Pseudogenes

Our chromosomes are full of the dead relics of genes. DNA analysis is beginning to unravel the origin and fate of these pseudogenes, and the influence that they may have on genome organization and evolution.     

Dynamics of Bacterial Swarming

When vegetative bacteria that can swim are grown in a rich medium on an agar surface, they become multinucleate, elongate, synthesize large numbers of flagella, produce wetting agents, and move across the surface in coordinated packs: they swarm. We examined the motion of swarming Escherichia coli, comparing the motion of individual cells to their motion during swimming. Swarming cells' speeds are comparable to bulk swimming speeds, but very broadly distributed. Their speeds and orientations are correlated over a short distance (several cell lengths), but this correlation is not isotropic. We observe the swirling that is conspicuous in many swarming systems, probably due to increasingly long-lived correlations among cells that associate into groups. The normal run-tumble behavior seen in swimming chemotaxis is largely suppressed, instead, cells are continually reoriented by random jostling by their neighbors, randomizing their directions in a few tenths of a second. At the edge of the swarm, cells often pause, then swim back toward the center of the swarm or along its edge. Local alignment among cells, a necessary condition of many flocking theories, is accomplished by cell body collisions and/or short-range hydrodynamic interactions.     

Selection-Driven Extinction Dynamics for Group II Introns in Enterobacteriales

Transposable elements (TEs) are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Some TEs were proposed to evolve under a pattern of periodic extinctions-recolonizations, in which elements recurrently invade and quickly proliferate within their host genomes, then start to disappear until total extinction. Depending on the model, TE extinction is assumed to be driven by purifying selection against colonized host genomes (Sel-DE model) or by saturation of host genomes (Sat-DE model). Bacterial group II introns are suspected to follow an extinction-recolonization model of evolution, but whether they follow Sel-DE or Sat-DE dynamics is not known. Our analysis of almost 200 group II intron copies from 90 sequenced Enterobacteriales genomes confirms their extinction-recolonization dynamics: patchy element distributions among genera and even among strains within genera, acquisition of new group II introns through plasmids or other mobile genetic elements, and evidence for recent proliferations in some genomes. Distributions of recent and past proliferations and of their respective homing sites further provide strong support for the Sel-DE model, suggesting that group II introns are deleterious to their hosts. Overall, our observations emphasize the critical impact of host properties on TE dynamics.     

双孢蘑菇培养料发酵过程中细菌群落动态变化

双孢蘑菇产量的最主要影响因素是培养料的堆肥发酵过程,而微生物是其中的主要推动力。为了揭示工厂化生产双孢蘑菇堆肥发酵过程中的微生物群落结构变化及演替规律,深入了解细菌在堆肥发酵过程中作用,文章以工厂化生产双孢蘑菇堆肥为研究对象,采用16S rRNA基因高通量测序技术分析堆肥前、一次发酵、二次发酵过程中细菌群落特征。共产生有效操作分类单元(OTUs) 854个,涵盖了19门259属的细菌。堆肥前优势类群为Proteobacteria,一次发酵优势类群为Firmicutes、Deinococcus-Thermus等,二次发酵时绿弯菌门Chloroflexi为主要类群。研究结果表明:微生物种类和数量随堆肥过程不断升高,并在二次发酵后降低,且微生物群落结构呈现连续变化的规律。高通量测序还发现了很多未分类细菌,说明双孢蘑菇培养料堆肥样品中还蕴含着大量未知的微生物种类。     

物种灭绝机制

对灭绝类型、灭绝率、灭绝特点等物种灭绝的基本概念进行了阐述,从灭绝与进化,灭绝与系统发育历程之间的关系等方面探讨了灭绝的内在机制,并从生物学、物理学及人类影响三方面对物种灭绝的外在机制进行了系统的说明。     

Seasonal Differences in Extinction and Colonization Drive Occupancy Dynamics of an Imperilled Amphibian

A detailed understanding of the population dynamics of many amphibian species is lacking despite concerns about declining amphibian biodiversity and abundance. This paper explores temporal patterns of occupancy and underlying extinction and colonization dynamics in a regionally imperiled amphibian species, the Northern leopard frog (Lithobates pipiens) in Alberta. Our study contributes to elucidating regional occupancy dynamics at northern latitudes, where climate extremes likely have a profound effect on seasonal occupancy. The primary advantage of our study is its wide geographic scale (60,000 km²) and the use of repeat visual surveys each spring and summer from 2009–2013. We find that occupancy varied more dramatically between seasons than years, with low spring and higher summer occupancy. Between spring and summer, colonization was high and extinction low; inversely, colonization was low and extinction high over the winter. The dynamics of extinction and colonization are complex, making conservation management challenging. Our results reveal that Northern leopard frog occupancy was constant over the last five years and thus there is no evidence of decline or recovery within our study area. Changes to equilibrium occupancy are most sensitive to increasing colonization in the spring or declining extinction in the summer. Therefore, conservation and management efforts should target actions that are likely to increase spring colonization; this could be achieved through translocations or improving the quality or access to breeding habitat. Because summer occupancy is already high, it may be difficult to improve further. Nevertheless, summer extinction could be reduced by predator control, increasing water quality or hydroperiod of wetlands, or increasing the quality or quantity of summer habitat.     

Model Studies of the Dynamics of Bacterial Flagellar Motors

The bacterial flagellar motor is a rotary molecular machine that rotates the helical filaments that propel swimming bacteria. Extensive experimental and theoretical studies exist on the structure, assembly, energy input, power generation, and switching mechanism of the motor. In a previous article, we explained the general physics underneath the observed torque-speed curves with a simple two-state Fokker-Planck model. Here, we further analyze that model, showing that 1), the model predicts that the two components of the ion motive force can affect the motor dynamics differently, in agreement with latest experiments; 2), with explicit consideration of the stator spring, the model also explains the lack of dependence of the zero-load speed on stator number in the proton motor, as recently observed; and 3), the model reproduces the stepping behavior of the motor even with the existence of the stator springs and predicts the dwell-time distribution. The predicted stepping behavior of motors with two stators is discussed, and we suggest future experimental procedures for verification.     

Protozoa Drive the Dynamics of Culturable Biocontrol Bacterial Communities

Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin (PRN) and hydrogen cyanide (HCN) in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks), as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.     

Dynamics of Seawater Bacterial Communities in a Shellfish Hatchery

Bacterial disease is a significant issue for larviculture of several species of shellfish, including oysters. One source of bacteria is the seawater used throughout the hatchery. In this study carried out at a commercial oyster hatchery in Tasmania, Australia, the diversity of the bacterial community and its relationship with larval production outcomes were studied over a 2-year period using terminal restriction fragment length polymorphism and tag-encoded pyrosequencing. The bacterial communities were very diverse, dominated by the Alphaproteobacteria, Gammaproteobacteria, Flavobacteria and Cyanobacteria. The communities were highly variable on scales of days, weeks and seasons. The difference between the intake seawater and treated clean seawater used in the hatchery was smaller than the observed temporal differences in the seawater throughout the year. No clear correlation was observed between production outcomes and the overall bacterial community structure. However, one group of Cyanobacterial sequences was more abundant when mass mortality events occurred than when healthy spat were produced although they were always present.     

Pseudogenes as Functionally Significant Elements of the Genome

Pseudogene is a gene copy that has lost its original function. For a long time, pseudogenes have been considered as “junk DNA” that inevitably arises as a result of ongoing evolutionary process. However, experimental data obtained during recent years indicate this understanding of the nature of pseudogenes is not entirely correct, and many pseudogenes perform important genetic functions. In the review, we have addressed classification of pseudogenes, methods of their detection in the genome, and the problem of their evolutionary conservatism and prevalence among species belonging to different taxonomic groups in the light of modern data. The mechanisms of gene expression regulation by pseudogenes and the role of pseudogenes in pathogenesis of various human diseases are discussed.     

The Effects of Vaccination and Immunity on Bacterial Infection Dynamics In Vivo

Salmonella enterica infections are a significant global health issue, and development of vaccines against these bacteria requires an improved understanding of how vaccination affects the growth and spread of the bacteria within the host. We have combined in vivo tracking of molecularly tagged bacterial subpopulations with mathematical modelling to gain a novel insight into how different classes of vaccines and branches of the immune response protect against secondary Salmonella enterica infections of the mouse. We have found that a live Salmonella vaccine significantly reduced bacteraemia during a secondary challenge and restrained inter-organ spread of the bacteria in the systemic organs. Further, fitting mechanistic models to the data indicated that live vaccine immunisation enhanced both the bacterial killing in the very early stages of the infection and bacteriostatic control over the first day post-challenge. T-cell immunity induced by this vaccine is not necessary for the enhanced bacteriostasis but is required for subsequent bactericidal clearance of Salmonella in the blood and tissues. Conversely, a non-living vaccine while able to enhance initial blood clearance and killing of virulent secondary challenge bacteria, was unable to alter the subsequent bacterial growth rate in the systemic organs, did not prevent the resurgence of extensive bacteraemia and failed to control the spread of the bacteria in the body.     

Bacterial Community Dynamics during Bioremediation of Diesel Oil-Contaminated Antarctic Soil

The effect of nutrient and inocula amendment in a bioremediation field trial using a nutrient-poor Antarctic soil chronically contaminated with hydrocarbons was tested. The analysis of the effects that the treatments caused in bacterial numbers and hydrocarbon removal was combined with the elucidation of the changes occurring on the bacterial community, by 16S rDNA-based terminal restriction fragment length polymorphism (T-RFLP) typing, and the detection of some of the genes involved in the catabolism of hydrocarbons. All treatments caused a significant increase in the number of bacteria able to grow on hydrocarbons and a significant decrease in the soil hydrocarbon content, as compared to the control. However, there were no significant differences between treatments. Comparison of the soil T-RFLP profiles indicated that there were changes in the structure and composition of bacterial communities during the bioremediation trial, although the communities in treated plots were highly similar irrespective of the treatment applied, and they had a similar temporal dynamics. These results showed that nutrient addition was the main factor contributing to the outcome of the bioremediation experiment. This was supported by the lack of evidence of the establishment of inoculated consortia in soils, since their characteristic electrophoretic peaks were only detectable in soil profiles at the beginning of the experiment. Genetic potential for naphthalene degradation, evidenced by detection of nahAc gene, was observed in all soil plots including the control. In treated plots, an increase in the detection of catechol degradation genes (nahH and catA) and in a key gene of denitrification (nosZ) was observed as well. These results indicate that treatments favored the degradation of aromatic hydrocarbons and probably stimulated denitrification, at least transiently. This mesocosm study shows that recovery of chronically contaminated Antarctic soils can be successfully accelerated using biostimulation with nutrients, and that this causes a change in the indigenous bacterial communities and in the genetic potential for hydrocarbon degradation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Structural and Functional Dynamics of Sulfate-Reducing Populations in Bacterial Biofilms

We describe the combined application of microsensors and molecular techniques to investigate the development of sulfate reduction and of sulfate-reducing bacterial populations in an aerobic bacterial biofilm. Microsensor measurements for oxygen showed that anaerobic zones developed in the biofilm within 1 week and that oxygen was depleted in the top 200 to 400 μm during all stages of biofilm development. Sulfate reduction was first detected after 6 weeks of growth, although favorable conditions for growth of sulfate-reducing bacteria (SRB) were present from the first week. In situ hybridization with a 16S rRNA probe for SRB revealed that sulfate reducers were present in high numbers (approximately 10⁸ SRB/ml) in all stages of development, both in the oxic and anoxic zones of the biofilm. Denaturing gradient gel electrophoresis (DGGE) showed that the genetic diversity of the microbial community increased during the development of the biofilm. Hybridization analysis of the DGGE profiles with taxon-specific oligonucleotide probes showed that Desulfobulbus and Desulfovibrio were the main sulfate-reducing bacteria in all biofilm samples as well as in the bulk activated sludge. However, different Desulfobulbus and Desulfovibrio species were found in the 6th and 8th weeks of incubation, respectively, coinciding with the development of sulfate reduction. Our data indicate that not all SRB detected by molecular analysis were sulfidogenically active in the biofilm.     

Extinction

In the life of any species, extinction is the final evolutionary process. It is a common one at present, as the world is entering a major extinction crisis. The pattern of extinction and threat is very non-random, with some taxa being more vulnerable than others. Explaining why some taxa are affected and some escape is a major goal of conservation biology. More ambitiously, a predictive model could, in principle, be built by integrating comparable studies of past and present extinctions. We review progress towards both explanatory and predictive frameworks, comparing correlates of extinction in different groups at different times. Progress towards explanatory models for the current crisis is promising, at least in some well-studied taxa, but the development of a truly predictive model is hampered by the formidable difficulties of integrating studies of present and past extinctions.     

Extinction

A significant proportion of conservationists' work is directed towards efforts to save disappearing species. This relies upon the belief that species extinction is undesirable. When justifications are offered for this belief, they very often rest upon the assumption that extinction brought about by humans is different in kind from other forms of extinction. This paper examines this assumption and reveals that there is indeed good reason to suppose current anthropogenic extinctions to be different in kind from extinctions brought about at other times or by other factors. Having considered – and rejected – quantity and rate of extinction as useful distinguishing factors, four alternative arguments are offered, each identifying a way in which anthropogenic extinction is significantly different from other forms of extinction, even mass extinction: (1) Humans are a different kind of natural cause from other causes of extinction; (2) Extinctions brought about by humans are uniquely persistent; (3) Anthropogenic extinctions are effectively random whereas past mass extinctions are rule-bound; (4) The impact of the current anthropogenic extinction event differs from the impact of other extinction events of the past, such that future recovery may not follow past patterns. Together, these four arguments suggest that the present-day extinction event brought about by humans may be unprecedented and that we cannot clearly extrapolate from past to present recovery from extinctions. Although insufficient as justification for the claim that present-day extinctions are undesirable, the arguments provide some ammunition for conservationists' conviction that species extinction – in which humans play an accelerating role – ought to be prevented.