Heterotrophic Aerobic Bacterium Research Articles

Increasing aggregate size reduces single-cell organic carbon incorporation by hydrogel-embedded wetland microbes.

Microbial degradation of organic carbon in sediments is impacted by the availability of oxygen and substrates for growth. To better understand how particle size and redox zonation impact microbial organic carbon incorporation, techniques that maintain spatial information are necessary to quantify elemental cycling at the microscale. In this study, we produced hydrogel microspheres of various diameters (100, 250, and 500μm) and inoculated them with an aerobic heterotrophic bacterium isolated from a freshwater wetland (Flavobacterium sp.), and in a second experiment with a microbial community from an urban lacustrine wetland. The hydrogel-embedded microbial populations were incubated with 13C-labeled substrates to quantify organic carbon incorporation into biomass via nanoSIMS. Additionally, luminescent nanosensors enabled spatially explicit measurements of oxygen concentrations inside the microspheres. The experimental data were then incorporated into a reactive-transport model to project long-term steady-state conditions. Smaller (100μm) particles exhibited the highest microbial cell-specific growth per volume, but also showed higher absolute activity near the surface compared to the larger particles (250 and 500μm). The experimental results and computational models demonstrate that organic carbon availability was not high enough to allow steep oxygen gradients and as a result, all particle sizes remained well-oxygenated. Our study provides a foundational framework for future studies investigating spatially dependent microbial activity in aggregates using isotopically labeled substrates to quantify growth.

Genomic and physiological characterization of an antimony and arsenite-oxidizing bacterium Roseomonas rhizosphaerae

Antimony (Sb) and arsenic (As) are two toxic metalloids, which are listed as priority environmental pollutants by the European Union and the U.S. Environmental Protection Agency (EPA). Antimony taken up by plants enters the food chain and poses a threat to human health. Microbial oxidation of antimonite (Sb(III)) and arsenite (As(III)) to the less toxic antimonate (Sb(V)) and arsenate (As(V)), has great potential for the immobilization of Sb and As in the environment. A heterotrophic aerobic bacterium, Roseomonas rhizosphaerae YW11, oxidized both Sb(III) and As(III) in the modified R2A medium. In the same medium, strain YW11 preferred to oxidize Sb(III), whereas the As(III) oxidation rate was only 50%. Genomic analysis of YW11 confirmed the presence of several As-resistance gene islands. The aioAB genes encoding As(III) oxidase were also induced by Sb(III). The role of aioA in Sb(III) oxidation and resistance was confirmed by disrupting this gene in strain YW11, resulting in the loss of Sb(III) oxidation abilities. This study documents an enzymatic basis for microbial Sb(III) oxidation in strain YW11, which is a novel bacterial strain showing simultaneous oxidation of Sb(III) and As(III), and may be a potential candidate for bioremediation of heavy metal-contaminated environments.

Isolation and Nitrogen Removal Characteristics of an Aerobic Heterotrophic Nitrifying-Denitrifying Bacterium, Klebsiella sp. TN-10.

Nitrogen removal by microorganisms has attracted increasing attention in wastewater treatment. In the present study, a heterotrophic nitrification bacterium was isolated from tannery wastewater and identified as Klebsiella sp. TN-10 based on phenotypic and phylogenetic characteristics. The optimal conditions for cell growth and nitrogen removal were investigated, and the results showed that the greatest ammonium removal rate and maximum biomass were achieved by using sodium pyruvate (7g/L) as carbon source, C/N 12, pH7, and temperature 30°C. Under optimal conditions, the removal rate of ammonia nitrogen reached 96%. Besides, the growth characteristic and the ability of utilizing nitrate and nitrite were investigated. The results demonstrated that strain TN-10 exhibited excellent characteristics to remove both nitrate and nitrite, with the removal rate of 95.44% and 99.87%, respectively. In addition, the nitrite reductase (NiR) and nitrate reductase (NR) involved in denitrification were both active, with the activities of 0.0815 and 0.0283U/mg proteins, respectively. Furthermore, the aggregation ability, auto-aggregation kinetics, and the relationship between zeta potentials and flocculating efficiency were determined. These results indicated that the strain Klebsiella sp. TN-10, with efficient heterotrophic nitrification-aerobic denitrification ability, has potential application in wastewater treatment.

High-efficiency inorganic nitrogen removal by newly isolated Pannonibacter phragmitetus B1

An aerobic heterotrophic nitrogen removal bacterium strain, B1, was isolated from aquaculture water and identified as Pannonibacter phragmitetus (99% similarity) by 16S rRNA sequencing analysis. When ammonium, nitrite or nitrate was the sole nitrogen source, with an initial nitrogen concentration of 14 mg/L, the nitrogen removal efficiencies were 98.66%, 99.96% and 98.73%, respectively, and the corresponding maximum removal rates reached as high as 1.16, 0.77 and 0.81 mg/L/h, respectively. In the presence of NH4+-N, the removal efficiency of 56 mg/L NO2−-N within 27 h increased by 83.50%, and the corresponding removal rate reached as high as 1.72 mg/L/h. Additionally, different carbon sources (dl-malic acid, sucrose, sodium citrate, and glucose) could be utilized in nitrogen removal. Sequence amplification indicates that the denitrification genes nirK, norB and narG are present in strain B1. All results demonstrate that strain B1 has high promise for future applications of removing inorganic nitrogen from wastewater.

Genomic Analysis of the Evolution of Phototrophy among Haloalkaliphilic Rhodobacterales.

A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photoheterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and facultatively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter thiooxidans, and aerobic heterotrophic bacterium Natronohydrobacter thiooxidans. These three haloalcaliphilic species are phylogenetically related and share many common characteristics with the Rhodobacter species, forming together the Rhodobacter-Rhodobaca (RR) group. A comparative genomic analysis showed close homology of photosynthetic proteins and similarity in photosynthesis gene organization among the investigated phototrophic RR species. On the other hand, Rhodobaca barguzinensis and Roseinatronobacter thiooxidans lack an inorganic carbon fixation pathway and outer light-harvesting genes. This documents the reduction of their photosynthetic machinery towards a mostly photoheterotrophic lifestyle. Moreover, both phototrophic species contain 5-aminolevulinate synthase (encoded by the hemA gene) incorporated into their photosynthesis gene clusters, which seems to be a common feature of all aerobic anoxygenic phototrophic Alphaproteobacteria. Interestingly, the chrR-rpoE (sigma24) operon, which is part of singlet oxygen defense in phototrophic species, was found in the heterotrophic strain Natronohydrobacter thiooxidans. This suggests that this organism evolved from a photoheterotrophic ancestor through the loss of its photosynthesis genes. The overall evolution of phototrophy among the haloalkaliphilic members of the RR group is discussed.

Synthesis of arborane triterpenols by a bacterial oxidosqualene cyclase

Cyclic triterpenoids are a broad class of polycyclic lipids produced by bacteria and eukaryotes. They are biologically relevant for their roles in cellular physiology, including membrane structure and function, and biochemically relevant for their exquisite enzymatic cyclization mechanism. Cyclic triterpenoids are also geobiologically significant as they are readily preserved in sediments and are used as biomarkers for ancient life throughout Earth's history. Isoarborinol is one such triterpenoid whose only known biological sources are certain angiosperms and whose diagenetic derivatives (arboranes) are often used as indicators of terrestrial input into aquatic environments. However, the occurrence of arborane biomarkers in Permian and Triassic sediments, which predates the accepted origin of angiosperms, suggests that microbial sources of these lipids may also exist. In this study, we identify two isoarborinol-like lipids, eudoraenol and adriaticol, produced by the aerobic marine heterotrophic bacterium Eudoraea adriatica Phylogenetic analysis demonstrates that the E. adriatica eudoraenol synthase is an oxidosqualene cyclase homologous to bacterial lanosterol synthases and distinct from plant triterpenoid synthases. Using an Escherichia coli heterologous sterol expression system, we demonstrate that substitution of four amino acid residues in a bacterial lanosterol synthase enabled synthesis of pentacyclic arborinols in addition to tetracyclic sterols. This variant provides valuable mechanistic insight into triterpenoid synthesis and reveals diagnostic amino acid residues to differentiate between sterol and arborinol synthases in genomic and metagenomic datasets. Our data suggest that there may be additional bacterial arborinol producers in marine and freshwater environments that could expand our understanding of these geologically informative lipids.

Draft Genome Sequence of Halomonas sp. HG01, a Polyhydroxyalkanoate-Accumulating Strain Isolated from Peru.

Halomonas sp. strain HG01, isolated from a salt mine in Peru, is a halophilic aerobic heterotrophic bacterium accumulating poly-3-hydroxybutyrate and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from different carbon sources. Here, we report the draft genome sequence of this isolate, which was found to be 3,665,487 bp long, with a G+C content of 68%.

A putative multicopper oxidase, IoxA, is involved in iodide oxidation by Roseovarius sp. strain A-2.

Roseovarius sp. strain A-2 is an aerobic heterotrophic bacterium with a capacity for oxidizing iodide ion (I(-)) to form molecular iodine (I2). In this study, iodide-oxidizing enzyme of strain A-2 was characterized. The enzyme was an extracellular protein, and Cu(2+) ion significantly enhanced the enzyme activity in the culture supernatant. When iodide was used as the substrate, the crude enzyme showed Km and Vmax values of 4.78mM and 25.1Umg(-1), respectively. The enzyme was inhibited by NaN3, EDTA, KCN, and o-phenanthroline, and also had significant activities toward p-phenylenediamine and hydroquinone. Tandem mass spectrometric analysis of an active band excised from SDS-PAGE gel revealed that at least two proteins are involved in the enzyme. One of these proteins was closely related with IoxA, a multicopper oxidase previously found as a component of iodide-oxidizing enzyme of Alphaproteobacterium strain Q-1. Furthermore, a terrestrial bacterium Rhodanobacter denitrificans 116-2, which possesses an ioxA-like gene in its genome, was found to oxidize iodide. These results suggest that IoxA catalyzes the oxidation of iodide in phylogenetically distinct bacteria.

Roseovarius albus sp. nov., a new Alphaproteobacterium isolated from the Mediterranean Sea

Strain 4SM10(T), an aerobic marine, Gram-negative, heterotrophic and non pigmented bacterium isolated from seawater from Vinaroz in Castellón, Spain, was characterized using a polyphasic approach. Analysis of the 16S rRNA gene sequence placed the strain within the Roseobacter clade in the family Rhodobacteraceae. Phylogenetic analyses also showed that strain 4SM10(T) forms a stable clade with species of the genus Roseovarius, being related to Roseovarius nubinhibens ISM(T) and Roseovarius aestuarii SMK-122(T) at 97.5 and 97.4 % 16S rRNA sequence similarity, respectively. Average Nucleotide Identity (ANI) values, determined as a measure of overall genomic resemblance, confirmed that strain 4SM10(T) does not belong to the same species as R. aestuarii CECT 7745(T) and Roseovarius nubinhibens CECT 7750(T) displaying ANI values well below the 95 % boundary for genomic species. Strain 4SM10(T) requires Na(+) plus a divalent cation (either Mg(2+) or Ca(2+)) to grow, reduces nitrate to nitrite and uses a large number of amino acids and organic acids (but no carbohydrates) as sole carbon sources. Enzymatic activities displayed in API ZYM tests are alkaline phosphatase, leucine arylamidase and acid phosphatase. The major cellular fatty acids were identified as C18:1 ω7c and/or C18:1 ω6c (67.1 %). The DNA G+C content was determined to be 54.27 mol%. Based on the genotypic and phenotypic data obtained, the name Roseovarius albus sp. nov. is proposed for this novel taxon, with the type strain 4SM10(T) (=CECT 7450(T) = KCTC 22653(T)).

Xanthobacter xylophilus sp. nov., a member of the xylotrophic mycobacterial community of low-mineral oligotrophic waters

A novel obligately aerobic heterotrophic bacterium belonging to the genus Xanthobacter, strain Z-0055, was isolated from the bacterial community of dystrophic waters formed by xylotrophic fungi grown on decaying spruce wood. The cells are small (0.4 ±0.7 fum), ovoid, grarrmegative, and nonmotile. The strain reproduces by nonuniform division. Strain Z-0055 is a moderately acidophilic microorganism and grows in a pH range of 4.8–6.8, with an optimum at pH 5.5. The temperature range for growth is 10–28°C, with an optimum at 20°C. The bacterium utilizes salts of organic acids (citrate, oxalate, succinate, and gluconate), as well as xylose and xylan as carbon and energy sources. No growth was detected at NaCl concentrations higher than 1.5 g/l. The DNA G+C base content is 63.6 mol %. According to phylogenetic analysis of the 16S rRNA gene sequences, strain Z-0055 belongs to the cluster containing X. flavus, X. aminoxidans, X. autotrophicus, and X. viscosus. The levels of similarity between the studied strain and these species are almost the same (96.0–97.0%). The genetic and ecophysiological properties of strain Z-0055 support classification of this acid-tolerant inhabitant of oligotrophic waters within the genus Xanthobacter as a new species X. xylophilus sp. nov.

Heterotrophic ammonium removal characteristics of an aerobic heterotrophic nitrifying-denitrifying bacterium, Providencia rettgeri YL

Bacterium Providencia rettgeri YL was found to exhibit an unusual ability to heterotrophically nitrify and aerobically denitrify various concentrations of ammonium (NH4+-N). In order to further understand its removal ability, several experiments were conducted to identify the growth and ammonium removal response at different carbon to nitrogen (C/N) mass ratios, shaking speeds, temperatures, ammonium concentrations and to qualitatively verify the production of nitrogen gas using gas chromatography techniques. Results showed that under optimum conditions (C/N 10, 30 degrees C, 120 r/min), YL can significantly remove low and high concentrations of ammonium within 12 to 48 h of growth, respectively. The nitrification products hydroxylamine (NH2OH), nitrite (NO2(-)) and nitrate (NO3(-)) as well as the denitrification product, nitrogen gas (N2), were detected under completely aerobic conditions.

Impact of light/dark regimen on growth rate, biomass formation and bacteriochlorophyll synthesis in Erythromicrobium hydrolyticum

The impact of illumination on specific growth rate, biomass formation, and synthesis of photopigment was studied in Erythromicrobium hydrolyticum, an obligately aerobic heterotrophic bacterium having the ability to synthesize bacteriochlorophyll a. In dark-grown continuous cultures the concentration of protein increased with increasing dilution rate, the concentration of bacteriochlorophyll a showed the opposite effect. At a dilution rate of 0.08 h-1 (68% of μmax in the dark) and SR-acetate of 11.8 mM, the concentration of BChla of illuminated cultures in steady-state was 11–22 nM, compared to 230–241 nM in cultures incubated in darkness. No significant differences were observed in the concentration of protein. A shift from darkness to light conditions resulted in increased specific growth rates resulting in increased biomass formation, thus showing that light enhances growth by serving as an additional energy source. This phenomenon, however, was temporary because bacteriochlorophyll synthesis is inhibited by light. In contrast to incubation in continuous light or dark, incubation under light/dark regimen resulted in permanently enhanced biomass formation. In the dark periods, bacteriochlorophyll was synthesized at elevated rates (compared to constant darkness), thus compensating the inhibitory effect of light in the preceding period. It thus appears that the organism is well-adpated to life in environments with alternating light/dark conditions. The ecological relevance of the observations is discussed.

Occurrence of bacteriochlorophyll a in a strain of an aerobic heterotrophic bacterium.

Occurrence of bacteriochlorophyll a in a strain of an aerobic heterotrophic bacterium.