A bunch of tiny individuals—Individual-based modeling for microbes

The individual-based (aka agent-based) approach is now well established in ecological modeling. Traditionally, most applications have been to organisms at higher trophic levels, where the importance of population heterogeneity (intra-population variability), complete life cycles and behavior adapted to internal and external conditions has been recognized for some time. However, advances in molecular biology and biochemistry have brought about an increase in the application of individual-based modeling (IBM) to microbes as well. This literature review summarizes 46 IBM papers for bacteria in wastewater treatment plants, phytoplankton in ocean and inland waters, bacteria in biofilms, bacteria in food and other environs, and “digital organisms” and “domesticated computer viruses” in silico. The use of IBM in these applications was motivated by population heterogeneity (45%), emergence (24%), absence of a continuum (5%), and other unknown reasons (26%). In general, the challenges and concepts of IBM modeling for microbes and higher trophic levels are similar. However, there are differences in the microbe population dynamics and their environment that create somewhat different challenges, which have led to somewhat different modeling concepts. Several topics are discussed, including producing, maintaining and changing population heterogeneity (different life histories, internal variability, positive feedback, inter-generation memory), dealing with very large numbers of individuals (different up-scaling methods, including representative space vs. super-individual, number vs. biomass based, discrete vs. continuous kinetics, various agent accounting methods), handling space, simulating interactions with the extracellular environment (hybrid Eulerian–Lagrangian approach), modeling agent–agent interaction (self-shading, predation, shoving) and passive transport (random walk with spatially variable diffusivity, well-mixed reactors). Overall, the literature indicates that the application of IBM to microbes is developing into a mature field. However, several challenges remain, including simulating various types of agent–agent interactions (formation and function of colonies or filaments, sexual reproduction) and even smaller individuals (viruses, genes). Further increases in intracellular detail and complexity in microbe IBMs may be considered the combination of systems biology and systems ecology, or the new field of systems bioecology.     

Energy dissipation estimates in oscillating grid setup: LDV and PIV measurements

The dissipation of turbulent kinetic energy has been increasingly used as a scaling parameter to integrate microbiological accrual and metabolic rates with fluid-flow motion in natural and engineered aquatic ecosystems. The estimation of turbulent kinetic energy under field conditions and the generation of energy dissipation rates under controlled laboratory conditions with microbiological organisms are necessities required to integrate environmental/ecological laboratory protocols with a moving fluid in the environment. Turbulent fluid-flow conditions were generated in an oscillating grid setup, and turbulence variables were quantified using laser-Doppler velocimetry (LDV) and particle image velocimetry (PIV) measuring techniques. The rate of dissipation of the turbulent kinetic energy in the setup ranged from 10⁻⁹ to 10⁻⁴ m²/s³ and was similar to the levels of energy dissipation commonly reported in engineered and natural aquatic ecosystems. Time-averaged velocities were close to zero with the root-mean-square velocity ratios about 1, indicating nearly isotropic fluid-flow conditions in the setup. The velocity spectra, obtained by stationary LDV measurements for the vertical and horizontal velocity components across the setup revealed the existence of inertial subrange with the frequency power scaling law of “ω ^−5/3.” The estimated Eulerian frequency spectrum followed the theoretical functional relation and confirmed the applicability of inertial dissipation method for the estimation of turbulent kinetic energy dissipation rates. PIV was used for a direct estimation of dissipation by evaluating spatially distributed velocity gradients. The direct dissipation estimate in conjunction with the estimated Eulerian frequency spectrum provided evaluation of a “universal” constant, α, commonly used for the estimation of an energy dissipation rate over the inertial subrange of the Eulerian spectrum. The results demonstrated a range of values, rather than a universal constant, of α with a lognormal probability distribution for vertical and horizontal velocity components. In order to encompass a 0.955 probability range under the lognormal distribution the universal constant, α, should be in the range 2.91 ≥ α _u ≥ 0.43 and 4.44 ≥ α _w ≥ 0.42 for horizontal and vertical velocity components, respectively.     

铅锌矿区土壤微生物区系及酶活性调查

通过对四川省汉源县富泉乡万顺铅锌矿区土壤微生物区系及微生物活性的调查,结果表明,铅锌矿区土壤几种重金属含量明显高于临近非矿区土壤。该矿区土壤微生物区系组成和微生物活性显著不同于临近非矿区土壤,随着重金属含量的增加,土壤微生物数量、微生物多样性指数、微生物生物量碳以及纤维素分解强度均显著降低,但土壤基础呼吸却明显升高;土壤脲酶、碱性磷酸酶、多酚氧化酶对铅锌矿较为敏感,而蔗糖酶和过氧化氢酶受到的抑制作用不明显。     

Incorporating dormancy in dynamic microbial community models

Biogeochemical activity in natural and engineered systems depends on the abundances, functional capabilities and physiological states of the indigenous microorganisms. Typically, only a fraction of the microbial population is active at any given time. As environmental conditions change, previously active microorganisms may switch to an inactive or dormant state, while dormant ones may become active. Here, we present an extended modeling concept for the growth and decay of microorganisms that explicitly accounts for their ability to switch between active and dormant states. The equations describing the switching between physiological states are implemented into a biogeochemical reaction simulator. The model was used to reproduce published data from two laboratory experiments in which microorganisms were subjected to intermittent substrate supply or reactivated after a prolonged period of starvation. Parameter values obtained from the simulation of these experiments were used for subsequent sensitivity analyses and for the simulation of hypothetical scenarios. Results for hypothetical microbial communities consisting of two competing species exposed to periodic feeding imply that, under certain conditions, an effective dormancy-reactivation strategy may have a competitive advantage over a fast growth strategy. That is, organisms that can switch rapidly in response to fluctuations in external conditions may outcompete fast-growing organisms. Furthermore, certain combinations of growth and dormancy strategies may lead to the long-term coexistence of the two competing species. Overall, the simulated population dynamics show that dormancy is an important feature of microbial communities, which can lead to complex responses to environmental fluctuations.     

Synthesis of nanoparticles by microorganisms and their application in enhancing microbiological reaction rates

Nanotechnology has attracted a great interest in recent years due to its expected impact on many areas such as energy, medicine, electronics, and space industries. This review provides the state-of-art knowledge on the synthesis of nanoparticles by microorganisms including bacteria, fungi, actinomycetes, and yeast, and their effect on microbiological processes. The available microbes and their predicted nanoparticle biosynthesis mechanism, the conditions to control the size/shape and monodispersity of particles, and microbiological reaction rate enhancement using nanoparticles as catalysts are presented. The current limitations and future scope for specific research are also discussed.     

有效微生物技术在城市环境治理领域中的应用

随着经济的快速发展,人口数量急剧增长,我国城市水污染及生活垃圾的安全处置问题日益严重,因此找到一种简单、经济的处理方法是目前迫切需要解决的问题。介绍了有效微生物的种群特点以及处理污水的机理,阐述了有效微生物对污水处理效果的影响因素,综述了有效微生物技术在污水处理、河湖富营养化治理、生活垃圾处置等方面的研究现状,并指出了该技术在城市环境治理领域的发展趋势和研究方向。     

利用微生物除臭技术研究与应用

简述了微生物在降解生产和生活中臭气方面的研究与应用,特别着重介绍了EM复合菌群在除臭方面的卓越效果,表明了生物除臭与物理、化学方法除臭相比具有彻底性、实用性与经济性的特点,在环境保护与资源的重复利用方面有着巨大的应用潜力。     

多级曝气-固定化优势微生物强化固定生物膜处理工艺的应用

广州白云山一峰污水处理工程采用了新型污水处理工艺-多级曝气-微生物制剂强化固定生物膜处理工艺,对该工艺的特点及设计体会进行了讨论。设计进水COD、BOD5、SS、NH3-N、TP、动植物油为400～600mg/L、300～400mg/L、250～400mg/L、20～30mg/L、3～5mg/L、70～100 mg/L,出水为90mg/L、20mg/L、10mg/L、10mg/L、0.5mg/L、10 mg/L。实际运行结果表明：主要出水指标COD、BOD5、SS、NH3-N、TP、动植物油的去除率分别可达到88.1%、94.4%、97.9%、88.6%、94.6%、91.5%。该工艺具有占地少、建设成本低、结构简单、施工容易、能耗低、噪声低、运行可靠、稳定达标、剩余污泥极少、运行成本底、维护简便等优点。     

Fate of pathogenic microorganisms and indicators in secondary activated sludge wastewater treatment plants

This study was undertaken to investigate the removal of pathogenic microorganisms and their indicators in a laboratory scale biological treatment system that simulated the secondary treatment process of a wastewater treatment plant (WWTP). Four groups of microorganisms including bacteria, viruses, protozoa and helminths as well as the selected indicators were employed in the investigation. The results demonstrated that approximately 2-3 log10 removal of the microbial indicators was achieved in the treatment process. The log removal of Clostridium perfringens spores was low due to their irreversible adsorption to sludge flocs. The laboratory treatment system demonstrated a similar removal capability for Escherichia coli and the bacterial indicators (total coliforms, enterococci and particles <2.73 microm/L). The MS-2 bacteriophage, measured as a viral indicator, showed a lower removal than poliovirus, which may be considered as a worst case scenario for virus removal. The results of using particle profiling as an indicator for protozoa and helminths appeared to be inaccurate. The removal performance for bacterial and protozoan pathogens and their indicators in a full scale WWTP and the laboratory treatment system was compared.     

Microbial Removal of Arsenic

Bangladesh is currently the subject of the world's largest mass arsenic poisoning in history. Groundwater throughout Bangladesh and West Bengal is contaminated with naturally occurring arsenic from the alluvial and deltaic sediments that form the region's aquifers. It has been estimated that 75 million people are at risk of developing health effects associated with the ingestion of arsenic. This project focuses on the use of microorganisms such as bacteria and algae to remove arsenic from water. Arsenic in the arsenite form was used in the studies. Experiments were conducted with a common alga and wastewater bacteria. A common green algae Scenedesmus abundans was used for determining arsenic uptake in batch experiments. Results of the experiments indicated that the algae biosorption could be modeled by the conventional Langmuir isotherm model. Algae morphology studies indicated that the algae cells were impacted due to the presence of arsenic as evidenced by clumping or loss of cell clusters. The wastewater bacteria also were capable of high percent of arsenic removal. Results indicate that microbial uptake of arsenic may be a viable method of pretreatment of arsenic contaminated water. However algae and sludge disposal would pose a problem and will have to be dealt with accordingly.