Azospirillum-plant relationships: physiological, molecular, agricultural, and environmental advances (1997-2003)

This review presents a critical and comprehensive documentation and analysis of the developments in agricultural, environmental, molecular, and physiological studies related to Azospirillum cells, and to Azospirillum interactions with plants, based solely on information published between 1997 and 2003. It was designed as an update of previous reviews (Bashan and Levanony 1990; Bashan and Holguin 1997a), with a similar scope of interest. Apart from an update and critical analysis of the current knowledge, this review focuses on the central issues of Azospirillum research today, such as, (i) physiological and molecular studies as a general model for rhizosphere bacteria; (ii) co-inoculation with other microorganisms; (iii) hormonal studies and re-consideration of the nitrogen contribution by the bacteria under specific environmental conditions; (iv) proposed Azospirillum as a non-specific plant-growth-promoting bacterium; (v) re-introduction of the "Additive Hypothesis," which suggests involvement of multiple mechanisms employed by the bacteria to affect plant growth; (vi) comment on the less researched areas, such as inoculant and pesticide research; and (vii) proposes possible avenues for the exploitation of this bacterium in environmental areas other than agriculture.     

Talking with the Donkey: Cooperative Approaches to Environmental Protection

In recent years, governments throughout the world have expressed growing interest in cooperative approaches to environmental protection, including negotiated rulemaking, flexible approaches t o enforcement, and voluntary codes and agreements. It is often argued that cooperative approaches are more cost effective, more conducive t o innovation, and better able t o promote fundamental attitudinal change than traditional "command and control" regulation. However, the overly broad term "cooperative approaches" fails t o acknowledge fundamental differences among these novel po I icies, including distinct ions between mandatory and voluntary programs and between those that involve bipartite negotiations between government and business and those that invite participation by a broader range of interests. This article analyzes these cooperative approaches first by offering a framework to distinguish among various cooperative policy instruments. Second, the article critically examines theoretical arguments and empirical evidence concerning one class o f cooperative approaches, voluntary challenges and agreements. The most striking finding is how little we know about the effectiveness of voluntary approaches. This is a function not only of the quite recent experience with these approaches, but also of more fundamental inattention t o program evaluation and obstacles to evaluation inherent in voluntary programs. The article concludes with a call for a more rigorous program of research to examine the effectiveness of the new policy instruments and t o compare them with traditional regulation and market-based incentives.     

Social setting,intuition and experience in laboratory experiments interact to shape cooperative decision-making

Recent studies suggest that cooperative decision-making in one-shot interactions is a history-dependent dynamic process: promoting intuition versus deliberation typically has a positive effect on cooperation (dynamism) among people living in a cooperative setting and with no previous experience in economic games on cooperation (history dependence). Here, we report on a laboratory experiment exploring how these findings transfer to a non-cooperative setting. We find two major results: (i) promoting intuition versus deliberation has no effect on cooperative behaviour among inexperienced subjects living in a non-cooperative setting; (ii) experienced subjects cooperate more than inexperienced subjects, but only under time pressure. These results suggest that cooperation is a learning process, rather than an instinctive impulse or a self-controlled choice, and that experience operates primarily via the channel of intuition. Our findings shed further light on the cognitive basis of human cooperative decision-making and provide further support for the recently proposed social heuristics hypothesis.     

Aphid-symbiotic bacteria cultured in insect cell lines

The cells and tissues of many aphids contain bacteria known as "secondary symbionts," which under specific environmental circumstances may be beneficial to the host insect. Such symbiotic bacteria are traditionally described as intractable to cultivation in vitro. Here we show that two types of aphid secondary symbionts, known informally as T type and U type, can be cultured and maintained in three insect cell lines. The identities of the cultured bacteria were confirmed by PCR with sequencing of 16S rRNA gene fragments and fluorescence in situ hybridization. In cell lines infected with bacteria derived from aphids harboring both T type and U type, the U type persisted, while the T type was lost. We suggest that the two bacteria persist in aphids because competition between them is limited by differences in tropism for insect tissues or cell types. The culture of these bacteria in insect cell lines provides a new and unique research opportunity, offering a source of unibacterial material for genomic studies and a model system to investigate the interactions between animal cells and bacteria. We propose the provisional taxon names "Candidatus Consessoris aphidicola" for T type and "Candidatus Adiaceo aphidicola" for U type.     

Temporal environmental variability drives the evolution of cooperative breeding in birds

Many vertebrates breed in cooperative groups in which more than two members provide care for young. Studies of cooperative breeding behavior within species have long highlighted the importance of environmental factors in mediating the paradox of why some such individuals delay independent breeding to help raise the offspring of others. In contrast, studies involving comparisons among species have not shown a similarly clear evolutionary-scale relationship between the interspecific incidence of cooperative breeding and any environmental factors. Here, we use a phylogenetically controlled comparative analysis of a complete, socially diverse group of birds-45 species of African starlings-to show that cooperative breeding is positively associated with living in semiarid savanna habitats and with temporal variability in rainfall. Savanna habitats are not only highly seasonal, but also temporally variable and unpredictable, and this temporal variability directly influences individual reproductive decisions in starlings and helps explain interspecific patterns of sociality. Cooperative breeding is likely to be adaptive in temporally variable environments because it allows for both reproduction in harsh years and sustained breeding during benign years. This "temporal variability" hypothesis might help explain the phylogenetic and geographic concentrations of cooperatively breeding vertebrates in savanna-like habitats and other temporally variable environments worldwide.     

Friendship, cliquishness, and the emergence of cooperation

The evolution of cooperation is a central problem in biology and the social sciences. While theoretical work using the iterated prisoner's dilemma (IPD) has shown that cooperation among non-kin can be sustained among reciprocal strategies (i.e. tit-for-tat), these results are sensitive to errors in strategy execution, cyclical invasions by free riders, and the specific ecology of strategies. Moreover, the IPD assumes that a strategy's probability of playing the PD game with other individuals is independent of the decisions made by others. Here, we remove the assumption of independent pairing by studying a more plausible cooperative dilemma in which players can preferentially interact with a limited set of known partners and also deploy longer-term accounting strategies that can counteract the effects of random errors. We show that cooperative strategies readily emerge and persist in a range of noisy environments, with successful cooperative strategies (henceforth, cliquers) maintaining medium-term memories for partners and low thresholds for acceptable cooperation (i.e. forgiveness). The success of these strategies relies on their cliquishness-a propensity to defect with strangers if they already have an adequate number of partners. Notably, this combination of medium-term accounting, forgiveness, and cliquishness fits with empirical studies of friendship and other long-term relationships among humans.     

A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps

For many species, multiple maps are available, often constructed independently by different research groups using different sets of markers and different source material. Integration of these maps provides a higher density of markers and greater genome coverage than is possible using a single study. In this article, we describe a novel approach to comparing and integrating maps by using abstract graphs. A map is modeled as a directed graph in which nodes represent mapped markers and edges define the order of adjacent markers. Independently constructed graphs representing corresponding maps from different studies are merged on the basis of their common loci. Absence of a path between two nodes indicates that their order is undetermined. A cycle indicates inconsistency among the mapping studies with regard to the order of the loci involved. The integrated graph thus produced represents a complete picture of all of the mapping studies that comprise it, including all of the ambiguities and inconsistencies among them. The objective of this representation is to guide additional research aimed at interpreting these ambiguities and inconsistencies in locus order rather than presenting a "consensus order" that ignores these problems.     

Oxygen-utilizing reactions and symbiotic colonization of the squid light organ by Vibrio fischeri.

A major goal in microbiology is to understand the processes by which bacteria successfully colonize host tissue. Although a wealth of studies focusing on pathogenic microorganisms has revealed much about the rare interactions that result in disease, far less is known about the regulation of the ubiquitous, long-term, cooperative associations of bacteria with their animal hosts.     

Epidemiology of Pathogenic Enterobacteria in Humans,Livestock, and Peridomestic Rodents in Rural Madagascar

Background

Among the families of enteric bacteria are globally important diarrheal agents. Despite their potential for zoonotic and environmental transmission, few studies have examined the epidemiology of these pathogens in rural systems characterized by extensive overlap among humans, domesticated and peridomestic animals. We investigated patterns of infection with Enterotoxigenic Escherichia coli, Shigella spp., Salmonella enterica, Vibrio cholerae, and Yersinia spp. (enterocolitica, and pseudotuberculosis) in Southeastern Madagascar where the potential for the aforementioned interactions is high. In this pilot project we conducted surveys to examine behaviors potentially associated with risk of infection and if infection with specific enterobacteria species was associated with diarrheal disease.

Methodology/Principal Findings

PCR was conducted on DNA from human, livestock, and rodent fecal samples from three villages. Overall, human prevalence was highest (77%), followed by rodents (51%) and livestock (18%). Rodents were ∼2.8 times more likely than livestock to carry one of the bacteria. The incidence of individual species varied between villages, with the observation that, E. coli and Shigella spp. were consistently associated with co-infections. As an aggregate, there was a significant risk of infection linked to a water source in one village. Individually, different pathogens were associated with certain behaviors, including: those who had used medication, experienced diarrhea in the past four weeks, or do not use toilets.

Conclusions/Significance

Different bacteria were associated with an elevated risk of infection for various human activities or characteristics. Certain bacteria may also predispose people to co-infections. These data suggest that a high potential for transmission among these groups, either directly or via contaminated water sources. As these bacteria were most prevalent in humans, it is possible that they are maintained in humans and that transmission to other species is infrequent. Further studies are needed to understand bacterial persistence, transmission dynamics, and associated consequences in this and similar systems.     

Cooperative transport in ants: a review of proximate mechanisms

The behavioral mechanisms that lead to cooperation in social insects are often unknown or poorly understood. Cooperative transport, or the movement of an object by two or more individuals, is a particularly impressive example of collaboration among workers. Many ant species perform this behavior, but there is extreme interspecific variation in efficiency. Why are some ant species so efficient at cooperative transport, while others are so inefficient? Surprisingly, the scientific community has little proximate understanding of the adaptations that make certain species excel at this behavior. This work provides a review of the behavioral rules that separate the efficient cooperative transporters from the inefficient. We present two measures of efficiency of cooperative transport as well as a flowchart of the cooperative transport process. By identifying the steps and flow of information, the flowchart enables careful modeling of cooperative transport from a mechanistic perspective. Previous studies of each of the four phases of cooperative transport are discussed, including decision, recruitment, organization, and transport. We also present hypotheses regarding behavioral mechanisms that may modulate efficiency.     

Ecological constraints, life history traits and the evolution of cooperative breeding

The ecological constraints hypothesis is widely accepted as an explanation for the evolution of delayed dispersal in cooperatively breeding birds. Intraspecific studies offer the strongest support. Observational studies have demonstrated a positive association between the severity of ecological constraints and the prevalence of cooperation, and experimental studies in which constraints on independent breeding were relaxed resulted in helpers moving to adopt the vacant breeding opportunities. However, this hypothesis has proved less successful in explaining why cooperative breeding has evolved in some species or lineages but not in others. Comparative studies have failed to identify ecological factors that differ consistently between cooperative and noncooperative species. The life history hypothesis, which emphasizes the role of life history traits in the evolution of cooperative breeding, offers a solution to this difficulty. A recent analysis showed that low adult mortality and low dispersal predisposed certain lineages to show cooperative behaviour, given the right ecological conditions. This represents an important advance, not least by offering an explanation for the patchy phylogenetic distribution of cooperative breeding. We discuss the complementary nature of these two hypotheses and suggest that rather than regarding life history traits as predisposing and ecological factors as facilitating cooperation, they are more likely to act in concert. While acknowledging that different cooperative systems may be a consequence of different selective pressures, we suggest that to identify the key differences between cooperative and noncooperative species, a broad constraints hypothesis that incorporates ecological and life history traits in a single measure of 'turnover of breeding opportunities' may provide the most promising avenue for future comparative studies. Copyright 2000 The Association for the Study of Animal Behaviour.     

Rejuvenating rice proteomics: facts, challenges, and visions

Proteomics is progressing at an unprecedented pace, as can be exemplified by the progress in model organisms such as yeast, bacteria, and mammals. Proteomics research in plants, however, has not progressed at the same pace. Unscrambling of the genome sequences of the dicotyledoneous Arabidopsis thaliana (L.) and monocotyledoneous rice (Oryza sativa L.) plant species, respectively, has made them accessible reference organisms to study plant proteomics. Study of these two reference plants is expected to unravel the mystery of plant biology. Rice, a critically important food crop on the earth, has been termed a "cornerstone" and the "Rosetta stone" for functional genomics of cereal crops. Here, we look at the progress in unraveling rice proteomes and present the facts, challenges, and vision. The text is divided into two major parts: the first part presents the facts and the second part discusses the challenges and vision. The facts include the technology and its use in developing proteomes, which have been critically and constructively reviewed. The challenges and vision deal with the establishment of technologies to exhaustively investigate the protein components of a proteome, to generate high-resolution gel-based reference maps, and to give rice proteomics a functional dimension by studying PTMs and isolation of multiprotein complexes. Finally, we direct a vision on rice proteomics. This is our third review in series on rice proteomics, which aims to stimulate an objective discussion among rice researchers and to understand the necessity and impact of unraveling rice proteomes to their full potential.     

Negotiation, sanctions, and context dependency in the legume-Rhizobium mutualism

Two important questions about mutualisms are how the fitness costs and benefits to the mutualist partners are determined and how these mechanisms affect the evolutionary dynamics of the mutualism. We tackle these questions with a model of the legume-rhizobium symbiosis that regards the mutualism outcome as a result of biochemical negotiations between the plant and its nodules. We explore the fitness consequences of this mechanism to the plant and rhizobia and obtain four main results. First, negotiations permit the plant to differentially reward more-cooperative rhizobia--a phenomenon termed "plant sanctions"--but only when more-cooperative rhizobia also provide the plant with good outside options during negotiations with other nodules. Second, negotiations may result in seemingly paradoxical cases where the plant is worse off when it has a "choice" between two strains of rhizobia than when infected by either strain alone. Third, even when sanctions are effective, they are by themselves not sufficient to maintain cooperative rhizobia in a population: less cooperative strains always have an advantage at the population level. Finally, partner fidelity feedback, together with genetic correlations between a rhizobium strain's cooperativeness and the outside options it provides, can maintain cooperative rhizobia. Our results show how joint control over the outcome of a mutualism through the proximate mechanism of negotiation can affect the evolutionary dynamics of interspecific cooperation.     

Effective norm emergence in cell systems under limited communication

Background

The cooperation of cells in biological systems is similar to that of agents in cooperative multi-agent systems. Research findings in multi-agent systems literature can provide valuable inspirations to biological research. The well-coordinated states in cell systems can be viewed as desirable social norms in cooperative multi-agent systems. One important research question is how a norm can rapidly emerge with limited communication resources.

Results

In this work, we propose a learning approach which can trade off the agents’ performance of coordinating on a consistent norm and the communication cost involved. During the learning process, the agents can dynamically adjust their coordination set according to their own observations and pick out the most crucial agents to coordinate with. In this way, our method significantly reduces the coordination dependence among agents.

Conclusion

The experiment results show that our method can efficiently facilitate the social norm emergence among agents, and also scale well to large-scale populations.

     

Antibiotic Resistance is Widespread in Urban Aquatic Environments of Rio de Janeiro,Brazil

Bacterial resistance to antibiotics has become a public health issue. Over the years, pathogenic organisms with resistance traits have been studied due to the threat they pose to human well-being. However, several studies raised awareness to the often disregarded importance of environmental bacteria as sources of resistance mechanisms. In this work, we analyze the diversity of antibiotic-resistant bacteria occurring in aquatic environments of the state of Rio de Janeiro, Brazil, that are subjected to distinct degrees of anthropogenic impacts. We access the diversity of aquatic bacteria capable of growing in increasing ampicillin concentrations through 16S rRNA gene libraries. This analysis is complemented by the characterization of antibiotic resistance profiles of isolates obtained from urban aquatic environments. We detect communities capable of tolerating antibiotic concentrations up to 600 times higher than the clinical levels. Among the resistant organisms are included potentially pathogenic species, some of them classified as multiresistant. Our results extend the knowledge of the diversity of antibiotic resistance among environmental microorganisms and provide evidence that the diversity of drug-resistant bacteria in aquatic habitats can be influenced by pollution.     

Differences in the electrostatic surfaces of the type III secretion needle proteins PrgI, BsaL, and MxiH

Gram-negative bacteria use a needle-like protein assembly, the type III secretion apparatus, to inject virulence factors into target cells to initiate human disease. The needle is formed by the polymerization of approximately 120 copies of a small acidic protein that is conserved among diverse pathogens. We previously reported the structure of the BsaL needle monomer from Burkholderia pseudomallei by nuclear magnetic resonance (NMR) spectroscopy and others have determined the crystal structure of the Shigella flexneri MxiH needle. Here, we report the NMR structure of the PrgI needle protein of Salmonella typhimurium, a human pathogen associated with food poisoning. PrgI, BsaL, and MxiH form similar two helix bundles, however, the electrostatic surfaces of PrgI differ radically from those of BsaL or MxiH. In BsaL and MxiH, a large negative area is on a face formed by the helix alpha1-alpha2 interface. In PrgI, the major negatively charged surface is not on the "face" but instead is on the "side" of the two-helix bundle, and only residues from helix alpha1 contribute to this negative region. Despite being highly acidic proteins, these molecules contain large basic regions, suggesting that electrostatic contacts are important in needle assembly. Our results also suggest that needle-packing interactions may be different among these bacteria and provide the structural basis for why PrgI and MxiH, despite 63% sequence identity, are not interchangeable in S. typhimurium and S. flexneri.     

Direct observations of cooperative effects in oral streptococcal adhesion to glass by analysis of the spatial arrangement of adhering bacteria

The spatial arrangement of two strains of oral bacteria adhering on glass was studied in order to investigate cooperative effects in their adhesion mechanisms. Streptococcus salivarius HB was a strain which possessed several classes of fibrillar surface appendages, whereas on the cell surface of S. mutants NS no surface appendages could be identified. The bacteria were deposited from a flowing suspension with various buffer concentrations on the bottom glass plate of a parallel plate flow cell and were observed directly with a video camera mounted on a phase contrast microscope. The positions of all adhering bacteria were determined by means of automated real time image analysis and subsequently employed for calculating radial and angular pair distribution functions. Pair distribution functions indicate the average relative number density of bacteria around one deposited bacterium as a function of the radial distance or the angular orientation relative to the flow direction. From the calculated pair distribution functions of both bacterial strains it was concluded that cooperative effects contributed to the adhesion of S. salivarius HB, but not to adhesion of S. mutants NS. It was suggested that these cooperative effects originate from the surface appendages of S. salivarius HB.     

Phylogenetic diversity, host-specificity and community profiling of sponge-associated bacteria in the northern Gulf of Mexico

Background

Marine sponges can associate with abundant and diverse consortia of microbial symbionts. However, associated bacteria remain unexamined for the majority of host sponges and few studies use phylogenetic metrics to quantify symbiont community diversity. DNA fingerprinting techniques, such as terminal restriction fragment length polymorphisms (T-RFLP), might provide rapid profiling of these communities, but have not been explicitly compared to traditional methods.

Methodology/Principal Findings

We investigated the bacterial communities associated with the marine sponges Hymeniacidon heliophila and Haliclona tubifera, a sympatric tunicate, Didemnum sp., and ambient seawater from the northern Gulf of Mexico by combining replicated clone libraries with T-RFLP analyses of 16S rRNA gene sequences. Clone libraries revealed that bacterial communities associated with the two sponges exhibited lower species richness and lower species diversity than seawater and tunicate assemblages, with differences in species composition among all four source groups. T-RFLP profiles clustered microbial communities by source; individual T-RFs were matched to the majority (80.6%) of clone library sequences, indicating that T-RFLP analysis can be used to rapidly profile these communities. Phylogenetic metrics of community diversity indicated that the two sponge-associated bacterial communities include dominant and host-specific bacterial lineages that are distinct from bacteria recovered from seawater, tunicates, and unrelated sponge hosts. In addition, a large proportion of the symbionts associated with H. heliophila were shared with distant, conspecific host populations in the southwestern Atlantic (Brazil).

Conclusions/Significance

The low diversity and species-specific nature of bacterial communities associated with H. heliophila and H. tubifera represent a distinctly different pattern from other, reportedly universal, sponge-associated bacterial communities. Our replicated sampling strategy, which included samples that reflect the ambient environment, allowed us to differentiate resident symbionts from potentially transient or prey bacteria. Pairing replicated clone library construction with rapid community profiling via T-RFLP analyses will greatly facilitate future studies of sponge-microbe symbioses.     

Sensor domain of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknD, forms a highly symmetric beta propeller

Diverse pathogenic bacteria produce transmembrane receptor Ser/Thr protein kinases (STPKs), but little is known about the signals mediated by these "eukaryotic-like" proteins. To explore the basis for signaling in the bacterial STPK receptor family, we determined the structure of the sensor domain of Mycobacterium tuberculosis PknD. In two crystal forms, the PknD sensor domain forms a rigid, six-bladed beta-propeller with a flexible tether to the transmembrane domain. The PknD sensor domain is the most symmetric beta-propeller structure described. All residues that vary most among the blade subdomains cluster in the large "cup" motif, analogous to the ligand-binding surface in many beta-propeller proteins. These results suggest that PknD binds a multivalent ligand that signals by changing the quaternary structure of the intracellular kinase domain.     

Interactions of Tetrahymena pyriformis, Escherichia coli, Azotobacter vinelandii, and Glucose in a Minimal Medium

A study was made of the food web formed from a protozoon, two bacteria, and a glucose minimal medium in chemostat culture. The system was also divided into simpler parts, first by omitting the protozoon to obtain a competition system, and then by omitting one or the other of the bacteria to obtain two food chains. In the competition studies, one bacterium was displaced by the other at all holding times used. In the food chain studies, sustained oscillations of the population densities of predator and prey developed at short holding times, and then changed to damped oscillations at longer holding times. In addition, the level of residual glucose remained high at long holding times. A new model of microbial growth is necessary to explain these results. In the food web studies, predation of the protozoon on the two bacteria stabilized the competition between the latter and allowed their coexistence in the same habitat. Thus, Gause's principle was circumvented.