Bacterial motility: links to the environment and a driving force for microbial physics

Bacterial motility was recognized 300 years ago. Throughout this history, research into motility has led to advances in microbiology and physics. Thirty years ago, this union helped to make run and tumble chemotaxis the paradigm for bacterial movement. This review highlights how this paradigm has expanded and changed, and emphasizes the following points. The absolute magnitude of swimming speed is ecologically important because it helps determine vulnerability to Brownian motion, sensitivity to gradients, the type of receptors used and the cost of moving, with some bacteria moving at 1 mm s(-1). High costs for high speeds are offset by the benefit of resource translocation across submillimetre redox and other environmental gradients. Much of environmental chemotaxis appears adapted to respond to gradients of micrometres, rather than migrations of centimetres. In such gradients, control of ion pumps is particularly important. Motility, at least in the ocean, is highly intermittent and the speed is variable within a run. Subtleties in flagellar physics provide a variety of reorientation mechanisms. Finally, while careful physical analysis has contributed to our current understanding of bacterial movement, tactic bacteria are increasingly widely used as experimental and theoretical model systems in physics.     

Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution

A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or 'fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.     

Molecular evolution in bacteria

Recent advances in microbiology and molecular biology have a unifying influence on our understanding of genetic diversity/similarity and evolutionary relationships in microorganisms. This article attempts to unify information from diverse areas such as microbiology, molecular biology, microbial physiology, clay crystal genes, metals-microbe-clay interactions and bacterial DNA restriction-modification systems (R-M) as they may apply to molecular evolution of bacteria. The possibility is discussed that the first informational molecules may have been catalytic RNA (micro-assembler) not DNA (now the master copy) and these first micro-assemblers may have been precursors of ribosomes.     

寡营养细菌及其生态作用和应用的研究进展

寡营养细菌是自然环境中特别是在寡营养环境中广泛分布的一种细菌,对寡营养生态环境起着至关重要的作用。近年来,随着分子生物学技术的飞速发展,寡营养细菌开始被广泛深入的研究。其分离培养技术,细菌形态特征,在生态中的作用和应用是目前微生物领域和环境科学领域的前沿课题,本文对这几个方面近年来的研究状况进行了综述,并展望了未来的发展趋势。     

Electrical/electrochemical impedance for rapid detection of foodborne pathogenic bacteria

The realization of rapid, sensitive, and specific methods to detect foodborne pathogenic bacteria is central to implementing effective practice to ensure food safety and security. As a principle of transduction, the impedance technique has been applied in the field of microbiology as a means to detect and/or quantify foodborne pathogenic bacteria. The integration of impedance with biological recognition technology for detection of bacteria has led to the development of impedance biosensors that are finding wide-spread use in the recent years. This paper reviews the progress and applications of impedance microbiology for foodborne pathogenic bacteria detection, particularly the new aspects that have been added to this subject in the past few years, including the use of interdigitated microelectrodes, the development of chip-based impedance microbiology, and the use of equivalent circuits for analysis of the impedance systems. This paper also reviews the significant developments of impedance biosensors for bacteria detection in the past 5 years, focusing on microfabricated microelectrodes-based and microfluidic-based Faradaic electrochemical impedance biosensors, non-Faradaic impedance biosensors, and the integration of impedance biosensors with other techniques such as dielectrophoresis and electropermeabilization.     

Native protein mass spectrometry: from intact oligomers to functional machineries

The development of electrospray ionization coupled to mass spectrometry has enabled the analysis of very large intact protein complexes, even when they are held together by weak non-covalent interactions. Together with equally spectacular advances in mass spectrometric instrumentation, a new field has emerged, termed native protein mass spectrometry, which focuses on the structural and functional analysis of the dynamics and interactions occurring in protein complexes. In the past two years, several important progressive steps in technologies have been reported that have led to exciting applications ranging from the detailed study of equilibria between different quaternary structures as influenced by environmental changes or binding of substrates or cofactors, to the analysis of intact nano-machineries, such as whole virus particles, proteasomes and ribosomes.     

Use of flow cytometric methods for single-cell analysis in environmental microbiology

Flow cytometry (FCM) is emerging as an important tool in environmental microbiology. Although flow cytometry applications have to date largely been restricted to certain specialized fields of microbiology, such as the bacterial cell cycle and marine phytoplankton communities, technical advances in instrumentation and methodology are leading to its increased popularity and extending its range of applications. Here we will focus on a number of recent flow cytometry developments important for addressing questions in environmental microbiology. These include (i) the study of microbial physiology under environmentally relevant conditions, (ii) new methods to identify active microbial populations and to isolate previously uncultured microorganisms, and (iii) the development of high-throughput autofluorescence bioreporter assays.     

A Guide to the Natural History of Freshwater Lake Bacteria

Summary: Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.     

Microbial Stabilization and Kinetic Enhancement of Marine Methane Hydrates

Abstract

In clathrate hydrates, a water host lattice encages small guest molecules in cavities. Methane hydrates are the most widespread in-situ clathrate in the permafrost and continental-shelf ocean regions, constituting a significant energy resource, and prompting recent marine-hydrate gas-production trials. Despite exciting engineering advances and a few marine-mimicking laboratory studies of methane-hydrate kinetics and stabilization, from microbial perspectives, little is known about a potential microbial origin of marine hydrates, nor their possible formation kinetics or potential stabilization by microbial sources. Here, for the first time, we show that an exported, extra-cytoplasmic porin – produced by a marine methylotrophic bacterium culture – provides the basis for kinetic enhancement and stabilization of methane hydrates under conditions simulating the seabed environment. We then identify the key protein at play, and we therefore suggest microbe-based stabilization of marine hydrates is evidently a property likely to be found in many marine bacteria. Our research opens the possibility of managing marine-hydrate deposits using microbiological strategies for environmental and societal benefit.     

Ecology of Infectious Disease: Forging an Alliance

The Ecology of Infectious Diseases (EID) program is a joint National Science Foundation–National Institutes of Health initiative to produce predictive understanding of disease dynamics, with a focus on diseases with an environmental component. The interdisciplinary research projects funded by this program take advantage of the wide range of theoretical and methodological advances developed over the past 30 years. The challenge for disease ecology is to unravel these systems, discover how complex they truly are, and to determine if they can be predicted and controlled using targeted environmental, public health, or medical interventions. Between 1999 and 2005, a total of 42 research awards were made under the EID program. EID projects have had affects on policy in two areas: adoption of novel interventions on a local scale and use of models by government agencies for the purpose of allocating public health resources. The past 6 years have been an exciting time for the field of disease ecology; we expect the coming years to be even more exciting and productive. As US federal government employees writing an article as part of our official duties, copyright of all publications is retained by the US government. The views expressed here by Samuel M. Scheiner and Joshua P. Rosenthal are those of the authors and do not represent official views or policies of the National Science Foundation, the National Institutes of Health, or the United States Government.     

Beyond ancient microbial DNA: nonnucleotidic biomolecules for paleomicrobiology

Identifying the causes of past epidemics depends on the specific detection of pathogens in buried individuals; this field of research is known as paleomicrobiology, an emerging field that has benefited from technological advances in microbiology. For almost 15 years, the detection, identification, and characterization of microbes in ancient environmental and human specimens emerged on the basis of ancient DNA (aDNA) analyses. aDNA limitations due to potential contamination by modern DNA and altered aDNA led to the development of alternative methods for the detection and characterization of nonnucleotidic biomolecules, including mycolic acids (of ancient mycobacteria) and proteins. Accordingly, immunohistochemistry, immunochromatography, and enzyme-linked immunosorbent assay techniques have been developed for the specific detection of microbes from ancient human and environmental specimens. Protein analysis by mass spectrometry, a standard for ancient animal identification, has also recently emerged as a technique for ancient mycobacteria detection, while immuno-PCR is yet another promising technique. As with aDNA, strict protocols must be enforced to ensure authenticity of the data. Here we review the analysis of nonnucleotidic biomolecules from ancient microbes and the ability of these analyses to complement aDNA analyses, which opens new opportunities for identification of ancient microbes as well as new avenues to potentially resolve controversies regarding the cause of some historical pandemics and study the coevolution of microbes and hosts.     

How do species interactions affect species distribution models?

One of the most promising recent advances in biogeography has been the increased interest and understanding of species distribution models – estimates of the probability that a species is present given environmental data. Unfortunately, such analyses ignore many aspects of ecology, and so are difficult to interpret. In particular, we know that species interactions have a profound influence on distributions, but it is not usually possible to incorporate this knowledge into species distribution models. What is needed is a rigorous understanding of how unmeasured biotic interactions affect the inferences generated by species distribution models. To fill this gap, we develop a general mathematical approach that uses probability theory to determine how unmeasured biotic interactions affect inferences from species distribution models. Using this approach, we reanalyze one of the most important classes of mechanistic models of competition: models of consumer resource dynamics. We determine how measurements of one aspect of the environment – a single environmental variable – can be used to estimate the probability that an environment is suitable with species distribution models. We show that species distribution models, which ignore numerous facets of consumer resource dynamics such as the presence of a competitor or the dynamics of depletable resources, can furnish useful predictions for the probability that an environment is suitable in some circumstances. These results provide a rigorous link between complex mechanistic models of species interactions and species distribution models. In so doing they demonstrate that unmeasured biotic interactions can have strong and counterintuitive consequences on species distribution models.     

Microgeographical diversification of threespine stickleback: body shape–habitat correlations in a small, ecologically diverse Alaskan drainage

Adaptive radiations are a major source of evolutionary diversity in nature, and understanding how they originate and how organisms diversify during the early stages of adaptive radiation is a major problem in evolutionary biology. The relationship between habitat type and body shape variation was investigated in a postglacial radiation of threespine stickleback in the upper Fish Creek drainage of Cook Inlet, Alaska. Although small, the upper Fish Creek drainage includes ecologically diverse lakes and streams in close proximity to one another that harbour abundant stickleback. Specimens from ancestral anadromous and derived resident freshwater populations differed substantially and could be distinguished by body shape alone, suggesting that the initial stages of adaptation contribute disproportionately to evolutionary divergence. Body shape divergence among resident freshwater populations was also considerable, and phenotypic distances among samples from freshwater populations were associated with habitat type but not geographical distance. As expected, stream stickleback from slow-moving, structurally complex environments tended to have the deepest bodies, stickleback from lakes with a mostly benthic habitat were similar but less extreme, and stickleback from lakes with a mostly limnetic habitat were the most shallow-bodied, elongate fish. Beyond adapting rapidly to conditions in freshwater environments, stickleback can diversify rapidly over small geographical scales in freshwater systems despite opportunities for gene flow. This study highlights the importance of ecological heterogeneity over small geographical scales for evolutionary diversification during the early stages of adaptive radiation, and lays the foundation for future research on this ecologically diverse, postglacial system.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 139–151.     

Gene array technology to determine host responses to Salmonella.

Gene expression array technology is a powerful new tool that has already been used to expand our understanding of host-pathogen interactions. There has been a rapid increase in published reports describing use of this approach to profile host responses to pathogenic bacteria and viruses. The large number of array studies currently in progress coupled with increasing accessibility of this new technology promises a plethora of gene expression data on host response to infection in the near future. Recent insights into macrophage and epithelial cell responses to Salmonella infection garnered from array studies are outlined and used as a basis to discuss various future research directions using gene arrays that will advance the field of cellular microbiology. There is an exciting potential for the gene expression data generated in such studies to provide insights into host physiology, the pathophysiology of disease and novel therapeutics.     

Genomics-fueled approaches to current challenges in marine ecology

As a result of recent advances in genomic technology, a 'tool set' is emerging that can be used by marine ecologists to gain new perspectives on central questions in the field. Techniques such as gene expression profiling using DNA microarrays, when placed in an ecological context, stand to advance greatly our understanding of how organisms respond to abiotic and biotic stresses. Here, we target areas in which adding genomics to ecological and physiological investigations will significantly advance our understanding of crucial issues ranging from the general biological effects of environmental temperature changes on individuals and communities to the interactions between symbionts in coral bleaching. At a time when both short- and long-term perturbations of marine ecosystems are increasing in severity, this kind of integrative approach could generate new and exciting hypotheses about the functioning of marine organisms and communities.     

Respiration response imaging for real-time detection of microbial function at the single-cell level

The ability to detect specific functions of uncultured microbial cells in complex natural communities remains one of the most difficult tasks of environmental microbiology. Here we present respiration response imaging (RRI) as a novel fluorescence microscopy-based approach for the identification of microbial function, such as the ability to use C(1) substrates, at a single-cell level. We demonstrate that RRI could be used for the investigation of heterogeneity of a single microbial population or for functional profiling of microbial cells from complex environmental communities, such as freshwater lake sediment.     

Microbial endocrinology and infectious disease in the 21st century

More than 70 years ago, a new age in endocrinology was just beginning with the first purification of a hormone, adrenaline. As early as 1930, almost immediately following its first use, cases of adrenaline-associated sepsis were reported. From this time, there have been reports associating the elaboration of neuroendocrine hormones, such as adrenaline, with infectious disease. The most widely accepted theory to explain the ability of hormones to influence the course of infection involves the suppression of the immune system. The theory that the infectious microorganism itself might be equally responsive to the host's neuroendocrine environment has not been considered. It is the intent of this article to introduce a new perspective to the current understanding of the factors that mediate the ability of bacteria to cause disease, and to demonstrate that neuroendocrinology and microbiology intersect to form the interdisciplinary field of microbial endocrinology.     

Conservation of Aquatic Resources through the Use of Freshwater Protected Areas: Opportunities and Challenges

Freshwater environments are currently experiencing an alarming decline in biodiversity. As a result, scientists and managers must look for alternative management techniques to protect these aquatic systems. One such option that has potential to protect freshwater environments from numerous threats is the use of freshwater protected areas (FPAs). FPAs are portions of the freshwater environment partitioned to minimize disturbances and allow natural processes to govern populations and ecosystems. While similar conservation practices are well established in the terrestrial and marine environments, the use of FPAs for conservation of freshwater environments has been relatively slow. Despite this, numerous examples exist in which FPAs have been incorporated into successful management approaches for freshwater environments. In this paper, we outline some of the past success stories where FPAs have been used to protect freshwater environments, discuss some of the reasons that this technique has not proliferated to the same degree as marine protected areas, and present some of the challenges that managers and scientists must overcome if they wish to implement FPAs. We recommend that the term Freshwater Protected Area be adopted to such conservation efforts, thereby standardizing terminology and facilitating literature searches and dissemination of research findings. Furthermore, we encourage freshwater scientists, conservationists and managers to develop and implement FPAs in innovative and creative situations thereby permitting the growth of the research base for this valuable conservation technique.