Early Eukaryotes in the Lakhanda Biota (Mesoproterozoic,Southeastern Siberia)—Morphological and Geochemical Evidence

Doklady Biological Sciences - The Mesoproterozoic Lakhanda Group (~1030 Ma) preserves one of the most diverse communities of pre-Ediacaran eukaryotes. More precisely, the Lakhanda Biota includes...     

Fungal remains from the Late Riphean

The paper describes organic remains of one billion years old from the Lakhanda microbiota of the Uchur-Maya Region of southeastern Siberia. The microfossils were discovered on organic sapropelic films. The preserved morphological characters and some developmental stages of the ancient organisms, which are fixed in fossil state, suggest that some of them resembled zygomycetes. Other microfossils under consideration are comparable to reproductive structures of myxomycetes in the type of fusion of spheroid cells and formation of various types of aggregation (sori). Colonies of unicellular microfossils that are arranged in a branching pseudomycelium superficially resemble yeasts. The presence in the same biota of fungal remains belonging to the Myxomycota and Mycota, as well as members of xanthophyte vaucherian algae, indicates that various branches of eukaryotes might have developed in parallel even earlier than the Late Riphean.     

Records of a new spongelike group in the Riphean biota

New microfossils of presumably sponge organization grade have been recorded in the Meso-Neoproterozoic boundary beds of the Riphean Lakhanda Formation (Maya River, Uchur-Maya Region, southeastern Siberia). Because of the microscopic size, they remained invisible for a long time among abundant green algae on the surface of individual acritarchs in associations with nematode-like organisms and zygotes and suspensors of fungal microfossils. The specimens were found during a reexamination of the type material of Annulusia annulata Timofeev et Hermann, 1979, fixed on biofilms. The biofilms have shown the presence of very small, abundant, colonial organisms represented by aggregations of cells tightly connected in a soft tissue structure. In morphological characters, mode of life, occurrence of spicule-like structures, symmetry of their body, with a central canal positioned at the apex and interpreted here as an osculum, they are considered to be similar to the sponges Demospongiae and Hexactinellida. The microfossils with a syncytium and collagen-fibrous network (amorphous body) resemble the sponge class Hexactinellida.     

Formation of an unusual form of Riphean Eosolenides

A specific group of tubular microfossil Eosolenides, which display a series of biological innovations for these organic-walled microorganisms, is reported from the Meso-Neoproterozoic boundary beds (Lakhanda Microbiota, 1 Ga). This morphologically diverse group is recognized by the presence of unicellular symbionts and by an external narrowly-segmented integument, a supposed cuticle. Appearance of outer covers in the evolution of early organisms could be related to calcium, and calcium imbalance could explain sharp changes in morphology of some Eosolenides.     

Holism and Kantian teleology in C.J. Van De Klaauw's structuralization of oecology

The Dutch biologist C J. van der Klaauw (1893–1972) structuralized the epistemology of oecology using concepts which exceeded the limits of a strictly teleological interpretation of nature. This article relates to his theory of holistic oecology which van der Klaauw formulated departing from a critical confrontation with Kant's teleological view on nature. He substituted this extra-scientifically heuristic maxim by the holistic notion of network-like associations between organisms within a community. The analogous similarities between the organization of individual organisms and communities drawn up by van der Klaauw, merely remained propaedeutics for a genuine holistic oecology, which would only employ epistemological principles specifically referring to the organization of supra-individual communities of organisms. This article discusses the process of structuralizing the theory of holistic oecology by van der Klaauw in his dialogue with Kantian philosophy.     

Evolutionary anthropology and genes: Investigating the genetics of human evolution from excavated skeletal remains

The development of molecular tools for the extraction, analysis and interpretation of DNA from the remains of ancient organisms (paleogenetics) has revolutionised a range of disciplines as diverse as the fields of human evolution, bioarchaeology, epidemiology, microbiology, taxonomy and population genetics. The paper draws attention to some of the challenges associated with the extraction and interpretation of ancient DNA from archaeological material, and then reviews the influence of paleogenetics on the field of human evolution. It discusses the main contributions of molecular studies to reconstructing the evolutionary and phylogenetic relationships between extinct hominins (human ancestors) and anatomically modern humans. It also explores the evidence for evolutionary changes in the genetic structure of anatomically modern humans in recent millennia. This breadth of research has led to discoveries that would never have been possible using traditional approaches to human evolution.     

The application of trophic structure of fossil communities in paleoenvironmental reconstruction

The relative abundance of suspension- and deposit-feeding organisms in fossil communities has been used to interpret water turbulence in ancient environments. Trophic analysis of modern molluscan communities of San Francisco Bay and of Pliocene macroinvertebrate communities of the Kettleman Hills, California, suggests that the method is only partly valid for inshore environments, which may be more complex than those previously studied. Factors other than water turbulence must explain some differences in trophic proportions. Epifaunal communities consist largely of suspension-feeding organisms regardless of other environmental factors, and relict sediments or sediments out of equilibrium with the normal hydrologic conditions in the area may lead to erroneous interpretations. Analysis of the total benthic macroinvertebrate communities of the southern California shelf indicates that the trophic proportions of the potentially fossilizable part of each community are not the same as the total community and is not always diagnostic of the environment.     

Ancient life and moving fluids

Over 3.7 billion years of Earth history, life has evolved complex adaptations to help navigate and interact with the fluid environment. Consequently, fluid dynamics has become a powerful tool for studying ancient fossils, providing insights into the palaeobiology and palaeoecology of extinct organisms from across the tree of life. In recent years, this approach has been extended to the Ediacara biota, an enigmatic assemblage of Neoproterozoic soft-bodied organisms that represent the first major radiation of macroscopic eukaryotes. Reconstructing the ways in which Ediacaran organisms interacted with the fluids provides new insights into how these organisms fed, moved, and interacted within communities. Here, we provide an in-depth review of fluid physics aimed at palaeobiologists, in which we dispel misconceptions related to the Reynolds number and associated flow conditions, and specify the governing equations of fluid dynamics. We then review recent advances in Ediacaran palaeobiology resulting from the application of computational fluid dynamics (CFD). We provide a worked example and account of best practice in CFD analyses of fossils, including the first large eddy simulation (LES) experiment performed on extinct organisms. Lastly, we identify key questions, barriers, and emerging techniques in fluid dynamics, which will not only allow us to understand the earliest animal ecosystems better, but will also help to develop new palaeobiological tools for studying ancient life.     

The ancient lakes of Indonesia: towards integrated research on speciation

Ancient lakes have provided considerable insights into the drivers of speciation and adaptive radiation in aquatic organisms. Most studies of species-flocks, however, focus only on a single group of organisms, and few have attempted to integrate geological, limnological, ecological, and genetic drivers of speciation on multiple species-flocks at various trophic levels. As such, there is a need for a comprehensive model system for research on speciation in aquatic environments where multiple radiations are investigated at various levels of biological organization (e.g., individual, population, and ecosystem) and placed in light of geographical and geological setting. The ancient Malili Lakes of Sulawesi, Indonesia, are ideal candidates for such a model, and represent the only hydrologically connected ancient lakes in the world. These lakes are characterized by ultra-oligotrophy and unique physicochemical conditions that govern the composition and production of planktonic communities. At higher trophic levels, there are three recurring trends: (1) low taxonomic richness and simple community structures, (2) adaptive radiations with trophic specialization, and (3) remarkably high endemism with evolutionary innovations throughout the lakes and species-flocks. Furthermore, the restricted geographic distributions of species-flocks within the Malili Lakes indicate that each lake constitutes a unique environment, and dispersal among lakes is limited, despite close contemporary connectivity. These observations suggest that ecological and evolutionary processes are regulated from the bottom up, and speciation is primarily facilitated by interspecific and intraspecific competition for limited resources. The Malili Lakes represent an outstanding natural model for integrative research into speciation as they offer the opportunity to explore the roles of geography, dispersal, and selection in the radiation of aquatic organisms.     

The barbs (Barbus spp.) of Lake Tana: a forgotten species flock?

Synopsis All living species occupy an ecological niche, and are positioned within a trophic hierarchy. Extinct organisms presumably held similar behavioral and coevolutionary characteristics in the past, and were susceptible to the same kinds of natural ecological pressures operating today. Paleoecological investigations are limited by the incompleteness of the fossil record, and particularly by a lack of behavioral data that are so fundamental to ecological studies of living communities and habitats. Opportunities to examine the coevolutionary structure of ancient communities from empirical data are extremely rare. One such opportunity is provided by the Lower Cretaceous Santana Formation of north-eastern Brazil, a series of richly fossiliferous strata approximately 110 million years old. Many fossil fishes from the Santana Formation contain identifiable prey, including decapod crustaceans and fishes. A trophic hierarchy of these organisms is reconstructed here, and their ecological relationships are discussed. Comparison is made with a similar fish fauna from the Upper Jurassic Solnhofen Limestone of Germany. Low-level, intermediate and high-level predators are identified in each fauna. Predator-prey relationships in the Santana fauna are strongly hierarchical, and are more focussed at the intermediate predator level than in Solnhofen. Comparison with a model of predator-prey relationships between fishes and benthic fauna of the Baltic Sea (which like the Araripe Basin represents a semi-enclosed environment) suggests that heavy predation on teleosts such asRhacolepis, occupying an intermediate trophic level, may have permitted benthic decapods to proliferate and exclude other benthic organisms. Less intense predation on fishes at the intermediate trophic level would allow their numbers to increase, thereby increasing the intensity of predation on the benthos at the base of the trophic hierarchy.     

Shotgun microbial profiling of fossil remains

Millions to billions of DNA sequences can now be generated from ancient skeletal remains thanks to the massive throughput of next‐generation sequencing platforms. Except in cases of exceptional endogenous DNA preservation, most of the sequences isolated from fossil material do not originate from the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200‐ to 13 000‐year‐old horse bones collected from northern Siberia. We use a robust, taxonomy‐based assignment approach to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial community profiling of the seven specimens revealed site‐specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using a shotgun sequencing approach. In future, it may be possible to correlate, for example, the accumulation of postmortem DNA damage with the presence and/or abundance of particular microbes.     

Potential applications of nonthermal plasmas against biofilm‐associated micro‐organisms in vitro

Biofilms as complex microbial communities attached to surfaces pose several challenges in different sectors, ranging from food and healthcare to desalination and power generation. The biofilm mode of growth allows microorganisms to survive in hostile environments and biofilm cells exhibit distinct physiology and behaviour in comparison with their planktonic counterparts. They are ubiquitous, resilient and difficult to eradicate due to their resistant phenotype. Several chemical‐based cleaning and disinfection regimens are conventionally used against biofilm‐dwelling micro‐organisms in vitro. Although such approaches are generally considered to be effective, they may contribute to the dissemination of antimicrobial resistance and environmental pollution. Consequently, advanced green technologies for biofilm control are constantly emerging. Disinfection using nonthermal plasmas (NTPs) is one of the novel strategies having a great potential for control of biofilms of a broad spectrum of micro‐organisms. This review discusses several aspects related to the inactivation of biofilm‐associated bacteria and fungi by different types of NTPs under in vitro conditions. A brief introduction summarizes prevailing methods in biofilm inactivation, followed by introduction to gas discharge plasmas, active plasma species and their inactivating mechanism. Subsequently, significance and aspects of NTP inactivation of biofilm‐associated bacteria, especially those of medical importance, including opportunistic pathogens, oral pathogenic bacteria, foodborne pathogens and implant bacteria, are discussed. The remainder of the review discusses majorly about the synergistic effect of NTPs and their activity against biofilm‐associated fungi, especially Candida species.     

Use of 16S rRNA Gene Based Clone Libraries to Assess Microbial Communities Potentially Involved in Anaerobic Methane Oxidation in a Mediterranean Cold Seep

This study provides data on the diversities of bacterial and archaeal communities in an active methane seep at the Kazan mud volcano in the deep Eastern Mediterranean sea. Layers of varying depths in the Kazan sediments were investigated in terms of (1) chemical parameters and (2) DNA-based microbial population structures. The latter was accomplished by analyzing the sequences of directly amplified 16S rRNA genes, resulting in the phylogenetic analysis of the prokaryotic communities. Sequences of organisms potentially associated with processes such as anaerobic methane oxidation and sulfate reduction were thus identified. Overall, the sediment layers revealed the presence of sequences of quite diverse bacterial and archaeal communities, which varied considerably with depth. Dominant types revealed in these communities are known as key organisms involved in the following processes: (1) anaerobic methane oxidation and sulfate reduction, (2) sulfide oxidation, and (3) a range of (aerobic) heterotrophic processes. In the communities in the lowest sediment layer sampled (22–34 cm), sulfate-reducing bacteria and archaea of the ANME-2 cluster (likely involved in anaerobic methane oxidation) were prevalent, whereas heterotrophic organisms abounded in the top sediment layer (0–6 cm). Communities in the middle layer (6–22 cm) contained organisms that could be linked to either of the aforementioned processes. We discuss how these phylogeny (sequence)-based findings can support the ongoing molecular work aimed at unraveling both the functioning and the functional diversities of the communities under study.     

真菌化石研究进展

随着真菌化石被不断发现,利用化石中的真菌研究真菌类群的起源和进化历程逐渐成为真菌进化生物学研究的一个热点。真菌化石还是研究古生态中真菌与其他生物之间相互作用的重要材料,而这种相互作用既能用于研究古生物间的协同进化,也能成为判断古生态、古气候的重要依据。本文综述了国内外真菌化石的研究进展,旨在为更加系统准确地确定不同真菌类群的分化时间,重建真菌的系统发育树提供参考,同时也为研究生物间相互作用以及推断古生态环境提供帮助。     

秦岭天然锐齿栎林群落区系研究

锐齿栎林是秦岭林区的主要森林类型之一。通过对秦岭天然锐齿栎林群落的野外调查,报道了组成该群落的植物种类１８３种,隶属于６０科,１３１属,并在此基础上对该群落区系特点作了较为详细的分析。分析表明：１．该群落区系具有明显的温带性质。２．该群落区系是奠基在秦岭古老植物区系的基础上,通过种间竞争、群落演替形成的。３．锐齿栎本身不是一个古老的类群,其出现的时间不会早于上新世。     

Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo‐) environmental conditions, including temperature, food availability, salinity and pollution, can be traced through the analysis of their shell (micro‐) structure and biogeochemical composition. Adding to this list, the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories. Here, we assess this potential by applying DNA extraction, high‐throughput shotgun DNA sequencing and metagenomic analyses to marine mollusc shells spanning the last ~7,000 years. We report successful DNA extraction from shells, including a variety of ancient specimens, and find that DNA recovery is highly dependent on their biomineral structure, carbonate layer preservation and disease state. We demonstrate positive taxonomic identification of mollusc species using a combination of mitochondrial DNA genomes, barcodes, genome‐scale data and metagenomic approaches. We also find shell biominerals to contain a diversity of microbial DNA from the marine environment. Finally, we reconstruct genomic sequences of organisms closely related to the Vibrio tapetis bacteria from Manila clam shells previously diagnosed with Brown Ring Disease. Our results reveal marine mollusc shells as novel genetic archives of the past, which opens new perspectives in ancient DNA research, with the potential to reconstruct the evolutionary history of molluscs, microbial communities and pathogens in the face of environmental changes. Other future applications include conservation of endangered mollusc species and aquaculture management.     

Spontaneous regeneration of dry grasslands on set-aside fields

Dry grasslands are among the most threatened plant communities of Central Europe. We explore the time scale of spontaneous regeneration of dry grasslands on abandoned fields in an area of Central Europe, where also ancient grassland communities occur (Saxony-Anhalt, Germany). On three permanent plots with shallow soils we monitored during 10 years change of species composition and analysed whether spontaneous succession leads to assemblages similar to the ancient dry grassland communities in the direct surroundings. We found that dry grassland species are able to invade the permanent plots and during the 10 years of succession the number of dry grassland species increased. But even after 10 years there was a clear difference between ancient dry grassland communities and the assemblages on the permanent plots. Our findings suggest two important conclusions: First, spontaneous succession on abandoned fields is a cheap possibility for the conservation of some dry grassland species, at least on shallow soils. Second, the time scale of the regeneration process, however, is rather long. Hence, conservation of remnants of ancient grassland communities needs special attention.     

Divergence,demography and gene loss along the human lineage

Genomic DNA sequences are an irreplaceable source for reconstructing the vanished past of living organisms. Based on updated sequence data, this paper summarizes our studies on species divergence time, ancient population size and functional loss of genes in the primate lineage leading to modern humans (Homo sapiens sapiens). The inter- and intraspecific comparisons of DNA sequences suggest that the human lineage experienced a rather severe bottleneck in the Middle Pleistocene, throughout which period the subdivided African population played a predominant role in shaping the genetic architecture of modern humans. Also, published and newly identified human-specific pseudogenes (HSPs) are enumerated in order to infer their significance for human evolution. Of the 121 candidate genes obtained, authentic HSPs turn out to comprise only 25 olfactory receptor genes, four T cell receptor genes and nine other genes. The fixation of HSPs has been too rare over the past 6–7 Myr to account for species differences between humans and chimpanzees.     

Culture-Free Survey Reveals Diverse and Distinctive Fungal Communities Associated with Developing Figs (Ficus spp.) in Panama

The ancient association of figs (Ficus spp.) and their pollinating wasps (fig wasps; Chalcidoidea, Hymenoptera) is one of the most interdependent plant–insect mutualisms known. In addition to pollinating wasps, a diverse community of organisms develops within the microcosm of the fig inflorescence and fruit. To better understand the multipartite context of the fig–fig wasp association, we used a culture-free approach to examine fungal communities associated with syconia of six species of Ficus and their pollinating wasps in lowland Panama. Diverse fungi were recovered from surface-sterilized flowers of all Ficus species, including gall- and seed flowers at four developmental stages. Fungal communities in syconia and on pollinating wasps were similar, dominated by diverse and previously unknown Saccharomycotina, and distinct from leaf- and stem endophyte communities in the same region. Before pollination, fungal communities were similar between gall- and seed flowers and among Ficus species. However, fungal communities differed significantly in flowers after pollination vs. before pollination, and between anciently diverged lineages of Ficus with active vs. passive pollination syndromes. Within groups of relatively closely related figs, there was little evidence for strict-sense host specificity between figs and particular fungal species. Instead, mixing of fungal communities among related figs, coupled with evidence for possible transfer by pollinating wasps, is consistent with recent suggestions of pollinator mixing within syconia. In turn, changes in fungal communities during fig development and ripening suggest an unexplored role of yeasts in the context of the fig–pollinator wasp mutualism.     

古DNA 及其在生物系统与进化研究中的应用

古DNA是指从已经死亡的古代生物的遗体和遗迹中得到的DNA。本文回顾了近20年古DNA研究所经历的3个阶段, 从早期参与研究的科学家较少并主要利用克隆技术, 到后来由于PCR技术的出现以及提取化石DNA技术的成熟从而出现大量有关古DNA的报道; 近几年由于发现不少问题, 并引起激烈的争论, 科学家们因此而开始考虑古DNA的真实性问题, 并且提出了开展古DNA研究的严格标准。本文还讨论了古DNA在人类起源、系统发育重建、动植物驯化及考古研究中的重要意义以及现状, 表明古DNA的研究给某些原先的观点如人类的非洲起源说提供了重要证据, 也对某些观点提出了挑战; 古DNA研究还提供了某些已经灭绝生物的形态学和分子资料, 为从序列上确定古代材料的系统位置并有效地补充仅用现代DNA建立起来的谱系提供了来自古生物的依据。在动植物驯化及考古方面, 古DNA证据也为科学家提供了许多有价值的信息。最后, 本文还对古DNA研究的应用前景进行了展望。