Symbiotic microorganisms: untapped resources for insect pest control

Symbiotic microorganisms offer one route to meet the anticipated heightened demand for novel insect pest management strategies created by growing human populations and global climate change. Two approaches have particular potential: the disruption of microbial symbionts required by insect pests, and manipulation of microorganisms with major impacts on insect traits contributing to their pest status (e.g. capacity to vector diseases, natural enemy resistance). Specific research priorities addressed in this article include identification of molecular targets against which highly specific antagonists can be designed or discovered, and management strategies to manipulate the incidence and properties of facultative microorganisms that influence insect pest traits. Collaboration with practitioners in pest management will ensure that the research agenda is married to agricultural and public health needs.     

Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation

Microorganisms have been mutating and evolving on Earth for billions of years. Now, a field of research has developed around the idea of using microorganisms to study evolution in action. Controlled and replicated experiments are using viruses, bacteria and yeast to investigate how their genomes and phenotypic properties evolve over hundreds and even thousands of generations. Here, we examine the dynamics of evolutionary adaptation, the genetic bases of adaptation, tradeoffs and the environmental specificity of adaptation, the origin and evolutionary consequences of mutators, and the process of drift decay in very small populations.     

Mechanisms for locating resources in space and time: Impacts on the abundance of insect herbivores

Herbivorous insects have the problem both of locating appropriate host plants and ensuring that the plant‐feeding stages of their life cycles are synchronized with the times when those hosts provide a high‐quality food resource. Because the taxonomic range of potential hosts is generally narrow, and the temporal window when those hosts are suitable is often relatively short, developmental (especially diapause) and dispersal mechanisms may be critical factors in determining whether or not a species population is successful in a particular plant community. The present paper considers the impact of diapause and dispersal mechanisms on the ability of insect herbivores to cope with two attributes of their host plants: (i) the diversity of the plant community within which the hosts are located; and (ii) the seasonal predictability of host suitability. Some common dispersal mechanisms used by insect herbivores are much more appropriate to low‐diversity than to high‐diversity plant communities and, similarly, some diapause cues are appropriate only to highly predictable plant phenology. Both agriculture and silviculture characteristically manipulate both these attributes of plant communities, that is, in order to make the human use of plants more efficient, cultivation strategies normally both reduce plant species diversity (often to a condition approaching monoculture) and increase the predictability of plant developmental patterns. Consequently, major pest species in managed systems may not be those that are most common in natural systems, and may be difficult to predict in advance.     

Effectiveness of journal ranking schemes as a tool for locating information

Background

The rise of electronic publishing [1], preprint archives, blogs, and wikis is raising concerns among publishers, editors, and scientists about the present day relevance of academic journals and traditional peer review [2]. These concerns are especially fuelled by the ability of search engines to automatically identify and sort information [1]. It appears that academic journals can only remain relevant if acceptance of research for publication within a journal allows readers to infer immediate, reliable information on the value of that research.

Methodology/Principal Findings

Here, we systematically evaluate the effectiveness of journals, through the work of editors and reviewers, at evaluating unpublished research. We find that the distribution of the number of citations to a paper published in a given journal in a specific year converges to a steady state after a journal-specific transient time, and demonstrate that in the steady state the logarithm of the number of citations has a journal-specific typical value. We then develop a model for the asymptotic number of citations accrued by papers published in a journal that closely matches the data.

Conclusions/Significance

Our model enables us to quantify both the typical impact and the range of impacts of papers published in a journal. Finally, we propose a journal-ranking scheme that maximizes the efficiency of locating high impact research.     

Overview: Spatial information and indicators for sustainable management of natural resources

Natural resource management (NRM) is becoming increasingly important at all scales, local, regional, national and global, because of an increasing human population and increasing per capita use of resources and space. Conflicts are intensifying between different interest groups. Production and conservation aspects are particularly debated because conservation often conflicts with economic and social sustainability. There is public demand for objective decision based NRM but limitations are all pervasive due to the spatial and temporal complexity and interdisciplinary nature.This special issue explores the use of spatial data and models to overcome some limitations of NRM decision making. The papers in this issue show modern approaches of natural resources management with a particular focus on spatial data collection, analysis and the development of spatial indicators. This issue presents a balanced mix of review and research papers that give examples of how to find or improve the spatial information base for evidence-based decision making.This overview makes the argument that understanding complex spatial pattern and processes, and the development of spatial indicators, is an essential aspect of evidence-based NRM. If spatial and temporal patterns are complex, ecological evidence from field data or experiments may have limited value for NRM and observational study designs become more appropriate for understanding complex spatial pattern and processes. Data quality should be documented as a combination of accuracy and spatio-temporal representativeness in order to be useful in the NRM decision process.     

Physiological bases of oligotrophy of microorganisms and the concept of microbial community

Three groups of physiological processes in microorganisms are considered the physiological basis of oligotrophy: the greater substrate affinity of the oligotrophs' transport systems, efficient or “economical” metabolism, and existence of a “master reaction” or “rate-determining steps” controlling the rate of metabolism. Heterotrophic microorganisms are divided into three unequal groups according to “reaction norma.” Two groups representing the extremes are small groups with the “narrow” reaction norma, regarding the concentrations and structure of the assimilated organic compounds and variability limits of the physiological characteristics mentioned above. The third, intermediate group includes the majority of microorganisms with the “wide” reaction norma.     

Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms

To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and their names validly published. Aside from these quantitative limitations, our understanding of phenotypic and functional diversity of prokaryotes is also highly biased as not a single species has been described for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal genome sequences become available at a faster rate than newly described species. The growing gap between the diversity of Bacteria and Archaea held in pure culture and that detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet-cultured taxa primarily based on sequence information. According to this proposal, the concept of Candidatus species would be extended to groups of closely related genome sequences and their names validly published following established rules of bacterial nomenclature. The corresponding sequences would be deposited in public databases as the type. The suggested alterations of the International Code of Nomenclature of Prokaryotes raise concerns regarding (1) the reliability and stability of nomenclature, (2) the technological and conceptual limitations as well as availability of reference genomes, (3) the information content of in silico functional predictions, and (4) the recognition of evolutionary units of microbial diversity. These challenges need to be overcome to arrive at a meaningful taxonomy of not-yet-cultured prokaryotes with so far poorly understood phenotypes.     

Role and functions of beneficial microorganisms in sustainable aquaculture

This paper aims to review the development of scientific concepts of microecology and ecology of microbes and the role and functions of beneficial microorganisms in aquaculture and mariculture. Beneficial microorganisms play a great role in natural and man-made aquatic ecosystems based on the co-evolution theory in living biosphere on earth. Their functions are to adjust algal population in water bodies so as to avoid unwanted algal bloom; to speed up decomposition of organic matter and to reduce CODmn, NH₃–N and NO₂–N in water and sediments so as to improve water quality; to suppress fish/shrimp diseases and water-borne pathogens; to enhance immune system of cultured aquatic animals and to produce bioactive compounds such as vitamins, hormones and enzymes that stimulate growth, thus to decrease the FCR of feed.     

A profile for molecular biology databases and information resources

This paper examines the requirements for building database managementsystems and multi-database information resources to supportmolecular biology research. The paper profiles the most importantfeatures of 16 integrated resources and 102 databases relatedto molecular biology research. The aspects surveyed in thispaper include the nature of information in these databases,their sizes, update properties, cross-references, database managementsystem heterogeneity, geographical distribution, data quality,use of temporal information and level of interpretation. Thepaper also comments on the access patterns to these databases.Since not all these aspects were available for all databases,specific comparisons sometimes compare fewer than the full 102databases. Consequently, the same set of databases is not necessarilyalways being compared with respect to every aspect. The paperis organized primarily according to these comparison aspectsand ends with some concluding remarks.     

Hydration of DNA bases: analysis of crystallographic data.

We present a systematic analysis of water structure around nucleic acid bases. We have examined 28 crystal structures of oligonucleotides, and have studied the patterns of water around the four bases, guanine, cytosine, adenine, and thymine. The geometries of water positions were calculated up to 4.00 A from base atoms. We have found conformation-dependent differences in both the geometry and extent of hydration of the bases.     

Interspecific resources: a major tool for quantitative trait locus cloning and speciation research

Positional cloning of the quantitative trait locus (QTL) still encounters numerous difficulties, which explains why thousands of QTL have been mapped, while only a few have been identified at the molecular level. Here, we focus on a specific mapping tool that exists in plant and animal model species: interspecific recombinant congenic strains (IRCSs) or interspecific nearly isogenic lines (NILs). Such panels exhibit a much higher sequence diversity than intraspecific sets, thus enhancing the contrasts between phenotypes. In animals, it allows statistical significance to be reached even when using a limited number of individuals. Therefore, we argue that interspecific resources may constitute a major genetic tool for positional cloning and for understanding some bases of speciation mechanisms.     

Enzyme production-based approach for determining the functions of microorganisms within a community

The functions of specific microorganisms in a microbial community were investigated during the composting process. Cerasibacillus quisquiliarum strain BLx(T) and Bacillus thermoamylovorans strain BTa were isolated and characterized in our previous studies based on their dominance in the composting system. Strain BLx(T) degrades gelatin, while strain BTa degrades starch. We hypothesized that these strains play roles in gelatinase and amylase production, respectively. The relationship between changes in the abundance ratios of each strain and those of each enzyme activity during the composting process was examined to address this hypothesis. The increase in gelatinase activity in the compost followed a dramatic increase in the abundance ratio of strain BLx(T). Zymograph analysis demonstrated that the pattern of active gelatinase bands from strain BLx(T) was similar to that from the compost. Gelatinases from both BLx(T) and compost were partially purified and compared. Homologous N-terminal amino acid sequences were found in one of the gelatinases from strain BLx(T) and that of compost. These results indicate strain BLx(T) produces gelatinases during the composting process. Meanwhile, the increase in the abundance ratio of strain BTa was not concurrent with that of amylase activity in the compost. Moreover, the amylase activity pattern of strain BTa on the zymogram was different from that of the compost sample. These results imply that strain BTa may not produce amylases during the composting process. To our knowledge, this is the first report demonstrating that the function of a specific microorganism is directly linked to a function in the community, as determined by culture-independent and enzyme-level approaches.     

Ethylene-induced leaf abscission in cotton seedlings : the physiological bases for age-dependent differences in sensitivity

The speed of ethylene-induced leaf abscission in cotton (Gossypium hirsutum L. cv LG-102) seedlings is dependent on leaf position (i.e. physiological age). Fumigation of intact seedlings for 18 hours with 10 microliters per liter of ethylene resulted in 40% abscission of the still-expanding third true (3°) leaves but had no effect on the fully expanded first true (1°) leaves. After 42 hours of fumigation with 50 microliters per liter of ethylene, total abscission of the 3° leaves occurred while <50% abscission of the 1° leaves was observed. On a leaf basis, endogenous levels of free IAA in 1° leaves were approximately twice those of 3° leaves. Free IAA levels were reduced equally (approximately 55%) in both leaf types after 18 hours of ethylene (10 microliters per liter) treatment. Ethylene treatment of intact seedlings inhibited the basipetal movement of [¹⁴C]IAA in petiole segments isolated from both leaf types in a dose-dependent manner. The auxin transport inhibitor N-1-naphthylphthalamic acid increased the rate and extent of ethylene-induced leaf abscission at both leaf positions but did not alter the relative pattern of abscission. Abscission-zone explants prepared from 3° leaves abscised faster than 1° leaf explants when exposed to ethylene. Ethyleneinduced abscission of 3° explants was not appreciably inhibited by exogenous IAA while 1° explants exhibited a pronounced and protracted inhibition. The synthetic auxins 2,4-D and 1-naphthaleneacetic acid completely inhibited ethylene-induced abscission of both 1° and 3° explants for 40 hours. It is proposed that the differential abscission response of cotton seedling leaves is primarily a result of the limited abscission-inhibiting effects of IAA in the abscission zone of the younger leaves.     

DRAGON View: information visualization for annotated microarray data

The DRAGON View information visualization tools aid in the comprehensive analysis of large-scale gene expression data that has been annotated with biologically relevant information through the generation of three types of complementary graphical outputs.