Responses of aerobic and anaerobic ammonia/ammonium-oxidizing microorganisms to anthropogenic pollution in coastal marine environments.

Up to date, numerous studies have shown that the community structure of aerobic ammonia oxidizers including ammonia-oxidizing Betaproteobacteria (Beta-AOB) and ammonia-oxidizing archaea (AOA) and, more recently, the anaerobic ammonium-oxidizing (anammox) bacteria is responsive to environmental conditions including salinity, pH, selected metal ions, concentrations of inorganic nitrogen, total phosphorus, the ratio of organic carbon and nitrogen, and sedimentological factors such as the sediment median grain size. Identification of these responses to known anthropogenic pollution is of particular interest to better understand the growth dynamics and activities of nitrogen transforming microorganisms in marine environments. This chapter discusses currently available methods including molecular ecological analysis using clone library constructions with specific molecular genetic markers for delineating community changes of Beta-AOB, AOA, and anammox bacteria.

Residence of habitat-specific anammox bacteria in the deep-sea subsurface sediments of the South China Sea: analyses of marker gene abundance with physical chemical parameters.

Anaerobic ammonium oxidation (anammox) has been recognized as an important process for the global nitrogen cycle. In this study, the occurrence and diversity of anammox bacteria in the deep-sea subsurface sediments of the South China Sea (SCS) were investigated. Results indicated that the anammox bacterial sequences recovered from this habitat by amplifying both 16S rRNA gene and hydrazine oxidoreductase encoding hzo gene were all closely related to the Candidatus Scalindua genus.

Seasonal dynamics of anammox bacteria in estuarial sediment of the Mai Po Nature Reserve revealed by analyzing the 16S rRNA and hydrazine oxidoreductase (hzo) genes.

The community and population dynamics of anammox bacteria in summer (wet) and winter (dry) seasons in estuarial mudflat sediment of the Mai Po Nature Reserve were investigated by 16S rRNA and hydrazine oxidoreductase (hzo) genes. 16S rRNA phylogenetic diversity showed that sequences related to 'Kuenenia' anammox bacteria were presented in summer but not winter while 'Scalindua' anammox bacteria occurred in both seasons and could be divided into six different clusters. Compared to the 16S rRNA genes, the hzo genes revealed a relatively uniform seasonal diversity, with sequences relating to 'Scalindua', 'Anammoxoglobus', and planctomycete KSU-1 found in both seasons.

Advances in methods for detection of anaerobic ammonium oxidizing (anammox) bacteria.

Anaerobic ammonium oxidation (anammox), the biochemical process oxidizing ammonium into dinitrogen gas using nitrite as an electron acceptor, has only been recognized for its significant role in the global nitrogen cycle not long ago, and its ubiquitous distribution in a wide range of environments has changed our knowledge about the contributors to the global nitrogen cycle. Currently, several groups of methods are used in detection of anammox bacteria based on their physiological and biochemical characteristics, cellular chemical composition, and both 16S rRNA gene and selective functional genes as biomarkers, including hydrazine oxidoreductase and nitrite reductase encoding genes hzo and nirS, respectively. Results from these methods coupling with advances in quantitative PCR, reverse transcription of mRNA genes and stable isotope labeling have improved our understanding on the distribution, diversity, and activity of anammox bacteria in different environments both natural and engineered ones.

Comparative analysis of binding affinities between styrene and mammalian CYP2E1 by bioinformatics approaches.

Cytochrome P450 2E1 (CYP2E1) is a cytochrome P450 enzyme involved in styrene metabolism. This study compared the binding affinities between styrene and 11 mammalian CYP2E1 systems using bioinformatics methods. Firstly, amino acid sequences of CYP2E1s were obtained from the Swiss-Prot database.

Cytochrome cd1-containing nitrite reductase encoding gene nirS as a new functional biomarker for detection of anaerobic ammonium oxidizing (Anammox) bacteria.

A newly designed primer set (AnnirS), together with a previously published primer set (ScnirS), was used to detect anammox bacterial nirS genes from sediments collected from three marine environments. Phylogenetic analysis demonstrated that all retrieved sequences were clearly different from typical denitrifiers' nirS, but do group together with the known anammox bacterial nirS. Sequences targeted by ScnirS are closely related to Scalindua nirS genes recovered from the Peruvian oxygen minimum zone (OMZ), whereas sequences targeted by AnnirS are more closely affiliated with the nirS of Candidatus 'Kuenenia stuttgartiensis' and even form a new phylogenetic nirS clade, which might be related to other genera of the anammox bacteria.

Spatial distribution and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in mangrove sediments.

We investigated the diversity, spatial distribution, and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediment samples of different depths collected from a transect with different distances to mangrove forest in the territories of Hong Kong. Both the archaeal and bacterial amoA genes (encoding ammonia monooxygenase subunit A) from all samples supported distinct phylogenetic groups, indicating the presences of niche-specific AOA and AOB in mangrove sediments. The higher AOB abundances than AOA in mangrove sediments, especially in the vicinity of the mangrove trees, might indicate the more important role of AOB on nitrification.

A new ColE1-like plasmid group revealed by comparative analysis of the replication proficient fragments of Vibrionaceae plasmids.

Plasmids play important roles in horizontal gene transfer among Vibrionaceae, but surprisingly little is known about their replication and incompatibility systems. In this study, we successfully developed a bioinformatics-assisted strategy of experimental identification of 7 Vibrio plasmid replicons. Comparative sequences analysis of the 7 Vibrio plasmid replicons obtained in this study together with 8 published Vibrionaceae plasmid sequences revealed replication participating elements involved in the ColE1-mode of replication initiation and regulation.

Molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in high-temperature petroleum reservoirs.

Anaerobic ammonium-oxidizing (anammox) process plays an important role in the nitrogen cycle of the worldwide anoxic and mesophilic habitats. Recently, the existence and activity of anammox bacteria have been detected in some thermophilic environments, but their existence in the geothermal subterranean oil reservoirs is still not reported. This study investigated the abundance, distribution and functional diversity of anammox bacteria in nine out of 17 high-temperature oil reservoirs by molecular ecology analysis.

Physiology and biochemistry of reduction of azo compounds by Shewanella strains relevant to electron transport chain.

Azo dyes are toxic, highly persistent, and ubiquitously distributed in the environments. The large-scale production and application of azo dyes result in serious environmental pollution of water and sediments. Bacterial azo reduction is an important process for removing this group of contaminants.

The contribution of mobile genetic elements to the evolution and ecology of Vibrios.

An increase in the frequency of seafood-borne gastroenteritis in humans and Vibrio-related disease of fish and invertebrates has generated interest in the ecology of disease-causing Vibrios and the mechanisms driving their evolution. Genome sequencing studies have indicated a substantial contribution of horizontal gene transfer (HGT) to the evolution of Vibrios. Of particular interest is the contribution of HGT to the evolution of Vibrios pathogens and the adaptation of disease-causing Vibrios for survival in diverse environments.

Microbial community analysis of fresh and old microbial biofilms on Bayon temple sandstone of Angkor Thom, Cambodia.

The temples of Angkor monuments including Angkor Thom and Bayon in Cambodia and surrounding countries were exclusively constructed using sandstone. They are severely threatened by biodeterioration caused by active growth of different microorganisms on the sandstone surfaces, but knowledge on the microbial community and composition of the biofilms on the sandstone is not available from this region. This study investigated the microbial community diversity by examining the fresh and old biofilms of the biodeteriorated bas-relief wall surfaces of the Bayon Temple by analysis of 16S and 18S rRNA gene sequences.

Oxidation of elemental sulfur by Fusarium solani strain THIF01 harboring endobacterium Bradyrhizobium sp.

Nineteen fungal strains having an ability to oxidize elemental sulfur in mineral salts medium were isolated from deteriorated sandstones of Angkor monuments. These fungi formed clearing zone on agar medium supplemented with powder sulfur due to the dissolution of sulfur. Representative of the isolates, strain THIF01, was identified as Fusarium solani on the basis of morphological characteristics and phylogenetic analyses.

Computational studies of interactions between endocrine disrupting chemicals and androgen receptor of different vertebrate species.

Homology modeling and molecular docking were used to in silico analyze the interactions between six endocrine disrupting chemicals (EDCs) and 11 androgen receptors (ARs) of different vertebrate species. The MODELLER 9V7 program was employed to construct the homology models of AR ligand binding domains (LBDs) from birds, amphibians, bony fishes and cartilaginous fishes. The Surflex-Dock program was applied to calculate and analyze the binding affinities between the six EDCs and AR LBDs.

A comparison of primer sets for detecting 16S rRNA and hydrazine oxidoreductase genes of anaerobic ammonium-oxidizing bacteria in marine sediments.

Published polymerase chain reaction primer sets for detecting the genes encoding 16S rRNA gene and hydrazine oxidoreductase (hzo) in anammox bacteria were compared by using the same coastal marine sediment samples. While four previously reported primer sets developed to detect the 16S rRNA gene showed varying specificities between 12% and 77%, an optimized primer combination resulted in up to 98% specificity, and the recovered anammox 16S rRNA gene sequences were >95% sequence identical to published sequences from anammox bacteria in the Candidatus "Scalindua" group. Furthermore, four primer sets used in detecting the hzo gene of anammox bacteria were highly specific (up to 92%) and efficient, and the newly designed primer set in this study amplified longer hzo gene segments suitable for phylogenetic analysis.

Surface properties of bacteria from activated sludge in relation to bioflocculation.

Two bacterial stains were isolated from the activated sludge and identified as Leucobacter sp. and Alcaligenesfaecalis by 16S rDNA sequencing. Pure cultures of these two strains, representing well or poorly settled bacteria, were used to investigate the mechanism of bioflocculation in activated sludge.

Disinfection characteristics of the dissolved organic fractions at several stages of a conventional drinking water treatment plant in Southern China.

Dissolved organic matter (DOM) influences many aspects of drinking water treatment, including the formation of harmful disinfection by-products (DBPs) when disinfectants are applied. DOM was isolated and fractionated using membrane ultra-filtration (UF) and reverse osmosis (RO) to eight individual fractions based on molecular weight cut-offs from a conventional surface water treatment plant (WTP) in Guangzhou of PR China. Molecular weights of these eight fractions were further calibrated using high performance size exclusion chromatography (HPSEC) and they ranged from 0.

[Bacterial anaerobic ammonia oxidation (Anammox) in the marine nitrogen cycle--a review].

Anaerobic ammonium oxidation (Anammox) is a microbial oxidation process of ammonium, with nitrite as the electron acceptor and dinitrogen gas as the main product, and is performed by a clade of deeply branched Planctomycetes, which possess an intracytoplasmic membrane-bounded organelle, the anammoxosome, for the Anammox process. The wide distribution of Anammox bacteria in different natural environments has been greatly modified the traditional view of biogeochemical cycling of nitrogen, in which microbial denitrifier is considered as the only organism to respire nitrate and nitrite to produce nitric and nitrous oxides, and eventually nitrogen gas. More evidences indicate that Anammox is responsible for the production of more than 50% of oceanic N2 and plays an important role in global nitrogen cycling.

Phylogenetic diversity and axial distribution of microbes in the intestinal tract of the polychaete Neanthes glandicincta.

The phylogenetic diversity and axial distribution of microorganisms in three sections of the gastrointestinal tracts of the polychaete Neanthes glandicincta was evaluated using both most probable number method and cloning analyses of 16S rRNA genes in this study. Quantification of the density of microorganisms in the gut showed that aerobic microorganisms decreased from anterior to posterior, while anaerobic ones showed a reverse trend. The total numbers of microorganisms decreased significantly (p < 0.

Effect of temperature on removal of iron cyanides from solution by maize plants.

Goal, Scope, And Background: Cyanide is commonly found in soils and groundwater complexed with iron as ferro- and ferri-cyanide. It is evident that plants are capable of tolerating, transporting, and assimilating iron cyanides. The objectives of this study were to investigate the influence of temperatures on the removal and bioaccumulation of two chemical forms of iron cyanides by maize seedlings.

Uptake, accumulation and metabolic response of ferricyanide in weeping willows.

The remediation potential and metabolic responses of plants to ferricyanide were investigated using pre-rooted weeping willows (Salix babylonica L.) grown hydroponically in growth chambers and treated with potassium ferricyanide. Positive responses were observed for the plants exposed to View Article and Find Full Text PDF

Complete sequence of plasmid pMP1 from the marine environmental Vibrio vulnificus and location of its replication origin.

A novel cryptic plasmid, pMP1, from an environmental Vibrio vulnificus MP-4 isolated from Mai Po Nature Reserve in Hong Kong, has been characterized. The 7.6-kb plasmid had guanine-cytosine content of 40.

Degradation of n-butyl benzyl phthalate using TiO2/UV.

n-Butyl benzyl phthalate (BBP) has been classified as endocrine disrupting compound and priority pollutant. Effects of TiO(2) dosage, pH, initial BBP concentration and co-existing substances on the degradation of BBP by TiO(2)/UV process were investigated. The optimal TiO(2) dosage and pH value for the BBP degradation were 2.

Differences in uptake and translocation of selenate and selenite by the weeping willow and hybrid willow.

Background, Aim, And Scope: Due to its essentiality, deficiency, and toxicity to living organisms and the extensive use in industrial activities, selenium (Se) has become an element of global environmental and health concern. Se removal from contaminated sites using physical, chemical, and engineering techniques is quite complicated and expensive. The goal of this study was to investigate uptake and translocation of Se in willows and to provide quantitative information for field application whether Se phytoremediation is feasible and ecologically safe.