北极海洋沉积物中锰细菌的分离与系统发育

对中国第二次北极科学考察采集的北极海洋沉积物中的锰细菌进行了筛选、分离和系统发育分析。根据其在筛选平板上菌落的形态学特征,分别从站位P11和S11采集的沉积物中分离到了21株和19株锰细菌。系统发育分析表明,两个站位的锰细菌群落组成有着明显的差别。站位P11分离的可培养锰细菌主要由细菌域（Bacteria）中变形杆菌门的γ-变形杆菌纲（γ-Proteobacteria）和放线菌纲（Actinobacteria）组成,二者分别占86％和14％;γ-变形杆菌纲主要包括嗜冷杆菌属（Psychrobacter）、希瓦氏菌属（Shewanella）、假交替单胞菌属（Pseudoaheromonas）、不动杆菌属（Acinetobacter）、海杆菌属（Marinobacter）,其中以嗜冷杆菌属为主,其比例可达67％。从站位S11分离到的可培养锰细菌主要包括细菌域中变形杆菌门的α-变形杆菌纲（α-Proteobacteria）和γ-变形杆菌纲以及拟杆菌门（Bacteroides）中的黄杆菌纲（Flavobaeteria）;γ-变形杆菌纲主要包括希瓦氏菌属、海单胞菌属（Marinomonas）和交替单胞菌属（Aheromonas）,α-变形杆菌纲主要为鞘氨醇单胞菌属（Sphingomonas）。实验菌株均对Mn^2＋有着较强的抗性,其中以菌株Marinomonas sp．S11-S-4耐受性最高。     

第六次北极科学考察海洋沉积物可培养细菌的多样性分析

【目的】研究北极海洋沉积物可培养细菌的菌种资源多样性。【方法】采用海水Zobell2216E培养基和涂布平板法对第六次北极科学考察获得的海洋沉积物开展细菌分离培养,通过16S rRNA基因系统发育分析了解可培养细菌的多样性。【结果】根据菌落形态特征,从40个站位的北极海洋沉积物样品中共分离并获得16S rRNA基因有效序列的细菌达445株;基于16S rRNA基因的相似性分析与系统发育研究结果表明,分离获得的细菌分属于细菌域的4个门、6个纲、13个目、28个科、49个属、91个种,其中γ-Proteobacteria占大多数;有12株与模式菌株的16S rRNA基因序列相似性小于97%,可能代表了6个潜在的细菌新物种;此次获得的细菌种类组成与以往第五次北极科考获得的相比,在属水平上差异较大。【结论】北极海洋沉积物中存在着丰富的微生物菌种资源,具有很多新型微生物仍未被发现,是亟待开发的微生物资源宝库。     

Diversity of Bacterial Communities in the Snowcover at Tianshan Number 1 Glacier and its Relation to Climate and Environment

The bacterial distribution, and its relationship with climate and environment factors were investigated in the snowcover at Tianshan Number 1 Glacier. The results showed that psychrotrophs were the preponderant bacteria in pit samples, though they were not the dominant species in the new fallen snow. The quantity and diversity of the cultivable bacteria decreased with the passage of time, indicating that the bacterial community acclimatized to low temperature by changing its structure. During this time, the peak number of the cultivable bacteria was associated with dirt layers, indicating that the bacterial input came with dust. Concurrently, the quantity and diversity of the cultivable bacteria showed a trend of variation similar to that shown by the δ¹⁸O values and the soluble ion concentrations, indicating that the bacterial distribution was related to both temperature and the amount of dust transported onto the glacier. Phylogentic analyses of 16S rRNA indicated that all the isolates fell into six categories: α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria, high G+C gram-positive bacteria, and low G+C gram-positive bacteria. In the snow pit, the abundance of the CFB group bacteria (mainly of the genus Flavobacterium) decreased from 55.5% to 1.49% with age, and fluctuated similar to the ion concentrations and the δ¹⁸O value. Meanwhile the α-Proteobacteria (mainly of the genus Brevundimonas) increased from 0.9% to 88.1%, indicating that Brevundimonas was the dominant psychrotroph in the study area, whose abundance varied inversely compared to the above-mentioned chemical properties. All the results suggest that bacterial abundance and diversity vary with climate and the physical chemical microenvironment. The pattern of bacterial distribution could be a biological index for the record of climate and environment change in the Tianshan Number 1 Glacier.     

Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments

Biology is believed to play a large role in the cycling of iron and manganese in many freshwater environments, but specific microbial groups indigenous to these systems have not been well characterized. To investigate the populations of Bacteria and Archaea associated with metal-rich sediments from Green Bay, WI, we extracted nucleic acids and analysed the phylogenetic relationships of cloned 16S rRNA genes. Because nucleic acids have not been routinely extracted from metal-rich samples, we investigated the bias inherent in DNA extraction and gene amplification from pure MnO₂ using defined populations of whole cells or naked DNA. From the sediments, we screened for manganese-oxidizing bacteria using indicator media and found three isolates that were capable of manganese oxidation. In the phylogenetic analysis of bacterial 16S rRNA gene clones, we found two groups related to known metal-oxidizing genera, Leptothrix of the β-Proteobacteria and Hyphomicrobium of the α-Proteobacteria, and a Fe(III)-reducing group related to the Magnetospirillum genus of the α-Proteobacteria. Groups related to the metal-reducing δ-Proteobacteria constituted 22% of the gene clones. In addition, gene sequences from one group of methanogens and a group of Crenarchaeota, identified in the archaeal gene clone library, were related to those found previously in Lake Michigan sediments.     

Metabolism of DMSP, DMS and DMSO by the cultivable bacterial community associated with the DMSP-producing dinoflagellate Scrippsiella trochoidea

Bacterial species associated with the dimethylsulfoniopropionate (DMSP)-producing phytoplankton Scrippsiella trochoidea were cultured and identified, with the aim of establishing their ability to metabolise DMSP, dimethylsulfide (DMS) and dimethylsulfoxide (DMSO). Results demonstrate that of the cultivable bacteria only α-Proteobacteria were capable of producing DMS from DMSP. The concentration of DMSP was shown to affect the amount of DMS produced. Lower DMSP concentrations (1.5?μmol?dm^?3) were completely assimilated, whereas higher concentrations (10?μmol?dm^?3) resulted in increasing amounts of DMS being produced. By contrast to the restricted set of bacteria that metabolised DMSP,?~?70% of the bacterial isolates were able to ‘consume’ DMS. However, 98-100% of the DMS removed was accounted for as DMSO. Notably, a number of these bacteria would only oxidise DMS in the presence of glucose, including members of the γ-Proteobacteria and Bacteroidetes. The observations from this study, coupled with published field data, identify DMS oxidation to DMSO as a major transformation pathway for DMS, and we speculate that the fate of DMS and DMSP in the field are tightly coupled to the available carbon produced by phytoplankton.     

Culture-Dependent and Independent Studies of Microbial Diversity in Highly Copper-Contaminated Chilean Marine Sediments

Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments.     

Characterization of halophilic bacteria from environmental samples from the brackish water of Pulicat Lake, India

Culture dependent phenotypic characterization and 16S rDNA based phylogenetic analyses were applied to study the aerobic halophilic bacterial population present in the Pulicat brackish-water Lake of India. Five different media were employed for isolation of bacteria. A total of 198 morphotypes were recovered, purified and screened for salt tolerance in nutrient agar medium amended with 5–25% NaCl. Based on 16S rDNA restriction fragment length polymorphism analysis with three restriction endonucleases, 51 isolates tolerant to 5% or more NaCl were grouped into 29 clusters. Phylogenetic analysis using 16S rRNA gene sequences revealed that 29 strains could further be allocated into two clades: 19 to Firmicutes and 10 to γ-Proteobacteria. Firmicutes included low G+C Gram-positive bacteria related to family Bacillaceae, which included five genera Bacillus, Virgibacillus, Rummelibacillus, Alkalibacillus and Halobacillus. Another genera included in Firmicutes was Salimicrobium halophilum. In the γ-Proteobacteria group, all the isolates belonged to one genus Halomonas, represented by six different species Halomonas salina, H. shengliensis, H. salifodinae, H. pacifica, H. aquamarina and H. halophila. Most of the isolates exhibited cellulase, xylanase, amylase and protease activities.     

Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria

Dissimilatory manganese reduction dominates anaerobic carbon oxidation in marine sediments with high manganese oxide concentrations, but the microorganisms responsible for this process are largely unknown. In this study, the acetate-utilizing manganese-reducing microbiota in geographically well-separated, manganese oxide-rich sediments from Gullmar Fjord (Sweden), Skagerrak (Norway) and Ulleung Basin (Korea) were analyzed by 16S rRNA-stable isotope probing (SIP). Manganese reduction was the prevailing terminal electron-accepting process in anoxic incubations of surface sediments, and even the addition of acetate stimulated neither iron nor sulfate reduction. The three geographically distinct sediments harbored surprisingly similar communities of acetate-utilizing manganese-reducing bacteria: 16S rRNA of members of the genera Colwellia and Arcobacter and of novel genera within the Oceanospirillaceae and Alteromonadales were detected in heavy RNA-SIP fractions from these three sediments. Most probable number (MPN) analysis yielded up to 10⁶ acetate-utilizing manganese-reducing cells cm⁻³ in Gullmar Fjord sediment. A 16S rRNA gene clone library that was established from the highest MPN dilutions was dominated by sequences of Colwellia and Arcobacter species and members of the Oceanospirillaceae, supporting the obtained RNA-SIP results. In conclusion, these findings strongly suggest that (i) acetate-dependent manganese reduction in manganese oxide-rich sediments is catalyzed by members of taxa (Arcobacter, Colwellia and Oceanospirillaceae) previously not known to possess this physiological function, (ii) similar acetate-utilizing manganese reducers thrive in geographically distinct regions and (iii) the identified manganese reducers differ greatly from the extensively explored iron reducers in marine sediments.     

Bacterial diversity in surface sediments from the Pacific Arctic Ocean

In order to assess bacterial diversity within four surface sediment samples (0–5 cm) collected from the Pacific Arctic Ocean, 16S ribosomal DNA clone library analysis was performed. Near full length 16S rDNA sequences were obtained for 463 clones from four libraries and 13 distinct major lineages of Bacteria were identified (α, β, γ, δ and ε-Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Firmicutes, Planctomycetes, Spirochetes, and Verrucomicrobia). α, γ, and δ-Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria were common phylogenetic groups from all the sediments. The γ-Proteobacteria were the dominant bacterial lineage, representing near or over 50% of the clones. Over 35% of γ-Proteobacteria clones of four clone library were closely related to cultured bacterial isolates with similarity values ranging from 94 to 100%. The community composition was different among sampling sites, which potentially was related to geochemical differences.     

Occurrence and diversity of mesophilic Shewanella strains isolated from the North-West Pacific Ocean

Although bacteria of the genus Shewanella belong to one of the readily cultivable groups of "Gammaproteobacteria", little is known about the occurrence and abundance of these microorganisms in the marine ecosystem. Studies revealed that of 654 isolates obtained from marine invertebrates (ophiuroid Amphiopholis kochii, sipuncula Phascolosoma japonicum, and holothurian Apostichopus japonicus, Cucumaria japonica), seawater and sediments of the North-West Pacific Ocean (i.e. the Sea of Japan and Iturup Is, Kurile Islands), 10.7% belonged to the genus Shewanella. The proportion of viable Shewanella species varied from 4% to 20% depending on the source of isolation. From the isolation study, representative strains of different phenotypes (from seventy presumptive Shewanella strains) were selected for detailed characterization using phenotypic, chemotaxonomic, and phylogenetic testing. 16S rDNA sequence-based phylogenetic analysis confirmed the results of tentative identification and placed the majority of these strains within only a few species of the genus Shewanella with 98-99% of 16S rDNA sequences identity mainly with S. japonica and S. colwelliana, suggesting that the strains studied might belong to these species. Numerically dominant strains of S. japonica were metabolically active and produced proteinases (gelatinases, caseinases), lipases, amylases, agarases, and alginases. Shewanella strains studied demonstrated weak antimicrobial and antifungal activities that might be an indication of their passive role in the colonization on living and non-living surfaces.     

Bacterial diversity in deep-sea sediments from different depths

Seven sediment samples have been examined, taken from different depths of the deep-sea in the range of 1159m to 6482m. A total of 75 different 16S rDNA sequences (149 clones) analyzed clustered into the Proteobacteria, Gram-positive bacteria, Cytophaga, Planctomyces, and Actinomycetes and many sequences were from microorganisms that showed no phylogenetic affiliation with known bacteria. Clones identical to 16S rDNA sequences of members of the genus Pseudomonas were observed in all of the sediments examined. The second group of common sequences cloned from six sediment samples was related to the 16S rDNA sequence of a chemoautotrophic bacterium, the Solemya velum symbiont. Five 16S rDNA sequences from three sediments were related to those of the Alvinella pompejana epibiont which is a member of the -Proteobacteria. Only one sequence was obtained that was closely related to the 16S rDNA of the barophilic bacterium, Shewanella benthica, which might be a minor population in the deeper sediments. -Proteobacteria-related sequences were cloned from sediments obtained from sites near man-made garbage deposits and a Calyptogena community. These environments obviously would be richer in nutrients than other sites, and might be expected to show more types of bacteria than other deep-sea sediments. A large number of cloned sequences in this study showed very low identity to known sequences. These sequences may represent communities of as-yet-uncultivated microorganisms in the sediments.     

Impact of Irradiation and Polycyclic Aromatic Hydrocarbon Spiking on Microbial Populations in Marine Sediment for Future Aging and Biodegradability Studies

Experiments were carried out to develop methods to generate well-characterized, polycyclic aromatic hydrocarbon (PAH)-spiked, aged but minimally altered sediments for fate, biodegradation, and bioavailability experiments. Changes in indigenous bacterial populations were monitored in mesocosms constructed of relatively clean San Diego Bay sediments, with and without exposure to gamma radiation, and then spiked with five different PAHs and hexadecane. While phenanthrene and chrysene degraders were present in the unspiked sediments and increased during handling, PAH spiking of nonirradiated sediments led to dramatic increases in their numbers. Phenotypic characterization of isolates able to grow on phenanthrene or chrysene placed them in several genera of marine bacteria: Vibrio, Marinobacter or Cycloclasticus, Pseudoalteromonas, Marinomonas, and Halomonas. This is the first time that marine PAH degraders have been identified as the latter two genera, expanding the diversity of marine bacteria with this ability. Even at the highest irradiation dose (10 megarads), heterotrophs and endospore formers reappeared within weeks. However, while bacteria from the unirradiated sediments had the capacity to both grow on and mineralize ¹⁴C-labeled phenanthrene and chrysene, irradiation prevented the reappearance of PAH degraders for up to 4 months, allowing spikes to age onto the sediments, which can be used to model biodegradation in marine sediments.     

Diversity of Both the Cultivable Protease-Producing Bacteria and Bacterial Extracellular Proteases in the Coastal Sediments of King George Island,Antarctica

Protease-producing bacteria play a vital role in degrading sedimentary organic nitrogen. However, the diversity of these bacteria and their extracellular proteases in most regions remain unknown. In this paper, the diversity of the cultivable protease-producing bacteria and of bacterial extracellular proteases in the sediments of Maxwell Bay, King George Island, Antarctica was investigated. The cultivable protease-producing bacteria reached 10⁵ cells/g in all 8 sediment samples. The cultivated protease-producing bacteria were mainly affiliated with the phyla Actinobacteria, Firmicutes, Bacteroidetes, and Proteobacteria, and the predominant genera were Bacillus (22.9%), Flavobacterium (21.0%) and Lacinutrix (16.2%). Among these strains, Pseudoalteromonas and Flavobacteria showed relatively high protease production. Inhibitor analysis showed that nearly all the extracellular proteases from the bacteria were serine proteases or metalloproteases. These results begin to address the diversity of protease-producing bacteria and bacterial extracellular proteases in the sediments of the Antarctic Sea.     

Decolorization of textile azo dye and Congo red by an isolated strain of the dissimilatory manganese-reducing bacterium Shewanella xiamenensis BC01

Shewanella xiamenensis BC01 (SXM) was isolated from sediment collected off Xiamen, China and was identified based on the phylogenetic tree of 16S rRNA sequences and the gyrB gene. This strain showed high activity in the decolorization of textile azo dyes, especially methyl orange, reactive red 198, and recalcitrant dye Congo red, decolorizing at rates of 96.2, 93.0, and 87.5 %, respectively. SXM had the best performance for the specific decolorization rate (SDR) of azo dyes compared to Proteus hauseri ZMd44 and Aeromonas hydrophila NIU01 strains and had an SDR similar to Shewanella oneidensis MR-1 in Congo red decolorization. Luria-Bertani medium was the optimal culture medium for SXM, as it reached a density of 4.69 g-DCW L^?1 at 16 h. A mediator (manganese) significantly enhanced the biodegradation and flocculation of Congo red. Further analysis with UV–VIS, Fourier Transform Infrared spectroscopy, and Gas chromatography–mass spectrometry demonstrated that Congo red was cleaved at the azo bond, producing 4,4′-diamino-1,1′-biphenyl and 1,2′-diamino naphthalene 4-sulfonic acid. Finally, SEM results revealed that nanowires exist between the bacteria, indicating that SXM degradation of the azo dyes was coupled with electron transfer through the nanowires. The purpose of this work is to explore the utilization of a novel, dissimilatory manganese-reducing bacterium in the treatment of wastewater containing azo dyes.     

Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution

Nowadays, because of substantial use of petroleum-derived fuels the number and extension of hydrocarbon polluted terrestrial ecosystems is in growth worldwide. In remediation of aforementioned sites bioremediation still tends to be an innovative, environmentally attractive technology. Although huge amount of information is available concerning the hydrocarbon degradation potential of cultivable hydrocarbonoclastic bacteria little is known about the in situ long-term effects of petroleum derived compounds on the structure of soil microbiota. Therefore, in this study our aim was to determine the long-term impact of total petroleum hydrocarbons (TPHs), volatile petroleum hydrocarbons (VPHs), total alkyl benzenes (TABs) as well as of polycyclic aromatic hydrocarbons (PAHs) on the structure of bacterial communities of four different contaminated soil samples. Our results indicated that a very high amount of TPH affected positively the diversity of hydrocarbonoclastic bacteria. This finding was supported by the occurrence of representatives of the α-, β-, γ-Proteobacteria, Actinobacteria, Flavobacteriia and Bacilli classes. High concentration of VPHs and TABs contributed to the predominance of actinobacterial isolates. In PAH impacted samples the concentration of PAHs negatively correlated with the diversity of bacterial species. Heavily PAH polluted soil samples were mainly inhabited by the representatives of the β-, γ-Proteobacteria (overwhelming dominance of Pseudomonas sp.) and Actinobacteria.     

Microbial Populations of the River-Recharged Fredericton Aquifer

The City of Fredericton, New Brunswick, Canada obtains its water from the Saint John River-recharged Fredericton aquifer. Water quality improves as it flows from the river into the aquifer in a process called bank filtration. Microorganisms contribute to water quality improvements during bank filtration by removing organic carbon. In the Fredericton aquifer, microbially catalyzed reductive dissolution of manganese oxide minerals negatively affects water quality. Aerobic and anaerobic microorganisms were cultured from Fredericton aquifer production well water, from associated bedrock groundwater, and from Saint John River sediment core and sediment groundwater samples. Aerobes were the largest culturable groups in all samples. The ratio of aerobes to other microbial groups, i.e., those reducing nitrate, Mn^{4 +}, Fe^{3 +}, or sulfate, did not vary significantly along the water flow path from the river to the aquifer. Analysis of microbial community composition along the flow path indicated an essentially identical community except in the immediate vicinity of the aquifer. This is in agreement with the absence of macroscale redox zones in the sediment below the Saint John River as determined by groundwater geochemical data. Bacteria isolated from groundwater samples, identified by 16S ribosomal RNA gene sequencing, were α -, β -, γ -, and δ -Proteobacteria, Actinobacteria, and Firmicutes. In contrast to groundwater samples, the majority of bacteria isolated from sediments were γ -Proteobacteria. Numbers of manganese-reducing bacteria, including Aeromonas spp., were small, however Mn^{4 +} reduction ability was widespread in bacteria enriched and isolated with other electron acceptors. The diverse Fredericton aquifer microbial community likely uses manganese oxide minerals as a sink for electrons derived from organic carbon oxidation.     

Cultivation of particle-associated heterotrophic bacteria during a spring phytoplankton bloom in the North Sea

Seawater contains free-living and particle-attached bacteria. Only a small fraction is cultivable on plates. As free-living and particle-associated bacteria differ in their physiological traits, their cultivability on plates may coincide with particle association. Using filtration and Imhoff sedimentation cones, particles were collected during a spring phytoplankton bloom off Helgoland (North Sea) in order to obtain particle-associated bacteria as inocula. Direct dilution plating resulted in 526 strains from 3 µm filtration retentates and 597 strains from settled particles. Motile Gammaproteobacteria from the genera Pseudoalteromonas, Shewanella, Psychrobacter, Vibrio and Colwellia, as well as particle-attached Flavobacteriia affiliating with the genera Tenacibaculum and Gramella, were frequently isolated. As a result, a diverse collection comprised of 266 strains was deposited. Two strains were most likely to represent novel genera and 78 strains were probably novel species. Recently, a high-throughput cultivation study from the same site using seawater as an inoculum had retrieved 271 operational phylogenetic units (OPUs) that represented 88% of the 4136 characterized strains at the species level. A comparison of 16S rRNA gene sequences revealed that the collection obtained matched 104 of the 271 seawater OPUs at the species level and an additional 113 at the genus level. This large overlap indicated a significant contribution of particle-associated bacteria to the cultivable microbiome from seawater. The presence of 49 genera not identified in the larger seawater study suggested that sample fractionation was an efficient strategy to cultivate rare members of the planktonic microbiome. The diverse collection of heterotrophic bacteria retrieved in this study will be a rich source for future studies on the biology of particle-associated bacteria.     

Community Structures and Distribution of Anaerobic Ammonium Oxidizing and nirS-Encoding Nitrite-Reducing Bacteria in Surface Sediments of the South China Sea

Anaerobic ammonium oxidation (anammox) and denitrification are two important processes responsible for nitrogen loss; monitoring of microbial communities carrying out these two processes offers a unique opportunity to understand the microbial nitrogen cycle. The aim of the current study was to characterize community structures and distribution of anammox and nirS-encoding nitrite-reducing bacteria in surface sediments of the northern South China Sea (SCS). The consistent phylogenetic results of three biomarkers of anammox bacteria, including 16S rRNA, hzo, and Scalindua-nirS genes, showed that Scalindua-like bacteria were the only anammox group presenting in surface sediments of the SCS. However, a relatively high micro-diversity was found within this group, including several SCS habitat-specific phylotypes, Candidatus “Scalindua zhenghei”. Comparing to 16S rRNA gene, hzo and Scalindua-nirS genes provided a relatively higher resolution to elucidate anammox bacteria. For the nirS-encoding nitrite-reducing bacteria, the detected nirS gene sequences were closely related to various marine nirS denitrifiers, especially those which originated from coastal and estuarine sediments with a much higher diversity than anammox bacteria. Anammox bacterial communities shifted along with the seawater depth, while nirS-encoding nitrite-reducing bacteria did not. Although nirS-encoding nitrite-reducing bacteria have a much higher abundance and diversity than anammox bacteria, they showed similar abundance variation patterns in research sites, suggesting the two microbial groups might be affected by the similar environmental factors. The significant correlations among the abundance of the two microbial groups with the molar ratio of NH₄ ⁺ to (NO₂ ^??+?NO₃ ^?), pH, and organic matters of sediments strongly supported this hypothesis.     

Diversity of cultivable bacteria associated with fruiting bodies of wild Himalayan Cantharellus spp.

The cultivable bacteria associated with fruiting bodies of different Cantharellus species collected from the forests of the north-western Himalayan region were studied. Repetitive extragenic palindromic (REP) and BOX-PCR fingerprinting analyses revealed that different strains were distributed within Cantharellus species. The number of bacteria varied from 0.5 to 1.1?×?10³?CFU/g of fresh tissue for different fruiting bodies. Thirty different operational taxonomic units (OTUs) were found among the bacteria analyzed. 16S rRNA sequence analysis revealed that most of the bacteria associated with different Cantharellus species were Gammaproteobacteria belong to the genera Hafnia, Enterobacter, Ewingella, Rahnella, Stenotrophomonas, and Pseudomonas, and γ-proteobacterium, followed by Betaproteobacteria (Alcaligenes) and Firmicutes, (Bacillus). The most common bacteria associated with the majority of Cantharellus species were Hafnia and Stenotrophomonas species.     

Bacterial diversity in biofilms formed on condenser tube surfaces in a nuclear power plant

To elucidate the bacterial diversity in biofilms formed on a condenser tube from a nuclear power plant, 16S rRNA gene sequences were examined using a PCR-cloning-sequencing approach. Twelve operational taxonomic units were retrieved in the clone library, and the estimated species richness was low (13.2). Most of the clones (94.7%) were affiliated with α-Proteobacteria; Planctomycetes and γ-Proteobacteria were much rarer. Interestingly, except for one clone belonging to Pseudoalteromonas, most of the sequences displayed sequence similarities <97% of those of the closest type strains. Based on 16S rRNA phylogenetic analysis, most bacteria were assigned to novel taxa above the species level. The low species richness and unusual bacterial composition may be attributable to selective pressure from chlorine in the cooling water. To prevent or control bacterial biofilms in cooling circuits, additional studies of the physiology and ecology of these species will be essential.