Nitrosubstituted Aromatic Compounds as Nitrogen Source for Bacteria

Bacteria which utilized nitroaromatic compounds (0.5 mM) as sole source of nitrogen were isolated from soil. With 2,6-dinitrophenol and succinate as carbon source, a Pseudomonas strain was isolated which liberated and assimilated nitrite. Approximately 2 mol of NO₂⁻ per mol of 2,6-dinitrophenol was released by resting cells. The xenobiotic compound was totally degraded, although specific growth yields were low even with succinate as a carbon source.     

Effect of Volatile Organic Compounds from Bacteria on Nematodes

The five studied bacterial strains could produce volatile organic compounds (VOCs) that kill nematodes. Based on their 16S rRNA sequences, these strains were identified as Pseudochrobactrum saccharolyticum, Wautersiella falsenii, Proteus hauseri, Arthrobacter nicotianae, and Achromobacter xylosoxidans. The bacterial VOCs were extracted using solid‐phase micro‐extraction (SPME) and subsequently identified by GC/MS analysis. The VOCs covered a wide range of aldehydes, ketones, alkyls, alcohols, alkenes, esters, alkynes, acids, ethers, as well as heterocyclic and phenolic compounds. Among the 53 VOCs identified, 19 candidates, produced by different bacteria, were selected to test their nematicidal activity (NA) against Caenorhabditis elegans and Meloidogyne incognita. The seven compounds with the highest NAs were acetophenone, S‐methyl thiobutyrate, dimethyl disulfide, ethyl 3,3‐dimethylacrylate, nonan‐2‐one, 1‐methoxy‐4‐methylbenzene, and butyl isovalerate. Among them, S‐methyl thiobutyrate showed a stronger NA than the commercial insecticide dimethyl disulfide. It was reported for the first time here that the five bacterial strains as well as S‐methyl thiobutyrate, ethyl 3,3‐dimethylacrylate, 1‐methoxy‐4‐methylbenzene, and butyl isovalerate possess NA. These strains and compounds might provide new insights in the search for novel nematicides.     

Succession of Sulfur-Oxidizing Bacteria in the Microbial Community on Corroding Concrete in Sewer Systems

Microbially induced concrete corrosion (MICC) in sewer systems has been a serious problem for a long time. A better understanding of the succession of microbial community members responsible for the production of sulfuric acid is essential for the efficient control of MICC. In this study, the succession of sulfur-oxidizing bacteria (SOB) in the bacterial community on corroding concrete in a sewer system in situ was investigated over 1 year by culture-independent 16S rRNA gene-based molecular techniques. Results revealed that at least six phylotypes of SOB species were involved in the MICC process, and the predominant SOB species shifted in the following order: Thiothrix sp., Thiobacillus plumbophilus, Thiomonas intermedia, Halothiobacillus neapolitanus, Acidiphilium acidophilum, and Acidithiobacillus thiooxidans. A. thiooxidans, a hyperacidophilic SOB, was the most dominant (accounting for 70% of EUB338-mixed probe-hybridized cells) in the heavily corroded concrete after 1 year. This succession of SOB species could be dependent on the pH of the concrete surface as well as on trophic properties (e.g., autotrophic or mixotrophic) and on the ability of the SOB to utilize different sulfur compounds (e.g., H₂S, S⁰, and S₂O₃²⁻). In addition, diverse heterotrophic bacterial species (e.g., halo-tolerant, neutrophilic, and acidophilic bacteria) were associated with these SOB. The microbial succession of these microorganisms was involved in the colonization of the concrete and the production of sulfuric acid. Furthermore, the vertical distribution of microbial community members revealed that A. thiooxidans was the most dominant throughout the heavily corroded concrete (gypsum) layer and that A. thiooxidans was most abundant at the highest surface (1.5-mm) layer and decreased logarithmically with depth because of oxygen and H₂S transport limitations. This suggested that the production of sulfuric acid by A. thiooxidans occurred mainly on the concrete surface and the sulfuric acid produced penetrated through the corroded concrete layer and reacted with the sound concrete below.     

固相反硝化系统中微生物群落结构的研究进展

固相反硝化是一种新型的异养反硝化工艺,采用固体有机物同时作为反硝化微生物的碳源和生物膜载体,可用于地下水和低C/N比污水的脱氮处理。固相反硝化系统生物膜的微生物群落结构决定固体碳源的降解效率,进而决定反硝化脱氮的速率和系统的稳定运行。因此,微生物群落结构的研究对于固相反硝化工艺的优化以及反应机理的解析具有重要意义。对不同固相反硝化系统微生物群落结构的研究现状和进展进行了综述,并探讨了当前研究中存在的问题和发展趋势。     

Plant Community Responses to Simultaneous Changes in Temperature,Nitrogen Availability,and Invasion

Background

Increasing rates of change in climate have been observed across the planet and have contributed to the ongoing range shifts observed for many species. Although ecologists are now using a variety of approaches to study how much and through what mechanisms increasing temperature and nutrient pollution may influence the invasions inherent in range shifts, accurate predictions are still lacking.

Methods and Results

In this study, we conducted a factorial experiment, simultaneously manipulating warming, nitrogen addition and introduction of Pityopsis aspera, to determine how range-shifting species affect a plant community. We quantified the resident community using ordination scores, then used structural equation modeling to examine hypotheses related to how plants respond to a network of experimental treatments and environmental variables. Variation in soil pH explained plant community response to nitrogen addition in the absence of invasion. However, in the presence of invasion, the direct effect of nitrogen on the community was negligible and soil moisture was important for explaining nitrogen effects. We did not find effects of warming on the native plant community in the absence of invasion. In the presence of invasion, however, warming had negative effects on functional richness directly and invasion and herbivory explained the overall positive effect of warming on the plant community.

Conclusions and Significance

This work highlights the variation in the biotic and abiotic factors responsible for explaining independent and collective climate change effects over a short time scale. Future work should consider the complex and non-additive relationships among factors of climate change and invasion in order to capture more ecologically relevant features of our changing environment.     

Role of Productivity and Protozoan Abundance for the Occurrence of Predation-resistant Bacteria in Aquatic Systems

Top-down control of lower trophic levels, e.g., bacteria, has been suggested to increase along aquatic productivity gradients. The response by the bacterial community may be to become more predation resistant in highly productive environments. To test this hypothesis, samples were taken from 20 aquatic systems along a productivity gradient (dissolved organic carbon from 7 to 71 mg/L), during late summer. The results showed that the biomass of bacteria, phytoplankton, and ciliates increased along the gradient (r2 = 0.532, 0.426, and 0.758, P < 0.01, respectively). However, the organisms did not increase equally, and the ratio of protozoan to bacterial biomass showed a 100-fold increase along the gradient. Ciliates dominated the protozoan biomass in the more nutrient-rich waters. The edibility of colony-forming bacteria was tested using a ciliate predator, Tetrahymena pyriformis. Bacterial edibility was found to decrease with increases in nutrient richness and ciliate biomass in the aquatic systems (r2 = 0.358, P < 0.01; r2 = 0.242, P < 0.05, respectively). Quantile regression analysis indicated that the selection pressures on edible bacteria were increasing along the productivity gradient. Thus, inedible forms of bacteria were selected for in the transition from oligotrophic to eutrophic conditions. Isolated bacteria were distributed among the alpha-, beta-, and gamma- Proteobacteria and the Actinobacteria and Firmicutes taxa. We conclude that bacterial predation resistance increases in nutrient-rich waters with high protozoan predation.     

Comparison of Blue Nucleic Acid Dyes for Flow Cytometric Enumeration of Bacteria in Aquatic Systems

Seven blue nucleic acid dyes from Molecular Probes Inc. (SYTO-9, SYTO-11, SYTO-13, SYTO-16, SYTO-BC, SYBR-I and SYBR-II) were compared with the DAPI (4′,6-diamidino-2-phenylindole) method for flow cytometric enumeration of live and fixed bacteria in aquatic systems. It was shown that SYBR-II and SYTO-9 are the most appropriate dyes for bacterial enumeration in nonsaline waters and can be applied to both live and dead bacteria. The fluorescence signal/noise ratio was improved when SYTO-9 was used to stain living bacteria in nonsaline waters. Inversely, SYBR-II is more appropriate than SYTO dyes for bacterial enumeration of unfixed and fixed seawater samples.     

The Structure of Nitrogen Fixing Root Nodules on the Aquatic Mimosoid Legume Neptunia plena

Nodules of the aquatic mimosoid legume Neptunia plena (L.) Benth.were always found associated with roots but not stems. Theyappeared macroscopically 10 and 20 d after inoculation on plantsgrown hydroponically and in vermiculite, respectively. The developmentof nitrogen-fixing cells occurred in a series of stages notyet reported in legume nodule formation: initial infection wasapparently intercellular and rhizobia spread between cells andthrough intercellular spaces before penetrating individual hostcells by means of infection threads. Subsequently nodule developmentwas broadly similar to that described for indeterminate papilionoidnodules. The infection threads of Neptunia and pea nodules containeda matrix with a common epitope, which was, in Neptunia, extrudedfrom the infection thread at the point of bacterial release. The central tissue contained infected and interstitial cellsand was surrounded by a three-layered cortex and a phellem.Bounding the infected region was a layer two to three cellsthick with large, unoccluded intercellular spaces. Externalto this was a layer, one or more cells thick, in which the cellwalls were interlocked, reducing the number of radially orientedintercellular spaces. The outer layer, several cells thick,contained intercellular spaces many of which were occluded.These features did not vary with growth conditions in a waywhich might influence oxygen diffusion characteristics. However,the phellem of water-cultured nodules was much more aerenchymatousthan that of vermiculite-grown nodules. Aquatic legume, Neptunia plena, nitrogen fixation, oxygen, root nodules, Rhizobium     

Diversity and Community Structure of Primary Wood-Inhabiting Bacteria in Boreal Forest

DNA-based pyrosequencing analysis of the V1- V3 16S rRNA gene region was used to identify bacteria community and shift during early stages of wood colonization in boreal forest soils. The dataset comprised 142,447 sequences and was affiliated to 11 bacteria phyla, 25 classes and 233 genera. The dominant groups across all samples were Proteobacteria, followed by Bacteroidetes, Acidobacteria, Actinobacteria, Amatimonadetes, Planctomycetes and TM7 group. The community structure of the primary wood-inhabiting bacteria differed between types of forest soils and the composition of bacteria remained stable over prolonged incubation time. The results suggest that variations in soil bacterial community composition have an influence on the wood-inhabiting bacterial structure.     

阿尔山不同时期落叶松根际土壤固氮菌的多样性研究

利用传统的细菌分离培养,结合16S rDNA序列分析等方法,对阿尔山地区不同时期落叶松根际可培养固氮菌群落的多样性进行分析,以揭示落叶松根际固氮菌的多样性及群落结构的季节变化规律,为森林生态系统的可持续发展提供理论依据。结果显示:(1)从阿尔山落叶松根际土壤中共计分离纯化细菌菌株112株,分属于14属41种,包括假单胞菌属、伯克氏菌属、根瘤菌属、叶杆菌属、节杆菌属、类芽孢杆菌属、沙雷菌属、欧文菌属、短小杆菌属、芽孢杆菌属、肠杆菌属、不动杆菌属、柄杆菌属、红球菌属;其中优势菌群为假单胞菌属,次优势菌群为叶杆菌属、伯克氏菌属和节杆菌属。(2)季节变化对落叶松固氮菌群的变化有显著影响,表现为4月份和10月份最优势类群为γ-变形菌纲(γ-proteobacteria)中的假单胞菌属,6月份和8月份的最优势类群相同,但组成有所差别,其中6月份优势菌群包括假单胞菌属、短小杆菌属、红球菌属、节杆菌属,8月份的优势菌群为假单胞菌属、不动杆菌属、肠杆菌属、短小杆菌属、红球菌属和节杆菌属。(3)不同时期的物种均匀度指数(McIntosh index)差异显著,8月份最大,4月份最小,变化范围在0.83～1.164之间;物种丰富度指数(Shannon-Wiener index) 6月份和8月份显著高于4月份和10月份;优势度指数(Simpson index) 4月份和10月份显著高于6月份和8月份。研究表明,阿尔山地区落叶松根际微生物的多样性较高,群落相对复杂,分离的14个菌属多为根际促生菌,且不同时期固氮菌的群落组成受季节的影响明显。     

Coliform Bacteria and Nitrogen Fixation in Pulp and Paper Mill Effluent Treatment Systems

The majority of pulp and paper mills now biotreat their combined effluents using activated sludge. On the assumption that their wood-based effluents have negligible fixed N, and that activated-sludge microorganisms will not fix significant N, these mills routinely spend large amounts adding ammonia or urea to their aeration tanks (bioreactors) to permit normal biomass growth. N₂ fixation in seven Eastern Canadian pulp and paper mill effluent treatment systems was analyzed using acetylene reduction assays, quantitative nitrogenase (nifH) gene probing, and bacterial isolations. In situ N₂ fixation was undetectable in all seven bioreactors but was present in six associated primary clarifiers. One primary clarifier was studied in greater detail. Approximately 50% of all culturable cells in the clarifier contained nifH, of which >90% were Klebsiella strains. All primary-clarifier coliform bacteria growing on MacConkey agar were identified as klebsiellas, and all those probed contained nifH. In contrast, analysis of 48 random coliform isolates from other mill water system locations showed that only 24 (50%) possessed the nifH gene, and only 13 (27%) showed inducible N₂-fixing activity. Thus, all the pulp and paper mill primary clarifiers tested appeared to be sites of active N₂ fixation (0.87 to 4.90 mg of N liter⁻¹ day⁻¹) and a microbial community strongly biased toward this activity. This may also explain why coliform bacteria, especially klebsiellas, are indigenous in pulp and paper mill water systems.     

Community Structure and Activity Dynamics of Nitrifying Bacteria in a Phosphate-Removing Biofilm

The microbial community structure and activity dynamics of a phosphate-removing biofilm from a sequencing batch biofilm reactor were investigated with special focus on the nitrifying community. O₂, NO₂⁻, and NO₃⁻ profiles in the biofilm were measured with microsensors at various times during the nonaerated-aerated reactor cycle. In the aeration period, nitrification was oxygen limited and restricted to the first 200 μm at the biofilm surface. Additionally, a delayed onset of nitrification after the start of the aeration was observed. Nitrate accumulating in the biofilm in this period was denitrified during the nonaeration period of the next reactor cycle. Fluorescence in situ hybridization (FISH) revealed three distinct ammonia-oxidizing populations, related to the Nitrosomonas europaea, Nitrosomonas oligotropha, and Nitrosomonas communis lineages. This was confirmed by analysis of the genes coding for 16S rRNA and for ammonia monooxygenase (amoA). Based upon these results, a new 16S rRNA-targeted oligonucleotide probe specific for the Nitrosomonas oligotropha lineage was designed. FISH analysis revealed that the first 100 μm at the biofilm surface was dominated by members of the N. europaea and the N. oligotropha lineages, with a minor fraction related to N. communis. In deeper biofilm layers, exclusively members of the N. oligotropha lineage were found. This separation in space and a potential separation of activities in time are suggested as mechanisms that allow coexistence of the different ammonia-oxidizing populations. Nitrite-oxidizing bacteria belonged exclusively to the genus Nitrospira and could be assigned to a 16S rRNA sequence cluster also found in other sequencing batch systems.     

长期不同施氮水平对草原植物群落结构的影响

为探讨施氮对贝加尔针茅草原植物群落结构的影响,该研究于内蒙古贝加尔针茅草原设置不同施氮水平0(N0)、15(N15)、30(N30)、50(N50)、100(N100)、150(N150)、200(N200)和300(N300)kg·hm-2·a-1,研究连续施氮9年后贝加尔针茅草原群落物种组成、重要值、多样性及生物量等指标对不同施氮水平的响应。结果表明:(1)长期施氮导致植物群落物种组成发生了明显的变化,在高浓度氮素添加量下群落物种数最低,但可显著提高优势种在群落中的重要值(P<0.05)。(2)长期施氮使贝加尔针茅草原植物多样性指数不同程度地降低,使优势度指数增加,其中N300添加水平效果最为明显(P<0.05)。(3)长期施氮使草原植被生产力(地上、地下生物量)整体呈先上升后下降的趋势,地上生物量在N100水平时出现峰值,地下生物量在N50水平时出现最大值(P<0.05),且根系分布具有明显的表聚特征(0~10 cm)。(4)RDA分析表明,寸草苔和狭叶柴胡地上生物量与土壤pH呈显著正相关关系(P<0.05);展枝唐松草和二裂委陵菜地上生物量与土壤有机质含量呈显著正相关关系(P<0.05)。研究认为,长期不同施氮水平均可改变贝加尔针茅草原群落物种组成,降低物种多样性,对植物群落结构有着明显的影响。     

The Impact of Bioaugmentation on Metal Cyanide Degradation and Soil Bacteria Community Structure

Metal cyanides are significant contaminants of many soils found at the site of former industrial activity. In this study we isolated bacteria capable of degrading ferric ferrocyanide and K₂Ni(CN)₄. One of these bacteria a Rhodococcus spp. was subsequently used to bioaugment a minimal medium broth, spiked with K₂Ni(CN)₄, containing 1 g of either an uncontaminated topsoil or a former coke works site soil. Degradation of the K₂Ni(CN)₄ was observed in both soils, however, bioaugmentation did not significantly impact the rate or degree of K₂Ni(CN)₄ removal. Statistical analysis of denaturing gradient gel electrophoresis profiles showed that the topsoil bacterial community had a higher biodiversity, and its structure was not significantly affected by either K₂Ni(CN)₄ or bioaugmentation. In contrast, profiles from the coke works site indicated significant changes in the bacterial community in response to these additions. Moreover, in both soils although bioaugmentation did not affect rates of biodegradation the Rhodococcus spp. did become established in the communities in broths containing both top and coke works soil. We conclude that bacterial communities from contaminated soils with low biodiversity are much more readily perturbed through interventions such as contamination events or bioaugmentation treatments and discuss the implications of these findings for bioremediation studies.     

Effect of Nitrogen Source on Growth and Trichloroethylene Degradation by Methane-Oxidizing Bacteria

The effect of nitrogen source on methane-oxidizing bacteria with respect to cellular growth and trichloroethylene (TCE) degradation ability were examined. One mixed chemostat culture and two pure type II methane-oxidizing strains, Methylosinus trichosporium OB3b and strain CAC-2, which was isolated from the chemostat culture, were used in this study. All cultures were able to grow with each of three different nitrogen sources: ammonia, nitrate, and molecular nitrogen. Both M. trichosporium OB3b and strain CAC-2 showed slightly lower net cellular growth rates and cell yields but exhibited higher methane uptake rates, levels of poly-β-hydroxybutyrate (PHB) production, and naphthalene oxidation rates when grown under nitrogen-fixing conditions. The TCE-degrading ability of each culture was measured in terms of initial TCE oxidation rates and TCE transformation capacities (mass of TCE degraded/biomass inactivated), measured both with and without external energy sources. Higher initial TCE oxidation rates and TCE transformation capacities were observed in nitrogen-fixing mixed, M. trichosporium OB3b, and CAC-2 cultures than in nitrate- or ammonia-supplied cells. TCE transformation capacities were found to correlate with cellular PHB content in all three cultures. The results of this study suggest that the nitrogen-fixing capabilities of methane-oxidizing bacteria can be used to select for high-activity TCE degraders for the enhancement of bioremediation in fixed-nitrogen-limited environments.     

Nitrogen Cycling and Community Structure of Proteobacterial β-Subgroup Ammonia-Oxidizing Bacteria within Polluted Marine Fish Farm Sediments

A multidisciplinary approach was used to study the effects of pollution from a marine fish farm on nitrification rates and on the community structure of ammonia-oxidizing bacteria in the underlying sediment. Organic content, ammonium concentrations, nitrification rates, and ammonia oxidizer most-probable-number counts were determined in samples of sediment collected from beneath a fish cage and on a transect at 20 and 40 m from the cage. The data suggest that nitrogen cycling was significantly disrupted directly beneath the fish cage, with inhibition of nitrification and denitrification. Although visual examination indicated some slight changes in sediment appearance at 20 m, all other measurements were similar to those obtained at 40 m, where the sediment was considered pristine. The community structures of proteobacterial β-subgroup ammonia-oxidizing bacteria at the sampling sites were compared by PCR amplification of 16S ribosomal DNA (rDNA), using primers which target this group. PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE) and with oligonucleotide hybridization probes specific for different ammonia oxidizers. A DGGE doublet observed in PCR products from the highly polluted fish cage sediment sample was present at a lower intensity in the 20-m sample but was absent from the pristine 40-m sample station. Band migration, hybridization, and sequencing demonstrated that the doublet corresponded to a marine Nitrosomonas group which was originally observed in 16S rDNA clone libraries prepared from the same sediment samples but with different PCR primers. Our data suggest that this novel Nitrosomonas subgroup was selected for within polluted fish farm sediments and that the relative abundance of this group was influenced by the extent of pollution.