems including air, soil, marine water and sediments. Degradation of PAHs generally occurs through processes like photolysis, adsorption, volatilization, chemical degradation and microbial degradation. Microbial degradation of PAHs is done by the utilization of diverse microorganisms like algae, bacteria, fungi which are readily compatible with biodegrading/bio transforming PAHs into H2O, CO2 under aerobic, or CH4 under anaerobic environment. The rate of PAHs degradation using microbes is mainly governed by various cultivation conditions like temperature, pH, nutrients availability, microbial population, chemical nature of PAHs, oxygen and degree of acclimation. Several microbial species including Selenastrum capricornutum, Ralstonia basilensis, Acinetobacter haemolyticus, Pseudomonas migulae, Sphingomonas yanoikuyae and Chlorella sorokiniana are known to degrade PAHs via biosorption and enzyme-mediated degradation. Numerous bacterial mediated PAHs degradation methods are studied globally. Among them, PAHs degradation by bacterial species like Pseudomonas fluorescence, Pseudomonas aeruginosa, Rhodococcus spp., Paenibacillus spp., Mycobacterium spp., and Haemophilus spp., by various degradation modes like biosurfactant, bioaugmentation, biostimulation and biofilms mediated are also investigated. In contrarily, PAHs degradation by fungal species such as Pleurotus ostreatus, Polyporus sulphureus, Fusarium oxysporum occurs using the activity of its ligninolytic enzymes such as lignin peroxidase, laccase, and manganese peroxidase. The present review highlighted on the PAHs degradation activity by the algal, fungal, bacterial species and also focused on their mode of degradation.

The current study demonstrates the enhanced production capability of strain Cupriavidus sp. ISTL7 for polyhydroxyalkanoates (PHA) using acetate and glucose (4.93 ± 0.4571 g L-1) which was characterised analytically by GC–MS, FTIR and NMR analysis. Whole genome sequencing of strain ISTL7 unveiled an array of PHA metabolism genes which included phaA, phaB and phaC. Life cycle assessment of the protocol established that the production was most sustainable with the carbon source acetate. + Glucose as compared to acetate/glucose alone. It also concluded that solvent extraction of PHA and energy consumption during the process requires optimization to sustain the production on ecological fronts. Additionally, acetoacetyl-CoA reductase (phaB) gene was molecularly cloned, expressed and purified (27 KDa, 2.63 mg/ml). Conclusively, Cupriavidus sp. ISTL7 is a potential strain for PHA production with a scope of improvement on energy fronts which would transform the production environmentally and economically appealing.

Culturable bacteria are widely used in the remediation of heavy metal-contaminated soil associated with different plants. In this study, a pot experiment of castor bean (Ricinus communis L.) was performed to determine the effect of culturable bacterial communities on the growth of castor bean, as well as their response to the presence of Pb and Zn during the 21-day incubation. The results indicated that the inoculation of the cultivable bacterial communities promoted plant growth, whether Pb/Zn-contaminated or not, and a well-developed root system was also detected in the bacterial community after treatment. Under heavy metal stress, the root surface area of castor bean decreased significantly, but after inoculation, it was close to the level of the normal (uncontaminated) samples. Sequence analysis at the phylum and genus taxonomic levels illustrated 13 identified phyla and 125 genera were observed in the control and Pb/Zn-contaminated soil. The input of contaminants affected the bacterial community structure, suggesting that although Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla in the two samples, the Ensifer and Cupriavidus genera were decreased in contaminated soil. However, Arcticibacter, a phosphate-solubilizing bacterium, was enriched by the Pb/Zn treatment. Compared with the control group, Pb and Zn exposure in the treatment group resulted in a new community structure. A microflora consisting of a number of microorganisms undergoing a long duration period of adaptation and symbiosis can possess systematic functions with high stabilities, so it has considerably high potential in intensifying the effect of phytoremediation.

Comparative analyses determined the relationship between the structure of bisphenol A (BPA) as well as of seven bisphenol analogues (bisphenol B (BPB), bisphenol C (BPC), bisphenol E (BPE), bisphenol F (BPF), bisphenol Z (BPZ), bisphenol AP (BPAP), bisphenol PH (BPPH)) and their biotransformability by the biphenyl-degrading bacterium Cupriavidus basilensis SBUG 290. All bisphenols were substrates for bacterial transformation with conversion rates ranging from 6 to 98% within 216 h and 36 different metabolites were characterized. Transformation by biphenyl-grown cells comprised four different pathways: (a) formation of ortho-hydroxylated bisphenols, hydroxylating either one or both phenols of the compounds; (b) ring fission; (c) transamination followed by acetylation or dimerization; and (d) oxidation of ring substituents, such as methyl groups and aromatic ring systems, present on the 3-position. However, the microbial attack of bisphenols by C. basilensis was limited to the phenol rings and its substituents, while substituents on the carbon bridge connecting the rings were not oxidized. All bisphenol analogues with modifications at the carbon bridge could be oxidized up to ring cleavage, while substituents at the 3-position of the phenol ring other than hydroxyl groups did not allow this reaction. Replacing one methyl group at the carbon bridge of BPA by a hydrophobic aromatic or alicyclic ring system inhibited both dimerization and transamination followed by acetylation. While most of the bisphenol analogues exhibited estrogenic activity, four biotransformation products tested were not estrogenically active.