Are paradoxes of amoeboid cognition, memristors, and memory mandating a re-conceptualization of actions and behaviors?

Background From intelligent behaviors of individual molecules and primitive organisms to those with a nervous system and brain, nature displays a fascinating collective memory across time and space. Using certain electronic circuits called memristors, it has been possible to emulate several processes of memory and learning, including a predictive form of intelligence of simple amoebas. Purpose What is the core of such intelligent performances? Although memristors are able to effectively describe puzzling biologic behaviors, recent results challenge their very existence altogether. This paper asks what can be gleaned from the underlying controversy itself, which will be argued is analogous to the observer principle in quantum physics. It is hypothesized that the material phenomena of resonance and sync have a counterpart involving behavior and memory. This questions the prominent role of a causative agent, and which type of behavior or memory is being occasioned. Results Building on the theory of memristors, the challenge of their actualization, and puzzling behaviors of amoebas, this paper proposes that 'resonating actions' - that is, similar or interlinked behaviors beyond space and time - are enabled by an underlying field of potentiation or domain of influence, and not by a cause-effect relationship. Such linked behaviors resemble a form of 'action coherence.' Habituated actions, memory, and behavior may arise out of a similar field of consciousness (here, modeled as memristors). These principles may be at the core of many hitherto unexplained mysteries of collective learning and behavior beyond space and time. Although this study is based on amoebas, the key postulates are also of great relevance to human thinking, behavior, and performance (including the representation of illness), and have independently been confirmed in the fields of consciousness research and spirituality.

Morphological stasis in the first myxomycete from the Mesozoic, and the likely role of cryptobiosis.

Myxomycetes constitute a group within the Amoebozoa well known for their motile plasmodia and morphologically complex fruiting bodies. One obstacle hindering studies of myxomycete evolution is that their fossils are exceedingly rare, so evolutionary analyses of this supposedly ancient lineage of amoebozoans are restricted to extant taxa. Molecular data have significantly advanced myxomycete systematics, but the evolutionary history of individual lineages and their ecological adaptations remain unknown. Here, we report exquisitely preserved myxomycete sporocarps in amber from Myanmar, ca. 100 million years old, one of the few fossil myxomycetes, and the only definitive Mesozoic one. Six densely-arranged stalked sporocarps were engulfed in tree resin while young, with almost the entire spore mass still inside the sporotheca. All morphological features are indistinguishable from those of the modern, cosmopolitan genus Stemonitis, demonstrating that sporocarp morphology has been static since at least the mid-Cretaceous. The ability of myxomycetes to develop into dormant stages, which can last years, may account for the phenotypic stasis between living Stemonitis species and this fossil one, similar to the situation found in other organisms that have cryptobiosis. We also interpret Stemonitis morphological stasis as evidence of strong environmental selection favouring the maintenance of adaptations that promote wind dispersal.

Plasmodial slime molds and the evolution of microbial husbandry.

Detailed analyses into the life cycle of the soil-dwelling microbe Dictyostelium discoideum led to the conclusion that this "social amoeba" practices some form of "non-monoculture farming" via the transfer of bacteria to novel environments. Herein, we show that in myxomycetes (plasmodial slime molds or myxogastrids) a similar "farming symbiosis" has evolved. Based on laboratory studies of two representative species in the genera Fuligo and Didymium, the sexual life cycle of these enigmatic microbes that feed on bacteria was reconstructed, with reference to plasmo- and karyogamy. We document that the spores carry and transfer bacteria and hence may inoculate new habitats. The significance of this finding with respect to Ernst Haeckel's work on myxomycetes and his concept of ecology are addressed.

A four year survey reveals a coherent pattern between occurrence of fruit bodies and soil amoebae populations for nivicolous myxomycetes.

Among soil-inhabiting protists, myxomycetes stand out by their macroscopic fructifications which have allowed studies on their ecology and distribution for more than two hundred years. One of the most distinct ecological guilds in myxomycetes are the nivicolous or "snowbank" myxomycete species, which produce fruit bodies at the edge of melting snowbanks in spring. Relationship between the occurrence of fructifications and myxamoebae remain unknown. In this study we used modern molecular techniques, by direct DNA amplification from soil extracts (NGS metabarcoding) to compare the distribution of soil-inhabiting myxamoebae found in 2016 with fructifications from the same sites collected over the course of four years (2013, 2015-17) along an elevational transect in the northern German Alps. A coherent community composition between fructification and soil myxamoebae, though with species-specific differences in relative abundance, was revealed. Although patterns varied among species, myxamoebae were found at both low and high elevations, whereas fruit bodies were mainly found at higher elevations, likely explained by the presence of a stable and long-lasting snow cover. In addition, a year to year comparison of fructification records support the hypothesis that the abundance of fructifications strongly depends on the onset of snowfall in the previous autumn and the soil temperature regime throughout the winter.

A Method for Growing Bio-memristors from Slime Mold.

Our research is aimed at gaining a better understanding of the electronic properties of organisms in order to engineer novel bioelectronic systems and computing architectures based on biology. This specific paper focuses on harnessing the unicellular slime mold Physarum polycephalum to develop bio-memristors (or biological memristors) and bio-computing devices. The memristor is a resistor that possesses memory. It is the 4th fundamental passive circuit element (the other three are the resistor, the capacitor, and the inductor), which is paving the way for the design of new kinds of computing systems; e.g., computers that might relinquish the distinction between storage and a central processing unit. When applied with an AC voltage, the current vs. voltage characteristic of a memristor is a pinched hysteresis loop. It has been shown that P. polycephalum produces pinched hysteresis loops under AC voltages and displays adaptive behavior that is comparable with the functioning of a memristor. This paper presents the method that we developed for implementing bio-memristors with P. polycephalum and introduces the development of a receptacle to culture the organism, which facilitates its deployment as an electronic circuit component. Our method has proven to decrease growth time, increase component lifespan, and standardize electrical observations.

The Species Problem in Myxomycetes Revisited.

Species identification in the myxomycetes (plasmodial slime molds or myxogastrids) poses particular challenges to researchers as a result of their morphological plasticity and frequent alteration between sexual and asexual life strategies. Traditionally, myxomycete morphology has been used as the primary method of species delimitation. However, with the increasing availability of genetic information, traditional myxomycete taxonomy is being increasingly challenged, and new hypotheses continue to emerge. Due to conflicts that sometimes occur between traditional and more modern species concepts that are based largely on molecular data, there is a pressing need to revisit the discussion surrounding the species concept used for myxomycetes. Biological diversity is being increasingly studied with molecular methods and data accumulates at ever-faster rates, making resolution of this matter urgent. In this review, currently used and potentially useful species concepts (biological, morphological, phylogenetic and ecological) are reviewed, and an integrated approach to resolve the myxomycete species problem is discussed.

Crown fire and surface fire: effects on myxomycetes inhabiting pine plantations.

Myxomycetes are heterotrophic eukaryote organisms that have three life stages, none of which are known to be resistant to fire. The response of myxobiota to different severity of fire is not well known either. We examined myxomycetes in Pinus mugo plantations following a crown fire and in Pinus sylvestris plantations following a surface fire during the first three years after the wildfire event in forested coastal sand dunes in western Lithuania. Additionally, we investigated myxomycetes in corresponding unburned stands. All studied sites (unburned and burned) bore rather different myxomycete assemblages but the disparities of the species compositions between both burn types were more pronounced showing that fire severity had stronger impact on myxomycete species composition than the pre-fire stand type. Analysis of myxomycete assemblages (including the results from field collections, bark and litter cultures) showed that surface fire sites bore the highest number of post-fire species compared to crown fire and unburned sites. Dynamic annual changes in species composition were observed in all studied sites but only crown fire plots showed a clear chronosequence of post-fire myxomycete assemblages. Fire impact promoted establishment and/or sporulation of myxomycete species that are rare in similar unburned stands, or are usually confined to other types of forests and substrata. In addition, individual myxomycete species tended to switch substratum usage during the course of vegetation succession, with a final return to their usual substrata. This possibly signaled the end of early stage of post-fire succession.

Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa).

Myxomycetes or plasmodial slime molds are widespread and very common soil amoebae with the ability to form macroscopic fruiting bodies. Even if their phylogenetic position as a monophyletic group in Amoebozoa is well established, their internal relationships are still not entirely resolved. At the base of the most intensively studied dark-spored clade lies the order Echinosteliales, whose highly divergent small subunit ribosomal (18S) RNA genes represent a challenge for phylogenetic reconstructions. This is because they are characterized by unusually long variable helices of unknown secondary structure and a high inter- and infraspecific divergence. Current classification recognizes two families: the monogeneric Echinosteliaceae and the Clastodermataceae with the genera Barbeyella and Clastoderma. To better resolve the phylogeny of the Echinosteliales, we obtained three new small subunit ribosomal (18S) RNA gene sequences of Clastoderma and Echinostelium corynophorum. Our phylogenetic analyses suggested the polyphyly of the family Clastodermataceae, as Barbeyella was more closely related to Echinostelium arboreum than to Clastoderma, while Clastoderma debaryanum was the earliest branching clade in Echinosteliales. We also found that E. corynophorum was the closest relative of the enigmatic Semimorula liquescens, a stalkless-modified Echinosteliales. We discuss possible evolutionary pathways in dark-spored Myxomycetes and propose a taxonomic update.

Microhabitats occupied by Myxomycetes in the Brazilian Atlantic Forest: Heliconiaceae inflorescences.

The occurrence of Myxomycetes in Heliconia psittacorum L.f. inflorescences was researched within four conservation units located in Northeast Brazil, aiming at evaluating the occupation of this microhabitat in fragments of Atlantic Forest along an altitude between 30-750 m. Inflorescences attached to the plant were examined; dead flowers and bracts were collected to assemble moist chambers (368). Four families, four genera and 10 species were recorded. A preference was evidenced for a basic pH substrate and a predominance of calcareous species (5:1). The composition of the myxobiota in fragments pertaining to altitudes above 400 m was similar and differed significantly from the one found in fragments of lowland forests (<100 m). Physarum compressum and Arcyria cinerea are the most characteristic species of the studied myxobiota.

Myxomycetes from mangroves: species occurring in the state of Maranhão, northeastern Brazil.

Mangrove swamps and forests cover over 137,000 km2 distributed latitudinally among subtropical zones, 7% of which are in Brazil, with a greater density in the country's northernmost region. Considering that the community of Myxomycetes recorded for this environment is hardly known, three areas located in the state of Maranhão were investigated. Two field trips were conducted, one at the beginning of the rainy season and another during the dry season. In each area, two plots (125 m2) equidistant 100 m apart from each other were surveyed. In these areas, standing dead tree trunks and dead branches still attached to the mother plant that were above the tideline, were examined. On these same occasions, samples of the aerial litter and from the cortex of living trees (Rhizophora) were collected for the preparation of moist chambers cultures. Twenty-one specimens were obtained from field and moist chambers, belonging to 11 species, distributed in nine genera and five families. Seven species are new records from Maranhão. There was a predominance of r-strategist (73%) over K-strategist (27%) species. Cribraria violacea, Comatricha tenerrima, Echinostelium minutum, and Fuligo septica are new worldwide records from mangrove environments, and Oligonema flavidum is reported for the first time from Brazil.

Microhabitats occupied by Myxomycetes in the Brazilian Atlantic Forest: Heliconiaceae inflorescences / Microhabitats ocupados por Myxomycetes na Floresta Atlântica Brasileira: inflorescências de Heliconiaceae

Abstract The occurrence of Myxomycetes in Heliconia psittacorum L.f. inflorescences was researched within four conservation units located in Northeast Brazil, aiming at evaluating the occupation of this microhabitat in fragments of Atlantic Forest along an altitude between 30-750 m. Inflorescences attached to the plant were examined; dead flowers and bracts were collected to assemble moist chambers (368). Four families, four genera and 10 species were recorded. A preference was evidenced for a basic pH substrate and a predominance of calcareous species (5:1). The composition of the myxobiota in fragments pertaining to altitudes above 400 m was similar and differed significantly from the one found in fragments of lowland forests (<100 m). Physarum compressum and Arcyria cinerea are the most characteristic species of the studied myxobiota.

Resumo A ocorrência de mixomicetos em inflorescências de Heliconia psittacorum L.f. foi pesquisada em quatro unidades de conservação situadas no Nordeste do Brasil, visando avaliar a ocupação deste microhabitat em fragmentos de Floresta Atlântica, numa faixa altitudinal de 30-750 m. Foram examinadas partes mortas de inflorescências ainda presas à planta; flores e brácteas mortas foram colhidas para montagem de câmaras-úmidas (368). Foram registrados quatro famílias, quatro gêneros e 10 espécies. Evidenciou-se preferência para substrato com pH básico e predominância de espécies calcárias (5:1). A composição da mixobiota nos fragmentos de altitudes acima de 400 m foi semelhante e diferiu significativamente da encontrada nos fragmentos de florestas de terras baixas (<100 m). Physarum compressum e Arcyria cinerea são as espécies mais características da mixobiota estudada.

Myxomycetes from mangroves: species occurring in the state of Maranhão, northeastern Brazil / Myxomycetes em manguezais: espécies ocorrentes no estado do Maranhão, nordeste do Brasil

Abstract Mangrove swamps and forests cover over 137,000 km2 distributed latitudinally among subtropical zones, 7% of which are in Brazil, with a greater density in the country’s northernmost region. Considering that the community of Myxomycetes recorded for this environment is hardly known, three areas located in the state of Maranhão were investigated. Two field trips were conducted, one at the beginning of the rainy season and another during the dry season. In each area, two plots (125 m2) equidistant 100 m apart from each other were surveyed. In these areas, standing dead tree trunks and dead branches still attached to the mother plant that were above the tideline, were examined. On these same occasions, samples of the aerial litter and from the cortex of living trees (Rhizophora) were collected for the preparation of moist chambers cultures. Twenty-one specimens were obtained from field and moist chambers, belonging to 11 species, distributed in nine genera and five families. Seven species are new records from Maranhão. There was a predominance of r-strategist (73%) over K-strategist (27%) species. Cribraria violacea, Comatricha tenerrima, Echinostelium minutum, and Fuligo septica are new worldwide records from mangrove environments, and Oligonema flavidum is reported for the first time from Brazil.

Resumo Os manguezais ocupam mais de 137.000 km2, distribuídos latitudinalmente entre as zonas subtropicais e 7% encontra-se no Brasil, com maior densidade entre os estados do Pará e Maranhão, na região norte do país. Considerando que a comunidade de mixomicetos registrada para este ambiente é pouco conhecida, três áreas localizadas no estado do Maranhão foram investigadas. Duas excursões foram realizadas, uma no início da estação chuvosa e outra na estiagem. Em cada área, foram georeferenciadas e exploradas duas parcelas (125 m2) equidistantes 100 m uma da outra foram avaliadas. Nestas, foram explorados troncos mortos em pé e galhos mortos ainda presos à planta-mãe, acima da linha da maré. Nas mesmas ocasiões foram coletadas amostras de folhedo aéreo e córtex de árvores vivas (Rhizophora) para montagem de câmaras-úmidas. Foram obtidos 21 espécimes de campo e câmara-úmida, pertencentes a 11 espécies, distribuídas em nove gêneros e cinco famílias. Sete espécies são novos registros para o Maranhão. Predominaram espécies r-estrategistas (73%), e 27% K-estrategistas. Cribraria violacea, Comatricha tenerrima, Echinostelium minutum e Fuligo septica são novos registros para o ambiente de manguezal, e Oligonema flavidum é registrada pela primeira vez no Brasil.

Stable isotope composition (δ(13)C and δ(15)N values) of slime molds: placing bacterivorous soil protozoans in the food web context.

RATIONALE: Data on the bulk stable isotope composition of soil bacteria and bacterivorous soil animals are required to estimate the nutrient and energy fluxes via bacterial channels within detrital food webs. We measured the isotopic composition of slime molds (Myxogastria, Amoebozoa), a group of soil protozoans forming macroscopic spore-bearing fruiting bodies. An analysis of largely bacterivorous slime molds can provide information on the bulk stable isotope composition of soil bacteria. METHODS: Fruiting bodies of slime molds were collected in a monsoon tropical forest of Cat Tien National Park, Vietnam, and analyzed by continuous-flow isotope ratio mass spectrometry. Prior to stable isotope analysis, carbonates were removed from a subset of samples by acidification. To estimate the trophic position of slime molds, their δ(13) C and δ(15) N values were compared with those of plant debris, soil, microbial destructors (litter-decomposing, humus-decomposing, and ectomycorrhizal fungi) and members of higher trophic levels (oribatid mites, termites, predatory macroinvertebrates). RESULTS: Eight species of slime molds represented by at least three independent samples were 3-6‰ enriched in (13) C and (15) N relative to plant litter. A small but significant difference in the δ(13) C and δ(15) N values suggests that different species of myxomycetes can differ in feeding behavior. The slime molds were enriched in (15) N compared with litter-decomposing fungi, and depleted in (15) N compared with mycorrhizal or humus-decomposing fungi. Slime mold sporocarps and plasmodia largely overlapped with oribatid mites in the isotopic bi-plot, but were depleted in (15) N compared with predatory invertebrates and humiphagous termites. CONCLUSIONS: A comparison with reference groups of soil organisms suggests strong trophic links of slime molds to saprotrophic microorganisms which decompose plant litter, but not to humus-decomposing microorganisms or to mycorrhizal fungi. Under the assumption that slime molds are primarily feeding on bacteria, the isotopic similarity of slime molds and mycophagous soil animals indicates that saprotrophic soil bacteria and fungi are similar in bulk isotopic composition.

Slime moulds use heuristics based on within-patch experience to decide when to leave.

Animals foraging in patchy, non-renewing or slowly renewing environments must make decisions about how long to remain within a patch. Organisms can use heuristics ('rules of thumb') based on available information to decide when to leave the patch. Here, we investigated proximate patch-departure heuristics in two species of giant, brainless amoeba: the slime moulds Didymium bahiense and Physarum polycephalum. We explicitly tested the importance of information obtained through experience by eliminating chemosensory cues of patch quality. In P. polycephalum, patch departure was influenced by the consumption of high, and to a much lesser extent low, quality food items such that engulfing a food item increased patch-residency time. Physarum polycephalum also tended to forage for longer in darkened, 'safe' patches. In D. bahiense, engulfment of any food item increased patch residency irrespective of that food item's quality. Exposure to light had no effect on the patch-residency time of D. bahiense. Given that these organisms lack a brain, our results illustrate how the use of simple heuristics can give the impression that individuals make sophisticated foraging decisions.

Using environmental niche models to test the 'everything is everywhere' hypothesis for Badhamia.

It is often discussed whether the biogeography of free-living protists is better explained by the 'everything is everywhere'(EiE) hypothesis, which postulates that only ecology drives their distribution, or by the alternative hypothesis of 'moderate endemicity' in which geographic barriers can limit their dispersal. To formally test this, it would be necessary not only to find organisms restricted to a geographical area but also to check for their presence in any other place with a similar ecology. We propose the use of environmental niche models to generate and test null EiE distributions. Here we have analysed the distribution of 18S rDNA variants (ribotypes) of the myxomycete Badhamia melanospora (belonging to the protozoan phylum Amoebozoa) using 125 specimens from 91 localities. Two geographically structured groups of ribotypes congruent with slight morphological differences in the spores can be distinguished. One group comprises all populations from Argentina and Chile, and the other is formed by populations from North America together with human-introduced populations from other parts of the world. Environmental climatic niche models constructed separately for the two groups have significant differences, but show several overlapping areas. However, only specimens from one group were found in an intensively surveyed area in South America where both niche models overlap. It can be concluded that everything is not everywhere for B. melanospora. This taxon constitutes a complex formed by at least two cryptic species that probably diverged allopatrically in North and South America.

Photonic simulation method applied to the study of structural color in Myxomycetes.

We present a novel simulation method to investigate the multicolored effect of the Diachea leucopoda (Physarales order, Myxomycetes class), which is a microorganism that has a characteristic pointillistic iridescent appearance. It was shown that this appearance is of structural origin, and is produced within the peridium -protective layer that encloses the mass of spores-, which is basically a corrugated sheet of a transparent material. The main characteristics of the observed color were explained in terms of interference effects using a simple model of homogeneous planar slab. In this paper we apply a novel simulation method to investigate the electromagnetic response of such structure in more detail, i.e., taking into account the inhomogeneities of the biological material within the peridium and its curvature. We show that both features, which could not be considered within the simplified model, affect the observed color. The proposed method is of great potential for the study of biological structures, which present a high degree of complexity in the geometrical shapes as well as in the materials involved.

Ecological niche models reveal the importance of climate variability for the biogeography of protosteloid amoebae.

Habitat availability and environmental preferences of species are among the most important factors in determining the success of dispersal processes and therefore in shaping the distribution of protists. We explored the differences in fundamental niches and potential distributions of an ecological guild of slime moulds-protosteloid amoebae-in the Iberian Peninsula. A large set of samples collected in a north-east to south-west transect of approximately 1000 km along the peninsula was used to test the hypothesis that, together with the existence of suitable microhabitats, climate conditions may determine the probability of survival of species. Although protosteloid amoebae share similar morphologies and life history strategies, canonical correspondence analyses showed that they have varied ecological optima, and that climate conditions have an important effect in niche differentiation. Maxent environmental niche models provided consistent predictions of the probability of presence of the species based on climate data, and they were used to generate maps of potential distribution in an 'everything is everywhere' scenario. The most important climatic factors were, in both analyses, variables that measure changes in conditions throughout the year, confirming that the alternation of fruiting bodies, cysts and amoeboid stages in the life cycles of protosteloid amoebae constitutes an advantage for surviving in a changing environment. Microhabitat affinity seems to be influenced by climatic conditions, which suggests that the micro-environment may vary at a local scale and change together with the external climate at a larger scale.

Structural color in Myxomycetes.

In this paper we report evidence of structural color in Myxomycetes, a group of eukaryotic microorganisms with an uncertain taxonomic position. We investigated the Diachea leucopoda, which belongs to the Physarales order, Myxomycetes class, and found that its peridium -protective layer that encloses the mass of spores- is basically a corrugated layer of a transparent material, which produces a multicolored pointillistic effect, characteristic of this species. Scanning (SEM) and transmission (TEM) electron microscopy techniques have been employed to characterize the samples. A simple optical model of a planar slab is proposed to calculate the reflectance. The chromaticity coordinates are obtained, and the results confirm that the color observed is a result of an interference effect.

Two new species of nivicolous Lamproderma (myxomycetes) from the mountains of Europe and America.

As a result of the revision of European and American collections of genus Lamproderma two new nivicolous myxomycete species, Lamproderma argenteobrunneum and L. kowalskii, are described. The new species are characterized by the silvery-brown sporothecae, the areolate peridium and the ferruginous-brown spores in mass. They differ from one another mainly in spore size and ornamentation, the form of the capillitium and the stalk length and ratio of the stalk length to the total height of the sporocarp. The morphology of the new species was examined with light microscopy and scanning electron microscopy (SEM), and micrographs of relevant details are included. Lamproderma argenteobrunneum also was obtained in moist chamber culture, and the mature sporocarps displayed all features typical of field-collected samples. The known geographical distribution of L. argenteobrunneum includes the main ranges of the European alpine system (Alps, Carpathians, Pyrenees) as well as those of North America, while L. kowalskii has been recorded so far from several sites in California in the United States.

Description and life cycle of a new Didymium (Myxomycetes) from arid areas of Argentina and Chile.

A new species of Didymium (Myxomycetes), D. infundibuliforme, is described herein, and details are provided on its life cycle as observed in spore to spore culture on agar. The new species was recorded during intensive studies of areas of the Monte Desert in Argentina and the Atacama Desert in Chile. It has been collected directly in the field in both countries on several occasions over 4 y and isolated in moist chamber cultures prepared with material from native plant species. The characters that make this species unique in the genus are its funnel-shape sporocarps with white stalks, the apical circumscissile dehiscence of the sporotheca that causes the base to resemble a calyculus and the ornamentation on the spores. The morphology of specimens of this new myxomycete was examined with scanning electron microscopy and light microscopy, and micrographs of relevant details are included in this paper.