Competition between Two Isolates of Denitrifying Bacteria Added to Soil

We examined the competitive relationship between two isolates of denitrifying bacteria, both of which grow well under aerobic conditions but differ in their ability to grow under denitrifying conditions. The growth and persistence of the two isolates, added to sterile soil or added to soil previously colonized by the other isolate, were monitored under aerobic and denitrifying (anaerobic) conditions. When isolates were added together to sterile soil, the isolate added at the higher density reduced the growth of the isolate added at the lower density. The magnitude of the growth reduction varied depending on the competitive abilities of the individual isolates and the aeration state of the soil. Prior colonization of soil with one of the isolates conferred a competitive advantage on the colonized isolate but did not lead to the disappearance of the challenging isolate. Fluctuations in aeration state caused large changes in the population density of one isolate and altered the competitive relationship between the two isolates. The competitive effectiveness of each isolate varied with cell density, the degree of prior colonization of the soil by the other isolate, and the aeration state of the soil.     

Community Composition and Functioning of Denitrifying Bacteria from Adjacent Meadow and Forest Soils

We investigated communities of denitrifying bacteria from adjacent meadow and forest soils. Our objectives were to explore spatial gradients in denitrifier communities from meadow to forest, examine whether community composition was related to ecological properties (such as vegetation type and process rates), and determine phylogenetic relationships among denitrifiers. nosZ, a key gene in the denitrification pathway for nitrous oxide reductase, served as a marker for denitrifying bacteria. Denitrifying enzyme activity (DEA) was measured as a proxy for function. Other variables, such as nitrification potential and soil C/N ratio, were also measured. Soil samples were taken along transects that spanned meadow-forest boundaries at two sites in the H. J. Andrews Experimental Forest in the Western Cascade Mountains of Oregon. Results indicated strong functional and structural community differences between the meadow and forest soils. Levels of DEA were an order of magnitude higher in the meadow soils. Denitrifying community composition was related to process rates and vegetation type as determined on the basis of multivariate analyses of nosZ terminal restriction fragment length polymorphism profiles. Denitrifier communities formed distinct groups according to vegetation type and site. Screening 225 nosZ clones yielded 47 unique denitrifying genotypes; the most dominant genotype occurred 31 times, and half the genotypes occurred once. Several dominant and less-dominant denitrifying genotypes were more characteristic of either meadow or forest soils. The majority of nosZ fragments sequenced from meadow or forest soils were most similar to nosZ from the Rhizobiaceae group in α-Proteobacteria species. Denitrifying community composition, as well as environmental factors, may contribute to the variability of denitrification rates in these systems.     

Heterotrophic Nitrification in an Acid Forest Soil and by an Acid-Tolerant Fungus

Nitrate was formed from ammonium at pH 3.2 to 6.1 in suspensions of a naturally acid forest soil; the maximum rates of formation occurred at ca. pH 4 to 5. Nitrate was also formed from soil nitrogen in suspensions incubated at 50°C. Autotrophic nitrifying bacteria could not be isolated from this soil. Enrichment cultures produced nitrate in a medium with β-alanine if much soil was added to the medium, and nitrite but not nitrate was formed in the presence of small amounts of soil. Nitrification by these enrichments was abolished by eucaryotic but not procaryotic inhibitors. A strain of Absidia cylindrospora isolated from this soil was found to produce nitrate and nitrite in a medium with β-alanine at pH values ranging from 4.0 to 4.8. Nitrate production by A. cylindrospora required the presence of sterile soil. Free and bound hydroxylamine, hydroxamic acids, and primary aliphatic nitro compounds did not accumulate during the conversion of β-alanine to nitrite by the fungus. The organism also formed nitrite from ammonium in a medium containing acetate. We suggest that nitrification in this soil is a heterotrophic process catalyzed by acid-tolerant fungi and not by autotrophs or heterotrophs in nonacid microsites.     

Isolation of Denitrifying Photosynthetic Bacteria

An alkaline proteinase produced by Bacillus sp. was purified and crystallyzed through isopropanol or ammonium sulfate precipitation, decolorization with DEAE-cellulose and gel filtration with Sephadex G-100. The optimum pH for caseinhydrolysis was 11.5 and the activity was completely inactivated after incubation with DFP. The specific activity on Hammersten casein was about 4,500 units/mg enzyme protein. The enzyme also hydrolyzed synthetic ester substrate such as Ac-Tyr-OEt, Ac-Phe-OEt or Bz-Met-OMe. The isoelectric point was pH 10.7, and the molecular weight was estimated to be about 17,500 by the sedimentation equilibrium method and 16,000 by gel filtration method. Some physicochemical properties and the amino acid composition of the enzyme were investigated, indicating that the enzyme is distinguishable from alkaline proteinase of Bacillus species so far reported.     

Dynamics and Biodiversity of Populations of Lactic Acid Bacteria and Acetic Acid Bacteria Involved in Spontaneous Heap Fermentation of Cocoa Beans in Ghana

The Ghanaian cocoa bean heap fermentation process was studied through a multiphasic approach, encompassing both microbiological and metabolite target analyses. A culture-dependent (plating and incubation, followed by repetitive-sequence-based PCR analyses of picked-up colonies) and culture-independent (denaturing gradient gel electrophoresis [DGGE] of 16S rRNA gene amplicons, PCR-DGGE) approach revealed a limited biodiversity and targeted population dynamics of both lactic acid bacteria (LAB) and acetic acid bacteria (AAB) during fermentation. Four main clusters were identified among the LAB isolated: Lactobacillus plantarum, Lactobacillus fermentum, Leuconostoc pseudomesenteroides, and Enterococcus casseliflavus. Other taxa encompassed, for instance, Weissella. Only four clusters were found among the AAB identified: Acetobacter pasteurianus, Acetobacter syzygii-like bacteria, and two small clusters of Acetobacter tropicalis-like bacteria. Particular strains of L. plantarum, L. fermentum, and A. pasteurianus, originating from the environment, were well adapted to the environmental conditions prevailing during Ghanaian cocoa bean heap fermentation and apparently played a significant role in the cocoa bean fermentation process. Yeasts produced ethanol from sugars, and LAB produced lactic acid, acetic acid, ethanol, and mannitol from sugars and/or citrate. Whereas L. plantarum strains were abundant in the beginning of the fermentation, L. fermentum strains converted fructose into mannitol upon prolonged fermentation. A. pasteurianus grew on ethanol, mannitol, and lactate and converted ethanol into acetic acid. A newly proposed Weissella sp., referred to as “Weissella ghanaensis,” was detected through PCR-DGGE analysis in some of the fermentations and was only occasionally picked up through culture-based isolation. Two new species of Acetobacter were found as well, namely, the species tentatively named “Acetobacter senegalensis” (A. tropicalis-like) and “Acetobacter ghanaensis” (A. syzygii-like).     

Isolation and Characterization of Phenol-Degrading Denitrifying Bacteria

Phenol is a man-made as well as a naturally occurring aromatic compound and an important intermediate in the biodegradation of natural and industrial aromatic compounds. Whereas many microorganisms that are capable of aerobic phenol degradation have been isolated, only a few phenol-degrading anaerobic organisms have been described to date. In this study, three novel nitrate-reducing microorganisms that are capable of using phenol as a sole source of carbon were isolated and characterized. Phenol-degrading denitrifying pure cultures were obtained by enrichment culture from anaerobic sediments obtained from three different geographic locations, the East River in New York, N.Y., a Florida orange grove, and a rain forest in Costa Rica. The three strains were shown to be different from each other based on physiologic and metabolic properties. Even though analysis of membrane fatty acids did not result in identification of the organisms, the fatty acid profiles were found to be similar to those of Azoarcus species. Sequence analysis of 16S ribosomal DNA also indicated that the phenol-degrading isolates were closely related to members of the genus Azoarcus. The results of this study add three new members to the genus Azoarcus, which previously comprised only nitrogen-fixing species associated with plant roots and denitrifying toluene degraders.     

Effect of the Spartina alterniflora Root-Rhizome System on Salt Marsh Soil Denitrifying Bacteria

Nitrous oxide (N₂O) reductase activity was used as an index of the denitrification potential in salt marsh soils. In a short Spartina alterniflora marsh, the seasonal distribution of N₂O reductase activity indicated a causal relationship between S. alterniflora root-rhizome production and the denitrification potential of the soil system. The relationship was not discerned in samples from a tall S. alterniflora marsh. To further examine the in situ plant-denitrifier interaction in the short S. alterniflora marsh, plots with and without living S. alterniflora were established and analyzed for N₂O reductase activity 5 and 18 months later. In the plots without living Spartina there was a significant reduction in the soil denitrification potential after 18 months, indicating that in the SS marsh the denitrifiers are tightly coupled to the seasonal production of below-ground Spartina macroorganic matter. In plots with intact Spartina, the soil denitrification potential was not altered by NH₄NO₃ or glucose enrichment. However, in plots without living Spartina, there were significant changes in soil N₂O reductase activity, thus indicating that the plants can serve as a “buffer” against this form of pulse perturbation.     

Biodiversity,Bioactivity, and Metabolites of High Desert Derived Oregonian Soil Bacteria

From arid, high desert soil samples collected near Bend, Oregon, 19 unique bacteria were isolated. Each strain was identified by 16S rRNA gene sequencing, and their organic extracts were tested for antibacterial and antiproliferative activities. Noteworthy, six extracts (30 %) exhibited strong inhibition resulting in less than 50 % cell proliferation in more than one cancer cell model, tested at 10 μg/mL. Principal component analysis (PCA) of LC/MS data revealed drastic differences in the metabolic profiles found in the organic extracts of these soil bacteria. In total, fourteen potent antibacterial and/or cytotoxic metabolites were isolated via bioactivity-guided fractionation, including two new natural products: a pyrazinone containing tetrapeptide and 7-methoxy-2,3-dimethyl-4H-chromen-4-one, as well as twelve known compounds: furanonaphthoquinone I, bafilomycin C1 and D, FD-594, oligomycin A, chloramphenicol, MY12-62A, rac-sclerone, isosclerone, tunicamycin VII, tunicamycin VIII, and (6S,16S)-anthrabenzoxocinone 1.264-C.     

Anaerobic Mineralization of Quaternary Carbon Atoms: Isolation of Denitrifying Bacteria on Pivalic Acid (2,2-Dimethylpropionic Acid)

The degradability of pivalic acid was established by the isolation of several facultative denitrifying strains belonging to Zoogloea resiniphila, to Thauera and Herbaspirillum, and to Comamonadaceae, related to [Aquaspirillum] and Acidovorax, and of a nitrate-reducing bacterium affiliated with Moraxella osloensis. Pivalic acid was completely mineralized to carbon dioxide. The catabolic pathways may involve an oxidation to dimethylmalonate or a carbon skeleton rearrangement, a putative 2,2-dimethylpropionyl coenzyme A mutase.     

Isolation and Characterization of Dinitrogen-Fixing Bacteria from the Rhizosphere of Temperate Cereals and Forage Grasses

N₂(C₂H₂)-fixing bacteria were isolated from the rhizosphere of various cereals and forage grasses grown in the greenhouse and from the rhizosphere of field-grown wheat in Sweden. All 46 isolates from the greenhouse plants lost their nitrogenase activity during purification. By imposing a stronger selection pressure, we obtained pure isolates with nitrogenase activity from field-grown wheat. Some isolates were identified as Enterobacter agglomerans and Bacillus polymyxa, but several bacteria of uncertain taxonomy also occurred. One of the isolates grew and reduced acetylene only in the presence of other bacteria or certain vitamins. Species of Azotobacter or Azospirillum could not be isolated from the rhizosphere of any of the cereals and forage grasses studied.     

好氧反硝化菌的分离鉴定及特性研究

从土壤中分离到1株能以硝酸钠为氮源进行好氧反硝化作用的细菌,命名为Rhodococcussp.DN,分离菌株革兰氏染色为阳性,球状或杆状,菌落颜色为橙红色。该细菌能以乙酰胺为惟一碳源和氮源,能进行氨化和硝化作用并产生亚硝酸。部分长度的16S rDNA序列分析表明,所分离的细菌与Rhodococcus ruber的16S rDNA序列具有99%相似性。     

反硝化细菌在污水脱氮中的作用

反硝化是在反硝化细菌的作用下,以硝酸盐作为最终电子受体而进行的无氧呼吸过程。从污水脱氮的角度论述反硝化在污水脱氮中的作用、污水脱氮的机理、污水脱氮过程中反硝化作用的影响因素等。从反硝化的角度出发,论述了反硝化细菌的类群、反硝化作用的机理、反硝化细菌细胞中参与反硝化过程的关键酶。另外,还论述了近年来发现的有氧反硝化细菌、自养反硝化细菌及反硝化除磷细菌等方面的研究进展。     

Identification of Denitrifying Bacteria Diversity in an Activated Sludge System by using Nitrite Reductase Genes

Nitrite reduction is the key step in the denitrification reaction with two predominant types of nitrite reductase genes: nirS and nirK. The diversity of denitrifying bacteria in a municipal wastewater treatment plant is described by using both these genes. Of the cultured colonies, 22.5% contained the NirS gene and 12.5% the nirK gene. These nitrite reductase-containing colonies could be further divided into five different types by using both restriction fragment length polymorphism and denaturing gradient gel electrophoresis analysis. Phylogenetic analysis showed that these five types of denitrifying bacteria were phylogenetically diverse. Finally, one nirS gene was obtained and compared with the published sequences.     

福州森林红壤细菌的菌群结构及其功能分析

福建地区是我国的第二大林区,土壤类型主要表现为红壤.对福州地区森林中因木材腐朽而形成的树洞中的土壤样品进行筛选,构建了一份具有强木质纤维素降解能力的酸性红壤的细菌16S rKNA基因文库,利用限制性片段长度多态性(RFLP)对随机克隆进行筛选;对该生态环境下的细菌菌群进行了系统发育分析.结果表明土壤pH偏酸性严重影响了细菌类群的多样性,酸杆菌门Acidobacteria(71.5%)和变形菌门Proteobacteria(24.1%)是该酸性土样中的优势菌群,其中酸杆菌门在该生态系统中占有绝对优势.变形菌菌群中的主要类群为光合细菌,固氮细菌和溶菌细菌.研究表明,在木质纤维素自然降解的过程中,存在于酸性树洞土壤中的细菌参与了碳素和氮素的固定与循环,并对其微生态的稳定起到重要作用.     

Myxobacterial Biodiversity in an Established Oak-Hickory Forest and a Savanna Restoration Site

The purpose of this study was to establish the myxobacterial biodiversity of an established oak-hickory forest and a savanna restoration site that has been cut and subsequently burned on four occasions between 1993 and 1998 in an attempt to restore the land to the native savanna ecosystem. Soil and bark samples were processed through standard methods specifically for myxobacteria and numbers and types of species were recorded for both locations. Species were identified through morphology of fruiting bodies, SDS-PAGE of whole cell protein profiles, and 16S rRNA gene sequences. Statistical analyses were employed and suggested that significantly greater numbers and types of myxobacteria are present on the bark of the trees in the established oak-hickory forest than the bark of trees in the savanna restoration site, while little difference in numbers and types of species were observed between the soil samples of the two locations.