Understanding the Evolution of Industrial Symbiosis Research

This study analyzes the evolution of the research field of industrial symbiosis (IS). We elucidate its embedding in industrial ecology (IE), trace the development of research themes, and reveal the evolution of the research network through analysis of the core literature and journals that appeared from 1997 to 2012 by citation analysis, cocitation analysis, and network analysis. In the first period (1997–2005), IS research held a minority share in the IE literature. The research revolved around the concept of IS, the assessment of eco‐industrial park projects, and the establishment of waste treatment and recycling networks. In the second period (2006–2012), diverse research approaches and theories enriched the field, which has led to a maturation in theory building. Our findings clearly illustrate that IS evolved from practice‐oriented research toward coherent theory building through a systematic underpinning and linking of diverse topics. As scientific attention shifted from exploring a phenomenon to elucidating underlying mechanisms, IS knowledge found worldwide practical implementation. The coauthorship network shows that the academic communities of IS are distributed worldwide and that international collaboration is widespread. Through bibliometric and network analysis of IS, we have created a systemic, quantitative image of the evolution of the IS research field and community, which gives IS researchers an underpinned overview of the IS research and may help them to identify new directions and synergy in worldwide research.     

From the Cell to the Ecosystem: The Physiological Evolution of Symbiosis

Living organisms constantly interact with their habitats, selectively taking up compounds from their surroundings to meet their particular needs but also excreting metabolic products and thus modifying their environment. The small size, ubiquity, metabolic versatility, flexibility, and genetic plasticity (horizontal transfer) of microbes allow them to tolerate and quickly adapt to unfavorable and/or changing environmental conditions. The consumption of resources and the formation of metabolic products by spatially separated microbial populations constitute the driving forces that lead to chemical gradient formation. Communication and cooperation, both within and among bacterial species, have produced the properties that give these organisms a selective advantage. Observations of a wide range of natural habitats have established that bacteria do not function as individuals; rather, the vast majority of bacteria in natural and pathogenic ecosystems live in biofilms, defined as surface-associated, complex aggregates of bacterial communities that are attached to solid substrates and embedded in a polymer matrix of their own production. The spatial configurations of biofilms reach levels of complexity nearing those of multicellular eukaryotes. Microbial consortia have played important roles throughout the history of life on Earth, from the microbial mats (a type of biofilm) that were probably the first ecosystems in the early Archean, to the complex microbiota of the intestinal tract of different animals.     

The Evolution of Facilitated Industrial Symbiosis

While much work has been done on the conditions surrounding the emergence and establishment of industrial symbiosis (IS), new attention is being paid to understanding the evolution of IS over time. We demonstrate empirically how a new, facilitated IS initiative developed and evolved over an 8‐year period. We explore its network evolution by considering how the facilitator's actions enabled and precluded two fundamental network processes—serendipitous and goal‐directed processes. We discuss implications for a more generalized theory of IS development by exploring why and how different evolutionary trajectories may unfold.     

Evolution of Mutualistic Symbiosis without Vertical Transmission

Mutualistic symbioses are considered to evolve from parasitic relationships. Vertical transmission, defined as the direct transfer of infection from a parent organism to its progeny, has been suggested as a key factor causing reduction of symbiont virulence and evolution of mutualism. On the other hand, there are several mutualistic associations without vertical transmission, such as those between plants and mycorrhizal fungi, legumes and rhizobia, and some corals and dinoflagellates. It is expected that all mutualisms evolve perfect vertical transmission if the relationship is really mutualistic, because hosts may fail to acquire symbionts if they do not transmit the symbionts by vertical transmission. We have developed a mathematical model to clarify the conditions under which mutualistic symbiosis without vertical transmission should evolve. The evolution may occur when and only when (i) vertical transmission involves some costs in the host, (ii) the symbiont suffers direct negative effects if it exploits the host too intensively, (iii) the host establishes the ability to make use of waste products from the symbiont, and (iv) the mechanism of vertical transmission is controlled by the host. We also clarify the conditions under which mutualistic symbiosis with vertical transmission evolves.     

VA菌根共生的起源和进化

ＶＡ菌根共生的起源和进化赵之伟（云南大学生物学系,昆明６５００９１）ＯｒｉｇｉｎａｎｄＥｖｏｌｕｔｉｏｎｏｆｔｈｅＶＡＭｙｃｏｒｒｈｉｚａｌＳｙｍｂｉｏｓｉｓ．ＺｈａｏＺｈｉｗｅｉ（ＢｉｏｌｏｇｙＤｅｐａｒｔｍｅｎｔｏｆＹｕｎｎａｎＵｎｉｖｅｒｓｉｔ...     

The Evolution of Insect-Fungus Associations: From Contact to Stable Symbiosis

Insect-fungus interactions range from agonistic to mutualistic,and include several spectacular examples of complex symbioses.A potential benefit of mycophagy (the ingestion of fungal tissue)is the augmentation of digestive capacity by the ingestion offungal enzymes that remain active in the gut following ingestion.Cellulose digestion is mediated by ingested fungal enzymes inthe wood-boring larvae of cerambycid beetles and siricid woodwasps,in detritus-feeding stonefly nymphs, and in the workers of fungus-growingtermites. In this paper I discuss a plausible scenario for theevolution of stable symbiotic insect-fungus associations, inwhich the augmentation of digestive capacity through the ingestionof fungal enzymes is an important factor leading to the establishmentof interdependence between the interacting partners in a mutualism.Ingested fungal enzymes play a different role in the mutualisticassociation of the attine ants and their symbiotic fungi. Analyses of the associations of the siricid woodwasps, fungus-growingtermites, and fungus-growing ants with their symbiotic fungipermit the testing of Law's (1985) predictions concerning theconsequences of evolution in a mutualistic environment. As predicted,the rate of speciation has been slower in the protected partnerthan in the host partner, selection has favored asexual reproductionin the protected partner, and, at least in the attine ant-fungussymbiosis, the protected partner exhibits a low degree of specificitytoward different host species. Insect-fungus interactions provide rich material for the studyof both mechanistic and theoretical aspects of mutualism.     

Extracellular and Mixotrophic Symbiosis in the Whale-Fall Mussel Adipicola pacifica: A Trend in Evolution from Extra- to Intracellular Symbiosis

Background

Deep-sea mussels harboring chemoautotrophic symbionts from hydrothermal vents and seeps are assumed to have evolved from shallow-water asymbiotic relatives by way of biogenic reducing environments such as sunken wood and whale falls. Such symbiotic associations have been well characterized in mussels collected from vents, seeps and sunken wood but in only a few from whale falls.

Methodology/Principal Finding

Here we report symbioses in the gill tissues of two mussels, Adipicola crypta and Adipicola pacifica, collected from whale-falls on the continental shelf in the northwestern Pacific. The molecular, morphological and stable isotopic characteristics of bacterial symbionts were analyzed. A single phylotype of thioautotrophic bacteria was found in A. crypta gill tissue and two distinct phylotypes of bacteria (referred to as Symbiont A and Symbiont C) in A. pacifica. Symbiont A and the A. crypta symbiont were affiliated with thioautotrophic symbionts of bathymodiolin mussels from deep-sea reducing environments, while Symbiont C was closely related to free-living heterotrophic bacteria. The symbionts in A. crypta were intracellular within epithelial cells of the apical region of the gills and were extracellular in A. pacifica. No spatial partitioning was observed between the two phylotypes in A. pacifica in fluorescence in situ hybridization experiments. Stable isotopic analyses of carbon and sulfur indicated the chemoautotrophic nature of A. crypta and mixotrophic nature of A. pacifica. Molecular phylogenetic analyses of the host mussels showed that A. crypta constituted a monophyletic clade with other intracellular symbiotic (endosymbiotic) mussels and that A. pacifica was the sister group of all endosymbiotic mussels.

Conclusions/Significance

These results strongly suggest that the symbiosis in A. pacifica is at an earlier stage in evolution than other endosymbiotic mussels. Whale falls and other modern biogenic reducing environments may act as refugia for primal chemoautotrophic symbioses between eukaryotes and prokaryotes since the extinction of ancient large marine vertebrates.     

Evolution of polyembryony: Consequences to the fitness of mother and offspring

Polyembryony, referring here to situations where a nucellar embryo is formed along with the zygotic embryo, has different consequences for the fitness of the maternal parent and offspring. We have developed genetic and inclusive fitness models to derive the conditions that permit the evolution of polyembryony under maternal and offspring control. We have also derived expressions for the optimal allocation (evolutionarily stable strategy, ESS) of resources between zygotic and nucellar embryos. It is seen that (i) Polyembryony can evolve more easily under maternal control than under that of either the offspring or the ‘selfish’ endosperm. Under maternal regulation, evolution of polyembryony can occur for any clutch size. Under offspring control polyembryony is more likely to evolve for high clutch sizes, and is unlikely for low clutch sizes (<3). This conflict between mother and offspring decreases with increase in clutch size and favours the evolution of polyembryony at high clutch sizes, (ii) Polyembryony can evolve for values of “x” (the power of the function relating fitness to seed resource) greater than 0.5758; the possibility of its occurrence increases with “x”, indicating that a more efficient conversion of resource into fitness favours polyembryony. (iii) Under both maternal parent and offspring control, the evolution of polyembryony becomes increasingly unlikely as the level of inbreeding increases, (iv) The proportion of resources allocated to the nucellar embryo at ESS is always higher than that which maximizes the rate of spread of the allele against a non-polyembryonic allele.     

Consequences of Parasitism to Marine Invertebrates: Host Evolution?

Parasitism among aquatic invertebrates is common, if not ubiquitous,and can be pathological to hosts. However, host evolution inresponse to parasitism has received little attention, particularlyfor marine invertebrates. Drawing on the rich literature demonstratingprey adaptations to predators, I develop analogous predictionsfor the ways in which host life histories may be molded by theirparasites. Such adaptations are expected when the effects ofparasites are severe and when the probability of infection ishigh. Predicted life history changes include the evolution ofsemelparity, reduced age at first reproduction and reduced sizeat first reproduction. Using Recent and fossil populations oftwo bivalves species in the genusTransennella, I show that theincidence of trematode parasites may explain a trend of reducedsize through time and contribute to the maintenance of sexualdimorphism for size.     

Symbiosis as a General Principle in Eukaryotic Evolution

Eukaryotes have evolved and diversified in the context of persistent colonization by non-pathogenic microorganisms. Various resident microorganisms provide a metabolic capability absent from the host, resulting in increased ecological amplitude and often evolutionary diversification of the host. Some microorganisms confer primary metabolic pathways, such as photosynthesis and cellulose degradation, and others expand the repertoire of secondary metabolism, including the synthesis of toxins that confer protection against natural enemies. A further route by which microorganisms affect host fitness arises from their modulation of the eukaryotic-signaling networks that regulate growth, development, behavior, and other functions. These effects are not necessarily based on interactions beneficial to the host, but can be a consequence of either eukaryotic utilization of microbial products as cues or host–microbial conflict. By these routes, eukaryote–microbial interactions play an integral role in the function and evolutionary diversification of eukaryotes.Eukaryotes do not live alone. They bear living cells of bacteria (Eubacteria and Archaea), and often eukaryotic microorganisms, on their surfaces and internally without any apparent ill effect. Furthermore, there is now persuasive evidence that all extant eukaryotes are derived from an association with intracellular bacteria within the Rickettsiales that evolved into mitochondria (Williams et al. 2007), with the implication that this propensity to form persistent associations has very ancient evolutionary roots. In this respect, the eukaryotes are different from the bacteria, among which only a subset associate with eukaryotes, specifically members of about 11 of an estimated 52 phyla of Eubacteria (Sachs et al. 2011) and a tiny minority of Archaea (Gill and Brinkman 2011).The current interest in the microbiota associated with eukaryotes stems from key technological advances for culture-independent analysis of microbial communities, especially high-throughput sequencing methods to identify and quantify microorganisms (Caporaso et al. 2011; Zaneveld et al. 2011). The Human Microbiome Project (commonfund.nih.gov), MetaHIT (metahit.eu), and other initiatives are yielding unprecedented information on the taxonomic diversity and functional capabilities of microorganisms associated with humans, other animals, and also plants, fungi, and unicellular eukaryotes (the protists), as well as abiotic habitats (Qin et al. 2010; Muegge et al. 2011; Human Microbiome Project 2012a; Lundberg et al. 2012; Bourne et al. 2013). Much of this research has focused on the Eubacteria, but eukaryotic members of the microbiota, especially the fungi, are increasingly being investigated (Iliev et al. 2012; Findley et al. 2013).Although driven by technological change, these culture-independent studies of the microbiota of humans and other eukaryotes are having profound consequences for our conceptual understanding. In particular, there is a growing appreciation that the germ theory of disease, which has played a crucial role in improving public health and food production through the 20th century, has also led to the widespread but erroneous belief that all microorganisms associated with animals and plants are pathogens. This outmoded perception is increasingly being replaced by the recognition that eukaryotes are chronically infected with benign and beneficial microorganisms, and that disease can result from disturbance to the composition or activities of the microbiota (McFall-Ngai et al. 2013; Stecher et al. 2013).This article reviews the pervasive impact of symbiosis with microorganisms on the traits of their eukaryotic hosts and the resultant consequences for the evolutionary history of eukaryotes. For the great majority of associations, the effects of symbiosis can be attributed to two types of interaction. The first interaction—“symbiosis as a source of novel capabilities”—is founded on metabolic or other traits possessed by the microbial partner but not the eukaryotic host. By gaining access to these capabilities, eukaryotes have repeatedly derived enhanced nutrition, defense against natural enemies, or other selectively important characteristics. The second interaction—“the symbiotic basis of health”—comprises the improved vigor and fitness that eukaryote hosts gain through microbial modulation of multiple traits, including growth rates, immune function, nutrient allocation, and behavior, even though the effects cannot be ascribed to specific microbial capabilities absent from the host. There is increasing evidence that the health benefits of symbiosis are commonly a consequence of microbial modulation of the signaling networks by which the growth and physiological function of eukaryote hosts are coordinated.This article comprises three sections: the two types of interaction are considered in turn, with the key patterns and processes illustrated by specific examples from a range of symbioses in animals, plants, and other eukaryotes; and the concluding comments address some key unanswered questions about symbiosis in eukaryotes. This article does not review the full diversity of associations made in this article on the general principles of symbiosis in eukaryotic evolution; interested readers are referred to Douglas (2010).     

Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria

The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as Agrobacterium are plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of the Rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes. Agrobacterium strains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain, A. tumefaciens C58, has been previously sequenced. In this study, the genomes of the biovar II strain A. radiobacter K84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strain A. vitis S4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of the Alphaproteobacteria provides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in select Beta- and Gammaproteobacteria species. Together, these results define the evolution of chromosome architecture and gene content among the Rhizobiaceae and support a generalized mechanism for second-chromosome formation among bacteria.     

Global Distribution and Evolution of a Toxinogenic Burkholderia-Rhizopus Symbiosis

Toxinogenic endobacteria were isolated from a collection of Rhizopus spp. representing highly diverse geographic origins and ecological niches. All endosymbionts belonged to the Burkholderia rhizoxinica complex according to matrix-assisted laser desorption ionization-time of flight biotyping and multilocus sequence typing, suggesting a common ancestor. Comparison of host and symbiont phylogenies provides insights into possible cospeciation and horizontal-transmission events.Bacterial symbionts and their metabolic potential play essential roles for many organisms. They may benefit from improved fitness, survival, and even acquired virulence (7, 12, 22). In the course of our studies of the biosynthesis of rhizoxin, the causative agent of rice seedling blight (10), we found that the phytotoxin is produced not by the fungus Rhizopus microsporus but by symbiotic bacteria (Burkholderia rhizoxinica) that reside within the fungus cytosol (13, 15, 23). Furthermore, cloning and sequencing of the rhizoxin biosynthesis gene cluster revealed the molecular basis of bacterial toxin production (14). In sum, this represents an unparalleled example for a symbiosis in which a fungus harbors bacteria for the production of a virulence factor. In analogy, we found that the first reported “mycotoxins” from lower fungi, the highly toxic cyclopeptides rhizonin A and B (25, 28), are also produced by symbiotic bacteria (Burkholderia endofungorum) and not by the fungus (16). While both rhizoxins and rhizonins have been believed to promote zygomycoses (21), there is no indication for toxin-producing endosymbiotic bacteria in clinical isolates (18).In nature, toxin production plays a pivotal role in the development of the fungus-bacterium association. Studies of the evolution of host resistance indicate that the association resulted from a pathogenicity mutualism shift in insensitive zygomycetes (24). The fungus lost its ability to sporulate independently and became totally dependent on endobacteria for reproduction through spores, thus warranting the persistence of the symbiosis and its efficient distribution through vegetative spores (17).To gain a broader view of the occurrence, biosynthetic potential, and relationship of toxinogenic endofungal bacteria, we investigated a collection of Rhizopus spp. consisting of 20 isolates classified as R. microsporus (of which 13 belong to R. microsporus var. microsporus, four to R. microsporus var. chinensis, two to R. microsporus var. oligosporus, and one to R. microsporus var. rhizopodiformis), one isolate classified as Rhizopus sp., and one Rhizopus oryzae strain. We initially monitored the presence of bacterial symbionts by PCR using universal primers (16S rRNA genes) and rhizoxin production in all available Rhizopus strains. Liquid cultivation of fungi in production medium with and without antibiotic followed by organic solvent extraction yielded crude extracts that were analyzed by high-performance liquid chromatography (HPLC) and mass spectrometry (MS). In total, eight fungal strains were identified or confirmed as rhizoxin positive and thus expected to harbor endosymbionts. In all cases, this assumption was verified by PCR and confocal scanning microscopy. By means of an optimized protocol, we finally succeeded in the isolation and cultivation of all eight bacterial symbiont strains in pure cultures (isolates B1 to B8) (Table ​(Table11).

TABLE 1.

Fungal strains and their bacterial endosymbionts

The Evolution and Consequences of Sex-Specific Reproductive Variance

Natural selection favors alleles that increase the number of offspring produced by their carriers. But in a world that is inherently uncertain within generations, selection also favors alleles that reduce the variance in the number of offspring produced. If previous studies have established this principle, they have largely ignored fundamental aspects of sexual reproduction and therefore how selection on sex-specific reproductive variance operates. To study the evolution and consequences of sex-specific reproductive variance, we present a population-genetic model of phenotypic evolution in a dioecious population that incorporates previously neglected components of reproductive variance. First, we derive the probability of fixation for mutations that affect male and/or female reproductive phenotypes under sex-specific selection. We find that even in the simplest scenarios, the direction of selection is altered when reproductive variance is taken into account. In particular, previously unaccounted for covariances between the reproductive outputs of different individuals are expected to play a significant role in determining the direction of selection. Then, the probability of fixation is used to develop a stochastic model of joint male and female phenotypic evolution. We find that sex-specific reproductive variance can be responsible for changes in the course of long-term evolution. Finally, the model is applied to an example of parental-care evolution. Overall, our model allows for the evolutionary analysis of social traits in finite and dioecious populations, where interactions can occur within and between sexes under a realistic scenario of reproduction.