The maturing of microbial ecology.

A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.     

Molecular evolution: concepts and the origin of disciplines

This paper focuses on the consolidation of Molecular Evolution, a field originating in the 1960s at the interface of molecular biology, biochemistry, evolutionary biology, biophysics and studies on the origin of life and exobiology. The claim is made that Molecular Evolution became a discipline by integrating different sorts of scientific traditions: experimental, theoretical and comparative. The author critically incorporates Timothy Lenoir’s treatment of disciplines (1997), as well as ideas developed by Stephen Toulmin (1962) on the same subject. On their account disciplines are spaces where the social and epistemic dimensions of science are deeply and complexly interwoven. However, a more detailed account of discipline formation and the dynamics of an emerging disciplinary field is lacking in their analysis. The present essay suggests focusing on the role of scientific concepts in the double configuration of disciplines: the social/political and the epistemic order. In the case of Molecular Evolution the concepts of molecular clock and informational molecules played a central role, both in differentiating molecular from classical evolutionists, and in promoting communication between the different sorts of traditions integrated in Molecular Evolution. The paper finishes with a reflection on the historicity of disciplines, and the historicity of our concepts of disciplines.     

Microbial landscapes on the outer tissue surfaces of the reef-building coral <Emphasis Type="Italic">Porites compressa</Emphasis>

Microbial-coral interactions are increasingly recognized as important for coral health and disease. Visualizing these interactions is important for understanding where, when, and how the coral animal and microbes interact. Porites compressa, preserved using Parducz fixative and examined by scanning electron microscopy, revealed a changing microbial landscape. The external cell layers of this coral were invariably clean of directly adhering microbes, unlike coral-associated mucus. In colonies with expanded polyps, secreted mucus rapidly dissipated, although blobs of new mucus were common; the coral epidermal cells expressed cilia, which are presumably used to clean the surface, and coral-associated microbes were present as flocs, possibly enmeshed in mucus. In colonies with permanently contracted polyps, the coral epidermis had lost cilia and a stable, multi-lamellar mucous sheet covered the surface of the animal. This sheet became heavily colonized by both prokaryotic and eukaryotic microbes, however these microbes did not penetrate the mucous sheet and the animal’s epidermal cell surfaces remained sterile. These observations show that relationships between this coral animal and associated microbes are highly dynamic.     

Probing the Topological Properties of Complex Networks Modeling Short Written Texts

In recent years, graph theory has been widely employed to probe several language properties. More specifically, the so-called word adjacency model has been proven useful for tackling several practical problems, especially those relying on textual stylistic analysis. The most common approach to treat texts as networks has simply considered either large pieces of texts or entire books. This approach has certainly worked well—many informative discoveries have been made this way—but it raises an uncomfortable question: could there be important topological patterns in small pieces of texts? To address this problem, the topological properties of subtexts sampled from entire books was probed. Statistical analyses performed on a dataset comprising 50 novels revealed that most of the traditional topological measurements are stable for short subtexts. When the performance of the authorship recognition task was analyzed, it was found that a proper sampling yields a discriminability similar to the one found with full texts. Surprisingly, the support vector machine classification based on the characterization of short texts outperformed the one performed with entire books. These findings suggest that a local topological analysis of large documents might improve its global characterization. Most importantly, it was verified, as a proof of principle, that short texts can be analyzed with the methods and concepts of complex networks. As a consequence, the techniques described here can be extended in a straightforward fashion to analyze texts as time-varying complex networks.     

土地整治的生态环境效应:作用机制及应用路径

随着生态文明理念的不断落实和土地多功能管理的转型,土地整治的生态化发展开始进入全面创新与实践探索的关键时期.系统梳理土地整治的生态环境效应理论研究与实践探索的发展过程,明确“新时代”下学科研究的服务方向和实施路径,对于实施“生态化”土地整治战略非常重要.本文以2000年以来国内外有关土地整治生态环境效应的文献为分析对象,采用Citespace 1.0软件的文献计量分析及文献归纳方法,对土地整治的生态环境效应研究热点进行识别,并从生态环境要素、生态景观、生态系统服务3个方面总结并提炼了土地整治生态环境影响的作用机制.在此基础上,从区域生态系统服务水平测度及障碍因子诊断、土地整治对区域生态系统服务的影响效应及其机制、基于生态系统服务提升的生态化土地整治模式构建等方面提出未来“生态化”土地整治的应用路径,旨在为我国“山水林田湖草”生命共同体的修复与建设提供科学依据.     

Smartphones and tablets: Reshaping radiation oncologists’ lives

BackgroundSmartphones and tablets are new handheld devices always connected to an information source and capable of providing instant updates, they allow doctors to access the most updated information and provide decision support at the point of care.AimThe practice of radiation oncology has always been a discipline that relies on advanced technology. Smartphones provide substantial processing power, incorporating innovative user interfaces and applications.Materials and methodsThe most popular smartphone and tablet app stores were searched for “radiation oncology” and “oncology” related apps. A web search was also performed searching for smartphones, tablets, oncology, radiology and radiation oncology.ResultsSmartphones and tablets allow rapid access to information in the form of podcasts, apps, protocols, reference texts, recent research and more.ConclusionWith the rapidly changing advances in radiation oncology, the trend toward accessing resources via smartphones and tablets will only increase, future will show if this technology will improve clinical care.     

Life's unity and flexibility: the ecological link.

The small size, ubiquity, metabolic versatility and flexibility, and genetic plasticity (horizontal transfer) of microbes allow them to tolerate and quickly adapt to unfavorable and/or changing environmental conditions. Prokaryotes are endowed with sophisticated cellular envelopes that contain molecules not found elsewhere in the biological world. Although prokaryotic cells lack the organelles that characterize their eukaryotic counterparts, their interiors are surprisingly complex. Prokaryotes sense their environment and respond as individual cells to specific environmental challenges; but prokaryotes also act cooperatively, displaying communal activities. In many microbial ecosystems, the functionally active unit is not a single species or population (clonal descendence of the same bacterium) but a consortium of two or more types of cells living in close symbiotic association. Only recently have we become aware that microbes are the basis for the functioning of the biosphere. Thus, we are at a unique time in the history of science, in which the interaction of technological advances and the exponential growth in our knowledge of the present microbial diversity will lead to significant advances not only in microbiology but also in biology and other sciences in general.     

The emergence of ecological engineering as a discipline

Pioneering efforts in ecological engineering (a precedent setting engineering and applied science discipline in which the self-engineering capabilities of ecosystems are managed for the benefit of the environment and humankind) research and practice have proven to be tremendous strides toward establishing a new engineering discipline with a science base in ecology. Case studies, demonstrations and applications pertaining to restoration, rehabilitation, conservation, sustainability, reconstruction, remediation and reclamation of ecosystems using ecological engineering techniques are numerous. This has brought the field to the current level where many scientists and engineers adequately support the concept of, and need for, ecological engineering, and generally agree that ecological engineering has been sufficiently defined. There is also general agreement that full emergence as an engineering discipline remains a difficult task. Certain general characteristics of existing engineering disciplines can guide the emergence of ecological engineering and thus are a vital context covered in this paper. From the context of engineering practice, three concepts are evident including: (1) establishment of formal foundations for ecological engineering research and development; (2) development of core ecological engineering sciences and curricula; and (3) certification in ecological design. These elements are important components of a formal approach to develop ecological engineering as a principled, quantitative, recognized, practical, novel, and formal engineering discipline that coalesces past and future research and practice into cohesive underpinnings.     

The era of microbiology: a golden phoenix.

The discoveries over the last decade have demonstrated that microbiology is a central scientific discipline with practical applications in agriculture, medicine, bioremediation, biotechnology, engineering, and other fields. It is clear that the roles of microbes in nature are so diverse that the process of mining this genetic variation for new applications will continue long into the future. Moreover, the rapid rate of microbial evolution ensures that there will be no permanent solution to agricultural, medical, or environmental problems caused by microbes. These problems will demand a continual stream of creative new approaches that evolve along with the microbes. Thus, the excitement of this field will continue long into the future. However, these opportunities and imperatives demand a deep understanding of basic microbial physiology, genetics, and ecology. Major challenges that lay ahead are to impart the broad training needed to entice and enable the next generation of microbiologists, and to educate the public and government representatives about the continued and critical importance of this field for health and the economy.     

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

Microbes are the unseen majority in soil and comprise a large portion of life's genetic diversity. Despite their abundance, the impact of soil microbes on ecosystem processes is still poorly understood. Here we explore the various roles that soil microbes play in terrestrial ecosystems with special emphasis on their contribution to plant productivity and diversity. Soil microbes are important regulators of plant productivity, especially in nutrient poor ecosystems where plant symbionts are responsible for the acquisition of limiting nutrients. Mycorrhizal fungi and nitrogen-fixing bacteria are responsible for c. 5–20% (grassland and savannah) to 80% (temperate and boreal forests) of all nitrogen, and up to 75% of phosphorus, that is acquired by plants annually. Free-living microbes also strongly regulate plant productivity, through the mineralization of, and competition for, nutrients that sustain plant productivity. Soil microbes, including microbial pathogens, are also important regulators of plant community dynamics and plant diversity, determining plant abundance and, in some cases, facilitating invasion by exotic plants. Conservative estimates suggest that c. 20 000 plant species are completely dependent on microbial symbionts for growth and survival pointing to the importance of soil microbes as regulators of plant species richness on Earth. Overall, this review shows that soil microbes must be considered as important drivers of plant diversity and productivity in terrestrial ecosystems.     

Naked in the Old and the New World: Differences and Analogies in Descriptions of European and American <Emphasis Type="BoldItalic">herbae nudae</Emphasis> in the Sixteenth Century

The sixteenth century could be understand as a period of renaissance of interest in nature and as a period of development of natural history as a discipline. The spreading of the printing press was connected to the preparation of new editions of Classical texts and to the act of correcting and commenting on these texts. This forced scholars to confront texts with living nature and to subject it to more careful investigation. The discovery of America uncovered new horizons and brought new natural products, which were exotic and unknown to Classical tradition. The aim of this study is to compare strategies and categories, which were used in describing plants of the Old and the New World. Attention will be paid to the first reactions to the new flora, to the methods of naming and describing plants, to the ways of gaining knowledge about plants from local sources or by means of one’s own observation. The confrontation with novelty puts naturalists in the Old World and in the New World in a similar situation. It reveals the limits of traditional knowledge based on Classical authorities. A closer investigation, however, brings to light not only the sometimes unexpected similarities, but also the differences which were due to the radical otherness of American plants.     

Impact of genomics on microbial food safety

Genome sequences are now available for many of the microbes that cause food-borne diseases. The information contained in pathogen genome sequences, together with the development of themed and whole-genome DNA microarrays and improved proteomics techniques, might provide tools for the rapid detection and identification of such organisms, for assessing their biological diversity and for understanding their ability to respond to stress. The genomic information also provides insight into the metabolic capacity and versatility of microbes; for example, specific metabolic pathways might contribute to the growth and survival of pathogens in a range of niches, such as food-processing environments and the human host. New concepts are emerging about how pathogens function, both within foods and in interactions with the host. The future should bring the first practical benefits of genome sequencing to the field of microbial food safety, including strategies and tools for the identification and control of emerging pathogens.     

森林凋落物研究进展

对森林凋落物的概念、研究方法及主要研究内容作了阐述,特别就凋落物收集面积和分解袋孔径大小、凋落量时空动态和凋落物分解速率等问题进行了综合分析。目前森林凋落物研究的重要结论有：海拔和纬度因子是通过对光、温、水等生态因子的再分配来影响凋落量,其中主导气候因子是年均温。凋落物的分解与化学组成和环境因子有关,C／N和N含量在凋落物分解过程中起着重要作用。土壤水分是影响凋落物分解主要环境因子之一;土壤微生物对凋落物的影响,前期是通过真菌破碎凋落物表层使内居性动物得以侵入凋落物内部,后期则以细菌降解有机物为主。凋落量、凋落物分解的影响因子,以及凋落物的生态作用等内容应是凋落物研究的重要方向。     

The relativity of Darwinian populations and the ecology of endosymbiosis

If there is a single discipline of science calling the basic concepts of biology into question, it is without doubt microbiology. Indeed, developments in microbiology have recently forced us to rethink such fundamental concepts as the organism, individual, and genome. In this paper I show how microorganisms are changing our understanding of natural aggregations and develop the concept of a Darwinian population to embrace these discoveries. I start by showing that it is hard to set the boundaries of a Darwinian population, and I suggest thinking of a Darwinian population as a relative property of a Darwinian individual. Then I argue, in contrast to the commonly held view, that Darwinian populations are multispecies units, and that in order to accept the multispecies account of Darwinian populations we have to separate fitness from natural selection. Finally, I show how all these ideas provide a theoretical framework leading to a more precise understanding of the ecology of endosymbiosis than is afforded by poetic metaphors such as ‘slavery’.     

Biofilms.

Outside of the laboratory, most microbes grow as organised biofilm communities on surfaces. The past year has seen important advances in our understanding of how cells initiate biofilm formation. We have also begun to appreciate how cells can co-ordinate their activities and build the complex structures of mature biofilms that afford protection for their inhabitants.     

100th anniversary of Robert Koch's Nobel Prize for the discovery of the tubercle bacillus

The year 2005 marks the 100th anniversary of Robert Koch's Nobel Prize. Here, we describe the scientific career of Robert Koch, the discoverer of the etiologic agent of tuberculosis but also of those of anthrax, cholera and wound infections. Equally important, Koch developed the methodologies and concepts that made medical microbiology a scientific discipline. Despite great efforts, however, Koch failed to conquer tuberculosis, which still causes enormous health problems worldwide 100 years after his Nobel award.     

On Achieving Balance

In a rapidly changing world, the question concerning the “right” balance between modeling and empirical work has never been more important. But achieving that balance is not just a matter of student training—it involves examining the incentives in, and structures of, the discipline as a whole.     

George Gaylord Simpson as mentor and apologist for paleoanthropology

The influence of George Gaylord Simpson (1902–1984) on paleoanthropology provides a well-documented, historical example of how one scientific discipline can impact upon another, bringing the latter quickly “up to speed” without having to retrace ground covered by the former. Paleoanthropologists were bystanders during the formulation of the evolutionary synthesis (1936–1947). After World War II, the younger paleoanthropologists looked to George Gaylord Simpson as one of several mentors regarding the implications of the synthesis for their own discipline. But why Simpson? Having earlier defined the superfamily Hominoidea (1931) as holding the Pongidae and Hominidae and monographed lower primate fossils (e.g., “Studies on the earliest primates,” 1940), Simpson's “Principles of classification and a classification of mammals” (1945) further solidified his reputation as a mammalian systematist. Simpson's Meaning of Evolution (1949) was widely read as an introduction to the synthesis, and his Tempo and Mode in Evolution (1944) made accessible the more complex aspects. Consequently, in the 1950s and 1960s paleoanthropologists invited Simpson to participate in their symposia (e.g., “Some principles of historical biology bearing on human origins,” 1951; “The meaning of taxonomic statements,” 1964), used his books as classroom texts, and cited his publications to support claims for their own work. Later in the 1960s, Simpson moved from mentor to apologist, as the paleoanthropologists were by then familiar with the synthesis and incorporated its theoretical concepts in their interpretations of the many newly discovered hominoid fossils. Simpson now took special care to celebrate these results in his more general, less technical writings, acting as a forceful apologist for the materialistic view of human origins (e.g., “The biological nature of man,” 1966; “The evolutionary concept of man,” 1972). During the 1970s, Simpson's influence waned, and he became just another practitioner at the margin of the discipline. However, anthropologists acknowledged Simpson's earlier impact, for example, when he was invited, yet again, to address them at the 50th anniversary celebration of the American Association of Physical Anthropologists in 1981.     

嗜酸性硫杆菌群体感应系统研究进展

嗜酸性硫杆菌(Acidithiobacillus spp.)是一类重要的极端环境微生物与工业微生物。该类细菌通过氧化硫或亚铁获得电子以固定二氧化碳进行自养生长,是驱动矿山环境酸化和重金属溶出的关键菌群,也是生物冶金等微生物浸出技术中的核心菌群。群体感应(quorum sensing, QS)系统是细菌种内及种间信息交流的重要方式,广泛分布于嗜酸性硫杆菌等化能自养微生物中,比如类似于LuxI/R的AfeI/R系统。系统介绍近年来嗜酸性硫杆菌菌体感应系统研究成果,尤其是在AfeI/R种群分布、生物学功能、调节机制及其应用研究中的新发现与新理论。讨论今后嗜酸性硫杆菌群体感应系统研究的主要方向及需要解决的关键科学问题,以促进极端微生物群体感应系统理论研究的开展与产业应用技术的开发。