Community history affects the predictability of microbial ecosystem development

Microbial communities mediate crucial biogeochemical, biomedical and biotechnological processes, yet our understanding of their assembly, and our ability to control its outcome, remain poor. Existing evidence presents conflicting views on whether microbial ecosystem assembly is predictable, or inherently unpredictable. We address this issue using a well-controlled laboratory model system, in which source microbial communities colonize a pristine environment to form complex, nutrient-cycling ecosystems. When the source communities colonize a novel environment, final community composition and function (as measured by redox potential) are unpredictable, although a signature of the community''s previous history is maintained. However, when the source communities are pre-conditioned to their new habitat, community development is more reproducible. This situation contrasts with some studies of communities of macro-organisms, where strong selection under novel environmental conditions leads to reproducible community structure, whereas communities under weaker selection show more variability. Our results suggest that the microbial rare biosphere may have an important role in the predictability of microbial community development, and that pre-conditioning may help to reduce unpredictability in the design of microbial communities for biotechnological applications.     

Lower Silurian animal communities — three case histories

A temporal succession of three marine animal communities of early Silurian age is described from the Midland Valley of Scotland. These formed part of an offshore onshore series of communities developed on the platform of a prograding delta under regressive tectonic conditions. All three communities were trophically structured in the same way as their modern analogues. In the earliest (isorthid-Glassia) community filterers and collectors were dominant; the absence of swallowers is attributable to the nature of the substrate. Soft-bodied swallowers, revealed only by their network of fine burrows, dominated the succeeding ( Skenidioides-Dicaelosia ) community. Filterers, which so dominated the hard-bodied fauna, were of only secondary importance: they lived clustered together in small aggregations, the sediments around which were reworked by the swallowers. A major fall of volcanic ash followed by an increase in the variability of the physical environment resulted in the abrupt replacement of this community by the Eoplectodonta-Visbyella community. Filterers were again dominant, with collectors subordinate; swallowers were comparatively rare.     

Phenazines and other redox-active antibiotics promote microbial mineral reduction

Natural products with important therapeutic properties are known to be produced by a variety of soil bacteria, yet the ecological function of these compounds is not well understood. Here we show that phenazines and other redox-active antibiotics can promote microbial mineral reduction. Pseudomonas chlororaphis PCL1391, a root isolate that produces phenazine-1-carboxamide (PCN), is able to reductively dissolve poorly crystalline iron and manganese oxides, whereas a strain carrying a mutation in one of the phenazine-biosynthetic genes (phzB) is not; the addition of purified PCN restores this ability to the mutant strain. The small amount of PCN produced relative to the large amount of ferric iron reduced in cultures of P. chlororaphis implies that PCN is recycled multiple times; moreover, poorly crystalline iron (hydr)oxide can be reduced abiotically by reduced PCN. This ability suggests that PCN functions as an electron shuttle rather than an iron chelator, a finding that is consistent with the observation that dissolved ferric iron is undetectable in culture fluids. Multiple phenazines and the glycopeptidic antibiotic bleomycin can also stimulate mineral reduction by the dissimilatory iron-reducing bacterium Shewanella oneidensis MR1. Because diverse bacterial strains that cannot grow on iron can reduce phenazines, and because thermodynamic calculations suggest that phenazines have lower redox potentials than those of poorly crystalline iron (hydr)oxides in a range of relevant environmental pH (5 to 9), we suggest that natural products like phenazines may promote microbial mineral reduction in the environment.     

Phenazines and Other Redox-Active Antibiotics Promote Microbial Mineral Reduction

Natural products with important therapeutic properties are known to be produced by a variety of soil bacteria, yet the ecological function of these compounds is not well understood. Here we show that phenazines and other redox-active antibiotics can promote microbial mineral reduction. Pseudomonas chlororaphis PCL1391, a root isolate that produces phenazine-1-carboxamide (PCN), is able to reductively dissolve poorly crystalline iron and manganese oxides, whereas a strain carrying a mutation in one of the phenazine-biosynthetic genes (phzB) is not; the addition of purified PCN restores this ability to the mutant strain. The small amount of PCN produced relative to the large amount of ferric iron reduced in cultures of P. chlororaphis implies that PCN is recycled multiple times; moreover, poorly crystalline iron (hydr)oxide can be reduced abiotically by reduced PCN. This ability suggests that PCN functions as an electron shuttle rather than an iron chelator, a finding that is consistent with the observation that dissolved ferric iron is undetectable in culture fluids. Multiple phenazines and the glycopeptidic antibiotic bleomycin can also stimulate mineral reduction by the dissimilatory iron-reducing bacterium Shewanella oneidensis MR1. Because diverse bacterial strains that cannot grow on iron can reduce phenazines, and because thermodynamic calculations suggest that phenazines have lower redox potentials than those of poorly crystalline iron (hydr)oxides in a range of relevant environmental pH (5 to 9), we suggest that natural products like phenazines may promote microbial mineral reduction in the environment.     

Multicellular microorganisms: laboratory versus nature

Our present in-depth knowledge of the physiology and regulatory mechanisms of microorganisms has arisen from our ability to remove them from their natural, complex ecosystems into pure liquid cultures. These cultures are grown under optimized laboratory conditions and allow us to study microorganisms as individuals. However, microorganisms naturally grow in conditions that are far from optimal, which causes them to become organized into multicellular communities that are better protected against the harmful environment. Moreover, this multicellular existence allows individual cells to differentiate and acquire specific properties, such as forming resistant spores, which benefit the whole population. The relocation of natural microorganisms to the laboratory can result in their adaptation to these favourable conditions, which is accompanied by complex changes that include the repression of some protective mechanisms that are essential in nature. Laboratory microorganisms that have been cultured for long periods under optimized conditions might therefore differ markedly from those that exist in natural ecosystems.     

Timing of snowmelt affects species composition via plant strategy filtering

Plant strategy schemes aim to classify plants according to measurable traits and group species according to their shared evolutionary responses to selective pressures. In this way, it becomes possible to make meaningful comparisons among ecosystems and communities and to predict how plant communities might respond to changes in their environment. Here, we classified common alpine plants which occur in snowpatches (Early and Late snowmelt sites) and in adjacent vegetation (Snow-free sites which melt early in the growing season) using Grime’s CSR plant strategy scheme. Alpine plant communities are largely driven by environmental filters associated with a relatively constant gradient of snowmelt timing. Since snow persistence influences the abiotic environment and plant assemblages alike, we hypothesised that these patterns would be reflected in community CSR scores. Weighted community CSR scores were clustered towards the stress-tolerator (S) corner of the triangular CSR space, and Snow-free communities were significantly more stress-tolerant than Early and Late snowmelt communities. This suggests that snowpatch communities are functionally distinct from surrounding vegetation when considering the major axes of plant variation identified by CSR theory. These results lend further support to the importance of the timing of snowmelt as a key filter, influencing how species and plant strategy types distribute themselves across the alpine landscape.     

An experimental model for the spatial structuring and selection of bacterial communities

Community-level selection is an important concept in evolutionary biology and has been predicted to arise in systems that are spatially structured. Here we develop an experimental model for spatially-structured bacterial communities based on coaggregating strains and test their relative fitness under a defined selection pressure. As selection we apply protozoan grazing in a defined, continuous culturing system. We demonstrate that a slow-growing bacterial strain Blastomonas natatoria 2.1, which forms coaggregates with Micrococcus luteus, can outcompete a fast-growing, closely related strain Blastomonas natatoria 2.8 under conditions of protozoan grazing. The competitive benefit provided by spatial structuring has implications for the evolution of natural bacterial communities in the environment.     

Detection of Peptidic Sequences in the Ancient Acidic Sediments of Río Tinto,Spain

Biomarkers are molecules that are produced by or can be associated with biological activities. They can be used as tracers that give us an idea of the ancient biological communities that produced them, the paleoenvironmental conditions where they lived, or the mechanism involved in their transformation and preservation. As a consequence, the preservation potential of molecules over time depends largely on their nature, but also on the conditions of the environment, which controls the decomposition kinetics. In this context, proteins and nucleic acids, which are biomolecules bearing biological information, are among the most labile molecules. In this research, we report the presence of short-chained peptides obtained from extracts of ferruginous sedimentary deposits that have been produced under the acidic and oxidizing solutions of Río Tinto, Spain. These preliminary results go against the paradigmatic idea that considers the acidic and oxidizing environments inappropriate for the preservation of molecular information.     

Response of Microbial Community Composition and Function to Soil Climate Change

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak–grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying ¹³C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their “life history” envelopes.     

松嫩平原西部生态脆弱带景观结构与生态耦合分析

研究了松嫩平原西部生态脆弱带生态景观结构,认为景观地球化学的空间分异及相互复合。决定了西部复杂而有规律的生态景观结构．景观地球化学梯度和生态梯度的耦合结果反映出大多植物沿景观地球化学梯度的生长状况表现为钟形或生态分布形曲线．现代条件下,西部植物群落的演替与土壤景观地球化学条件的改变几乎是同时发生的,二者在一定条件下互为因果关系.     

Parasites and Conservation Biology: The ‘Ibex-Ecosystem’

Parasites, as organisms with a particular way of life, form an important part of biodiversity, not only regarding the number of known species, but also because of their relevant role within ecological processes. These two facts should justify conservation of parasites, at least within natural and protected areas. Little is known about such complex communities of parasites but they are often considered as pests, even out of the fields of public (human) health and animal production, that is, just in the natural environment or under natural conditions. It is increasingly assumed that wildlife diseases, including those produced by parasites, are one of the main bases for managing animal populations. Parasitic diseases may also be managed and, at this point, we can find multiple technical problems which, in certain occasions, lead into philosophical questions or true dilemmas. These considerations are illustrated by revising parasites of the Spanish ibex (Capra pyrenaica), an Iberian mountain ungulate the parasitofauna of which is relatively well known. As a big game species, its trophies become more and more appreciated. Therefore, human dimensions involved in management of its populations are considerably increased. Finally, reasons and opportunities for managing parasitic diseases affecting ibex are revised and discussed, under a global goal or perspective of conserving parasites within natural areas, particularly those that are protected.     

Mechanisms determining the fate of dispersed bacterial communities in new environments

Recent work has shown that dispersal has an important role in shaping microbial communities. However, little is known about how dispersed bacteria cope with new environmental conditions and how they compete with local resident communities. To test this, we implemented two full-factorial transplant experiments with bacterial communities originating from two sources (freshwater or saline water), which were incubated, separately or in mixes, under both environmental conditions. Thus, we were able to separately test for the effects of the new environment with and without interactions with local communities. We determined community composition using 454-pyrosequencing of bacterial 16S rRNA to specifically target the active fraction of the communities, and measured several functional parameters. In absence of a local resident community, the net functional response was mainly affected by the environmental conditions, suggesting successful functional adaptation to the new environmental conditions. Community composition was influenced both by the source and the incubation environment, suggesting simultaneous effects of species sorting and functional plasticity. In presence of a local resident community, functional parameters were higher compared with those expected from proportional mixes of the unmixed communities in three out of four cases. This was accompanied by an increase in the relative abundance of generalists, suggesting that competitive interactions among local and immigrant taxa could explain the observed ‘functional overachievement''. In summary, our results suggest that environmental filtering, functional plasticity and competition are all important mechanisms influencing the fate of dispersed communities.     

Competition and allelopathy in aquatic plant communities

The paper reviews the published literature on the studies of competition and allelopathy in aquatic plant communities. Taking a broader view of the community, the studies on interactions between macrophytes and microphytes, macrophytes and macro-invertebrates and microbial communities are also reviewed. The role of these interactions in the structure and dynamics of aquatic communities has been discussed in light of the current hypotheses concerning competition in terrestrial communities. The available information suggests that the aquatic plants of various growth forms differ greatly among themselves in their responses and adaptations to competition and allelopathy. The possible application of these interactions in biological control of plant pests and in agriculture is also summarized. We conclude that the observed differences in these interactions between the terrestrial and aquatic environment are due to the effects of water as a non-resource variable as well as due to special adaptive characteristics of aquatic plants. Further we hypothesize that the aquatic plants adopt both competitive and allelopathic strategies under different conditions and in interactions with different plants. The review highlights that our knowledge of both competition and allelopathy among aquatic plant communities is inadequate and fragmentary, and therefore, both extensive and intensive studies are required.     

Anoxia can increase the rate of decay for cnidarian tissue: Using Actinia equina to understand the early fossil record

An experimental decay methodology is developed for a cnidarian model organism to serve as a comparison to the many previous such studies on bilaterians. This allows an examination of inherent bias against the fossilisation of cnidarian tissue and their diagnostic characters, under what conditions these occur, and in what way. The decay sequence of Actinia equina was examined under a series of controlled conditions. These experiments show that cnidarian decay begins with an initial rupturing of the epidermis, followed by rapid loss of recognisable internal morphological characters. This suggests that bacteria work quicker on the epidermis than autolysis does on the internal anatomy. The data also show that diploblastic tissue is not universally decayed more slowly under anoxic or reducing conditions than under oxic conditions. Indeed, some cnidarian characters decay more rapidly under anoxic conditions than they do under oxic conditions. This suggests the decay pathways acting may be different to those affecting soft bilaterian tissue such as soft epidermis and internal organs. What is most important in the decay of soft polyp anatomy is the microbial community, which can be dominated by oxic or anoxic bacteria. Different Lagerstätte, even of the same type, will inevitably have subtle difference in their bacterial communities, which among other factors, could be a control on soft polyp preservation leading to either an absence of compelling soft anthozoans (Burgess Shale) or an astonishing abundance (Qingjiang biota).     

Fish in Reservoirs

In all reservoirs the fish fauna is recruited from their riverine antecedents. The nature of the riverine environment, created by its unstable hydrological regime, favours the evolution of generalist species. Of these species, only a few are preadapted to lacustrine conditions. When riverine fish communities are trapped in a reservoir, most of the fish stay close to the shore, the mouth of tributaries and in shallows. The pelagic and deep waters are poorly utilized and the yield of fish is below the natural productivity of these water bodies, especially in the case of deep and large reservoirs. This occurs unless the dammed river contains fish species from families which are preadapted for lacustrine conditions. A positive correlation between the percentage of pelagic fish and the total yield of fish in reservoirs indicates that the pelagial represents a vacant habitat, only seldom invaded by riverine species. This situation probably applies to the deep water of reservoirs too, although sufficient data to demonstrate this are not available. The littoral region of reservoirs is utilized by some generalists of euryoecious species derived from the indigenous riverine fauna which may be preadapted for lacustrine conditions. If such preadapted lacustrine species are not present, the introduction of lacustrine species or those preadapted for the lacustrine environment is desirable under certain circumstances. However, caution must be exercised in any introduction.     

Engineering bacterial competitiveness and persistence in the phytosphere

Several tactics exist to improve the survival of an introduced microorganism of interest in the plant environment. One, derived from studies on the Agrobacterium-plant interaction and the role of opines in this interaction, proposes to promote growth of the inoculant in the plant environment via the establishment of a bias in the rhizosphere. It is supported by the occurrence of natural biases, such as those generated by opine-like molecules, by calestegins, or by mimosine. Opine-mediated biases have allowed several investigators to favor the growth of opine-degrading bacteria or communities under sterile or axenic environments or in microcosms mimicking near field conditions. Another way to favor a given microbe consists in impeding growth of competing microorganisms. Experiments performed using detergent or bacteriostatic agents as amendments under field or near field conditions yielded promising results. Research perspectives for engineering plant-microbe interactions also include specific engineering of predation and strategies designed to interfere with some of the signals perceived by the microbes, provided these signals control the expression of functions central to microbial fitness. In this respect, quorum-sensing signal molecules, such as N-acyl-homoserine lactones, may be valuable targets for the development of biocontrol agents and procedures.     

Structure of component parasite communities in the grayling, Thymallus thymallus L. (Salmoniformes, Thymallidae), and minnow, Phoxinus phoxinus L. (Cypriniformes, Cyprinidae), from the upper reaches of the Pechora River

A comparative analysis of parasite communities in the grayling and minnow has been performed. These communities differ in the number of constituent species and in the fact that the community of the minnow is dominated by one allogenic species, whereas that of the grayling usually has two dominants, both being autogenic species. The values of species diversity indices characterizing these communities are also different. Differences between the parasite communities of these fish species reflect the position of their hosts in the hydrobiocenosis. Species prevailing in both communities are classified as specialists, which is characteristic of parasite communities of the boreal-piedmont faunal complex. Both these communities consist of three species groups distinguished by their proportions in the total biomass, which indicates that parasitic communities are structured in a certain way and that the distribution of species in them is not random.