Functional succession of bacterioplankton on the basis of carbon source utilization ability by BIOLOG plates

Changes of bacterioplankton diversity in lake water were followed in triplicate, continuous-flow experimental tanks. Most probable numbers (MPN) were obtained for 95 different carbon sources using BIOLOG plates and were used to characterize bacterioplankton diversity. During 70 days of incubation, MPN declined for 15 of the 95 substrates while three of 95 appeared to be newly used, indicating functional succession in the bacterioplankton. Total bacterial cell abundance was constant from day 7 to day 70 of the incubation period. The succession of species composition of phyto- and zooplankton was also observed and suggested some involvement by phyto- and zooplankton species in the changes of bacterioplankton diversity. Thus, BIOLOG-based MPN assays is a simple but sensitive method for characterizing the changes in the bacterioplankton carbon utilization profile and is also useful for tracing the functional succession of bacterioplankton diversity within a community.     

Evidence of septic system failure determined by a bacterial biochemical fingerprinting method

AIMS: To provide evidence of septic system failure by comparing two faecal indicator bacteria, enterococci and Escherichia coli, from defective septic tanks and adjacent creeks. METHODS AND RESULTS: A biochemical fingerprinting method was used to type and compare enterococci and E. coli strains from 39 septic tanks with creek water samples. Phenotypic diversity of enterococci (0.5 +/- 0.3) and E. coli (0.5 +/- 0.3) in septic tanks were significantly lower than those found in water samples (0.8 +/- 0.1, P < 0.0001 for enterococci and 0.9 +/- 0.1, P < 0.0001 for E. coli). Among 1072 enterococci isolates tested from septic tanks, 203 biochemical phenotypes (BPTs) were found of which 98 BPTs from 33 septic tanks were identical to several water samples. Similarly, among 621 E. coli isolates tested from septic tanks, 159 BPTs were found of which 53 BPTs from 26 septic tanks were also identical to water samples. The number of the latter bacteria was significantly (P = 0.01) higher in water samples collected from downstream compared with that of upstream in the study area. A high similarity between the populations of both indicator bacteria was also found between defective septic tanks and downstream water samples further indicating the contamination of both creeks by defective septic systems. CONCLUSIONS: Biochemical fingerprinting of faecal indicator bacteria is a useful and rapid method to provide direct evidence for septic system failure. Combination of both faecal indicator bacteria (enterococci and E. coli) provides a better judgement of the performance of a septic system. SIGNIFICANCE AND IMPACT OF THE STUDY: This study is the first to provide direct evidence of septic system failure by identifying the presence of specific bacterial types in septic tanks and surface waters. Based on our findings, we suggest that the performance evaluation of a septic system should be accompanied by direct analysis of faecal indicator bacteria.     

Island size and bacterial diversity in an archipelago of engineering machines

There is an increasing realization that progress in bacterial ecology can be further advanced by applying theories and models developed in ecology. Consequently, there is a significant need to assess the applicability of such tools, developed specifically for macroorganisms, for investigating the underlying issues that determine bacterial diversity and community assemblage. In this study, we employed the island biogeography species-area model, originally conceived to assess colonization of islands by macroorganisms, to assess bacterial communities colonizing metal-cutting fluids from machines of increasing sump tank size, taking these to be analogous to islands of variable size. This system was selected because it is well studied and compared with other natural bacterial communities has a relatively low (manageable) diversity. Our findings show that island biogeography theory holds for the bacterial communities studied, in that smaller sump tanks contained lower and putatively less stable diversity, and larger sumps had greater diversity and were temporally stable. It was found that the calculated power law indices (i.e. z-values) were similar for all sample sets, and strikingly, typical of those observed in classical ecology. This was not expected as bacteria have significant distinguishing features such as huge population sizes, rapid asexual reproduction and small body size that facilitate dispersal, and are particularly resistant to extinction.     

Monitoring Biolog patterns and r/K-strategists in the intensive culture of Artemia juveniles

Artemia juveniles were cultured under intensive conditions in three series of six tanks at different times. Both plate counts and Biolog GN microtitre plates were used to monitor the microbial community. Repetitions of the Artemia cultures in time revealed significant differences in Biolog patterns and bacterial counts, showing that normal culture practices, including chlorination of the sea water, does not allow control of the associated microbial community. However, the similarity among the Biolog fingerprints of all 18 tanks as determined by the Pearson correlation coefficient was always high. Both observations together indicate that the microbial community which colonizes the culture tanks seems to be determined by both deterministic factors (e.g. salinity, temperature, oxygen concentration, composition of the feed) and stochastic factors (micro-organisms still present in the sea water after chlorination, on the walls of the culture tanks or in the air around the culture tanks). When a high proportion of microbial r -strategists was present in the water at the beginning of the Artemia culture, the smallest differences in Biolog patterns among the tanks of one series throughout the culture period were observed. A parallelism between Artemia rearing success, functional fingerprint of the bacterial community and the proportion of r-strategists present, was observed. This suggests an important role of the bacterial community in the overall Artemia rearing success.     

Thermoduric and Psychrotrophic Organisms on Poorly Cleansed Milking Plants and Farm Bulk Milk Tanks

S ummary . Poorly cleansed pipeline milking plants gave much higher total and thermoduric colony counts than the internal surfaces of refrigerated farm bulk milk tanks, higher counts being recorded for milking plants after circulation cleaning than after cleansing by the acidified boiling water (ABW) method. Psychrotrophic counts were highest for farm milk tanks and lowest for milking plants cleansed by the ABW method. There was much variation in the proportion of thermoduric and psychrotrophic organisms in the total bacterial content of milking plants determined at 30°, thermodurics being much more prevalent in 21% of the rinses and psychrotrophs in 16%. Both groups formed about equal proportions in 9% of the pipeline rinses. The bacterial content of the farm bulk milk tanks was characterized by many psychrotrophs and few thermodurics.     

季节性冻结初期川西亚高山/高山森林土壤细菌多样性

高山/亚高山显著的季节性冻结过程可能对土壤细菌多样性产生重要影响。为了解季节性冻结初期土壤完全冻结前后川西亚高山/高山森林群落土壤细菌多样性变化特征,于2008年11月5日(土壤冻结前期)—11月25日(土壤完全冻结期)期间,采用PCR-DGGE技术同步研究了原始冷杉(Abies faxoniana)林(PF)、针阔混交林(MF)和次生冷杉林(SF)的土壤细菌群落多样性变化特征。土壤完全冻结后,3个森林群落仍然具有较高的土壤细菌多样性。3个森林的土壤细菌类群总数在土壤冻结前表现为MFSFPF,但在土壤完全冻结后表现为PFMFSF。土壤冻结明显降低了土壤细菌多样性,但提高了土壤细菌群落的优势度。冻结作用对土壤细菌群落的影响随着土壤深度增加而降低,随着海拔升高而降低。这些结果表明季节性冻结过程对亚高山/高山森林土壤细菌多样性有着显著的影响,这对深入认识冬季土壤生态过程具有重要意义。     

传统分离培养结合DGGE法检测榨菜腌制过程的细菌多样性

采用传统分离培养和基于16S rRNA 作为分子标记的变性梯度凝胶电泳(Denaturing gradient gel electrophoresis, DGGE)的方法, 分析榨菜腌制过程中不同时期的可培养细菌数量、多样性及其群落结构。结果表明, 用传统分离与分子鉴定方法获得7个属的细菌类群, 其中乳杆菌属(Acidobacterium)是优势菌群, 明串珠菌属(Leuconostoc)是次优势菌群。对通过DGGE方法得到的11条16S rRNA优势条带序列进行了比对, 结果表明明串珠菌属(Leucon     

轮套作对黄瓜根际土壤细菌种群的影响

以黄瓜为试材,采用PCR-DGGE技术研究了小麦、大豆、毛苕子、三叶草和苜蓿与黄瓜轮作及大蒜、毛葱与黄瓜套作对黄瓜根际土壤细菌种群的影响.结果表明:轮套作对黄瓜根际土壤细菌种群的种类、数量和黄瓜产量具有一定的影响,提高了土壤细菌种群多样性指数、均匀度指数和黄瓜产量.对DGGE条带进行测序的结果表明,它们大多与不可培养的细菌种属具有较高的同源性,大多为鞘氨醇杆菌属（Sphingobacterium）和变形细菌纲（Proteobacteria）, High bacterium G+C只在以毛葱为套作作物的黄瓜根际中出现.不同轮套作中细菌种群多样性随黄瓜生育期的变化而变化,在盛瓜期达最高值.以小麦为轮作作物和以毛葱为套作作物的黄瓜轮套作栽培模式最佳.     

Analysis of bacterial community structure in the natural circulation system wastewater bioreactor by using a 16S rRNA gene clone library

A variety of physical and chemical parameters are routinely monitored during operation of the Natural Circulation System, a wastewater purification bioreactor in which only natural materials and no synthetic chemicals are used. However, the microbial community structures existing in the Natural Circulation System have not been well characterized. Thus, bacterial community structure and composition in this system were studied using clone library analysis of 16S ribosomal RNA genes amplified using PCR with universal bacterial primer sets. The PCR products were then subcloned into the pGEM-T vector. Each unique restriction fragment length polymorphism pattern, created by using two pairs of restriction endonucleases, was designated as an operational taxonomic unit (OTU). The Natural Circulation System comprises five tanks, the second and third of which play a major role in the bioreactor. Clone library pro-files and principal component analysis revealed differences in the bacterial community structures of the second (anaerobic chamber) and the third (aerobic chamber) tanks. However, the beta-proteobacteria, Bacteroidetes/ Chlorobi and gamma-proteobacteria groups were dominant in both tanks. Bacterial composition was more complex in the second tank (107 OTUs) than in the third tank (68 OTUs). Of a total of 154 OTUs in the clone libraries, only 21 were common to the two tanks. The results obtained in this study should provide important information for future research into and management of the Natural Circulation System wastewater bioreactor.     

DGGE analysis of 16S rDNA of ammonia-oxidizing bacteria in chemical–biological flocculation and chemical coagulation systems

Microbial community DNA was extracted from activated sludge samples taken from a chemical bioflocculation process and a chemical coagulation process in Shanghai, China. 16S rDNA of ammonia-oxidizing bacteria (AOB)was amplified by nested polymerase chain reaction and fingerprinted by denaturing gradient gel electrophoresis for microbial structure analysis. The Shannon diversity index of each sample was determined. The results indicated that the microbial structure of AOB in chemical bioflocculation process was comparable at two operational conditions. The ammonia-oxidizing bacterial communities were similar in three channels of the chemical bioflocculation process and in three serial tanks in the chemical coagulation process at the same condition. The diversity of microbial structures in the chemical bioflocculation process was higher than in the chemical coagulation process, in which the microbial structure was similar to that in the influent. Although the microbial study provides insights to the nitrification removal, higher microbial diversity of AOB does not necessarily mean higher ammonia oxidization. Molecular analysis should be combined with chemical assays to optimize operational conditions.     

Convergent dynamics of the juvenile European sea bass gut microbiota induced by poly-β-hydroxybutyrate

Poly-β-hydroxybutyrate (PHB) is a bacterial energy and carbon storage compound which exhibits a controlling effect on the gastrointestinal microbiota. Its beneficial activities for aquaculture have already been shown in terms of increased disease resistance and growth performance in a number of studies. However, the action of PHB on the intestinal microbial community in the treated animals has not yet been studied in depth. In this research, the effects of PHB on the microbiota composition in the intestinal tract of juvenile sea bass were examined. It was found that fish cohabiting in the same tank were on average 87% similar regarding the intestinal microbiota. When subjected to the same treatment and environmental conditions but reared in different tanks, the compositions of the enteric communities diverged. The provision of PHB overruled this tank effect by sustaining a microbial core community in the gut that represented 60% of the total bacterial diversity at the highest PHB level of 10%. The microbial community compositions converged between replicate tanks upon supplementation of PHB and were characterized by high dynamics and increased evenness. The results are discussed in the framework of hypotheses that try to relate the intestinal microbial community composition to the health status of the host organisms.     

Configuration of biological wastewater treatment line and influent composition as the main factors driving bacterial community structure of activated sludge

The structure of microbial consortia in wastewater treatment facilities is a resultant of environmental conditions created by the operational parameters of the purification process. In the research, activated sludge from nine Polish wastewater treatment plants (WWTPs) was investigated at a molecular level to determine the impact of the complexity of biological treatment line and the influent composition on the species structure and the diversity of bacterial consortia. The community fingerprints and technological data were subjected to the canonical correspondence and correlation analyses. The number of separated biological processes realized in the treatment line and the presence of industrial wastewater in the influent were the key factors determining the species structure of total and ammonia-oxidizing bacteria in biomass. The N₂O-reducers community composition depended significantly on the design of the facility; the highest species richness of denitrifiers was noted in the WWTPs with separated denitrification tanks. The contribution of industrial streams to the inflow affected the diversity of total and denitrifying bacterial consortia and diminished the diversity of ammonia oxidizers. The obtained data are valuable for engineers since they revealed the main factors, including the design of wastewater treatment plant, influencing the microbial groups critical for the stability of purification processes.     

Bacterioplankton Dynamics in Estuarine Mesocosms: Effects of Tank Shape and Size

Mesocosms provide a powerful tool for investigating bacterial dynamics at small scales; however, even these controlled studies are not exempt from spatial influences. Differences in mesocosm shape and size may have profound effects on the enclosed community since these features may influence the behavior of the system. Studies were conducted in mesocosms of varying dimensions (narrow, deep and wide, shallow tanks) and volumes (0.1, 1, and 10 m3) in an attempt to decipher effects attributable to changes in container size and shape. Both mesocosm volume and shape affected the course of bacterial growth following containment. Bacterial abundance and production were high in both groups of 0.1 m3 tanks and in the large, wide, shallow tanks with the greatest light supply at depth. Differences in bacterial growth between differently shaped tanks (i.e., differing wall area to volume ratios) were observed among equal volume enclosures, with faster growth in the wide/shallow tanks. Light availability, phytoplankton growth, and primary production differed among tanks, and bacterial growth and production were correlated with these properties. During high nutrient conditions, mesocosm volume and shape influenced bacterial growth, possibly because of periphyton growth on walls in small tanks and elevated light levels in wide/shallow tanks. These results suggest the importance of considering container dimensions when designing and interpreting mesocosm experiments and may allow deeper understanding of the fundamental processes underlying patterns observed in the real world.     

Corrosion of aluminum alloy 2024 by microorganisms isolated from aircraft fuel tanks

Microorganisms frequently contaminate jet fuel and cause corrosion of fuel tank metals. In the past, jet fuel contaminants included a diverse group of bacteria and fungi. The most common contaminant was the fungus Hormoconis resinae. However, the jet fuel community has been altered by changes in the composition of the fuel and is now dominated by bacterial contaminants. The purpose of this research was to determine the composition of the microbial community found in fuel tanks containing jet propellant-8 (JP-8) and to determine the potential of this community to cause corrosion of aluminum alloy 2024 (AA2024). Isolates cultured from fuel tanks containing JP-8 were closely related to the genus Bacillus and the fungi Aureobasidium and Penicillium. Biocidal activity of the fuel system icing inhibitor diethylene glycol monomethyl ether is the most likely cause of the prevalence of endospore forming bacteria. Electrochemical impedance spectroscopy and metallographic analysis of AA2024 exposed to the fuel tank environment indicated that the isolates caused corrosion of AA2024. Despite the limited taxonomic diversity of microorganisms recovered from jet fuel, the community has the potential to corrode fuel tanks.     

Effects of two different application methods of Burkholderia ambifaria MCI 7 on plant growth and rhizospheric bacterial diversity

In order to acquire a better understanding of the effects of the different delivery modes of bacterial inoculants on plant growth and on the community structure of rhizosphere bacterial populations, Burkholderia ambifaria MCI 7 (formerly B. cepacia MCI 7) was inoculated into the rhizosphere of maize plants by either seed adhesion or incorporation into soil. Plant growth was evaluated at different inoculum concentrations. The community structure of rhizosphere bacterial populations was evaluated by analysing the restriction patterns of the DNA coding for 16S rRNA amplified by polymerase chain reaction (PCR) (ARDRA) of 745 bacterial isolates. A number of diversity indices (richness, Shannon diversity, evenness and mean genetic distance) were calculated for each bacterial population isolated from control and treated plants according to the concept of the r/K strategy. Moreover, the analysis of molecular variance (AMOVA) method was applied to estimate the genetic differences among the various bacterial populations. Our results showed that the method of application can be an essential element in determining the effects of the inoculant on plant growth. In fact, when applied as a maize seed treatment, B. ambifaria MCI 7 promoted plant growth significantly; on the contrary, when incorporated into soil, the same strain reduced plant growth markedly. As far as the bacterial community structure is concerned, B. ambifaria MCI 7 affected the indigenous microflora of treated plants according to the application method: seed treatment brought about an abrupt decrease in bacterial diversity, whereas incorporation into soil increased bacterial diversity. Moreover, changes in bacterial diversity were limited to r-strategist bacteria. In conclusion, B. ambifaria MCI 7 can act as both a plant growth-promoting rhizobacterium and a deleterious rhizobacterium depending on the inoculation method.     

Effects of environmental conditions on the nitrifying population dynamics in a pilot wastewater treatment plant

The effect of environmental conditions, especially ammonium concentration, on community composition and nitrification activity of nitrifying bacterial biofilms in a pilot wastewater treatment plant was examined. A decreasing ammonium gradient was created when four aerated tanks with suspended carrier material were serially fed with wastewater. Community composition was analysed using fluorescence in situ hybridization (FISH) probes as well as partial 16S rRNA and amoA gene analysis using polymerase chain reaction-denaturating gradient gel electrophoresis (PCR-DGGE) and sequencing. Fluorescence in situ hybridization probes identified at least five ammonia-oxidizing bacterial (AOB) and two nitrite-oxidizing bacterial (NOB) populations. A change in nitrifying community was detected in the tanks, indicating that ammonium was an important structuring factor. Further, we found support for different autoecology within the Nitrosomonas oligotropha lineage, as at least one population within this lineage increased in relative abundance with ammonium concentration while another population decreased. Absolute numbers of AOB and NOB growing in biofilms on the carriers were determined and the cell specific nitrification rates calculated seemed strongly correlated to ammonium concentration. Oxygen could also be limiting in the biofilms of the first tank with high ammonium concentrations. The response of the nitrifying community to increased ammonium concentrations differed between the tanks, indicating that activity correlates with community structure.     

Development of a Bacterial Cell Enrichment Method and its Application to the Community Analysis in Soybean Stems

A method was developed for enriching bacterial cells from soybean stems which was recalcitrant for a culture-independent analysis of bacterial community due to the interference with plant DNA. Stem homogenates were fractionated by a series of differential centrifugations followed by a Nycodenz density gradient centrifugation. The efficiency of bacterial cell enrichment was assessed by ribosomal intergenic spacer analysis (RISA). The intensity and the number of bacterial amplicons of RISA were markedly increased in the DNA extracted from the enriched bacterial cells compared to that in the DNA directly extracted from soybean stems. The phylogenetic diversity of the enriched bacterial cells was evaluated by analyzing a clone library of 16S rRNA gene in comparison with those of the culturable fractions of the enriched and non-enriched stem-associated bacteria, endophytic bacteria, and epiphytic bacteria. The results indicated that the method was able to enrich both endophytic and epiphytic bacteria from soybean stems, and was useful to assess the bacterial diversity based on a 16S rRNA gene clone library. When the sequence data from all clones (1,332 sequences) were combined, 72 operational taxonomic units were affiliated with Proteobacteria (Alpha-, Beta-, and Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes, which also provided the most comprehensive set of data on the bacterial diversity in the aerial parts of soybeans.     

TGGE分析焦化废水处理系统活性污泥细菌种群动态变化及多样性

应用TGGE指纹图谱技术对两个曝气池细菌种群的动态变化及多样性进行了研究。每3d进行1次,共8个监测时期中同一曝气池活性污泥的16SrDNAV3-PCRTGGE指纹图谱基本一致,图谱间的相似性系数(Cs)为100％。同一曝气池不同位点活性污泥的TGGE指纹图谱也完全一致。功能不同曝气池活性污泥TGGE指纹图谱存在差异,Cs为83．3％。对TJ1活性污泥TGGE图谱中9条主要条带回收、扩增、克隆建库,每个条带选4个转化子进行序列分析,结果显示TGGE条带是由序列不同的片段组成。32个序列在97％的相似性下分成16个分类操作单元(OTU),14个OTU与GenBank中已登录的细菌种群的同源性≥97％,2个OTU的同源性为95％和94％。与10个OTU同源性较高的细菌类群是在活性污泥或污染环境分离或发现的,与8个OTU相似的细菌类群目前尚无法分离培养。     

Bacterial diversity and bioaugmentation in floodwater of a paddy field in the presence of the herbicide molinate

This work aimed at studying variations on the diversity and composition of the bacterial community of a rice paddy field floodwater, subjected to conventional management, namely by using the herbicide molinate. The promotion of the herbicide biodegradation either by the autochthonous microbiota or by a bioaugmentation process was also assessed. This study comprehended four sampling campaigns at key dates of the farming procedures (seeding, immediately and 6 days after application of the herbicide molinate, and after synthetic fertilization) and the subsequent physic-chemical and microbiological characterization (pH, DOC and molinate contents, total cells, cultivable bacteria and DGGE profiling) of the samples. Multivariate analysis of the DGGE profiles showed temporal variations in the bacterial community structure and the Shannon’s index values indicated that the bacterial diversity reached its minimum at the molinate application day. The highest bacterial diversity coincided with the periods with undetectable concentrations of the herbicide, although microcosm assays suggested that other factors than molinate may have been responsible for the decrease of the bacterial diversity. The ability of autochthonous microorganisms to degrade molinate and the influence of the herbicide on the bacterial community composition were assessed in microcosm assays using floodwater collected at the same dates. Given molinate was not degraded by autochthonous microorganisms, and considering it represents an environmental contaminant, bioaugmentation microcosms were assayed aiming the assessment of the feasibility of a bioremediation process to clean contaminated floodwater. A molinate-mineralizing culture, previously isolated, promoted molinate removal, induced alterations in the autochthonous bacterial community structure and diversity, and was undetected after 7 days of incubation, suggesting the feasibility of the process.     

The differentiation of bacterial isolates encountered in fieldwork

A numerical value for each isolate is obtained by adding the appropriate value for each positive test given by each organism.

The advantages and disadvantages of the method compared with more conventional methods of bacterial identification are discussed and some modifications or improvements are suggested. This simplified approach is presented as being suitable for obtaining information about the diversity of bacterial types on student fieldwork.