The survival of plant growth promoting microorganisms in peat inoculant as measured by selective plate counting and enzyme-linked immunoassay

Achieving specific counting of plant growth promoting (PGP) microorganisms maintained at high numbers in inert carriers such as peat is an important objective for the inoculation of field crops such as cereals. In this paper, methods based on selective media together with strain-specific counting using enzyme-linked immunoassay (ELISA) were examined. Selective plate counting was developed by screening four commercial PGP biofertiliser strains for resistance to antibiotics. ELISAs for each strain were developed and calibrated by purifying polyclonal antibodies, testing sample pre-treatment strategies, and investigating the effect of culture age on standard curves. Selective plate counting proved to be more accurate than the ELISA methodology, confirming that all microbial strains survived for at least 1 month in sterile peat without loss in viable numbers, and further demonstrated growth inhibition of the strain Candida tropicalis HY when co-inoculated with the other strains Pseudomonas fluorescens 1 N, Bacillus amyloliquefaciens E19 and Bacillus subtilis B9. This is the first known study to have investigated the dynamics of PGP microorganisms in multi-strain inoculants and demonstrates the utility and hitherto unmentioned drawbacks of two different low-cost counting methods for biofertiliser quality control. Such information is vital for the adoption and success of non-rhizobial PGP biofertilisers for sustainable agriculture.     

What,if anything,is a social niche?

The term “social niche” is rapidly increasing in usage, particularly in the context of “social niche construction.” But what (if anything) is a social niche? Here, we survey papers that have used the term to uncover commonalities and discrepancies in its definition. We aim to alert researchers to the need for more consistency in how the term is used in the literature, and we provide a working definition of “social niche:” the set of social environments in which the focal individual has non-zero inclusive fitness. We consider the extent to which a social niche is analogous to an ecological niche, discuss whether a population-level social niche can be meaningfully identified, and describe conceptual insights about the properties of social niches, focusing on social niche construction. We highlight questions about social niches that demand more theoretical and empirical attention.     

Proposal of a comprehensive definition of modified and other forms of mycotoxins including “masked” mycotoxins

As the term “masked mycotoxins” encompasses only conjugated mycotoxins generated by plants and no other possible forms of mycotoxins and their modifications, we hereby propose for all these forms a systematic definition consisting of four hierarchic levels. The highest level differentiates the free and unmodified forms of mycotoxins from those being matrix-associated and from those being modified in their chemical structure. The following lower levels further differentiate, in particular, “modified mycotoxins” into “biologically modified” and “chemically modified” with all variations of metabolites of the former and dividing the latter into “thermally formed” and “non-thermally formed” ones. To harmonize future scientific wording and subsequent legislation, we suggest that the term “modified mycotoxins” should be used in the future and the term “masked mycotoxins” to be kept for the fraction of biologically modified mycotoxins that were conjugated by plants.     

The Obesity Paradox: A Misleading Term That Should Be Abandoned

The term “obesity paradox” is a figure of speech, not a scientific term. The term has no precise definition and has been used to describe numerous observations that have little in common other than the finding of an association of obesity with a favorable outcome. The terminology has led to misunderstandings among researchers and the public alike. It's time for authors and editors to abandon the use of this term. Simply labeling counterintuitive findings as the “obesity paradox” adds no value. Unexpected findings should not be viewed negatively; such findings can lead to new knowledge, better treatments, and scientific advances.     

How can “Super Corals” facilitate global coral reef survival under rapid environmental and climatic change?

Coral reefs are in a state of rapid global decline via environmental and climate change, and efforts have intensified to identify or engineer coral populations with increased resilience. Concurrent with these efforts has been increasing use of the popularized term “Super Coral” in both popular media and scientific literature without a unifying definition. However, how this subjective term is currently applied has the potential to mislead inference over factors contributing to coral survivorship, and the future trajectory of coral reef form and functioning. Here, we discuss that the information required to support a single definition does not exist, and in fact may never be appropriate, i.e. “How Super is Super”? Instead, we advocate caution of this term, and suggest a workflow that enables contextualization and clarification of superiority to ensure that inferred or asserted survivorship is appropriate into future reef projections. This is crucial to robustly unlock how “Super Corals” can be integrated into the suite of management options required to facilitate coral survival under rapid environmental and climate change.     

Is a community still a community? Reviewing definitions of key terms in community ecology

Community ecology is an inherently complicated field, confounded by the conflicting use of fundamental terms. Nearly two decades ago, Fauth et al. (1996) demonstrated that imprecise language led to the virtual synonymy of important terms and so attempted to clearly define four keywords in community ecology; “community,” “assemblage,” “guild,” and “ensemble”. We revisit Fauth et al.'s conclusion and discuss how the use of these terms has changed over time since their review. An updated analysis of term definition from a selection of popular ecological textbooks suggests that definitions have drifted away from those encountered pre‐1996, and slightly disagreed with results from a survey of 100 ecology professionals (comprising of academic professors, nonacademic PhDs, graduate and undergraduate biology students). Results suggest that confusion about these terms is still widespread in ecology. We conclude with clear suggestions for definitions of each term to be adopted hereafter to provide greater cohesion among research groups.     

Qu’est-ce que l’Ivoire ?

What is ivory? Though the term “ivory” has been generally applied to animal dental materials of commercial value, many specialists reserve the term “true ivory” for the enlarged incisors of elephants and extinct proboscideans. Compared even to the check teeth of the same species, these specialized incisors have chemical and structural properties that are unique, and which have substantial implications for the identification, analysis and interpretation of archaeological artifacts made of true ivory. Below, we present a definition of “true ivory” and an overview of its chemical and structural characteristics and the diagnostic features that can be used in its identification.     

TOWARD AN EVOLUTIONARY DEFINITION OF CHEATING

The term “cheating” is used in the evolutionary and ecological literature to describe a wide range of exploitative or deceitful traits. Although many find this a useful short hand, others have suggested that it implies cognitive intent in a misleading way, and is used inconsistently. We provide a formal justification of the use of the term “cheat” from the perspective of an individual as a maximizing agent. We provide a definition for cheating that can be applied widely, and show that cheats can be broadly classified on the basis of four distinctions: (i) whether cooperation is an option; (ii) whether deception is involved; (iii) whether members of the same or different species are cheated; and (iv) whether the cheat is facultative or obligate. Our formal definition and classification provide a framework that allow us to resolve and clarify a number of issues, regarding the detection and evolutionary consequences of cheating, as well as illuminating common principles and similarities in the underlying selection pressures.     

“野生动物”的概念框架和术语定义

“野生动物”(wild animal)一词不止在我国, 在全球的英语使用者中也有不同的含义。通过梳理相关研究、国内法和国际法背景下的定义和适用范围, 结合人类对动物繁殖和生活条件的控制情况, 本文提出了“野生动物”的二维概念框架, 梳理了动物从“野生”到“驯化”的12个连续状态。以下状态即未经中长期人工选择的动物类群应被视为野生动物: (1)其在荒野自然或人工环境(如城市或乡村)中自由生存繁殖, 无论是否存在人工投喂、经救护或辅助生殖后被放归的个体; (2)被捕捉圈养在人工环境中生活, 或源自野外但在圈养条件下出生的个体; (3)直系血亲(《濒危野生动植物种国际贸易公约》解释为世系前四代)仍有野外来源的人工繁育后代; (4)放生、逃逸或引入到自然环境中的人工繁育个体。在野生动物物种保护的目标和语境之下, 经过长期人工选择的驯化动物, 无论其是否在人类控制下生活, 如家养猫狗、家禽家畜或模式实验动物, 以及流浪猫狗、放生禽畜和野化家养动物等都不是“野生动物”。但对于一些经过一定程度的人工选择, 所处人类控制情况和对野外种群的影响各异(如经过多代人工繁育的驯养动物、因人类活动导致的外来动物等), 其是否需被作为野生动物管理, 则需要根据生态安全、物种管理、立法目标等特别设定监管范围。《中华人民共和国野生动物保护法》的保护对象可以考虑为: 受到人类威胁濒临灭绝的, 或者具有重要生态作用的野生动物物种, 其状态可不限于是在野外还是人工控制条件下。其他动物的管理, 可根据遗传资源保护、疫病防控、动物福利和生态安全等需要, 另外设立《动物福利法》《生物安全法》等, 并和已有的法律法规如《动物防疫法》《渔业法》等做好衔接。本文还就《野生动物保护法》可能采用的“野生动物”定义提出建议。     

Synergistic plant-microbes interactions in the rhizosphere: a potential headway for the remediation of hydrocarbon polluted soils

Soil pollution is an unavoidable evil; many crude-oil exploring communities have been identified to be the most ecologically impacted regions around the world due to hydrocarbon pollution and their concurrent health risks. Several clean-up technologies have been reported on the removal of hydrocarbons in polluted soils but most of them are either very expensive, require the integration of advanced mechanization and/or cannot be implemented in small scale. However, “Bioremediation” has been reported as an efficient, cost-effective and environment-friendly technology for clean-up of hydrocarbon”s contaminated soils. Here, we suggest the implementation of synergistic mechanism of bioremediation such as the use of rhizosphere mechanism which involves the actions of plant and microorganisms, which involves the exploitation of plant and microorganisms for effective and speedy remediation of hydrocarbon”s contaminated soils. In this mechanism, plant”s action is synergized with the soil microorganisms through the root rhizosphere to promote soil remediation. The microorganisms benefit from the root metabolites (exudates) and the plant in turn benefits from the microbial recycling/solubilizing of mineral nutrients. Harnessing the abilities of plants and microorganisms is a potential headway for cost-effective clean-up of hydrocarbon”s polluted sites; such technology could be very important in countries with great oil producing activities/records over many years but still developing.     

Optimised separation procedures for the simultaneous assay of three plant hormones in liquid biofertilisers

Introduction – The overuse of petrochemical‐based synthetic fertilisers has caused detrimental effects to soil, water supplies, foods and animal health. This, in addition to increased awareness of organic farming, has generated considerable interest in the evaluation of renewable biofertilisers. Objective – The three objectives of the current research were: (1) to evaluate and optimise a solid phase extraction procedure for extraction of three plant hormones, IAA, GA₃ and ABA from two model biofertilisers produced from coconut shells and pineapple peels; (2) to develop an HPLC analysis procedure for the simultaneous separation and quantification of three plant hormones (IAA, GA₃ and ABA); and (3) to evaluate the changes in three plant hormones levels at four different fermentation time periods and varying number of general bacteria, lactic acid bacteria and yeast. Result – An optimised procedure for sample preparation, separation and simultaneous analysis of three plant hormones [indole‐3‐acetic acid (IAA), gibberellic acid (GA₃) and abscisic acid (ABA)] produced in liquid biofertilisers was developed. This method involves sample cleanup using a Sep‐pack Oasis^®MAX cartridge containing mixed‐mode anion‐exchange and reverse‐phase sorbents that provided optimum recovery of 85.6, 91.9 and 94.3%, respectively, for the three hormones, IAA, GA₃, and ABA. Baseline separation of three hormones was achieved using mobile phase consisting of 1% acetic acid and acetonitrile (75:25, v/v) at pH 4.0. The amounts of hormones produced in liquid biofertilisers were influenced by fruit types, fermentation time and total number of general bacteria, lactic acid bacteria and yeasts. The quantities of three plant hormones produced during fermentation correlated well with the total number of microorganisms present in the liquid biofertilisers. Conclusion – A simple and rapid sample preparation procedure followed by RP‐HPLC with UV detection was optimised and developed for simultaneous quantification and identification of three plant hormones namely, IAA, GA₃ and ABA in the liquid biofertilisers. This procedure allows quantification of the three plant hormones in their natural states without any prior derivatisation step. The results presented illustrate that the contents of the three plant hormones depended on the type of fruit wastes, fermentation time and the number of microorganisms found in liquid biofertilisers. This method can be extended to determine the quantity of three hormones in other matrices. This assay procedure will aid in the development of liquid biofertilisers, a valuable alternative fertilisers to promote plant growth. This process will help farmers to reduce production cost and pollution problems. Copyright © 2009 John Wiley & Sons, Ltd.     

The Cell and Protoplasm as Container,Object, and Substance, 1835–1861

This article revisits the development of the protoplasm concept as it originally arose from critiques of the cell theory, and examines how the term “protoplasm” transformed from a botanical term of art in the 1840s to the so-called “living substance” and “the physical basis of life” two decades later. I show that there were two major shifts in biological materialism that needed to occur before protoplasm theory could be elevated to have equal status with cell theory in the nineteenth century. First, I argue that biologists had to accept that life could inhere in matter alone, regardless of form. Second, I argue that in the 1840s, ideas of what formless, biological matter was capable of dramatically changed: going from a “coagulation paradigm” (Pickstone, 1973) that had existed since Theophrastus, to a more robust conception of matter that was itself capable of movement and self-maintenance. In addition to revisiting Schleiden and Schwann’s original writings on cell theory, this article looks especially closely at Hugo von Mohl’s definition of the protoplasm concept in 1846, how it differed from his primordial utricle theory of cell structure two years earlier. This article draws on Lakoff and Johnson’s theory of “ontological metaphors” to show that the cell, primordial utricle, and protoplasm can be understood as material container, object, and substance, and that these overlapping distinctions help explain the chaotic and confusing early history of cell theory.     

Expanded bed adsorption at production scale: Scale-up verification, process example and sanitization of column and adsorbent

Expanded bed adsorption is a technique for recovery of biomolecules directly from unclarified feedstocks. The work described here demonstrates that expanded bed adsorption is a scaleable technique. The methods used to test scaleability were “determination of degree of bed expansion”, “determination of axial dispersion” and “determination of protein breakthrough capacity”. The performance of a production scale expanded bed column with 600?mm diameter was tested using these methods and the results were found to be consistent with the results obtained from lab scale and pilot scale expanded bed columns. The scaleability and function of the expanded bed technique was also tested by performing a “process example”: a purification mimicking a real process using a yeast culture spiked with bovine serum albumin as feedstock. The results show that the 600?mm diameter production scale column was as efficient as a 25?mm diameter lab scale column in recovering bovine serum albumin from the unclarified yeast culture. The production scale runs were fully automated using a software controlled system containing an adaptor position sensor and an adsorbent sensor. A cleaning study was performed which showed that after use of a proper cleaning protocol, no surviving microorganisms could be detected in the column or in the adsorbent.     

Tree cricket baffles are manufactured tools

Tree crickets use sound to attract mates and make acoustic baffles to increase their sound production efficiency. It has been recently discovered that these insects use a flexible yet inherited behavioural programme to make acoustically optimal baffles. Whether these baffles qualify as tools, however, remains controversial. Here, baffle‐using and baffle‐making behaviours are analysed using the most current and authoritative definition of tool use. The current definition of tool use does not require the tool to be detached from the substrate and includes attached but manipulable external objects. Given this schema, tree cricket baffles, which are attached but manipulated prior to use, must be considered tools. The mode of manufacture for a baffle is “Subtract,” and the mode of use is “Drape”.     

Rhizosphere microbiome: revisiting the synergy of plant-microbe interactions

Sustainable enhancement in food production from less available arable land must encompass a balanced use of inorganic, organic, and biofertilizer sources of plant nutrients to augment and maintain soil fertility and productivity. The varied responses of microbial inoculants across fields and crops, however, have formed a major bottleneck that hinders its widespread adoption. This necessitates an intricate analysis of the inter-relationships between soil microbial communities and their impact on host plant productivity. The concept of “biased rhizosphere,” which evolved from the interactions among different components of the rhizosphere including plant roots and soil microflora, strives to garner a better understanding of the complex rhizospheric intercommunications. Moreover, knowledge on rhizosphere microbiome is essential for developing strategies for shaping the rhizosphere to benefit the plants. With the advent of molecular and “omics” tools, a better understanding of the plant-microbe association could be acquired which could play a crucial role in drafting the future “biofertilizers.” The present review, therefore aims to (a) to introduce the concepts of rhizosphere hotspots and microbiomes and (b) to detail out the methodologies for creating biased rhizospheres for plant-mediated selection of beneficial microorganisms and their roles in improving plant performance.

     

Evaluation of dehydrogenase as a suitable indicator of soil microflora activity

Dehydrogenase activity was determined in a variety of soil samples to assess the assay's suitability as an indicator of soil microorganism activity. This technique, like others in soil ecology, has shortcomings. The work outlined below demonstrates that the dehydrogenase assay can provide a valid indication of soil microorganism activity. Although dehydrogenase activity can be correlated with the numbers of microorganisms isolated, the application of herbicides, which are not greatly toxic to microorganisms, results in a reduction in dehydrogenase activity but little alteration in the number of microorganisms isolated. As this reduction can be accounted for, the use of the assay could be advocated in determining soil microbial activity in ecological investigations.     

When can noise induce chaos and why does it matter: a critique

Noise‐induced chaos illustrates how small amounts of exogenous noise can have disproportionate qualitative impacts on the long term dynamics of a nonlinear system. This property is particularly clear in chaotic systems but is also important for the majority of ecological systems which are nonchaotic, and has direct implications for analyzing ecological time series and testing models against field data. Dennis et al. point out that a definition of chaos which we advocated allows a noise‐dominated system to be classified as chaotic when its Lyapunov exponent λ is positive, which misses what is really going on. As a solution, they propose to eliminate the concept of noise‐induced chaos: chaos “should retain its strictly deterministic definition”, hence “ecological populations cannot be strictly chaotic”. Instead, they suggest that ecologists ask whether ecological systems are strongly influenced by “underlying skeletons with chaotic dynamics or whatever other dynamics”– the skeleton being the hypothetical system that would result if all external and internal noise sources were eliminated. We agree with Dennis et al. about the problem – noise‐dominated systems should not be called chaotic – but not the solution. Even when an estimated skeleton predicts a system's short term dynamics with extremely high accuracy, the skeleton's long term dynamics and attractor may be very different from those of the actual noisy system. Using theoretical models and empirical data on microtine rodent cycles and laboratory populations of Tribolium, we illustrate how data analyses focusing on attributes of the skeleton and its attractor – such as the “deterministic Lyapunov exponent”λ₀ that Dennis et al. have used as their primary indicator of chaos – will frequently give misleading results. In contrast, quantitative measures of the actual noisy system, such as λ, provide useful information for characterizing observed dynamics and for testing proposed mechanistic explanations.