Screening environmental samples for source-specific bacteriophage hosts using a method for the simultaneous pouring of 12 petri plates

A simple apparatus was developed to allow 12 petri plates to be poured simultaneously by hand. It was used when screening bacterial isolates from sewage and dog feces for their ability to detect phages from these sources. This was done to assess the ease with which source-specific phage hosts can be isolated from these sources of fecal pollution. Host bacteria that consistently detected phages from sewage were easily isolated from sewage. These bacterial isolates did not detect phages from dog feces. Host bacteria were not isolated from dog feces even after screening hundreds of colonies from fecal samples from six dogs. Journal of Industrial Microbiology & Biotechnology (2000) 24, 124–126. Received 06 July 1999/ Accepted in revised form 05 November 1999     

The coupling of biogeochemical cycles of nutrients

For any element which is incorporated into biomass, the biogeochemical cycle of that element in a given ecosystem will be coupled to that of any other element similarly incorporated. The mutual interaction of two such cycles is examined using a simple model in which each cycle is constrained into four compartments. In each cycle the assimilation rate (primary productivity) is related in a non-linear fashion to the two nutrients and to biomass. The interactions are represented by combining a hyperbolic dependence for each nutrient (involving a "Michaelis constant") with a logistic equation governing the dependence of rate on biomass (involving a "carrying capacity"). The response of the model to perturbation (e.g. mobilization of an abiotic reserve) is strongly governed by the values assigned to these constants. The coupled cycles can exhibit positive feed-back with anomalous responses of the steady state and time-dependent solutions may exhibit complex oscillatory behaviour. Both the steady-state sensitivity and the kinetic behaviour of such coupled systems are simplified if the range of atomic ratios permitted by the assimilation process is restricted. It will therefore be of importance to determine under what conditions the assimilation rates for different elements are governed by mass-action effects (Liebig's Law) or by stoichiometric constraints (Redfield ratios).     

Some improvements in the quality of NAA procedures and the reliability of the results

After considering the need for quality control in NAA, the concept of quality in NAA procedures themselves is discussed, and some important factors identified. Two approaches to improve quality are then described in more detail. The first concerns the unique ability of NAA using different isotopic reactions and different modes (INAA/RNAA) to provide independent data sets in the same laboratory, thus allowing internal validation or crosschecking. The second discusses the need for chemical yield measurements in RNAA and the advantages of the radioisotopic tracer technique. Some recent advances and further possibilities for this use of tracers are listed.     

Didymosphenia geminata invasion in South America: Ecosystem impacts and potential biogeochemical state change in Patagonian rivers

The diatom Didymosphenia geminata has emerged as a major global concern, as both an aggressive invader of rivers and streams in the southern hemisphere, and for its ability to form nuisance blooms in oligotrophic systems in its native range. South American D. geminata blooms were first documented in Chilean Patagonia in May 2010, and have spread to over five regions and three provinces, in Chile and Argentina respectively. The Patagonian invasion represents a distinct challenge compared to other regions; not only are affected systems poorly characterized, but also a general synthesis of the nature and magnitude of ecosystem impacts is still lacking. The latter is essential in evaluating impacts to ecosystem services, forms the basis for a management response that is proportional to the potentially valid threats, or aids in the determination of whether action is warranted or feasible. Based on a revision of the recent literature, some of the most significant impacts may be mediated through physical changes: substantially increased algal biomass, trapping of fine sediment, altered hydrodynamics, and consequent effects on biogeochemical states and processes such as redox condition, pH and nutrient cycling in the benthic zone. Surveys conducted during the early invasion in Chile show a strong correlation between benthic biomass and associated fine sediments, both of which were one–two orders of magnitude higher within D. geminata blooms. Experimental phosphorous amendments showed significant abiotic uptake, while interstitial water in D. geminata mats had nearly 10–20 fold higher soluble reactive phosphorous and a pronounced pH cycle compared to the water column. A dominant and aggressive stalk-forming diatom with this combination of characteristics is in sharp contrast to the colonial cyanobacteria and bare gravel substrate that characterize many Patagonian streams. The potential displacement of native benthic algal communities with contrasting functional groups, increased primary producer biomass, and fine benthic sediment accumulation, all may have a significant effect on stream nutrient cycling and ecosystem function, in Patagonia and elsewhere where nuisance blooms have been reported.     

A guide to metabolic flux analysis in metabolic engineering: Methods,tools and applications

The field of metabolic engineering is primarily concerned with improving the biological production of value-added chemicals, fuels and pharmaceuticals through the design, construction and optimization of metabolic pathways, redirection of intracellular fluxes, and refinement of cellular properties relevant for industrial bioprocess implementation. Metabolic network models and metabolic fluxes are central concepts in metabolic engineering, as was emphasized in the first paper published in this journal, “Metabolic fluxes and metabolic engineering” (Metabolic Engineering, 1: 1–11, 1999). In the past two decades, a wide range of computational, analytical and experimental approaches have been developed to interrogate the capabilities of biological systems through analysis of metabolic network models using techniques such as flux balance analysis (FBA), and quantify metabolic fluxes using constrained-based modeling approaches such as metabolic flux analysis (MFA) and more advanced experimental techniques based on the use of stable-isotope tracers, i.e. ¹³C-metabolic flux analysis (¹³C-MFA). In this review, we describe the basic principles of metabolic flux analysis, discuss current best practices in flux quantification, highlight potential pitfalls and alternative approaches in the application of these tools, and give a broad overview of pragmatic applications of flux analysis in metabolic engineering practice.     

Tracing mangrove carbon in suspended matter and aquatic fauna of the Gautami–Godavari Delta,Bay of Bengal (India)

Stable carbon isotopic composition and C/N ratio were used to trace the input of carbon associated with mangrove litter into the estuary of the Godavari–Gautami delta system and Kakinada bay (Andhra Pradesh, India). Suspended organic matter in the mangrove channels was more depleted in ¹³C (average ¹³C = –24.5) than in Kakinada bay which showed ¹³C values for suspended matter (average ¹³C = –22.7) closer to those expected for marine phytoplankton. Suspended organic matter from mangrove channels was enriched in nitrogen (average C/N atom ratio 12.7) and ¹³C (average ¹³C = –24.5) relative to mangrove leaf litter, which had a C/N ratio of 75 and a ¹³C value of –28. Lowest C/N ratios for suspended matter were observed during southwest monsoon when rainfall was highest. Although in general, mangrove litter fall was also lower during this period, no clear correlation was observed between litter fall and C/N ratio of suspended matter. In general, the composition of suspended matter pointed towards phytoplankton as a major component. Isotopic composition of zooplankton suggested selective feeding on ¹³C-enriched, marine phytoplankton in open Kakinada bay and on ¹³C-depleted organic matter, such as estuarine phytoplankton and mangrove litter, in the mangrove channels. From the ¹³C signature, it appeared that mangrove carbon was present to some extent in zooplankton and macrofauna from the mangrove mudflats and channels, but the signal rapidly decreased in Kakinada bay. Nitrogen isotopic composition of zooplankton and macrofauna indicated a progressive enrichment of ¹⁵N away from the mangrove forest towards the northern part of Kakinada bay, in approach of Kakinada city. This is thought to reflect input of anthropogenic nitrogen enriched in ¹⁵N and subsequent uptake of this enriched nitrogen into the aquatic food chain.     

滇池水-植物系统金属元素的分布特征和相关性研究

对滇池优势水生植物凤眼莲、旱生莲子草、红线草、聚草和茭草及其对应水环境中的Ｋ、Ｎａ、Ｃａ、Ｍｇ、Ｆｅ、Ｍｎ、Ｚｎ、Ｃｕ、Ｐｂ、Ｃｄ进行了化学分析,初步揭示了滇池水－植物系统金属元素的分布特征和关性。结果表明,滇池水域属Ｋ、Ｃａ、Ｍｇ、Ｆｅ高背景生物地球化学区,植物体内金属元素的含量,既与植物种属特性有关,又明显地受环境因素的影响,植物对营养元素的吸收不一定与环境中相应元素的浓度呈简单的线性关系,而     

Relationships between benthic macrofauna and biogeochemical properties of sediments at different spatial scales and among different habitats in mangrove forests

In muddy intertidal sediments, there are reported complex interactions between the biological, physical and chemical properties of the sediment and the benthos that live in and on it. These are expected to be reflected in strong relationships between benthic animals and particular properties of the sediment, although some research has shown these relationships to be relatively weak. This study investigates the relationships between benthic macrofauna and biogeochemical properties of sediments within and among different habitats in multiple mangrove forests in a temperate estuary, in order to address the generality of any such relationships. Matched samples of benthos and sediment were collected from three habitats, which differed with respect to shading, the amounts of algae and leaf litter and the presence of pneumatophores. The sediment was sampled for water content, grain size, organic matter, chlorophylls a and b and colloidal and total carbohydrate.Spatial variation in sediment and benthos were significantly correlated across habitats in two of the three bays, but the sediment properties that contributed to differences between habitats and those that best correlated with the benthos varied among bays. In all bays, the single taxon that best correlated with the sediment was spionid polychaetes, but correlations were generally weak. There was no generality in the patterns of variation among the benthos or sedimentary properties among habitats. The benthos differed significantly among bays in all habitats, with large variation within and among sites. The sediment varied significantly at small scales in all habitats, but significant differences among bays were only found in two habitats. All spatial scales contributed to the total amount of variability in the sediment and there was little predictability from the patterns shown in one habitat to those in other habitats, or from one component of sediment to other components. Such variability suggests that there may be structural redundancy in this fauna, with different components of the benthos contributing to similar functions in different places. Such variability must be considered in experiments designed to understand relationships between ecological structure and function in these complex habitats and in any sampling studies to identify environmental impacts in these habitats.     

A biogeochemical framework for metal detoxification in sulfidic systems

We develop a comprehensive biogeochemical framework for understanding and quantitatively evaluating metals bio-protection in sulfidic microbial systems. We implement the biogeochemical framework in CCBATCH by expanding its chemical equilibrium and biological sub-models for surface complexation and the formation of soluble and solid products, respectively. We apply the expanded CCBATCH to understand the relative importance of the various key ligands of sulfidic systems in Zn detoxification. Our biogeochemical analysis emphasizes the relative importance of sulfide over other microbial products in Zn detoxification, because the sulfide yield is an order of magnitude higher than that of other microbial products, while its reactivity toward metals also is highest. In particular, metal-titration simulations using the expanded CCBATCH in a batch mode illustrate how sulfide detoxifies Zn, controlling its speciation as long as total sulfide is greater than added Zn. Only in the absence of sulfide does complexation of Zn to biogenic organic ligands play a role in detoxification. Our biogeochemical analysis conveys fundamental insight on the potential of the key ligands of sulfidic systems to effect Zn detoxification. Sulfide stands out for its reactivity and prevalence in sulfidic systems.     

Oak trees and soil interactions in Mediterranean forests: a positive feedback model

Questions: What is the spectrum of variability of chemical elements in a Mediterranean forest ecosystem across the different compartments? Do co‐existing tree species with different leaf chemical composition and nutrient cycling distinctly modify soil conditions? Could these species‐specific, tree‐generated soil changes create a potential positive feedback by affecting long‐term species distribution? Location: Mixed oak forests of southern Spain, Los Alcornocales Natural Park. Methods: We sampled and chemically analysed five different ecosystem components: leaves, leaf fall, litter and superficial (0–25 cm) and sub‐superficial (25–50 cm) soil beneath the canopies of evergreen Quercus suber and deciduous Q. canariensis trees. We used multiple co‐inertia analysis (MCoA) to conjointly analyse the patterns of variability and covariation of eight macro‐ and micronutrients determined in each of the sampled ecological materials. We implemented a path analysis to investigate alternative causal models of relationships among the chemical properties of the different ecosystem components. Results: Variability in the concentration of chemical elements was related to the nature of their biogeochemical cycles. However, the rank of element concentration was consistent across ecosystem components. Analysis of co‐inertia (MCoA) revealed that there was a common underlying multivariate pattern of nutrient enrichment in the ecosystem, which supported the hypothesis of a separation in biogeochemical niches between the two co‐existing oak species, with Q. canariensis having richer plant tissues and more fertile soil directly under each tree than Q. suber. The feasibility of a potential tree–soil positive feedback model was the only statistically validated among several alternative (non‐feedback) models tested. Conclusions: In the studied Mediterranean forests, oak species distinctly modify soil fertility conditions through different nutrient return pathways. Further investigation is needed to address whether these tree‐generated soil changes could affect seedling establishment and ultimately influence species distribution.