What drives bacteria to produce a biofilm?

Nearly 40 years ago, Dr. R.J. Gibbons made the first reports of the clinical relevance of what we now know as bacterial biofilms when he published his observations of the role of polysaccharide glycocalyx formation on teeth by Streptococcus mutans [Sci. Am. 238 (1978) 86]. As the clinical relevance of bacterial biofilm formation became increasingly apparent, interest in the phenomenon exploded. Studies are rapidly shedding light on the biomolecular pathways leading to this sessile mode of growth but many fundamental questions remain. The intent of this review is to consider the reasons why bacteria switch from a free-floating to a biofilm mode of growth. The currently available wealth of data pertaining to the molecular genetics of biofilm formation in commonly studied, clinically relevant, single-species biofilms will be discussed in an effort to decipher the motivation behind the transition from planktonic to sessile growth in the human body. Four potential incentives behind the formation of biofilms by bacteria during infection are considered: (1) protection from harmful conditions in the host (defense), (2) sequestration to a nutrient-rich area (colonization), (3) utilization of cooperative benefits (community), (4) biofilms normally grow as biofilms and planktonic cultures are an in vitro artifact (biofilms as the default mode of growth).     

Do hormonal control systems produce evolutionary inertia?

Hormonal control systems are complex in design and well integrated. Concern has been raised that these systems might act as evolutionary constraints when animals are subject to anthropogenic environmental change. Three systems are examined in vertebrates, especially birds, that are important for assessing this possibility: (i) the hypothalamic-pituitary-gonadal (HPG) axis, (ii) the activational effects of sex steroids on mating effort behaviour, and (iii) sexual differentiation. Consideration of how these systems actually work that takes adequate account of the brain's role and mechanisms suggests that the first two are unlikely to be impediments to evolution. The neural and molecular networks that regulate the HPG provide both phenotypic and evolutionary flexibility, and rapid evolutionary responses to selection have been documented in several species. The neuroendocrine and molecular cascades for behaviour provide many avenues for evolutionary change without requiring a change in peripheral hormone levels. Sexual differentiation has some potential to be a source of evolutionary inertia in birds and could contribute to the lack of diversity in certain reproductive (including life history) traits. It is unclear, however, whether that lack of diversity would impede adaptation to rapid environmental change given the role of behavioural flexibility in avian reproduction.     

Do YB2/0 cells produce alien sugars?

Olovnikova et al. (“Impact on N-glycosylation profile of monoclonal anti-D antibodies as a way to control their immunoregulatory and cytotoxic properties” (2012) Biochemistry (Moscow), 77, 925–933) mentioned the presence of “alien sugars” on monoclonal antibodies (mAbs) produced by YB2/0 cell line. We summarize in this paper our previous findings on the glycosylation profile of two anti-D mAbs produced in this cell line (LFB-R297 and LFB-R593, so-called Roledumab). Our results show the absence of any immunogenic glycotopes, and furthermore neither immunogenicity nor other serious adverse reactions were observed during clinical trials.     

Do ecto- and ericoid mycorrhizal fungi produce peroxidase activity?

 Several reports attest to the apparent ability of some ectomycorrhizal (ECM) and ericoid (ERM) mycorrhizal fungi to produce peroxidase enzyme activities during growth in axenic culture. In critically reviewing these data, we highlight that apparent peroxidase activities have been observed during growth in media containing 60–70 μM Fe. ECM and ERM fungi are known to produce H₂O₂ via carbohydrate oxidase activity and conditions in common culture media are favourable to the production of hydroxyl radicals, superoxide radicals and ferryl ions via the Fenton reaction. Free radicals so produced can mediate oxidation of substrates commonly used in presumptive peroxidase assays, leading to false-positive results. We argue that there is currently no evidence to support production of peroxidase activity by ECM or ERM fungi, but highlight circumstances in which peroxidase expression might be observed in future work. Accepted: 16 July 1998     

Do artificial substrates favor nonindigenous fouling species over native species?

Exotic species are prominent constituents of fouling communities. If exotic fouling organisms colonize or compete better on a wider range of substrate types than native species, this may partially account for their high abundance in estuaries and bays. We used four artificial and four naturally occurring substrate types to compare initial settlement and percent cover of native and exotic fouling species through six months of community development. Both the identity of common taxa and the total number of species colonizing artificial versus natural substrate types were similar. Despite the similarities in species richness, relative abundance patterns between natural and artificial substrate types varied, particularly as the communities developed. Native species were initially in equal abundance on natural and artificial substrate types. Initially, the two most common exotic species, the colonial tunicates, Botrylloides violaceus Ritter and Forsyth and Botryllus schlosseri (Pallas), were also in similar, but low, abundance on artificial and natural substrates. As the communities developed, there was little change in abundance of exotic or native species on natural substrates. However, on artificial substrates the exotic tunicates increased dramatically and native species declined in abundance. Artificial surfaces may provide a novel context for competitive interactions giving exotic species a more “level playing field” in an environment for which they otherwise might not be as well adapted compared to long-resident native species. Additions of artificial substrates to nearshore environments may disproportionately favor exotic species by increasing local sources of exotic propagules to colonize all types of substrates.     

Do we expect natural selection to produce rational behaviour?

We expect that natural selection should result in behavioural rules which perform well; however, animals (including humans) sometimes make bad decisions. Researchers account for these with a variety of explanations; we concentrate on two of them. One explanation is that the outcome is a side effect; what matters is how a rule performs (in terms of reproductive success). Several rules may perform well in the environment in which they have evolved, but their performance may differ in a 'new' environment (e.g. the laboratory). Some rules may perform very badly in this environment. We use the debate about whether animals follow the matching law rather than maximizing their gains as an illustration. Another possibility is that we were wrong about what is optimal. Here, the general idea is that the setting in which optimal decisions are investigated is too simple and may not include elements that add extra degrees of freedom to the situation.     

Do neutrophils produce ozone? An appraisal of current evidence

Recently, it was proposed that neutrophils generate ozone. Evidence for the proposal is based largely on three experimental systems using probes that are known to react with ozone. However, further assessment of the findings shows that in each case, there is a plausible alternative explanation. Oxidation of indigo carmine to isatin sulfonic can be accounted for by superoxide. Conversion of vinylbenzoic acid to p-carboxybenzaldehyde is analogous to the reactions of other styrene derivatives shown to be catalyzed by myeloperoxidase, and more rigorous assessment of alternative explanations is needed before the formation of secosterol oxidation products of cholesterol can be taken as proof of ozone production. We conclude that the evidence for ozone production by neutrophils is not convincing and studies using the same probes to implicate ozone in other biological processes should also be interpreted with caution.     

Do Heliconius butterfly species exchange mimicry alleles?

Hybridization has the potential to transfer beneficial alleles across species boundaries, and there are a growing number of examples in which this has apparently occurred. Recent studies suggest that Heliconius butterflies have transferred wing pattern mimicry alleles between species via hybridization, but ancestral polymorphism could also produce a signature of shared ancestry around mimicry genes. To distinguish between these alternative hypotheses, we measured DNA sequence divergence around putatively introgressed mimicry loci and compared this with the rest of the genome. Our results reveal that putatively introgressed regions show strongly reduced sequence divergence between co-mimetic species, suggesting that their divergence times are younger than the rest of the genome. This is consistent with introgression and not ancestral variation. We further show that this signature of introgression occurs at sites throughout the genome, not just around mimicry genes.     

Do fatal infectious diseases eradicate host species?

In simple SI epidemic and endemic models, three classes of incidence functions are identified for their potential to be associated with host extinction: weakly upper density-dependent incidences are never associated with host extinction. Power incidences that depend on the number of susceptibles and infectives by powers strictly between 0 and 1 are associated with initial-constellation-dependent host extinction for all parameter values. Homogeneous incidences, of which frequency-dependent incidence is a very particular case, and power incidences are associated with global host extinction for certain parameter constellations and with host survival for others. Laboratory infection experiments with salamander larvae are equally well fitted by power incidences and certain upper density-dependent incidences such as the negative binomial incidence and do not rule out homogeneous incidences such as an asymmetric frequency-dependent incidence either.

     

Do species distribution models explain spatial structure within tree species ranges?

Aim To evaluate the ability of species distribution models (SDMs) to predict the spatial structure of tree species within their geographical ranges (how trees are distributed within their ranges). Location Continental Spain. Methods We used an extensive dataset consisting of c. 90,000 plots (1 plot km^?2) where presence/absence data for 23 common Mediterranean and Atlantic tree species had been surveyed. We first generated SDMs relating the presence or absence of each species to a set of 16 environmental predictors, following a stepwise modelling process based on maximum likelihood methods. Superimposing spatial correlograms generated from the predictions of the SDMs over those generated from the raw data allowed a model–observation comparison of the nature, scale and intensity (level of aggregation) of spatial structure with the species ranges. Results SDMs predicted accurately the nature and scale of the spatial structure of trees. However, for most species, the observed intensity of spatial structure (level of aggregation of species in space) was substantially greater than that predicted by the SDMs. On average, the intensity of spatial aggregation was twice that predicted by SDMs. In addition, we also found a negative correlation between intensity of aggregation and species range size. Main conclusions Standard SDM predictions of spatial structure patterns differ among species. SDMs are apparently able to reproduce both the scale and intensity of species spatial structure within their ranges. However, one or more missing processes not included in SDMs results in species being substantially more aggregated in space than can be captured by the SDMs. This result adds to recent calls for a new generation of more biologically realistic SDMs. In particular, future SDMs should incorporate ecological processes that are likely to increase the intensity of spatial aggregation, such as source–sink dynamics, fine‐scale environmental heterogeneity and disequilibrium.     

Do persistent rare species experience stronger negative frequency dependence than common species?

Understanding why so many species are rare yet persistent remains a significant challenge for both theoretical and empirical ecologists. Yenni et al. (2012, Ecology, 93, 456–461) proposed that strong negative frequency dependence causes species to be rare while simultaneously buffering them against extinction. This hypothesis predicts that, on average, rare species should experience stronger negative frequency dependence than common species. However, it is unknown if ecological communities generally show this theoretical pattern. We discuss the implications of this phenomenon for community dynamics, and develop a method to test for a non‐random relationship between negative frequency dependence and relative abundance using species abundance data from 90 communities across a broad range of environments and taxonomic groups. To account for biases introduced by measurement error, we compared the observed correlation between species relative abundance and the strength of frequency dependence against expectations from a randomization procedure. In approximately half of the analysed communities, we found increasingly strong negative frequency dependence with decreasing relative abundance: rare species experienced stronger frequency dependence than common species. The randomization test never detected stronger negative frequency dependence in more common species. Our results suggest that strong negative frequency dependence is a signature of persistent, rare species in many communities.     

Do forest-dwelling plant species disperse along landscape corridors?

Woody corridors in fragmented landscapes have been proposed as alternative habitats for forest plants, but the great variation in species-specific responses blurs the overall assessment. The aim of this study was to estimate the dispersal success of forest-dwelling plants from a stand into and along an attached woody corridor, and to explain the observed patterns from the point of view of species’ dispersal traits and corridor properties. We sampled 47 forest–corridor transects in the agricultural landscapes of southeastern Estonia. Regionally common forest-dwelling species (observed in at least 10 % of seed-source forests) were classified on the basis of their ecological response profile—forest-restricted species (F-type) and forest-dwelling generalists (G-type). Species richness and the proportion of F-type species decreased sharply from the seed-source forest core to the forest edge and to the first 10–15 m of the corridor, while G-type species richness remained constant throughout the transect. Corridor structure had a species-specific effect—F species were promoted by old (≥50 years) and wide (≥10 m) corridors, while G species were supported by young and narrow corridors with ditch-related soil disturbances. Moderate shade (canopy cover <75 %) was optimal for all forest-dwelling species. Large dispersule weight, and not seed weight, dispersal vector or Ellenberg’s indicator values, was the trait that differentiated F species from G species. We conclude that most woody corridors are only dispersal stepping-stone habitats for habitat generalist species, and not for specialists. Only century old corridors can relieve the dispersal limitation of forest-restricted species.     

Two-step sampling can produce triphasic species–area relationship

两步采样可产生三段式种面积关系解析在不同尺度下引起三段式种面积关系(triphasic species–area relationship, triphasic SAR)的潜在机制对于理解生物多样性的空间格局非常重要。相较于理论构建和野外数据推导,本研究采用了种面积关系的幂函数来拟合对数正态分布的物种多度。研究结果表明,一步采样可引起两段式SAR,n步采样可引起2n段SAR。因为大面积时的Preston和Pan效应,实际的两步采样可产生三段式种面积关系。此外,我们在探索自然现象的生物学或生态学机制之前,我们应该识别或排除潜在的数学、统计或者采样原因。     

Do parasitoid preferences for different host species match virulence?

Abstract.  Leptopilina boulardi is a parasitoid wasp specialist of Drosophila larvae of the melanogaster subgroup. In Mediterranean areas, natural populations are highly virulent against their main host Drosophila melanogaster . In Congo, populations are less virulent against D. melanogaster but are able to develop successfully inside the tropical African species Drosophila yakuba . Host preferences are compared between two laboratory isofemale lines of L. boulardi , obtained from populations of Congo and Tunisia, respectively, and differing in virulence levels against D. melanogaster and D. yakuba . Host selection is studied by offering female parasitoids a choice between larvae of the two host species. In agreement with optimal foraging models, the line highly virulent against D. melanogaster shows a clear preference for this host species. The other line, less virulent against D. melanogaster but more virulent against D. yakuba , prefers to oviposit on D. yakuba . Such preferences can be observed after a period of host-patch exploitation only, suggesting that experience plays an important role in the host-selection process. These results evidence the existence of intraspecific variability in preference between two host species in L. boulardi , a major requisite in theoretical models of parasite specialization by the host. They also sustain the hypothesis that intraspecific variation in parasitoid preferences between host species might mirror intraspecific variation in virulence.     

Do large forest trees tend towards high species mingling?

Effects caused by human management and natural disturbances as well as by ecological mechanisms such as those described, for example, by the Janzen-Connell and the herd immunity hypotheses play an important role in maintaining species diversity. These processes are often accompanied by local size-hierarchy effects and as a likely consequence of them we hypothesised that large plants generally have a tendency to show high species mingling, where plants and their nearest neighbours are heterospecific. To carry out a first benchmark study in forests from different parts of Europe, Africa and North America, we selected spatial data from twelve forest ecosystems and analysed the mingling situation based on an index of spatial species mingling. Using stem diameter at breast height and stem diameter differentiation among the nearest neighbours as explanatory variables we then applied logistic regression to explain mingling probability. Overall we found significant support for the expectation that large trees and trees growing at low local densities often (75% of all analysed forest stands) have indeed a tendency towards high species mingling. This supports our expectation that the tendency of larger trees towards high species mingling generally is either a consequence of disturbances/forest management or of the aforementioned ecological processes, although a few forest stands also deviated from the expected pattern. We also found that size differentiation and species mingling are strongly related in local neighbourhoods. Thus the results of our study strongly support the view that local species richness promotes local size hierarchy irrespective of climate zone. This leads to situations where in local neighbourhoods with large size diversity there is also high mingling and vice versa. This allows conservation to focus on maintaining or improving one diversity aspect, e.g. size diversity, whilst obtaining the other, e.g. species mingling, as a by-product.     

Do allopatric male Calopteryx virgo damselflies learn species recognition?

There is a growing amount of empirical evidence that premating reproductive isolation of two closely related species can be reinforced by natural selection arising from avoidance of maladaptive hybridization. However, as an alternative for this popular reinforcement theory, it has been suggested that learning to prefer conspecifics or to discriminate heterospecifics could cause a similar pattern of reinforced premating isolation, but this possibility is much less studied. Here, we report results of a field experiment in which we examined (i) whether allopatric Calopteryx virgo damselfly males that have not encountered heterospecific females of the congener C. splendens initially show discrimination, and (ii) whether C. virgo males learn to discriminate heterospecifics or learn to associate with conspecifics during repeated experimental presentation of females. Our experiment revealed that there was a statistically nonsignificant tendency for C. virgo males to show initial discrimination against heterospecific females but because we did not use sexually naïve individuals in our experiment, we were not able to separate the effect of innate or associative learning. More importantly, however, our study revealed that species discrimination might be further strengthened by learning, especially so that C. virgo males increase their association with conspecific females during repeated presentation trials. The role of learning to discriminate C. splendens females was less clear. We conclude that learning might play a role in species recognition also when individuals are not naïve but have already encountered potential conspecific mates.     

Do major species concepts support one, two or more species within Cryptococcus neoformans?

Cryptococcus neoformans, the agent of cryptococcosis, had been considered a homogeneous species until 1949 when the existence of four serotypes was revealed based on the antigenic properties of its polysaccharide capsule. Such heterogeneity of the species, however, remained obscure until the two morphologically distinct teleomorphs of C. neoformans were discovered during the mid 1970s. The teleomorph Filobasidiella neoformans was found to be produced by strains of serotype A and D, and Filobasidiella bacillispora was found to be produced by strains of serotype B and C. Ensuing studies revealed numerous differences between the anamorphs of the two Filobasidiella species with regard to their ecology, epidemiology, pathobiology, biochemistry and genetics. At present, the etiologic agent of cryptococcosis is classified into two species, C. neoformans (serotypes A and D) and Cryptococcus gattii (serotypes B and C). Intraspecific genetic diversity has also been revealed as more genotyping methods have been applied for each serotype. As a result, the number of scientifically valid species within C. neoformans has become a controversial issue because of the differing opinions among taxonomists as to the appropriate definition of a species. There are three major species concepts that govern classification of organisms: phenetic (morphologic, phenotypic), biologic (interbreeding) and cladistic (evolutionary, phylogenetic). Classification of the two C. neoformans species has been based on the phenetic as well as the biologic species concept, which is also supported by the cladistic species concept. In this paper, we review and attest to the validity of the current two-species system in light of the three major species concepts.     

Do host species evolve a specific response to slave-making ants?

Background

Social parasitism is an important selective pressure for social insect species. It is particularly the case for the hosts of dulotic (so called slave-making) ants, which pillage the brood of host colonies to increase the worker force of their own colony. Such raids can have an important impact on the fitness of the host nest. An arms race which can lead to geographic variation in host defenses is thus expected between hosts and parasites. In this study we tested whether the presence of a social parasite (the dulotic ant Myrmoxenus ravouxi) within an ant community correlated with a specific behavioral defense strategy of local host or non-host populations of Temnothorax ants. Social recognition often leads to more or less pronounced agonistic interactions between non-nestmates ants. Here, we monitored agonistic behaviors to assess whether ants discriminate social parasites from other ants. It is now well-known that ants essentially rely on cuticular hydrocarbons to discriminate nestmates from aliens. If host species have evolved a specific recognition mechanism for their parasite, we hypothesize that the differences in behavioral responses would not be fully explained simply by quantitative dissimilarity in cuticular hydrocarbon profiles, but should also involve a qualitative response due to the detection of particular compounds. We scaled the behavioral results according to the quantitative chemical distance between host and parasite colonies to test this hypothesis.

Results

Cuticular hydrocarbon profiles were distinct between species, but host species did not show a clearly higher aggression rate towards the parasite than toward non-parasite intruders, unless the degree of response was scaled by the chemical distance between intruders and recipient colonies. By doing so, we show that workers of the host and of a non-host species in the parasitized site displayed more agonistic behaviors (bites and ejections) towards parasite than toward non-parasite intruders.

Conclusions

We used two different analyses of our behavioral data (standardized with the chemical distance between colonies or not) to test our hypothesis. Standardized data show behavioral differences which could indicate qualitative and specific parasite recognition. We finally stress the importance of considering the whole set of potentially interacting species to understand the coevolution between social parasites and their hosts.