On the early evolutionary stage of the geosphere and biosphere and the problem of early glaciations

The early evolutionary stages of the geosphere and biosphere are determined by three interrelated factors: (1) continuous cooling of the surface and interior (mantle) of the Earth (the mean temperatures of the mantle and surface decreased by a factor of 1.5–2 and 3–4, respectively; the mean heat flow was reduced by approximately one order of magnitude, and viscosity, by three orders); (2) continuous stepwise oxidation of the surface, which was particularly well pronounced from 3.8 to 1.8 Ga; and (3) periodic and correlated fluctuations of conditions in the geosphere and biosphere of varying extent and nature. The major boundaries of this evolution were about 4 Ga (the origin of rather thick and heterogeneous earth’s crust, the origin of life); about 3 Ga (appearance of a strong magnetic field, an increase in photosynthetic activity); about 1.8–1.9 Ga (appearance of an oxidized atmosphere, the first supercontinent, possibly, the first superplumes from the nucleus); and about 0.75 Ga (acceleration of subduction, “watering” of the upper mantle, elevation of continents with vast land masses, shelves, large rivers, and the first great glaciations). The significance and correlations of the earliest events (before and about 4 Ga) and events about 750 Ma are widely debated. In the Late Archean and Early Proterozoic (before 1.8 Ga), the biosphere was dominated by cyanobacteria, the dynamics and developmental peaks of which are marked by the presence of widespread stromatolite buildups in carbonaceous rocks (initially, mostly dolomitic matter). About 700–750 Ma, intense and frequent glaciations developed, marking the cooling of the Earth. The greatest glaciation apparently occurred about 640 Ma, which gave rise to the discussion of the model of the Snowball Earth. The emergence and evolution of skeletons in animals is sometimes thought to be connected with glaciations. These events are correlated and accounted for by great endogenous changes. One of the major events in endogenous history is the onset about 750 Ma of periodic manifestation of mantle flows (superplumes), which explain further periodicity of the biosphere evolution. In conclusion, extrapolation of future evolution and successive collapse of biosphere segments in the course of transformation of the Sun into a red star and warming of the Earth surface are proposed.     

Astrocatalysis—Abiogenic synthesis and chemical evolution at pregeological stages of the Earth’s formation

The Earth’s biosphere appeared in a self-organization process along with the appearance of the Solar System. It is shown, based on the methods of self-organization examination and existing knowledge, that major stages of the chemical evolution in the early development of the biosphere include the “cold prehistory of life” in dense molecular nebulae, “pre-planetary chemocoenosis,” “RNA-world” in a circumsolar nebula, and primary biocoenoses of protocells (life) on the planetary bodies. Estimates for carbon in the primordial biosphere on the young Earth’s surface give 2.4 × 10¹⁹ kg. The decay of the primordial Earth’s biomass and biogeochemical cycles in 2.5 Myr led to the “planet of bacteria” with 2.0 × 10¹⁵ kg of biota in the Proterozoic (at the time of an oxygenated atmosphere). The main parameters (pressure, temperature, and state of catalytic solid phase) are estimated for these stages of the early evolution of life. It is shown that the abiogenic synthesis of the primordial matter was preformed in the Solar System on a grand scale with practically every atom in nanoparticles-catalysts participating. Selection among catalytically active nanoparticles worked towards the ability to synthesize high molecular compounds in a protoplanetary disk. Autocatalysts participated in the preplanetary chemical evolution, beginning from such simple substances as ethylene or glycolaldehyde. Primary synthesis of autocatalysts depended on external sources of energy, e.g., on ultraviolet radiation.     

陆地生物圈模型的发展与应用

陆地生物圈与大气圈和水圈之间能量、水和碳氮等元素的交换和循环对整个地球系统产生了深刻的影响。陆地生物圈模型(TBM)是研究陆地生态系统如何响应和反馈全球变化的重要方法和工具。通过对从生态系统到区域和全球陆地生物圈不同空间尺度的植被动态、生物地球物理和生物地球化学循环过程、水循环和水文过程、自然干扰和人类活动等过程时间动态的模拟, 陆地生物圈模型被广泛地应用于评估和归因过去陆地生物圈的时空变化和预测陆地生物圈对未来全球变化的响应和反馈。该文简要回顾了陆地生物圈模型的发展, 总结了模型对陆地生态系统主要过程的刻画和模型在生态系统生态学的应用, 并对未来陆地生物圈模型的发展和应用进行了展望。     

Photosynthesis and Oxygenation of the Earth's Atmosphere

Based on the contemporary data concerning photosynthesis as a global biogeochemical mechanism of solar energy utilization and organic matter and oxygen production, the formation of photosynthesis in the Proterozoic is considered, as well as its role in transformation of the pre-Proterozoic oceanic hydrosphere and the Earth's atmosphere from a reduced to an oxidized state. Photosynthesis is considered the longest stage of organic world evolution. The problem of production of excessive oxygen is considered, which entered and is entering the atmosphere through the oceanic hydrosphere and determines the process of its organization.     

The Hierarchical Structure of Ecosystems: Connections to Evolution

Ecologic systems, which are involved mainly in the processing of energy and materials, are actually nested one inside another—they are simultaneously parts and wholes. This fundamental hierarchical organization is easy to detect in nature but has been undervalued by ecologists as a source of new insights about the structure and development of ecosystems and as a means of understanding the crucial connections between ecologic processes and large-scale evolutionary patterns. These ecologic systems include individual organisms bundled into local populations, populations as functional components of local communities or ecosystems, local systems making up the working parts of larger regional ecosystems, and so on, right up to the entire biosphere. Systems at any level of organization can be described and interpreted based on aspects of scale (size, duration, and “membership” in more inclusive entities), integration (all the vital connections both at a particular focal level and across levels of hierarchical organization), spatiotemporal continuity (the “life history” of each system), and boundaries (either membranes, skins, or some other kind of border criterion). Considering hierarchical organization as a general feature of ecologic systems could reinvigorate theoretical ecology, provide a realistic scaling framework for paleoecologic studies, and – most importantly – forge new and productive connections between ecology and evolutionary theory.     

Changes in terrestrial biota before the Permian-Triassic ecological crisis

The period around the Permian-Triassic boundary was marked by one of the most important and interesting events in the evolution of life. The diversity of both marine and continental biotas decreased. The changes were global and led to the establishment of the new Mesozoic World. Transformations of the organic world constituted a single process with changes in the inorganic components of the biosphere. The preceding glacial period had ended and the “cool,” zonal, and markedly seasonal climate was replaced by a “warm,” “equable,” virtually non-seasonal and azonal climate. The new climatic organization remained on Earth for more than two hundred million years. The biotic crisis was global: it involved the sea, the land, and inland waters. The changes on land began earlier and more superficial. The principal events were in the Kazanian and Vyatkian, before the end of the Permian. The crisis was caused to a greater extent by biospheric processes than by momentary external influences, the latter at most triggering the crisis.     

Linking limitation to species composition: importance of inter- and intra-specific variation in grazing resistance

Short-term responses of producers highlight that key nutrients (e.g., N, P)—or combinations of these nutrients—limit primary production in aquatic and terrestrial ecosystems. These discoveries continue to provide highly valuable insights, but it remains important to ask whether nutrients always predominantly limit producers despite wide variation in nutrient supply and herbivory among systems. After all, predictions from simple food chain models (derived here) readily predict that limitation by grazers can exceed that by nutrients, given sufficient enrichment. However, shifts in composition of producers and/or increasing dominance of invulnerable stages of a producer can, in theory, reduce grazer limitation and retain primacy of nutrient limitation along nutrient supply gradients. We observed both mechanisms (inter- and intra-species variation in vulnerability to herbivory) working in a two-part mesocosm experiment. We incubated diverse benthic algal assemblages for several months either in the presence or absence of benthic macro-grazers in mesocosms that spread a broad range of nutrient supply. We then conducted short-term assays of nutrient and grazer limitation on these communities. In the “historically grazed” assemblages, we found shifts from more edible, better competitors to more resistant producers over enrichment gradients (as anticipated by the food web model built with a tradeoff in resistance vs. competitive abilities). However, contrary to our expectations, “historically ungrazed” assemblages became dominated by producers with vulnerable juvenile forms but inedible adult forms (long filaments). Consequently, we observed higher resource limitation rather than grazer limitation over this nutrient supply gradient in both “historically grazed” (expected) and “historically ungrazed” (not initially expected). Thus, via multiple, general mechanisms involving resistance to grazing (changes in species composition or variation in stage-structured vulnerability), producer assemblages should remain more strongly or as strongly limited by nutrients than grazers, even over large enrichment gradients. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Understanding the Complexity of Economic, Ecological, and Social Systems

Hierarchies and adaptive cycles comprise the basis of ecosystems and social-ecological systems across scales. Together they form a panarchy. The panarchy describes how a healthy system can invent and experiment, benefiting from inventions that create opportunity while being kept safe from those that destabilize because of their nature or excessive exuberance. Each level is allowed to operate at its own pace, protected from above by slower, larger levels but invigorated from below by faster, smaller cycles of innovation. The whole panarchy is therefore both creative and conserving. The interactions between cycles in a panarchy combine learning with continuity. An analysis of this process helps to clarify the meaning of “sustainable development.” Sustainability is the capacity to create, test, and maintain adaptive capability. Development is the process of creating, testing, and maintaining opportunity. The phrase that combines the two, “sustainable development,” thus refers to the goal of fostering adaptive capabilities and creating opportunities. It is therefore not an oxymoron but a term that describes a logical partnership. Received 7 March 2001; accepted 16 March 2001.     

Keystone Interactions: Salmon and Bear in Riparian Forests of Alaska

The term “keystone species” is used to describe organisms that exert a disproportionately important influence on the ecosystems in which they live. Analogous concepts such as “keystone mutualism” and “mobile links” illustrate how, in many cases, the interactions of two or more species produce an effect greater than that of any one species individually. Because of their role in transporting nutrients from the ocean to river and riparian ecosystems, Pacific salmon (Oncorhynchus spp.) and brown bear (Ursus arctos) have been described as keystone species and mobile links, although few data are available to quantify the importance of this interaction relative to other nutrient vectors. Application of a mass balance model to data from a southwestern Alaskan stream suggests that nitrogen (N) influx to the riparian forest is significantly increased in the presence of both salmon and bear, but not by either species individually. The interactions of salmon and bear may provide up to 24% of riparian N budgets, but this percentage varies in time and space according to variations in salmon escapement, channel morphology and watershed vegetation characteristics, suggesting interdependence and functional redundancy among N sources. These findings illustrate the complexity of interspecific interactions, the importance of linkages across ecosystem boundaries and the necessity of examining the processes and interactions that shape ecological communities, rather than their specific component parts.     

The carbon cycle on early Earth--and on Mars?

One of the goals of the present Martian exploration is to search for evidence of extinct (or even extant) life. This could be redefined as a search for carbon. The carbon cycle (or, more properly, cycles) on Earth is a complex interaction among three reservoirs: the atmosphere; the hydrosphere; and the lithosphere. Superimposed on this is the biosphere, and its presence influences the fixing and release of carbon in these reservoirs over different time-scales. The overall carbon balance is kept at equilibrium on the surface by a combination of tectonic processes (which bury carbon), volcanism (which releases it) and biology (which mediates it). In contrast to Earth, Mars presently has no active tectonic system; neither does it possess a significant biosphere. However, these observations might not necessarily have held in the past. By looking at how Earth's carbon cycles have changed with time, as both the Earth's tectonic structure and a more sophisticated biology have evolved, and also by constructing a carbon cycle for Mars based on the carbon chemistry of Martian meteorites, we investigate whether or not there is evidence for a Martian biosphere.     

Milestones in the evolution of the biosphere and soil formation

The evolution of the biosphere implies successive occupation by biota of all the Earth’s parts: hydrosphere, atmosphere, and lithosphere. A certain type of soil was formed at each stage: the underwater type at hydrospheric stage, the swampy type at atmospheric stage, the land type at lithospheric stage. The composition and properties of soil corresponded to the level of development of biota and promoted the involvement of new potential habitats into the biospheric cycle.     

Ophel: a groundwater biome based on chemoautotrophic resources. The global significance of the Ayyalon cave finds,Israel

The discovery, in the inner coastal plain of Israel, of a deep, secluded subterranean ecosystem, supported by chemosynthetis producing by sulfide-oxidizing bacteria, suggests the existence of a new biome, “Ophel”, with an autonomous energy basis. This biome could provide an ecological and historical basis for explaining the high taxonomic diversity of subterranean faunas, especially of crustaceans. A continuum with the anchialine ecosystems, in which chemoautotrophy is also encountered, as well as with marine hot vents and cold seeps, implies the existence of a second, parallel chemosynthesis-based eukaryotic biosphere. Handling editor: K. Martens Dedicated to my teacher, the active nonagerian Acad. Prof. Nicolaie Botnariuc, Bucharest.     

Macroevolution via secondary endosymbiosis: a Neo-Goldschmidtian view of unicellular hopeful monsters and Darwin’s primordial intermediate form

Seventy-five years ago, the geneticist Richard Goldschmidt hypothesized that single mutations affecting development could result in major phenotypic changes in a single generation to produce unique organisms within animal populations that he called “hopeful monsters”. Three decades ago, Sarah P. Gibbs proposed that photosynthetic unicellular micro-organisms like euglenoids and dinoflagellates are the products of a process now called “secondary endosymbiosis” (i.e., the evolution of a chloroplast surrounded by three or four membranes resulting from the incorporation of a eukaryotic alga by a eukaryotic heterotrophic host cell). In this article, we explore the evidence for Goldschmidt’s “hopeful monster” concept and expand the scope of this theory to include the macroevolutionary emergence of organisms like Euglena and Chlorarachnion from secondary endosymbiotic events. We argue that a Neo-Goldschmidtian perspective leads to the conclusion that cell chimeras such as euglenids and dinoflagellates, which are important groups of phytoplankton in freshwater and marine ecosystems, should be interpreted as “successful monsters”. In addition, we argue that Charles Darwin had euglenoids (infusoria) in mind when he speculated on the “primordial intermediate form”, although his Proto-Euglena-hypothesis for the origin of the last common ancestor of all forms of life is no longer acceptable.     

A mathematical model of HIV dynamics in the presence of a rescuing virus with replication deficiency

Recently, an enzyme (Cre recombinase) has been developed by directed evolution that successfully removes the HIV genome from the nuclear DNA of infected cells. To explore this idea further, we hypothesized that a replication deficient virus (called “police virus”), added externally, can deliver such a recombinase which excises the integrated HIV DNA from the genome of infected cells. Such a “police virus” could attack and remove the integrated provirus which is not possible using contemporary strategies. The hypothesis was tested by developing a mathematical model that describes the dynamics of virus-host cell interaction and the consequences of introducing the “police virus”. The simulations show that such a therapeutic vector may eradicate all HIV viruses from the system in the long term. All components of the HIV infection (free virus, latently, and actively infected cells) can be cleared and the system ends up only with susceptible CD4+ cells. The proposed model may provide new insights in the dynamical behavior and future alternative treatments of HIV.     

Microbial biopshere

Evolution of the prokaryotic biosphere is regarded from the system point of view. It starts with the appearance of the first organisms, the ∼3.5 Ga date forming the boundary between the observed and imagined biosphere. The prokaryotic community dominated from the Archean to the Mesoproterozoic. Prokaryotes make a sustainable community due to the cooperative action of specialized forms. The main route for establishing a community is made by trophic links. The structure of the trophic links in the prokaryotic community making a trophic network is an invariant, with secondary adaptive deviations. Material balance is the ultimate requirement for a long living self-supporting system. The system of biogeospheric cycles is dictated by the constancy of biomass composition establishing a quantitative ratio between C_org:N_org:P_org. Biospheric processes are driven by the C_org-cycle. Carbon assimilation is limited by the size of the illuminated moist surface populated by producers, meaning that C_org-production remains within an order of magnitude of 10² Gt/yr. Evolution of primary producers forms a basis for the evolution of the biospheric-geospheric system, and cyanobacteria integrated as chloroplasts remain its driving force. Decomposition of organic compounds is performed by organotrophic destructors, anacrobic being less effective. Destructors determine the residual C_org accumulation. Recalcitrant C_org remaining in the sedimentary record is equilibrated by O₂ and other oxidized compounds as Fe-oxides or sulfates. Geospheric and biotic interactions include both direct and biotically mediated processes; the most important is the weathering-sedimentation pathway. Prokaryotic community makes a sustainable frame into which all other more complex forms of life fit. That makes the prokaryotic biosphere a permanent essence of the whole system. New participants might come in and substitute functional components only when they fit to the existing system. The evolution of a large system is additive rather than substitutive. The message of this is; “we all originated from the cyanobacterial community.” The text was submitted by the author in English.     

Global environmental changes in terrestrial ecosystems. International issues and strategic solutions: introduction

Human activities are having major impact on biogeochemical cycles and ecosystems worldwide. Rapid urbanization and changes in rural populations are affecting ecosystems in often-drastic ways. Ecologists are using long term monitoring and experimental studies to understand and to help mitigate the effects of these changes. The collection of 15 papers in this special volume “global changes in terrestrial ecosystems” describes some of these studies, particularly concentrating on effects on terrestrial ecosystems and landscapes, and demonstrating the importance of understanding the problems at both the multi-scale and international levels.     

Hierarchies and the Sloshing Bucket: Toward the Unification of Evolutionary Biology

Evolutionary biology presents a bewildering array of phenomena to scientists and students alike—ranging from molecules to species and ecosystems; and embracing 3.8 billion years of life’s history on earth. Biological systems are arranged hierarchically, with smaller units forming the components of larger systems. The evolutionary hierarchy, based on replication of genetic information and reproduction, is a complex of genes/organisms/demes/species and higher taxa. The ecological hierarchy, based on patterns of matter–energy transfer, is a complex of proteins/organisms/avatars/local ecosystems/regional ecosystems. All organisms are simultaneously parts of both hierarchical systems. Darwin’s original formulation of natural selection maps smoothly onto a diagram where the two hierarchical systems are placed side-by-side. The “sloshing bucket” theory of evolution emerges from empirical cases in biological history mapped onto this dual hierarchy scheme: little phenotypically discernible evolution occurs with minor ecological disturbance; conversely, greatest concentrations of change in evolutionary history follow mass extinctions, themselves based on physical perturbations of global extent. Most evolution occurs in intermediate-level regional “turnovers,” when species extinction leads to rapid evolution of new species. Hierarchy theory provides a way of integrating all fields of evolutionary biology into an easily understood—and taught—rubric.

Distant land use affects terrestrial and aquatic habitats of high naturalness

Biotas from all ecosystems need to respond to factors that determine habitat suitability. These factors originate from different scales. Effects can be assumed to be hierarchical in the order large-scale geographic > regional > local > small-scale in-habitat factors. We aimed at the identification of general patterns by comparisons between ecosystems (forest floor snails, hololimnic stream macroinvertebrates) and across scales, and include potential seasonal effects. Sampling sites displayed signs of naturalness, such as high levels of deadwood accumulation in the forests, or a lack of artificial stream bed fixation plus a “good” to “high” score for the assemblage-derived Multimetric Index (MMI) in the streams. Terrestrial and aquatic assemblages of non-emergent taxa fluctuated independent of seasonal effects. They differed in their relative correlation with environmental matrices with quasi-concentric effects in forests, and longitudinal effects in streams. Large-scale factors, namely geographic position, strongly influenced assemblage turnover, but the effect is based on a high covariation between geographic position and environmental factors. We thus extracted variables that best explained species turnover after correcting for spatio-temporal effects. The terrestrial community assembling was habitat-based and mainly responded to soil acidification, distance to disturbances, and regional scale deforestation and deciduous/mixed forest cover. The stream assemblages were structured by regional pasture cover, organic pollution, regional deciduous forest cover and microlithal cover. Apparently, community assembly occurs along with changes in regional forest cover and the transport of nutrients and matter that can originate from a distance, irrespective of ecosystem and assumed “naturalness”.     

Relationship between genome size and organismal complexity in the lineage leading from prokaryotes to mammals

The lack of a strict relationship between genome size and organismal complexity (level of organization) is largely due to size variability of the facultative part of the genome. However, there is a direct relationship between the level of organization and the minimal genome size (MGS) in the lineage leading from prokaryotes to mammals, in which the tendency towards increasing complexity is especially clear. The dynamics of MGS in this lineage can be adequately described by the model of hyperexponential growth. This implies the existence of nonlinear positive feedbacks that account for the acceleration of MGS growth. The nature of these feedbacks is discussed, including the formation of new genes by means of recombination of the fragments of existing genes, formation of “niches” for new genes in the course of evolution of gene networks, and the expansion of regulatory regions. Hyperexponential growth of different variables related to the level of organization of the biosphere and society (biodiversity, MGS, size and complexity of organisms, world population, technological development, urbanization, etc.) suggests that the evolution of the biosphere and humanity in the direction of increasing complexity is a self-accelerating (autocatalytic) process.     

Association between contrasting methane emissions of two rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) cultivars from the irrigated agroecosystem of northeast India and their growth and photosynthetic characteristics

Over two consecutive years in the North Bank Plain Zone of Assam, India, during the spring growing season (February–June) of- 2006 and 2007 we examined effects of morpho-physiological characteristics of rice (Oryza sativa L.) plants in relation to methane (CH₄) emission from paddy fields. Traditional cultivar “Agni” and modern improved cultivar “Ranjit” were grown in light textured loamy soil under irrigation. A higher seasonal integrated methane flux (E _sif) was recorded from “Agni” compared to “Ranjit”. Both cultivars exhibited an emission peak during active vegetative growth and a second peak at panicle initiation. Leaf and tiller number, leaf area, length, and volume of root were greater in “Agni”, but grain yield and yield-related parameters such as increased photosynthate partitioning to panicles at the expense of roots were greater in “Ranjit”. “Ranjit” also photosynthesed faster than “Agni” during panicle development but slower than “Agni” at tillering. In both the years, a higher soil organic carbon content was recorded in plots of “Agni”. Our results suggest that in “Agni” enhanced diversion of photosynthate to roots resulted in more substrate being available to methanogenic bacteria in the rhizosphere. Additionally, the more extensive vegetative growth of this cultivar may enhance methane transport from the soil to the above-ground atmosphere.