两株多环芳烃降解菌协同对菲-镉污染的去除特性北大核心

【目的】从污染土壤中分离筛选一株多环芳烃降解菌,并探究其与Pseudomonas aeruginosa B6-2构建的混菌体系对菲-镉复合污染的修复效能,以及微生物代谢特性对不同镉浓度赋存的响应特性,以期为复合污染的生物修复提供优良菌株资源及应用技术参考。【方法】采用富集驯化、筛选纯化方法得到一株多环芳烃降解菌,通过生理生化特征和16S rRNA基因序列分析进行鉴定。利用高效液相色谱法和电感耦合等离子体质谱法评估不同镉浓度赋存下各反应体系对菲和镉的去除效能;通过菌体细胞形态的扫描电镜观测及菌株代谢活性检测,探讨镉胁迫对菲生物降解过程的影响机制。【结果】筛选得到一株具有重金属耐受性和多环芳烃高效降解菌SZ-3,经鉴定为节杆菌属;降解菌协同体系(M)具有良好的菲降解效能和抗镉胁迫优势。镉胁迫浓度为0.5、10 mg/L时,M对菲和镉的去除率分别高于85%、80%;镉胁迫浓度为25、50 mg/L时,2种污染物的去除率均大于65%。扫描电镜分析表明,镉胁迫导致菌体表面粗糙且出现不同程度变形,菌体间黏附性和聚集性提高。反应周期内,邻苯二酚1,2-双加氧酶活性与电子传递体系活性随镉浓度增加而降低,两者变化与菲降解速率变化一致。【结论】Arthrobacter sp.SZ-3是一株PAHs高效降解菌,能与Pseudomonas aeruginosa B6-2协同高效修复菲-镉复合污染,随着初始镉胁迫浓度增加,混菌协同对目标污染物去除的优势显著。     

Identification of cellulolytic bacteria in soil by stable isotope probing

Plant residues, mainly made up of cellulose, are the largest fraction of organic carbon material in terrestrial ecosystems. Soil microorganisms are mainly responsible for the transfer of this carbon to the atmosphere, but their contribution is not accurately known. The aim of the present study was to identify bacterial populations that are actively involved in cellulose degradation, using the DNA-stable isotope probing (DNA-SIP) technique. ¹³C-cellulose was produced by Acetobacter xylinus and incubated in soil for 7, 14, 30 and 90 days. Total DNA was extracted from the soil, the ¹³C-labelled (heavy) and unlabelled (light) DNA fractions were separated by ultracentrifugation, and the structure of active bacterial communities was analysed by bacterial-automated ribosomal intergenic spacer analysis (B-ARISA) and characterized with denaturing gradient gel electrophoresis (DGGE). Cellulose degradation was associated with significant changes in bacterial community structure issued from heavy DNA, leading to the appearance of new bands and increase in relative intensities of other bands until day 30. The majority of bands decreased in relative intensity at day 90. Sequencing and phylogenetic analysis of 10 of these bands in DGGE profiles indicated that most sequences were closely related to sequences from organisms known for their ability to degrade cellulose or to uncultured soil bacteria.     

Identification of nitrogen-incorporating bacteria in petroleum-contaminated arctic soils by using [15N]DNA-based stable isotope probing and pyrosequencing

Arctic soils are increasingly susceptible to petroleum hydrocarbon contamination, as exploration and exploitation of the Arctic increase. Bioremediation in these soils is challenging due to logistical constraints and because soil temperatures only rise above 0°C for ∼2 months each year. Nitrogen is often added to contaminated soil in situ to stimulate the existing microbial community, but little is known about how the added nutrients are used by these microorganisms. Microbes vary widely in their ability to metabolize petroleum hydrocarbons, so the question becomes: which hydrocarbon-degrading microorganisms most effectively use this added nitrogen for growth? Using [¹⁵N]DNA-based stable isotope probing, we determined which taxonomic groups most readily incorporated nitrogen from the monoammonium phosphate added to contaminated and uncontaminated soil in Canadian Forces Station-Alert, Nunavut, Canada. Fractions from each sample were amplified with bacterial 16S rRNA and alkane monooxygenase B (alkB) gene-specific primers and then sequenced using lage-scale parallel-pyrosequencing. Sequence data was combined with 16S rRNA and alkB gene C quantitative PCR data to measure the presence of various phylogenetic groups in fractions at different buoyant densities. Several families of Proteobacteria and Actinobacteria that are directly involved in petroleum degradation incorporated the added nitrogen in contaminated soils, but it was the DNA of Sphingomonadaceae that was most enriched in ¹⁵N. Bacterial growth in uncontaminated soils was not stimulated by nutrient amendment. Our results suggest that nitrogen uptake efficiency differs between bacterial groups in contaminated soils. A better understanding of how groups of hydrocarbon-degraders contribute to the catabolism of petroleum will facilitate the design of more targeted bioremediation treatments.     

Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing

Movile Cave is an unusual groundwater ecosystem that is supported by in situ chemoautotrophic production. The cave atmosphere contains 1-2% methane (CH4), although much higher concentrations are found in gas bubbles that keep microbial mats afloat on the water surface. As previous analyses of stable carbon isotope ratios have suggested that methane oxidation occurs in this environment, we hypothesized that aerobic methane-oxidizing bacteria (methanotrophs) are active in Movile Cave. To identify the active methanotrophs in the water and mat material from Movile Cave, a microcosm was incubated with a 10%13CH4 headspace in a DNA-based stable isotope probing (DNA-SIP) experiment. Using improved centrifugation conditions, a 13C-labelled DNA fraction was collected and used as a template for polymerase chain reaction amplification. Analysis of genes encoding the small-subunit rRNA and key enzymes in the methane oxidation pathway of methanotrophs identified that strains of Methylomonas, Methylococcus and Methylocystis/Methylosinus had assimilated the 13CH4, and that these methanotrophs contain genes encoding both known types of methane monooxygenase (MMO). Sequences of non-methanotrophic bacteria and an alga provided evidence for turnover of CH4 due to possible cross-feeding on 13C-labelled metabolites or biomass. Our results suggest that aerobic methanotrophs actively convert CH4 into complex organic compounds in Movile Cave and thus help to sustain a diverse community of microorganisms in this closed ecosystem.     

Enrichment, isolation, and phylogenetic identification of polycyclic aromatic hydrocarbon-degrading bacteria from Elizabeth River sediments

The diversity of indigenous bacteria in sediments from several sites in the Elizabeth River (Virginia) able to degrade multiple polycyclic aromatic hydrocarbons (PAHs) was investigated by the use of classical selective enrichment and molecular analyses. Enrichment cultures containing naphthalene, phenanthrene, fluoranthene, or pyrene as a sole carbon and energy source were monitored by denaturing gradient gel electrophoresis (DGGE) to detect changes in the bacterial-community profile during enrichment and to determine whether the representative strains present were successfully cultured. The DGGE profiles of the final enrichments grown solely on naphthalene and pyrene showed no clear relationship with the site from which the inoculum was obtained. The enrichments grown solely on pyrene for two sample sites had >80% similarity, which suggests that common pyrene-degrading strains may be present in these sediments. The final enrichments grown on fluoranthene and phenanthrene remained diverse by site, suggesting that these strains may be influenced by environmental conditions. One hundred and one isolates were obtained, comprising representatives of the actinomycetes and alpha-, beta-, and gammaproteobacteria, including seven novel isolates with 16S rRNA gene sequences less than 98% similar to known strains. The ability to degrade multiple PAHs was demonstrated by mineralization of 14C-labeled substrate and growth in pure culture. This supports our hypothesis that a high diversity of bacterial strains with the ability to degrade multiple PAHs can be confirmed by the combined use of classical selective enrichment and molecular analyses. This large collection of diverse PAH-degrading strains provides a valuable resource for studies on mechanisms of PAH degradation and bioremediation.     

Pseudomonas, the dominant polycyclic aromatic hydrocarbon-degrading bacteria isolated from Antarctic soils and the role of large plasmids in horizontal gene transfer

Twenty-two polycyclic aromatic hydrocarbon (PAH)-degrading bacterial strains were isolated from Antarctic soils with naphthalene or phenanthrene as a sole carbon source, while no degrader was obtained from an unpolluted sampling site. Phylogenetic analysis showed that all belonged to the genus Pseudomonas except one that was identified as the genus of Rahnella. Some of them were closely related to previously reported cold-tolerant species, while some were separated in deeply rooted branches and represent new strains. All these strains showed a high efficiency to degrade naphthalene at 4 degrees C, and some additionally degraded phenanthrene. Using degenerate primers and polymerase chain reaction (PCR) amplification, ndo gene encoding naphthalene dioxygenase (NDO) was detected from all the isolates. Phylogenetic analysis grouped these genes into two clusters which shared 94% similarity to each other, and showed about 97% similarity within a cluster. However, no obvious difference was observed with mesophilic ndo genes; this indicates that the host cell is pivotal in cold adaptation. In addition, the mismatch between 16S rRNA and NDO phylogenetic trees strongly indicates horizontal gene transfer among these isolates and may have happened in situ. Further, Southern hybridization and plasmid curing confirmed that ndo genes were located on a large self-transmissible plasmid, which can be transferred to a mesophilic strains. The transconjugants acquired the ability to utilize naphthalene and phenanthrene. Results of this article imply that Pseudomonas plays an important role in PAH biodegradation in Antarctic soils, and the related genes might be originally transferred from outside Antarctica and spread among indigenous species.     

Hydroxylations of substituted naphthalenes by Escherichia coli expressing aromatic dihydroxylating dioxygenase genes from polycyclic aromatic hydrocarbon-utilizing marine bacteria

Bioconversion experiments of various mono- or di-substituted naphthalenes such as dimethylnaphthalenes were carried out using the cells of Escherichia coli that expressed aromatic dihydroxylating dioxygenase genes (phnA1A2A3A4 and phdABCD) from polycyclic aromatic hydrocarbon-utilizing marine bacteria, Nocardioides sp. KP7 and Cycloclasticus sp. A5, respectively. We found that the former dioxygenase PhnA1A2A3A4 had broad substrate preference for these compounds and often was able to hydroxylate their methyl groups. Specifically, 1,4-dimethylnaphthalene was predominantly bioconverted into 1,4-dihydroxymethylnaphthalene.     

Assimilatory nitrate utilization by bacteria on the West Florida Shelf as determined by stable isotope probing and functional microarray analysis

Dissolved inorganic nitrogen (DIN) uptake by marine heterotrophic bacteria has important implications for the global nitrogen (N) and carbon (C) cycles. Bacterial nitrate utilization is more prevalent in the marine environment than traditionally thought, but the taxonomic identity of bacteria that utilize nitrate is difficult to determine using traditional methodologies. (15) N-based DNA stable isotope probing was applied to document direct use of nitrate by heterotrophic bacteria on the West Florida Shelf. Seawater was incubated in the presence of 2 μM (15) N ammonium or (15) N nitrate. DNA was extracted, fractionated via CsCl ultracentrifugation, and each fraction was analyzed by terminal restriction fragment length polymorphism (TRFLP) analysis. TRFs that exhibited density shifts when compared to controls that had not received (15) N amendments were identified by comparison with 16S rRNA gene sequence libraries. Relevant marine proteobacterial lineages, notably Thalassobacter and Alteromonadales, displayed evidence of (15) N incorporation. RT-PCR and functional gene microarray analysis could not demonstrate the expression of the assimilatory nitrate reductase gene, nasA, but mRNA for dissimilatory pathways, i.e. nirS, nirK, narG, nosZ, napA, and nrfA was detected. These data directly implicate several bacterial populations in nitrate uptake, but suggest a more complex pattern for N flow than traditionally implied.     

浙江南部近海前肛鳗营养生态位变化研究——基于稳定同位素技术

基于2016年和2020年浙江南部近海收集的71尾前肛鳗样品,通过测定碳氮稳定同位素比值计算其营养生态位指标,对比分析前肛鳗不同发育过程、不同季节及不同年份营养生态位的差异,探究营养生态位的变动规律及对资源的利用情况。结果表明：(1)2016年和2020年前肛鳗平均δ¹³C值分别为(-15.19±0.31)‰、(-15.90±0.45)‰;平均δ¹⁵N值分别为(12.42±0.45)‰、(12.92±0.25)‰;(2)单因素方差分析表明,2016年前肛鳗不同发育过程δ¹³C值差异不显著(P>0.05),δ¹⁵N值差异显著(P<0.05),不同季节间δ¹³C值和δ¹⁵N值均存在显著差异(P<0.05),而2020年前肛鳗不同发育过程δ¹³C值和δ¹⁵N值差异均不显著(P>0.05),不同季节间δ¹³C值存在显著差异(P<0.05),δ¹⁵N...     

Short Communication: A method for extraction of DNA and PCR-based detection of polycyclic aromatic hydrocarbon-degrading bacteria in soil contaminated with oil and grease

A protocol for extraction of microbial DNA from oil-and grease-saturated soil is reported that can be used to target availability of specific genotypes of bacteria in extensively contaminated soils using the polymerase chain reaction. The methodology developed can be used in the biotreatibility studies for in situ bioremediation of hydrocarbon-contaminated sites.     

Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing

Carbohydrates, including starches, are an important energy source for humans, and are known for their interactions with the microbiota in the digestive tract. Largely, those interactions are thought to promote human health. Using 16S ribosomal RNA (rRNA)-based stable isotope probing (SIP), we identified starch-fermenting bacteria under human colon-like conditions. To the microbiota of the TIM-2 in vitro model of the human colon 7.4 g l⁻¹ of [U-¹³C]-starch was added. RNA extracted from lumen samples after 0 (control), 2, 4 and 8 h was subjected to density-gradient ultracentrifugation. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprinting and phylogenetic analyses of the labelled and unlabelled 16S rRNA suggested populations related to Ruminococcus bromii, Prevotella spp. and Eubacterium rectale to be involved in starch metabolism. Additionally, 16S rRNA related to that of Bifidobacterium adolescentis was abundant in all analysed fractions. While this might be due to the enrichment of high-GC RNA in high-density fractions, it could also indicate an active role in starch fermentation. Comparison of the T-RFLP fingerprints of experiments performed with labelled and unlabelled starch revealed Ruminococcus bromii as the primary degrader in starch fermentation in the studied model, as it was found to solely predominate in the labelled fractions. LC-MS analyses of the lumen and dialysate samples showed that, for both experiments, starch fermentation primarily yielded acetate, butyrate and propionate. Integration of molecular and metabolite data suggests metabolic cross-feeding in the system, where populations related to Ruminococcus bromii are the primary starch degrader, while those related to Prevotella spp., Bifidobacterium adolescentis and Eubacterium rectale might be further involved in the trophic chain.     

Nitrogen uptake by heterotrophic bacteria and phytoplankton in Arctic surface waters

We estimated rates of heterotrophic bacterial and phytoplanktonuptake of nitrate, ammonium, and urea using ¹⁵N-labelled nitrogenand specific metabolic inhibitors of prokaryote and eukaryotenitrogen metabolism in the surface waters of the North Water(northern Baffin Bay) during autumn that were characterizedby the absence of cyanobacteria (comprising prochlorophytes).The percentage of nitrate + ammonium uptake by heterotrophicbacteria ranged between 44 and 78% of the measured total uptakeand was the highest when the phytoplankton biomass was relativelylow (<2 µg Chlorophyll a L^–1). Phytoplanktonaccounted for a larger fraction (e.g., 58–95%) of ureauptake than heterotrophic bacteria. When our results are combinedwith those from previous studies carried out in diverse temperateand polar areas, it appears that heterotrophic bacteria accountfor 25% (14–40%; median and interquartile range) of thetotal nitrate uptake in surface waters with chlorophyll biomass<2 µg L^–1. Estimates of new production computedfrom phytoplankton carbon uptake and f-ratios may be stronglyoverestimated in regions where nitrate uptake by heterotrophicbacteria is high and the biomass of phytoplankton is low.     

Identifying fermenting bacteria in anoxic tidal-flat sediments by a combination of microcalorimetry and ribosome-based stable-isotope probing

A novel approach was developed to follow the successive utilization of organic carbon under anoxic conditions by microcalorimetry, chemical analyses of fermentation products and stable-isotope probing (SIP). The fermentation of (13) C-labeled glucose was monitored over 4 weeks by microcalorimetry in a stimulation experiment with tidal-flat sediments. Based on characteristic heat production phases, time points were selected for quantifying fermentation products and identifying substrate-assimilating bacteria by the isolation of intact ribosomes prior to rRNA-SIP. The preisolation of ribosomes resulted in rRNA with an excellent quality. Glucose was completely consumed within 2 days and was mainly fermented to acetate. Ethanol, formate, and hydrogen were detected intermittently. The amount of propionate that was built within the first 3 days stayed constant. Ribosome-based SIP of fully labeled and unlabeled rRNA was used for fingerprinting the glucose-degrading species and the inactive background community. The most abundant actively degrading bacterium was related to Psychromonas macrocephali (similarity 99%) as identified by DGGE and sequencing. The disappearance of Desulfovibrio-related bands in labeled rRNA after 3 days indicated that this group was active during the first degradation phase only. In summary, ribosome-based SIP in combination with microcalorimetry allows dissecting distinct phases in substrate turnover in a very sensitive manner.     

Investigation of an acetate-fed denitrifying microbial community by stable isotope probing, full-cycle rRNA analysis, and fluorescent in situ hybridization-microautoradiography

The acetate-utilizing microbial consortium in a full-scale activated sludge process was investigated without prior enrichment using stable isotope probing (SIP). [13C]acetate was used in SIP to label the DNA of the denitrifiers. The [13C]DNA fraction that was extracted was subjected to a full-cycle rRNA analysis. The dominant 16S rRNA gene phylotypes in the 13C library were closely related to the bacterial families Comamonadaceae and Rhodocyclaceae in the class Betaproteobacteria. Seven oligonucleotide probes for use in fluorescent in situ hybridization (FISH) were designed to specifically target these clones. Application of these probes to the sludge of a continuously fed denitrifying sequencing batch reactor (CFDSBR) operated for 16 days revealed that there was a significant positive correlation between the CFDSBR denitrification rate and the relative abundance of all probe-targeted bacteria in the CFDSBR community. FISH-microautoradiography demonstrated that the DEN581 and DEN124 probe-targeted cells that dominated the CFDSBR were capable of taking up [14C]acetate under anoxic conditions. Initially, DEN444 and DEN1454 probe-targeted bacteria also dominated the CFDSBR biomass, but eventually DEN581 and DEN124 probe-targeted bacteria were the dominant bacterial groups. All probe-targeted bacteria assessed in this study were denitrifiers capable of utilizing acetate as a source of carbon. The rapid increase in the number of organisms positively correlated with the immediate increase in denitrification rates observed by plant operators when acetate is used as an external source of carbon to enhance denitrification. We suggest that the impact of bacteria on activated sludge subjected to intermittent acetate supplementation should be assessed prior to the widespread use of acetate in the wastewater industry to enhance denitrification.     

Seasonal carbon allocation to arbuscular mycorrhizal fungi assessed by microscopic examination, stable isotope probing and fatty acid analysis

Background and Aim

Climate change models are limited by lack of baseline data, in particular carbon (C) allocation to – and dynamics within – soil microbial communities. We quantified seasonal C-assimilation and allocation by plants, and assessed how well this corresponds with intraradical arbuscular mycorrhizal fungal (AMF) storage and structural lipids (16:1ω5 NLFA and PLFA, respectively), as well as microscopic assessments of AMF root colonization.

Methods

Coastal Hypochoeris radicata plants were labeled with ¹³CO₂ in February, July and October, and ¹³C-allocation to fine roots and NLFA 16:1ω5, as well as overall lipid contents and AM colonization were quantified.

Results

C-allocation to fine roots and AMF storage lipids differed seasonally and mirrored plant C-assimilation, whereas AMF structural lipids and AM colonization showed no seasonal variation, and root colonization exceeded 80 % throughout the year. Molecular analyzes of the large subunit rDNA gene indicated no seasonal AMF community shifts.

Conclusions

Plants allocated C to AMF even at temperatures close to freezing, and fungal structures persisted in roots during times of low C-allocation. The lack of seasonal differences in PLFA and AM colonization indicates that NLFA analyses should be used to estimate fungal C-status. The implication of our findings for AM function is discussed.     

Pollution,sources, and ecological-health risks of polycyclic aromatic hydrocarbons in coastal waters along coastline of China

Abstract

This study investigated the distribution, sources, and potential risks of polycyclic aromatic hydrocarbons (PAHs) in coastal waters along over 18,000?km of coastline in China. Concentrations of PAHs in coastal waters ranged from 141.99 to 717.72?ng/L. Approximately 84.38% of sampling sites were determined at moderate PAH pollution level. PAHs in coastal waters at most of sampling sites mainly originated from combustion based on characteristic ratios of PAHs. Ecological risks posed by PAHs in coastal waters were evaluated as high level at 59.38% of sampling sites and moderate level at 40.63% of sampling sites although toxic equivalent quotients of PAHs only ranged from 2.86 to 126.52?ng/L benzo[a]pyrene that was not detected at all sampling sites. Maximal cancer risk/hazard quotient of total PAHs in coastal waters for adults and children reached 6.34?×?10^?4/5.85?×?10^?2 and 2.25?×?10^?3/7.72?×?10^?2, respectively. PAHs exerted high cancer risks for children at 31.25% of sampling sites. Health risks posed by PAHs in coastal waters of this study were higher than those of Japan, Belgium, Greece, Italy, Spain, USA, and Australia, but much lower than those of Singapore, Iran, Brazil, and Egypt. These findings indicate that PAH pollution has become a crucial stress affecting the sustainable development of coastal regions.     

Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing

Many bacteria and fungi are known to degrade cellulose in culture, but their combined response to cellulose in different soils is unknown. Replicate soil microcosms amended with [(13)C]cellulose were used to identify bacterial and fungal communities responsive to cellulose in five geographically and edaphically different soils. The diversity and composition of the cellulose-responsive communities were assessed by DNA-stable isotope probing combined with Sanger sequencing of small-subunit and large-subunit rRNA genes for the bacterial and fungal communities, respectively. In each soil, the (13)C-enriched, cellulose-responsive communities were of distinct composition compared to the original soil community or (12)C-nonenriched communities. The composition of cellulose-responsive taxa, as identified by sequence operational taxonomic unit (OTU) similarity, differed in each soil. When OTUs were grouped at the bacterial order level, we found that members of the Burkholderiales, Caulobacteriales, Rhizobiales, Sphingobacteriales, Xanthomonadales, and the subdivision 1 Acidobacteria were prevalent in the (13)C-enriched DNA in at least three of the soils. The cellulose-responsive fungi were identified as members of the Trichocladium, Chaetomium, Dactylaria, and Arthrobotrys genera, along with two novel Ascomycota clusters, unique to one soil. Although similarities were identified in higher-level taxa among some soils, the composition of cellulose-responsive bacteria and fungi was generally unique to a certain soil type, suggesting a strong potential influence of multiple edaphic factors in shaping the community.