细菌生物被膜基质的研究进展

细菌生物被膜(biofilm)附着在生物或者非生物表面,由细菌及其分泌的糖、蛋白质和核酸等多种基质组成的细菌群落,是造成病原细菌持续性感染、毒力和耐药性的重要原因之一.细菌的生物被膜基质由复杂的胞外聚合物(extracellular polymeric substances,EPS)构成,影响生物被膜的结构和功能.本文...     

Identification of early microbial colonizers in human dental biofilm

AIMS: To elucidate the first colonizers within in vivo dental biofilm and to establish potential population shifts that occur during the early phases of biofilm formation. METHODS AND RESULTS: A 'checkerboard' DNA-DNA hybridization assay was employed to identify 40 different bacterial strains. Dental biofilm samples were collected from 15 healthy subjects, 0, 2, 4 and 6 h after tooth cleaning and the composition of these samples was compared with that of whole saliva collected from the same individuals. The bacterial distribution in biofilm samples was distinct from that in saliva, confirming the selectivity of the adhesion process. In the very early stages, the predominant tooth colonizers were found to be Actinomyces species. The relative proportion of streptococci, in particular Streptococcus mitis and S. oralis, increased at the expense of Actinomyces species between 2 and 6 h while the absolute level of Actinomyces remained unaltered. Periodontal pathogens such as Tannerella forsythensis(Bacteroides forsythus), Porphyromonas gingivalis and Treponema denticola as well as Actinobacillus actinomycetemcomitans were present in extremely low levels at all the examined time intervals in this healthy group of subjects. CONCLUSION: The data provide a detailed insight into the bacterial population shifts occurring within the first few hours of biofilm formation and show that the early colonizers of the tooth surface predominantly consist of beneficial micro-organisms. SIGNIFICANCE AND IMPACT OF THE STUDY: The early colonizers of dental plaque are of great importance in the succession stages of biofilm formation and its overall effect on the oral health of the host.     

Influence of Cr3+ on microbial cluster formation in biofilm and on steel corrosion

Pit corrosion of mild steel in seawater increased with Cr³⁺ concentration. SEM observations showed that increasing Cr³⁺ concentration caused microbes in biofilm on the steel surface to aggregate forming clusters. AFM images suggested that pit corrosion occurred largely on the mild steel surface between clusters, and only little corrosion on the surface covered by microbes.     

硫酸盐还原细菌生物被膜的形成与调控研究进展

硫酸盐还原细菌(sulfate-reducing bacteria,SRB)形成的生物被膜是微生物导致金属锈蚀行为的主要原因,同时也是重金属污水微生物修复技术的关键因子。生物被膜形成及调控机制研究对SRB的防治和利用均十分重要。本文综述了近年来SRB生物被膜的研究进展,包括SRB生物被膜的胞外多聚物组成和控制因子,并着重阐述了目前已知的调控因子对SRB生物被膜形成的影响。     

Conduction-based modeling of the biofilm anode of a microbial fuel cell

The biofilm of a microbial fuel cell (MFC) experiences biofilm-related (growth and mass transport) and electrochemical (electron conduction and charger-transfer) processes. We developed a dynamic, one-dimensional, multi-species model for the biofilm in three steps. First, we formulated the biofilm on the anode as a "biofilm anode" with the following two properties: (1) The biofilm has a conductive solid matrix characterized by the biofilm conductivity (kappa(bio)). (2) The biofilm matrix accepts electrons from biofilm bacteria and conducts the electrons to the anode. Second, we derived the Nernst-Monod expression to describe the rate of electron-donor (ED) oxidation. Third, we linked these components using the principles of mass balance and Ohm's law. We then solved the model to study dual limitation in biofilm by the ED concentration and local potential. Our model illustrates that kappa(bio) strongly influences the ED and current fluxes, the type of limitation in biofilm, and the biomass distribution. A larger kappa(bio) increases the ED and current fluxes, and, consequently, the ED mass-transfer resistance becomes significant. A significant gradient in ED concentration, local potential, or both can develop in the biofilm anode, and the biomass actively respires only where ED concentration and local potential are high. When kappa(bio) is relatively large (i.e., > or =10(-3) mS cm(-1)), active biomass can persist up to tens of micrometers away from the anode. Increases in biofilm thickness and accumulation of inert biomass accentuate dual limitation and reduce the current density. These limitations can be alleviated with increases in the specific detachment rate and biofilm density.     

Molecular survey of concrete sewer biofilm microbial communities

The microbial composition of concrete biofilms within wastewater collection systems was studied using molecular assays. SSU rDNA clone libraries were generated from 16 concrete surfaces of manholes, a combined sewer overflow, and sections of a corroded sewer pipe. Of the 2457 sequences analyzed, α-, β-, γ-, and δ-Proteobacteria represented 15%, 22%, 11%, and 4% of the clones, respectively. β-Proteobacteria (47%) sequences were more abundant in the pipe crown than any of the other concrete surfaces. While 178 to 493 Operational Taxonomic Units (OTUs) were associated with the different concrete samples, only four sequences were shared among the different clone libraries. Bacteria implicated in concrete corrosion were found in the clone libraries while archaea, fungi, and several bacterial groups were also detected using group-specific assays. The results showed that concrete sewer biofilms are more diverse than previously reported. A more comprehensive molecular database will be needed to better study the dynamics of concrete biofilms.     

Membrane biofouling characterization: effects of sample preparation procedures on biofilm structure and the microbial community

Ensuring the quality and reproducibility of results from biofilm structure and microbial community analysis is essential to membrane biofouling studies. This study evaluated the impacts of three sample preparation factors (ie number of buffer rinses, storage time at 4°C, and DNA extraction method) on the downstream analysis of nitrifying biofilms grown on ultrafiltration membranes. Both rinse and storage affected biofilm structure, as suggested by their strong correlation with total biovolume, biofilm thickness, roughness and the spatial distribution of EPS. Significant variations in DNA yields and microbial community diversity were also observed among samples treated by different rinses, storage and DNA extraction methods. For the tested biofilms, two rinses, no storage and DNA extraction with both mechanical and chemical cell lysis from attached biofilm were the optimal sample preparation procedures for obtaining accurate information about biofilm structure, EPS distribution and the microbial community.     

Biodiversity and species competition regulate the resilience of microbial biofilm community

The relationship between biodiversity and ecosystem stability is poorly understood in microbial communities. Biofilm communities in small bioreactors called microbial electrolysis cells (MEC) contain moderate species numbers and easy tractable functional traits, thus providing an ideal platform for verifying ecological theories in microbial ecosystems. Here, we investigated the resilience of biofilm communities with a gradient of diversity, and explored the relationship between biodiversity and stability in response to a pH shock. The results showed that all bioreactors could recover to stable performance after pH disturbance, exhibiting a great resilience ability. A further analysis of microbial composition showed that the rebound of Geobacter and other exoelectrogens contributed to the resilient effectiveness, and that the presence of Methanobrevibacter might delay the functional recovery of biofilms. The microbial communities with higher diversity tended to be recovered faster, implying biofilms with high biodiversity showed better resilience in response to environmental disturbance. Network analysis revealed that the negative interactions between the two dominant genera of Geobacter and Methanobrevibacter increased when the recovery time became longer, implying the internal resource or spatial competition of key functional taxa might fundamentally impact the resilience performances of biofilm communities. This study provides new insights into our understanding of the relationship between diversity and ecosystem functioning.     

Poly-beta-hydroxy alkanoate and the support of river biofilm metabolism following radical changes in environmental conditions

Endogenous carbon reserves such as poly-beta-hydroxy alkanoate (PHA) can sustain microbial viability during conditions of nutrient deprivation. Microbial extracellular enzyme activities under one set of environmental conditions might be wholly inappropriate for another, and thus PHA might also serve as an energy source as the biofilm acclimates to a changed environment. In order to test this hypothesis, radical changes in environmental conditions were imposed upon river biofilms by transferring them between three rivers of acid, circum-neutral and alkaline pH. The findings supported the hypothesis; each of the transfers resulted in reduced PHA levels, while the physiology of the biofilm (metabolic activity, population density, phosphatase & glucosidase activities) acclimated to the environmental conditions of the recipient site. The greatest PHA depletion was observed when the magnitude of the imposed change resulted in an inability of phosphatase enzyme to respond to the change. The implicit greater dependence on the reserves of PHA, is similarly consistent with the hypothesis.     

生物膜型污水脱氮系统中膜结构及微生物生态研究进展

生物膜法污水脱氮系统主要利用生物膜中脱氮功能微生物的代谢活动去除氮素,从而达到净化水质的目的,研究脱氮生物膜的微观结构和微生物生态是揭示生物膜脱氮机理从而提高脱氮效率的重要途径.本文综述了生物膜型污水脱氮系统类型、生物膜微观结构特征及其影响因素、生物膜型污水脱氮系统内氮素传质过程、脱氮机理和生物膜数学模型等方面的研究进展.另外,本文介绍了生物膜型污水脱氮系统内生物膜脱氮功能微生物分布特征,不同生物膜脱氮系统、底物、运行条件和时间对功能微生物群落影响,及新型脱氮功能微生物等方面的研究进展,为生物膜脱氮技术的深入研究提供参考.     

Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem

Biofilms represent a metabolically active and structurally complex component of freshwater ecosystems. Ephemeral prairie streams are hydrologically harsh and prone to frequent perturbation. Elucidating both functional and structural community changes over time within prairie streams provides a general understanding of microbial responses to environmental disturbance. We examined microbial succession of biofilm communities at three sites in a third‐order stream at Konza Prairie over a 2‐ to 64‐day period. Microbial abundance (bacterial abundance, chlorophyll a concentrations) increased and never plateaued during the experiment. Net primary productivity (net balance of oxygen consumption and production) of the developing biofilms did not differ statistically from zero until 64 days suggesting a balance of the use of autochthonous and allochthonous energy sources until late succession. Bacterial communities (MiSeq analyses of the V4 region of 16S rRNA) established quickly. Bacterial richness, diversity and evenness were high after 2 days and increased over time. Several dominant bacterial phyla (Beta‐, Alphaproteobacteria, Bacteroidetes, Gemmatimonadetes, Acidobacteria, Chloroflexi) and genera (Luteolibacter, Flavobacterium, Gemmatimonas, Hydrogenophaga) differed in relative abundance over space and time. Bacterial community composition differed across both space and successional time. Pairwise comparisons of phylogenetic turnover in bacterial community composition indicated that early‐stage succession (≤16 days) was driven by stochastic processes, whereas later stages were driven by deterministic selection regardless of site. Our data suggest that microbial biofilms predictably develop both functionally and structurally indicating distinct successional trajectories of bacterial communities in this ecosystem.     

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land‐cover change affects belowground carbon storage and nutrient availability. We measured intra‐ and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well‐replicated, long‐term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter‐ and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land‐use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities.     

Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes

Ecosystems worldwide are receiving increasing amounts of reactive nitrogen (N) via anthropogenic activities with the added N having potentially important impacts on microbially mediated belowground carbon dynamics. However, a comprehensive understanding of how elevated N availability affects soil microbial processes and community dynamics remains incomplete. The mechanisms responsible for the observed responses are poorly resolved and we do not know if soil microbial communities respond in a similar manner across ecosystems. We collected 28 soils from a broad range of ecosystems in North America, amended soils with inorganic N, and incubated the soils under controlled conditions for 1 year. Consistent across nearly all soils, N addition decreased microbial respiration rates, with an average decrease of 11% over the year‐long incubation, and decreased microbial biomass by 35%. High‐throughput pyrosequencing showed that N addition consistently altered bacterial community composition, increasing the relative abundance of Actinobacteria and Firmicutes, and decreasing the relative abundance of Acidobacteria and Verrucomicrobia. Further, N‐amended soils consistently had lower activities in a broad suite of extracellular enzymes and had decreased temperature sensitivity, suggesting a shift to the preferential decomposition of more labile C pools. The observed trends held across strong gradients in climate and soil characteristics, indicating that the soil microbial responses to N addition are likely controlled by similar wide‐spread mechanisms. Our results support the hypothesis that N addition depresses soil microbial activity by shifting the metabolic capabilities of soil bacterial communities, yielding communities that are less capable of decomposing more recalcitrant soil carbon pools and leading to a potential increase in soil carbon sequestration rates.     

微生物电解池阳极生物膜功能菌群构建及群落特征分析

【目的】微生物电解电池(MEC)是近几年快速发展的利用电极呼吸微生物快速降解有机质,通过较小的辅助外加电压直接生成氢气的新工艺。MEC能够有效地富集高效率电子传递功能菌群,是未来工艺放大和快速启动的关键。【方法】采用不同驯化方法构建MEC电极微生物菌群,通过单链构象多肽性技术(Single-strand conformation poly-morphism,SSCP)快速检测分析启动后电子传递功能菌群特征。【结果】阳极生物膜接种MEC可以实现2 d的快速启动,库仑效率达到20%以上,7 d获得稳定产氢,氢气转化率达到30%,能量回收效率达到90%以上。通过SSCP群落分析发现,采用微生物燃料电池阳极生物膜构建的MEC主要电子传递功能相关的菌群包括Pseudomonas sp.、Flavobacterium sp.、Ochrobactrum sp.,而直接由产氢MEC阳极生物膜新启动的MEC功能菌群组成丰度更大,包括电子传递效能更高的Desulfovibrio、Pseudomonas和Shewanella成为主要优势电子传递菌群。通过稳定产氢运行,MEC阳极生物膜优势菌群中存在的较大比例的厌氧菌与电子传递辅助菌对体系的快速稳定运行十分重要。【结论】与MFC阳极生物膜相比,MEC生物膜作为启动菌源能够获得多样性更丰富的电极功能菌群,其库仑效率和产氢效率更具优势。     

Flux balancing of light and nutrients in a biofilm photobioreactor for maximizing photosynthetic productivity

This article reports a combined experimental and numerical study on the efficient operation of Porous Substrate Bioreactors. A comprehensive model integrating light transport, mass transport, and algal growth kinetics was used to understand the productivity of photosynthetic biofilms in response to delivery rates of photons and nutrients. The reactor under consideration was an evaporation driven Porous Substrate Bioreactor (PSBR) cultivating the cyanobacteria Anabaena variabilis as a biofilm on a porous substrate which delivers water and nutrients to the cells. In an unoptimized experimental case, this reactor was operated with a photosynthetic efficiency of 2.3%, competitive with conventional photobioreactors. Moreover, through a scaling analysis, the location at which the phosphate delivery rate decreased the growth rate to half of its uninhibited value was predicted as a function of microorganism and bioreactor properties. The numerical model along with the flux balancing techniques presented herein can serve as tools for designing and selecting operating parameters of biofilm based cultivation systems for maximum productivity. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:348–359, 2014     

Effect of bulk liquid BOD concentration on activity and microbial community structure of a nitrifying,membrane-aerated biofilm

Membrane-aerated biofilms (MABs) are an effective means to achieve nitrification and denitrification of wastewater. In this research, microsensors, fluorescence in situ hybridization (FISH), and modeling were used to assess the impact of bulk liquid biological oxygen demand (BOD) concentrations on the activity and microbial community structure of nitrifying MABs. With 1 g m⁻³ BOD in the bulk liquid, the nitrification rate was 1.3 g N m⁻² day⁻¹, slightly lower than the 1.5 g N m⁻² day⁻¹ reported for no bulk liquid BOD. With bulk liquid BOD concentrations of 3 and 10 g m⁻³, the rates decreased to 1 and 0.4 g N m⁻² day⁻¹, respectively. The percent denitrification increased from 20% to 100% when the BOD increased from 1 to 10 g m⁻³ BOD. FISH results indicated increasing abundance of heterotrophs with increasing bulk liquid BOD, consistent with the increased denitrification rates. Modeling was used to assess the effect of BOD on nitrification rates and to compare an MAB to a conventional biofilm. The model-predicted nitrification rates were consistent with the experimental results. Also, nitrification in the MAB was much less sensitive to BOD inhibition than the conventional biofilm. The MAB achieved concurrent nitrification and denitrification, whereas little denitrification occurred in the conventional biofilm.     

Perspectives and predictions on the microbial ecology of the hyporheic zone

1. Studies of hyporheic microbial ecology have suggested an important role for hyporheic microbial processes in stream ecosystem functioning. Using evidence from microbial communities in other aquatic habitats, some predictions are made concerning the diversity of microbial types and microbial processes likely to occur in the hyporheic zone, and the relative importance of these various types to the hyporheic ecosystem. 2. It is predicted that the biofilm growth form of interstitial micro-organisms will create a variety of microniches, allowing coexistence of a great diversity of microbial types, and promoting the activity of some otherwise poor competitors. It is further predicted that the confluence of reduced groundwaters and aerobic surface waters will favour chemolithotrophic processes in the hyporheic zone, but that these will contribute significantly to hyporheic production only if surface water is very low in dissolved organic carbon, or the groundwater is extremely reduced, such as by the influence of riparian wetlands. A variety of anaerobic respiratory pathways, such as nitrate, ferric ion, sulphate and even methanogenic respiration will be employed in the hyporheic zone, with biofilm dynamics permitting these to occur even in aerobic sediments. Anaerobic pathways may account for a significant proportion of total hyporheic organic matter mineralization. 3. The role of fungi in hyporheic dynamics is, as yet, almost completely unstudied. However, it is expected that they will be important in breaking down buried particulate organic matter (POM), which may account for a large proportion of total stream POM. 4. Physicochemical conditions in hyporheic sediments appear to be highly heterogeneous, and this heterogeneity may be very important in the cycling of certain nutrients, especially nitrogen, which involves a series of steps requiring different conditions. 5. Various new techniques are now available by which biofilm dynamics and in situ microbial processes may be measured. Studies are recommended of intact microbial communities both at the microscale of the biofilm and at the scale of the heterogeneities occurring in hyporheic sediments. Studies are needed that measure actual rates of microbial processes under in situ conditions.     

Effect of magnetic hyperthermia on the structure of biofilm and cellular viability of a food spoilage bacterium

This work evaluated the effect of magnetic hyperthermia (MH) on planktonic cells and biofilms of a major food spoilage bacterium Pseudomonas fluorescens and its performance compared to a conventional direct heating (DH) technique. The results showed that MH had a greater and faster bactericidal effect, promoting a significant reduction in cell viability (≥3 Log CFU) in planktonic and biofilm cells, and leading to a complete eradication of planktonic cells at 55 °C (after only ~8 min). Accordingly, when comparing the same final temperatures, MH was more harmful to the integrity of cell membranes than DH, as observed in confocal laser scanning microscope images. Additionally, scanning electron microscope images revealed that exposure to MH had promoted modifications of the bacterial cell surface as well as of the structure of the biofilm. These results present the possibility of using MH out of the biomedical field as a potential disinfection method in food-related environments.