Review: from chemosphere to biosphere

An understanding of how the Earth's chemosphere was transformed to a biosphere is central to our understanding of the origin of life and the search for extraterrestrial life or life signatures. Once early prokaryotic life originated and colonized the Earth, the biosphere was well on its way to being formed. In this paper, information and knowledge is integrated to examine the possibility how life first self-assembled and transformed a lifeless chemosphere into a complex biosphere that we still do not understand today.     

The illusion of balance in the history of the biosphere

Earth's surface has been irreversibly altered by the activity of organisms, a process that has accelerated as the power of the biosphere (the rate at which life extracts and deploys energy) has increased over time. This trend is incompatible with the expectation that the inputs to Earth's surface of life's materials from the crust and mantle be matched by export from Earth's surface to long-term reservoirs. Here, I suggest that the collective activity of organisms has always violated this balance. The biosphere's ability to extract, retain, recycle, and accumulate materials has allowed living biomass to increase and for exports to decrease over very long timescales. This collective metabolism implies a net transfer of materials from the planet's interior to its surface. The combination of metabolic innovations, competition, adaptive evolution, and the establishment of collaborative economic feedback in ecosystems created dynamic ecological stability despite great spatial and temporal heterogeneity in physical and biological inputs and export of nutrients into and out of the biosphere. Models of geochemical cycling must take the fundamental role of living organisms and the evolutionary changes in these roles into account to explain past and future conditions.     

Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates

Much of the phylogenetic diversity in microbial systems arises from rare taxa that comprise the long tail of taxon rank distribution curves. This vast diversity presents a challenge to testing hypotheses about the effects of perturbations on microbial community composition because variability of rare taxa among environmental replicates may be sufficiently large that it would require a prohibitive degree of sequencing to discern differences between samples. In this study we used pyrosequencing of 16S rRNA tags to examine the diversity and within-site variability of salt marsh sediment bacteria. Our goal was to determine whether pyrosequencing could produce similar patterns in community composition among replicate environmental samples from the same location. We hypothesized that repeated sampling from the same location would produce different snapshots of the rare community due to incomplete sequencing of the taxonomically rich rare biosphere. We demonstrate that the salt marsh sediments we sampled contain a remarkably diverse array of bacterial taxa and, in contrast to our hypothesis, repeated sampling from within the same site produces reliably similar patterns in bacterial community composition, even among rare organisms. These results demonstrate that deep sequencing of 16s tags is well suited to distinguish site-specific similarities and differences among rare taxa and is a valuable tool for hypothesis testing in microbial ecology.     

海底玄武岩玻璃中蚀变微结构:探索海洋深地生物圈的新材料

玄武岩玻璃中的生物蚀变微结构为微生物摄取玄武岩玻璃中营养成分,通过新陈代谢产生有机酸溶解玄武岩玻璃而形成的微米级孔洞或钻穴.生物蚀变微结构在现代海洋洋壳及代表古老洋壳残片的蛇绿岩和绿岩带中广泛存在.研究玄武岩玻璃中蚀变微结构的形态特征、形成机制及其时空分布,不仅对探索地球早期生命起源和演化具有重要启示意义,也为研究海洋...     

On the early stages of the evolution of the geosphere and biosphere

The conditions necessary for the existence of nucleic-protein life are as follows: the presence of liquid water, an atmosphere, and a magnetic field (all of which protect from meteorites, abrupt changes in temperature, and a flow of charged particles from space) and the availability of nutrients (macro-and microelements in the form of dissolved compounds). In the evolution of the geosphere, complex interference of irreversible processes (general cooling, gravitational differentiation of the Earth’s interior, dissipation of hydrogen, etc.) with cyclic processes of varying natures and periodicities (from the endogenic cycles “from Pangea to Pangea” to Milankovitch cycles), these conditions have repeatedly changed; hence, in the coevolution of the geosphere and biosphere, the vector of irreversible evolution was determined by the geosphere. Only with the appearance of the ocean as a global system of homeostasis, which provided the maintenance and leveling of nutrient concentrations in the hydrosphere, and the conveyor of nutrients from the mantle, “the film of life” could begin its expansion from the source of the nutrients. Life itself is a system of homeostasis, but not due to the global size and a vast buffer capacity, but because of the high rate of reactions and presence of a program (genome) that allowed its development (ontogeny) independent from the outside environment. The early stages of the origin and evolution of the biosphere (from the RNA-world to the development of the prokaryotic ecosystems) were characterized by the domination of chemotrophic ecosystems. The geographical ranges of these ecosystems were directly or indirectly (through the atmosphere and hydrosphere) tied to the sources of nutrients in the geosphere, which were in turn connected to various sources of volcanic and geotectonic activity (geothermal waters, “black smokers” along the rift zones, etc.). This gave the biosphere consisting of chemotrophic ecosystems a mosaic appearance composed of separate local oases of life. The decrease of methane and accumulation of O₂ in the atmosphere in the geological evolution of the Earth caused the extinction of chemotrophic ecosystems and directed evolution of the biosphere toward autotrophy. Autotrophic photosynthesis gave the biosphere an energy source that was not connected to the geosphere, and for the first time allowed its liberation from the geosphere by developing its own vector of evolution. This vector resulted in the biosphere forming a continuous film of life on the planet by capturing the continents and occupying pelagic and abyssal zones, and the appearance of eukaryotes. The geosphere formed biogeochemical cycles in parallel to the geochemical ones, and comparable in the annual balances of participating matter.     

The origins of animal domestication and husbandry: a major change in the history of humanity and the biosphere

This article aims to summarize the present archaeo(zoo)logical knowledge and reflections on the origins of Neolithic animal domestication. It targets the main characteristics of early Neolithic animal domestication set against a backdrop of two complementary scales, namely the global and macro-regional scales (the latter using the example of the Near East). It discusses the conceptual and methodological issues, arguing in favor of an anthropozoological approach taking into account the intentions and the dynamics of human societies and critically analyzes the reductionist neo-Darwinian concepts of co-evolution and human niche construction. It also provides a brief discussion on the birth of ungulate domestication and its roots, as well as appropriate bibliographic references to enlighten the current status of domestication research.     

A method of determining rooting depth from a terrestrial biosphere model and its impacts on the global water and carbon cycle

We outline a method of inferring rooting depth from a Terrestrial Biosphere Model by maximizing the benefit of the vegetation within the model. This corresponds to the evolutionary principle that vegetation has adapted to make best use of its local environment. We demonstrate this method with a simple coupled biosphere/soil hydrology model and find that deep rooted vegetation is predicted in most parts of the tropics. Even with a simple model like the one we use, it is possible to reproduce biome averages of observations fairly well. By using the optimized rooting depths global Annual Net Primary Production (and transpiration) increases substantially compared to a standard rooting depth of one meter, especially in tropical regions that have a dry season. The decreased river discharge due to the enhanced evaporation complies better with observations. We also found that the optimization process is primarily driven by the water deficit/surplus during the dry/wet season for humid and arid regions, respectively. Climate variability further enhances rooting depth estimates. In a sensitivity analysis where we simulate changes in the water use efficiency of the vegetation we find that vegetation with an optimized rooting depth is less vulnerable to variations in the forcing. We see the main application of this method in the modelling communities of land surface schemes of General Circulation Models and of global Terrestrial Biosphere Models. We conclude that in these models, the increased soil water storage is likely to have a significant impact on the simulated climate and the carbon budget, respectively. Also, effects of land use change like tropical deforestation are likely to be larger than previously thought.     

Reproductive skew and the threat of eviction: a new perspective

Most recent models of the partitioning of reproduction attempt to explain patterns of skew on the assumption that dominant individuals have complete control over breeding opportunities within the group, but may nevertheless concede a share of direct reproduction to subordinates as an incentive to remain peacefully in the association. Although these models may be applicable to some animal societies, we argue that they fail to provide a comprehensive theory of skew. Instead, we suggest that subordinates may often be able to claim unsanctioned reproduction for themselves, but will be forced to exercise a degree of reproductive restraint lest they incite ejection by the dominant. Reproductive skew, in other words, may reflect the threat of ejection (inducing subordinate restraint) rather than the threat of subordinate departure (inducing reproductive concessions by dominants). We present a simple ESS model of reproductive skew under these circumstances, which demonstrates that a shift in emphasis from reproductive concessions by dominants to reproductive restraint on the part of subordinates, radically alters the predictions of skew models. High group productivity, high relatedness and (when group members are related) strong ecological constraints are all expected to lead to reduced skew (the opposite conclusions to those of previous, concession-based analyses). The reason is that these factors reduce the benefits (or increase the costs) of ejection to the dominant, who therefore does best to tolerate more subordinate reproduction.     

Evidence of current impact of climate change on life: a walk from genes to the biosphere

We review the evidence of how organisms and populations are currently responding to climate change through phenotypic plasticity, genotypic evolution, changes in distribution and, in some cases, local extinction. Organisms alter their gene expression and metabolism to increase the concentrations of several antistress compounds and to change their physiology, phenology, growth and reproduction in response to climate change. Rapid adaptation and microevolution occur at the population level. Together with these phenotypic and genotypic adaptations, the movement of organisms and the turnover of populations can lead to migration toward habitats with better conditions unless hindered by barriers. Both migration and local extinction of populations have occurred. However, many unknowns for all these processes remain. The roles of phenotypic plasticity and genotypic evolution and their possible trade‐offs and links with population structure warrant further research. The application of omic techniques to ecological studies will greatly favor this research. It remains poorly understood how climate change will result in asymmetrical responses of species and how it will interact with other increasing global impacts, such as N eutrophication, changes in environmental N : P ratios and species invasion, among many others. The biogeochemical and biophysical feedbacks on climate of all these changes in vegetation are also poorly understood. We here review the evidence of responses to climate change and discuss the perspectives for increasing our knowledge of the interactions between climate change and life.     

Predicting ecosystem dynamics at regional scales: an evaluation of a terrestrial biosphere model for the forests of northeastern North America

Terrestrial biosphere models are important tools for diagnosing both the current state of the terrestrial carbon cycle and forecasting terrestrial ecosystem responses to global change. While there are a number of ongoing assessments of the short-term predictive capabilities of terrestrial biosphere models using flux-tower measurements, to date there have been relatively few assessments of their ability to predict longer term, decadal-scale biomass dynamics. Here, we present the results of a regional-scale evaluation of the Ecosystem Demography version 2 (ED2)-structured terrestrial biosphere model, evaluating the model's predictions against forest inventory measurements for the northeast USA and Quebec from 1985 to 1995. Simulations were conducted using a default parametrization, which used parameter values from the literature, and a constrained model parametrization, which had been developed by constraining the model's predictions against 2 years of measurements from a single site, Harvard Forest (42.5° N, 72.1° W). The analysis shows that the constrained model parametrization offered marked improvements over the default model formulation, capturing large-scale variation in patterns of biomass dynamics despite marked differences in climate forcing, land-use history and species-composition across the region. These results imply that data-constrained parametrizations of structured biosphere models such as ED2 can be successfully used for regional-scale ecosystem prediction and forecasting. We also assess the model's ability to capture sub-grid scale heterogeneity in the dynamics of biomass growth and mortality of different sizes and types of trees, and then discuss the implications of these analyses for further reducing the remaining biases in the model's predictions.     

Adolescents and the threat of nuclear war: the evolution of a perspective

The authors briefly review recent work in the area of the impact of the threat of nuclear war on children and adolescents. They explore some of the difficulties inherent in understanding the possible effects of the threat of nuclear war on children based on their research experience in the area.     

利用大气二氧化碳和羰基硫浓度评估陆地生态系统模型碳通量模拟的不确定性

生态系统模型是模拟全球陆地生态系统碳循环的重要工具,但是其在全球不同区域的模拟存在很大的不确定性。如何评估陆地生态系统模型的不确定性是一项重要的研究。以北美地区为例,利用8个高塔观测站点同步获取的大气CO₂和羰基硫(OCS)浓度数据,结合WRF-STILT大气粒子扩散模型,评估了CASA-GFED3、SiB3和SiBCASA三种陆地生态系统模型模拟总初级生产力(GPP)和净生态系统CO₂交换(NEE)通量的不确定性。结果表明,SiB3模型能很好地模拟北美陆地生态系统GPP和NEE的季节变化时相和幅度,在3种模型中具有最佳的模拟能力;CASA-GFED3模型模拟的NEE季节变化较为理想、但对生长季GPP的模拟存在较大的误差,SiBCASA模型在模拟冬季晚期和春季早期的NEE和GPP时表现较不理想。研究证明了大气CO₂和OCS在评估陆地生态系统模型碳通量模拟的不确定性中的作用,为利用大气CO₂和OCS观测数据优化计算陆地生态系统光合和呼吸碳通量提供了理论支撑。     

Non-indigenous ungulates as a threat to biodiversity

Non-indigenous ungulate species pose a problem for conservation. They can be socially and economically valuable, but are also potentially harmful to biodiversity. Therefore, their introduction requires an explicit assessment of risk relative to benefit. To conduct such risk assessments, information regarding the impacts of non-indigenous ungulates on biodiversity is required. Here, we review the available evidence for the biodiversity impacts of non-indigenous ungulates. Hybridization, exploitation and apparent competition, vegetation impacts, predation, facilitation, trophic cascades and soil system functioning were assessed using a hierarchical set of criteria for the strength of the evidence. Strong evidence was lacking for risks posed by competition. Numerous reports exist of hybridization in captivity between ungulate species that normally do not co-occur, but conclusive evidence for introgression in the wild was restricted to one case. Strong evidence (using exclosure experiments) for the impacts of introduced ungulates on vegetation structure and composition was found and in some cases introduced ungulates caused the extirpation of plant species. Predation by Sus scrofa is a substantial threat to island faunas and systems, and impacts on soil system functioning elsewhere have also been found. Facilitation by ungulates has been shown to be substantial in promoting invasive plant species. By contrast, little evidence exists for apparent competition. The largest impacts from introduced ungulates are likely to be in cases where they perform novel functions in the new environment. However, to determine which types of impacts are likely to be most problematic, further evidence is required, ideally from well-designed field experiments.     

Chiral safety of the biosphere as a biophysical problem

The biosphere with its inherent chiral asymmetry fixed in the process of biological evolution at the level of L-amino acids and D-hydrocarbons and some other biologically active compounds of biogenic origin is under strong pressure of chiral substances produced by chemical, pharmaceutical, and other branches of industry and agriculture. Effective use of enantiomers is accompanied by toxic and even mutagenic effects of their mirror-image enantiomorphs. Only small amounts of products are tested for chiral purity; there is no system of global biosphere monitoring as well as no common standards of permissible concenrations. The investigation of the molecular basis of chiral stereospecificity of enzymes and cell receptors is of great interest from the point of view of fundamental biophysics. On the other hand, the development of chiral-selective sensors for environmental monitoring is important from the viewpoint of applied biophysics.     

A new threat: assessing the main interactions between marine fish and plastic debris from a scientometric perspective

Reviews in Fish Biology and Fisheries - Impacts generated by plastic pollution constitute one of the most significant challenges that humanity must face in the next century, receiving increasing...     

Herbivory by hares as a threat to the native brooms

Adult mortality, seed production, and seedling establishment of two species of New Zealand broom (Carmichaelia juncea and C. vexillata) were studied in exclosure trials to determine the level of threat posed by herbivory by introduced mammals. While no effect on mortality was observed for either species, herbivory by hares drastically reduced seed production and subsequent seedling establishment in C. juncea. C. vexillata seemed less vulnerable to herbivore damage due to its plant architecture, as well as the timing and intensity of the herbivore impact. The results of this trial suggest that species characteristics and the dynamics of herbivore impacts need to be considered in planning targeted herbivore control.     

The Chikungunya threat: an ecological and evolutionary perspective

Chikungunya virus (CHIKV) is an emerging mosquito-borne alphavirus. Although primarily African and zoonotic, it is known chiefly for its non-African large urban outbreaks during which it is transmitted by the same vectors as those of Dengue viruses. Unlike Dengue viruses, CHIKV displays a re-emergence pattern that closely depends on long-distance migrations including recent re-immigrations from African (putatively zoonotic) sources. Genus-based differences also emerged when comparing the evolution of Dengue-related (Flaviviruses) and of CHIKV-related (Alphaviruses) arboviruses. In this review, we discuss current information on CHIKV genetics, ecology and human infection. Further investigations on African CHIKV ecology and the differences between Flavivirus and Alphavirus members in adaptive changes and evolutionary constraints are likely to help delineate the potential of further CHIKV (re-)emergence.     

Effects of anthropogenic disturbance on tree population structure and diversity of a rain forest biosphere reserve in Ghana,West Africa

We evaluated the impacts of anthropogenic disturbance on community structure and diversity along three management zones of the Bia biosphere reserve in Ghana. Sixty sample plots were distributed among the core, buffer and transition zones. We estimated the degree of disturbances from discernible indicators on the field and satellite images. All tree species ≥10 cm dbh (diameter at breast height) were identified and enumerated. Inventory data were compared across the zones and related to intensity of disturbances. A total of 1176 individual trees from 108 species and 33 families were encountered. Number of species varied from 27 in the highly disturbed (HD) to 61 in the least disturbed (LD) zone. Mean basal area (BA) varied from 11.71 in the HD to 28.26 in the LD. Both Margalef's species richness and Shannon‐Weiner's α‐diversity were highest in the moderately disturbed (MD) than either the least and most disturbed zones. Our study revealed significant differences in tree abundance, stem density, BA and species diversity, attributable to differences in degree of anthropogenic disturbances among zones. Given the different levels of anthropogenic disturbance and corresponding impacts across the reserve, we recommend an integrated management strategy for the conservation of biodiversity in the Bia biosphere reserve.     

The perils of payoff: corruption as a threat to global biodiversity

Corruption is a worldwide phenomenon, particularly in many developing countries, which contain a large proportion of global biodiversity. Most alarming, from a biodiversity-conservation perspective, is the frequent corruption of government officials who manage valuable natural resources, such as timber, oil and precious minerals. A recent study by Joyotee Smith and colleagues describes rampant corruption in the timber industry of Indonesia, and shifts in the prevalence of different types of corruption as the country has become destabilized politically. By placing corruption into a conceptual framework, Smith et al. provide important insights into how developing nations and their natural resources can be besieged by corruption.     

Culture and inattentional blindness: a global workspace perspective

A recent 'necessary conditions' mathematical treatment of Baars' global workspace consciousness model, analogous to Dretske's communication theory analysis of high level mental function, is used to explore the effects of embedding cultural heritage on inattentional blindness. Culture should express itself quite distinctly in this basic psychophysical phenomenon across a great variety of sensory modalities because the limited syntactic and grammatical bandpass of the rate distortion manifold characterizing conscious attention must conform to topological constraints generated by cultural context.