Life: past, present and future

Molecular methods of taxonomy and phylogeny have changed the way in which life on earth is viewed; they have allowed us to transition from a eukaryote-centric (five-kingdoms) view of the planet to one that is peculiarly prokarote-centric, containing three kingdoms, two of which are prokaryotic unicells. These prokaryotes are distinguished from their eukaryotic counterparts by their toughness, tenacity and metabolic diversity. Realization of these features has, in many ways, changed the way we feel about life on earth, about the nature of life past and about the possibility of finding life elsewhere. In essence, the limits of life on this planet have expanded to such a degree that our thoughts of both past and future life have been altered. The abilities of prokaryotes to withstand many extreme conditions has led to the term extremophiles, used to describe the organisms that thrive under conditions thought just a few years ago, to be inconsistent with life. Perhaps the most extensive adaptation to extreme conditions, however, is represented by the ability of many bacteria to survive nutrient conditions not compatible with eukaryotic life. Prokaryotes have evolved to use nearly every redox couple that is in abundance on earth, filling the metabolic niches left behind by the oxygen-using, carbon-eating eukaryotes. This metabolic plasticity leads to a common feature in physically stratified environments of layered microbial communities, chemical indicators of the metabolic diversity of the prokaryotes. Such 'metabolic extremophily' forms a backdrop by which we can view the energy flow of life on this planet, think about what the evolutionary past of the planet might have been, and plan ways to look for life elsewhere, using the knowledge of energy flow on earth.     

Population and community level approaches for analysing microbial diversity in natural environments

The enormous diversity available at the microbial level is just beginning to be realized. The richness of diversity amongst the bacteria that have been described so far is between 2 and 3000, whereas estimates indicates that millions of microorganisms still remains to be discovered. Microbiologists have realized that there are at least a dozen major evolutionary groups of the microbial life forms on earth (bacteria, fungi, algae and protozoa) that are even more diverse than the better known animal and plant kingdom. Indeed, we can state that microorganisms dominate the tree of life. Microorganisms have inhabited Earth for more than 3.7 billion years, whereas plants and animals have evolved rather recently in Earth's history. Possible reports of evidence for microbial life on Mars is also consistent with the concept that microorganisms precede plants and animals on Earth. The applications of molecular-phylogenetic techniques have provided the tools for studying natural microbial communities, including those that we are not able to grow in the laboratory. The utilization of these techniques has resulted in the discovery of many new evolutionary lineages, some of them only distantly related to known organisms. Here I discuss some environmental factors controlling bacterial diversity in different environments and the utility of modern methods developed for describing this diversity.     

Space flight effects on bacterial physiology

The study of bacterial behavior under space flight conditions is highly important for the early detection of changes in bacterial communities and bacteria with medical, environmental, or life support consequences for survival of the crew in closed space environments. Although many species of prokaryotes have been studied in ground simulation facilities or have been flown in space flights, at present only few hard research data are available to predict the effects of cosmic radiation, microgravity, vibration and hypervelocity on microbial behavior in space flight. The results that are available tend to be fragmentary and often lack a classical, controlled experimental context to interpret them. Thus, many basic questions concerning the effects of space on microbial behavior have yet to be resolved.     

Evolution of photosystem I and the control of global enthalpy in an oxidizing world

Life on earth is governed by light, chemical reactions, and the second law of thermodynamics, which defines the tendency for increasing entropy as an expression of disorder or randomness. Life is an expression of increasing order, and a constant influx of energy and loss of entropic wastes are required to maintain or increase order in living organisms. Most of the energy for life comes from sunlight and, thus, photosynthesis underlies the survival of all life forms. Oxygenic photosynthesis determines not only the global amount of enthalpy in living systems, but also the composition of the Earth’s atmosphere and surface. Photosynthesis was established on the Earth more than 3.5 billion years ago. The primordial reaction center has been suggested to comprise a homodimeric unit resembling the core complex of the current reaction centers in Chlorobi, Heliobacteria, and Acidobacteria. Here, an evolutionary scenario based on the known structures of the current reaction centers is proposed.     

Nitrogen fixation and hydrogen metabolism in photosynthetic bacteria.

The photosynthetic bacteria are found in a wide range of specialized aquatic environments. These bacteria represent important members of the microbial community since they are capable of carrying out two of the most important processes on earth, namely, photosynthesis and nitrogen fixation, at the expense of solar energy. Since the discovery that these bacteria could fix atmospheric nitrogen, there has been an intensification of studies relating to both the biochemistry and physiology of this process. The practical importance of this field is emphasized by a consideration of the tremendous energy input required for the production of artificial nitrogenous fertilizer. The present communication aims to briefly review the current state of knowledge relating to certain aspects of nitrogen fixation by the photosynthetic bacteria. The topics that will be discussed include a general survey of the nitrogenase system in the various photosynthetic bacteria, the regulation of both nitrogenase biosynthesis and activity, recent advances in the genetics of the nitrogen fixing system, and the hydrogen cycle in these bacteria. In addition, a brief discussion of some of some of the possible practical applications provided by the photosynthetic bacteria will be presented.     

Bacterial Exopolysaccharides from Extreme Marine Environments with Special Consideration of the Southern Ocean, Sea Ice, and Deep-Sea Hydrothermal Vents: A Review

Exopolysaccharides (EPSs) are high molecular weight carbohydrate polymers that make up a substantial component of the extracellular polymers surrounding most microbial cells in the marine environment. EPSs constitute a large fraction of the reduced carbon reservoir in the ocean and enhance the survival of marine bacteria by influencing the physicochemical environment around the bacterial cell. Microbial EPSs are abundant in the Antarctic marine environment, for example, in sea ice and ocean particles, where they may assist microbial communities to endure extremes of temperature, salinity, and nutrient availability. The microbial biodiversity of Antarctic ecosystems is relatively unexplored. Deep-sea hydrothermal vent environments are characterized by high pressure, extreme temperature, and heavy metals. The commercial value of microbial EPSs from these habitats has been established recently. Extreme environments offer novel microbial biodiversity that produces varied and promising EPSs. The biotechnological potential of these biopolymers from hydrothermal vent environments as well as from Antarctic marine ecosystems remains largely untapped.     

Extreme environments and exobiology

Ecological research on extreme environments can be applied to exobiological problems such as the question of life on Mars. If life forms (fossil or extant) are found on Mars, their study will help to solve fundamental questions about the nature of life on Earth. Extreme environments that are beyond the range of adaptability of their inhabitants are defined as "absolute extreme". Such environments can serve as terrestrial models for the last stages of life in the history of Mars, when the surface cooled down and atmosphere and water disappeared. The cryptoendolithic microbial community in porous rocks of the Ross Desert in Antarctica and the microbial mats at the bottom of frozen Antarctic lakes are such examples. The microbial communities of Siberian permafrost show that, in frozen but stable communities, long-term survival is possible. In the context of terraforming Mars, selected microorganisms isolated from absolute extreme environments are considered for use in creation of a biological carbon cycle.     

The obligate autotroph — the demise of a concept

Autotrophy is a life style in which inorganic compounds provide for all nutritional needs of an organism. Implicit in this definition is the capacity of an organism to derive all cell carbon from CO₂ and to obtain ATP either photosynthetically or chemolithotrophically. The existence of bacteria with such potentials has been known since the work of Winogradsky in the 1880's. The question explored in this paper is whether bacteria exist that must of necessity live autotrophically, i.e., the obligate autotrophsensu Winogradsky. The evidence is briefly reviewed and leads to four conclusions. One: there is no obligatory coupling between phototrophy and autotrophy or between chemolithotrophy and autotrophy. Two: autotrophic bacteria are not uniquely inhibited by organic matter. Three: all putative obligate autotrophic bacteria so far tested assimilate and metabolize exogenously supplied organic compounds. Four: mixotrophy can exist with respect to autotrophic and heterotrophic biosynthetic mechanisms and/or to chemolithotrophic and chemoorganotrophic energy-generating processes. Examples remain of bacteria that have not been cultured in the absence of an inorganic energy source or light. Such forms are appropriately described as obligate chemolithotrophs or obligate phototrophs. The available evidence, briefly categorized above, suggest that none of these bacteria is, at the same time, an obligate autotroph. From ecological and evolutionary considerations, an absolute dependence on carbon dioxide for all carbon makes little sense, and bacteria with such a requirement would be an anachronism on earth as it now exists. A lecture delivered before the third meeting of the Northwest European Microbiological Group, on August 18, 1971 at Utrecht, the Netherlands. The work reported from the author's laboratory was supported by grants from the National Science Foundation.     

Bacteriophage in polar inland waters

Bacteriophages are found wherever microbial life is present and play a significant role in aquatic ecosystems. They mediate microbial abundance, production, respiration, diversity, genetic transfer, nutrient cycling and particle size distribution. Most studies of bacteriophage ecology have been undertaken at temperate latitudes. Data on bacteriophages in polar inland waters are scant but the indications are that they play an active and dynamic role in these microbially dominated polar ecosystems. This review summarises what is presently known about polar inland bacteriophages, ranging from subglacial Antarctic lakes to glacial ecosystems in the Arctic. The review examines interactions between bacteriophages and their hosts and the abiotic and biotic variables that influence these interactions in polar inland waters. In addition, we consider the proportion of the bacteria in Arctic and Antarctic lake and glacial waters that are lysogenic and visibly infected with viruses. We assess the relevance of bacteriophages in the microbial loop in the extreme environments of Antarctic and Arctic inland waters with an emphasis on carbon cycling.     

Is biofilm formation intrinsic to the origin of life?

Biofilms are multicellular, often surface-associated, communities of autonomous cells. Their formation is the natural mode of growth of up to 80% of microorganisms living on this planet. Biofilms refractory towards antimicrobial agents and the actions of the immune system due to their tolerance against multiple environmental stresses. But how did biofilm formation arise? Here, I argue that the biofilm lifestyle has its foundation already in the fundamental, surface-triggered chemical reactions and energy preserving mechanisms that enabled the development of life on earth. Subsequently, prototypical biofilm formation has evolved and diversified concomitantly in composition, cell morphology and regulation with the expansion of prokaryotic organisms and their radiation by occupation of diverse ecological niches. This ancient origin of biofilm formation thus mirrors the harnessing environmental conditions that have been the rule rather than the exception in microbial life. The subsequent emergence of the association of microbes, including recent human pathogens, with higher organisms can be considered as the entry into a nutritional and largely stress-protecting heaven. Nevertheless, basic mechanisms of biofilm formation have surprisingly been conserved and refunctionalized to promote sustained survival in new environments.     

Errata corrige

Abstract

Ecological research on extreme environments can be applied to exobiological problems such as the question of life on Mars. If life forms (fossil or extant) are found on Mars, their study will help to solve fundamental questions about the nature of life on Earth. Extreme environments that are beyond the range of adaptability of their inhabitants are defined as “absolute extreme.” Such environments can serve as terrestrial models for the last stages of life in the history of Mars, when the surface cooled down and atmosphere and water disappeared. The cryptoendolithic microbial community in porous rocks of the Ross Desert in Antarctica and the microbial mats at the bottom of frozen Antarctic lakes are such examples. The microbial communities of Siberian permafrost show that, in frozen but stable communities, long-term survival is possible. In the context of terraforming Mars, selected microorganisms isolated from absolute extreme environments are considered for use in creation of a biological carbon cycle.     

RNA stable-isotope probing

At the heart of microbial ecology lies a true scientific dichotomy. On the one hand, we know microbes are responsible for processes on which all other life on Earth is dependent; their removal would mean the cessation of all known life. However, in opposition, the majority of extant microbial species in natural environments have never been cultured or studied in a laboratory as living organisms. Owing to these factors, the question of "who does what?" has been a major barrier to understanding how microbially mediated ecosystem level events occur. Recently, the use of stable isotopes (13C) to trace carbon from specific substrates into microbes that assimilate carbon from that substrate has significantly advanced our understanding of the relationship between environmental processes and microbial phylogeny.     

Adaptations to Hydrothermal Vent Life in Kiwa tyleri,a New Species of Yeti Crab from the East Scotia Ridge,Antarctica

Hydrothermal vents in the Southern Ocean are the physiologically most isolated chemosynthetic environments known. Here, we describe Kiwa tyleri sp. nov., the first species of yeti crab known from the Southern Ocean. Kiwa tyleri belongs to the family Kiwaidae and is the visually dominant macrofauna of two known vent sites situated on the northern and southern segments of the East Scotia Ridge (ESR). The species is known to depend on primary productivity by chemosynthetic bacteria and resides at the warm-eurythermal vent environment for most of its life; its short-range distribution away from vents (few metres) is physiologically constrained by the stable, cold waters of the surrounding Southern Ocean. Kiwa tylerihas been shown to present differential life history adaptations in response to this contrasting thermal environment. Morphological adaptations specific to life in warm-eurythermal waters, as found on – or in close proximity of – vent chimneys, are discussed in comparison with adaptations seen in the other two known members of the family (K. hirsuta, K. puravida), which show a preference for low temperature chemosynthetic environments.     

Iron metabolism in anoxic environments at near neutral pH

Anaerobic dissimilatory ferric iron-reducing and ferrous iron-oxidizing bacteria gain energy through reduction or oxidation of iron minerals and presumably play an important role in catalyzing iron transformations in anoxic environments. Numerous ferric iron-reducing bacteria have been isolated from a great diversity of anoxic environments, including sediments, soils, deep terrestrial subsurfaces, and hot springs. In contrast, only few ferrous iron-oxidizing bacteria are known so far. At neutral pH, iron minerals are barely soluble, and the mechanisms of electron transfer to or from iron minerals are still only poorly understood. In natural habitats, humic substances may act as electron carriers for ferric iron-reducing bacteria. Also fermenting bacteria were shown to channel electrons to ferric iron via humic acids. Whether quinones or cytochromes released from cells act as electron transfer components in ferric iron reduction is still a matter of debate. Anaerobic ferrous iron-oxidizing phototrophic bacteria, on the other hand, appear to excrete complexing agents to prevent precipitation of ferric iron oxides at their cell surfaces. The present review evaluates recent findings on the physiology of ferric iron-reducing and ferrous iron-oxidizing bacteria with respect to their relevance to microbial iron transformations in nature.     

Biofilme — die bevorzugte Lebensform der Bakterien: Flocken,Filme und Schlämme

„Biofilm”︁ describes microbial aggregates such as flocs, films and sludges; most microorganisms on earth prefer the mode of life in aggregates.They all have in common that the organisms are embedded in a matrix of extracellular polymeric substances (EPS) in which they can establish synergistic microconsortia. In this matrix, they are protected against biocides. Furthermore, the matrix acts as a sorbent for nutrients, retains exoenzymes and can be considered as a recycling yard for cellular components as well as for nutrients. Biofilms are ubiquitous and can be found even in extreme environments. In many cases, they are dominated by bacteria and/or algae, but they can also harbor higher trophical levels and represent a nutrient source for protozoa and metazoa. Biofilms are systems characterized by a vast spatial heterogeneity and temporal dynamics. Genes and signals are exchanged intensively. Thus, biofilms bear similarities to multicellular organisms.     

Is H2 the Universal Energy Source for Long-Term Survival?

Abstract This review revisits anabiosis (cryptobiosis or latent life); but more specifically with the discrepancy (time factor) between the finding of viable bacteria in ancient material and the racemization of amino acids and depurination of DNA that would have contributed to their death. The omnipresence of H₂ in the biosphere since life began, its ability to penetrate the microbial cell, its low energy of activation, its ability to form protons and electrons in the presence of Fe(II), and its (including electrons and protons) role in many biochemical reactions make H₂ the best candidate as the energy of survival for microbial cells. Although the concentration of H₂ in most environments is below the threshold level for microbial growth, the surviving cells have a long period of time to carry out the necessary metabolism to offset the racemization and depurination processes. This paper explores a hypothesis that explains this discrepancy. Received: 30 March 1999; Accepted: 27 July 1999; Online Publication: 30 November 1999     

微生物物种多样性、群落构建与功能性状研究进展

微生物主要包括细菌、真菌、古菌、病毒等类群, 是地球上出现时间最早、分布最广泛、个体数量最多, 以及物种和基因多样性十分丰富的生物类群。为了适应各种生境, 微生物衍生出腐生、寄生、共生等多样的生存策略, 在生物地球化学循环、生态系统演替与稳定性、环境修复以及人类健康等方面发挥着重要作用。传统的微生物监测方法限制了我们对微生物多样性的认知; 但是, 近年来高通量测序技术和生物信息学的发展极大推动了微生物多样性的研究进展。本文概述了近年来在微生物多样性分布格局与维持、群落构建以及功能属性多样性的最新进展; 总结分析了细菌、古菌、真菌的多样性纬度分布格局及其驱动因子, 选择、扩散、成种、漂变等过程对细菌、古菌、真菌的群落构建的贡献, 以及细菌和真菌的形态、生理生化、生长繁殖、扩散、基因组等功能性状的多样性; 提出了未来微生物多样性研究的重要领域: 环境宏真菌组研究, 微生物多样性与生态系统多功能性的关系研究, 以及微生物互作网络的生态功能研究。     

矿物电子能量协同微生物胞外电子传递与生长代谢

矿物是无机自然界吸收与转化能量的重要载体,其与微生物的胞外电子传递过程体现出矿物电子能量对微生物生长代谢与能量获取方式的影响。根据电子来源与产生途径,以往研究表明矿物中变价元素原子最外层或次外层价电子与半导体矿物导带上的光电子是微生物可以利用的两种不同胞外电子能量形式,其产生及传递方式与微生物胞外电子传递的电子载体密切相关。在协同微生物胞外电子传递过程中,矿物不同电子能量形式之间既有相似性亦存在着差异。反过来,微生物胞内-胞外电子传递途径也影响对矿物电子能量的吸收与获取,进而对微生物生长代谢等生命活动产生影响。本文在阐述矿物不同电子能量形式产生机制及其参与生物化学反应的共性和差异性特征基础上,综述了微生物获取矿物电子能量所需的不同电子载体类型与传递途径,探讨了矿物不同电子能量形式对微生物生长代谢等生命活动的影响,展望了自然条件下微生物利用矿物电子能量调节其生命活动、调控元素与能量循环的新方式。     

Microorganisms in the atmosphere over Antarctica

Antarctic microbial biodiversity is the result of a balance between evolution, extinction and colonization, and so it is not possible to gain a full understanding of the microbial biodiversity of a location, its biogeography, stability or evolutionary relationships without some understanding of the input of new biodiversity from the aerial environment. In addition, it is important to know whether the microorganisms already present are transient or resident – this is particularly true for the Antarctic environment, as selective pressures for survival in the air are similar to those that make microorganisms suitable for Antarctic colonization. The source of potential airborne colonists is widespread, as they may originate from plant surfaces, animals, water surfaces or soils and even from bacteria replicating within the clouds. On a global scale, transport of air masses from the well-mixed boundary layer to high-altitude sites has frequently been observed, particularly in the warm season, and these air masses contain microorganisms. Indeed, it has become evident that much of the microbial life within remote environments is transported by air currents. In this review, we examine the behaviour of microorganisms in the Antarctic aerial environment and the extent to which these microorganisms might influence Antarctic microbial biodiversity.     

Responses exhibited by various microbial groups relevant to uranium exposure

There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth’s crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.