Microbial community structure in polluted Baltic Sea sediments

Nearly half the seabed of the Baltic Proper is incapable of supporting life of higher organisms as a consequence of oxygen depletion resulting from eutrophication. However, these areas are actually teeming with microbial life. Here we used terminal-restriction fragment length polymorphism (T-RFLP) to investigate the dominant archaeal and bacterial groups, with respect to community structure, in surface layers of bottom sediments of the Baltic Sea along a coastal pollution gradient. Both archaeal and bacterial communities formed distinct clusters along the pollution gradient and the community compositions were different at the polluted sites compared with the relatively clean reference sites. The structures of the bacterial communities were most strongly correlated to water depth, followed by organic carbon, oxygen, salinity and silicate levels. In contrast, the structures of the archaeal communities were most strongly correlated to oxygen, salinity, organic carbon, silicate and nitrate levels. Some members of the microbial communities were identified using a combination of traditional and molecular approaches. Isolates obtained on different culture media were identified by partial sequencing of their 16S rRNA genes and some novel species were found. In addition, we developed a computer program, aplaus, to elucidate the putative identities of the most dominant community members by T-RFLP.     

Alternate life history phases of a common seaweed have distinct microbial surface communities

Macroalgal life histories are complex, often involving the alternation of distinct free‐living life history phases that differ in morphology, longevity and ploidy. The surfaces of marine macroalgae support diverse microbial biofilms, yet the degree of microbial variation between alternate phases is unknown. We quantified bacterial (16S rRNA gene) and microeukaryote (18S rRNA gene) communities on the surface of the common intertidal seaweed, Mastocarpus spp., which alternates between gametophyte (foliose, haploid) and sporophyte (encrusting, diploid) life history phases. A large portion (97%) of bacterial taxa on the surface Mastocarpus was also present in samples from the environment, indicating that macroalgal surface communities are largely assembled from the surrounding seawater. Still, changes in the relative abundance of bacterial taxa result in significantly different communities on alternate Mastocarpus life history phases, rocky substrate and seawater at all intertidal elevations. For microeukaryote assemblages, only high intertidal samples had significant differences between life history phases although sporophytes were not different from the rocky substrate at this elevation; gametophytes and sporophytes did not differ in microeukaryote communities in the mid and low zones. By sequencing three host genes, we identified three cryptic species of Mastocarpus in our data set, which co‐occur in the mid‐to‐low intertidal zone. In these samples, M. alaskensis sporophytes harboured distinct bacterial communities compared to M. agardhii and M. intermedius sporophytes, which were not distinguishable. Conversely, microeukaryote communities did not differ among species.     

Density‐dependent survival varies with species life‐history strategy in a tropical forest

Species coexistence in diverse communities likely results from multiple interacting factors. Mechanisms such as conspecific negative density dependence (CNDD) and varying life‐history strategies related to resource partitioning are known to influence plant fitness, and thereby community composition and diversity. However, we have little understanding of how these mechanisms interact and how they vary across life stages. Here, we document the interaction between CNDD and life‐history strategy, based on growth‐mortality trade‐offs, from seedling to adult tree for 47 species in a tropical forest. Species’ life‐history strategies remained consistent across stages: fast‐growing species had higher mortality than slow‐growing species at all stages. In contrast, mean CNDD was strongest at early life stages (i.e. seedling, sapling). Fast‐growing species tended to suffer greater CNDD than slow‐growing species at several, but not all life stages. Overall, our results demonstrate that coexistence mechanisms interact across multiple life stages to shape diverse tree communities.     

Environmental filtering structures fungal endophyte communities in tree bark

The factors that control the assembly and composition of endophyte communities across plant hosts remains poorly understood. This is especially true for endophyte communities inhabiting inner tree bark, one of the least studied components of the plant microbiome. Here, we test the hypothesis that bark of different tree species acts as an environmental filter structuring endophyte communities, as well as the alternative hypothesis, that bark acts as a passive reservoir that accumulates a diverse assemblage of spores and latent fungal life stages. We develop a means of extracting high‐quality DNA from surface sterilized tree bark to compile the first culture‐independent study of inner bark fungal communities. We sampled a total of 120 trees, spanning five dominant overstorey species across multiple sites in a mixed temperate hardwood forest. We find that each of the five tree species harbour unique assemblages of inner bark fungi and that angiosperm and gymnosperm hosts harbour significantly different fungal communities. Chemical components of tree bark (pH, total phenolic content) structure some of the differences detected among fungal communities residing in particular tree species. Inner bark fungal communities were highly diverse (mean of 117–171 operational taxonomic units per tree) and dominated by a range of Ascomycete fungi living asymptomatically as putative endophytes. Together, our evidence supports the hypothesis that tree bark acts as an environmental filter structuring inner bark fungal communities. The role of these potentially ubiquitous and plant‐specific fungal communities remains uncertain and merits further study.     

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.     

Community‐level spatial structure supports a model of stochastic geometry in species‐rich shrublands

In some ecosystems a small suite of species can determine community‐level patterns of species richness by acting as either ‘accumulators’ or ‘repellers’; that is, the richness of the immediate neighbourhood of such species departs from that expected on the basis of a given null model. Using the individual species‐area approach, we evaluated community‐level spatial pattern in four species‐rich shrublands (two 40 × 40 m and two 30 × 30 m plots) by assessing the frequency of accumulator and repeller species and whether any such species were associated with specific life‐history characteristics. Few species departed from the expectations of the null spatial model that we used, although, at three of the four sites, accumulators were more common than repellers. Departures from the null model we assessed were most prevalent within just 1 m of focal individuals and were not consistently associated with specific life‐history traits. Model‐based clustering suggests that there are distinct sub‐communities in each of the four communities, but while internally spatially cohesive, these sub‐communities intermingle and their membership is not predictable from the life‐history traits of their constituent species. Comparable analyses in other species‐rich systems have also detected a similar absence of spatial interactions. The disturbance regime in the shrubland communities we consider is markedly different from those in the forest ecosystems where previous studies have been concentrated (recurrent fire versus infrequent gap‐phase dynamics) and resources are more limiting. Thus, our results provide further support for the generality of a model of stochastic geometry, likely underpinned by stochastic dilution effects, in species‐rich plant communities.     

Microbial colonization of the salt deposits in the driest place of the Atacama Desert (Chile)

The Atacama Desert (Chile), one of the most arid places on Earth, shows hostile conditions for the development of epilithic microbial communities. In this study, we report the association of cyanobacteria (Chroococcidiopsis sp.) and bacteria belonging to Actinobacteria and Beta-Gammaproteobacteria and Firmicutes phyla inhabiting the near surface of salt (halite) deposits of the Salar Grande Basin, Atacama Desert (Chile). The halite deposits were investigated by using optical, confocal and field emission scanning electron microscopes, whereas culture-independent molecular techniques, 16S rDNA clone library, alongside RFLP analysis and 16S rRNA gene sequencing were applied to investigate the bacterial diversity. These microbial communities are an example of life that has adapted to extreme environmental conditions caused by dryness, high irradiation, and metal concentrations. Their adaptation is, therefore, important in the investigation of the environmental conditions that might be expected for life outside of Earth.     

High Diversity of Testate Amoebae (Amoebozoa,Arcellinida) Detected by HTS Analyses in a New England Fen using Newly Designed Taxon‐specific Primers

Testate (shell‐building) amoebae, such as the Arcellinida (Amoebozoa), are useful bioindicators for climate change. Though past work has relied on morphological analyses to characterize Arcellinida diversity, genetic analyses revealed the presence of multiple cryptic species underlying morphospecies. Here, we design and deploy Arcellinida‐specific primers for the SSU‐rDNA gene to assess the community composition on the molecular level in a pilot study of two samplings from a New England fen: (1) 36‐cm horizontal transects and vertical cores; and (2) 26‐m horizontal transects fractioned into four size classes (2–10, 10–35, 35–100, and 100–300 μm). Analyses of these data show the following: (1) a considerable genetic diversity within Arcellinida, much of which comes from morphospecies lacking sequences on GenBank; (2) communities characterized by DNA (i.e. active + quiescent) are distinct from those characterized by RNA (i.e. active, indicator of biomass); (3) active communities on the surface tend to be more similar to one another than to core communities, despite considerable heterogeneity; and (4) analyses of communities fractioned by size find some lineages (OTUs) that are abundant in disjunct size categories, suggesting the possibility of life‐history stages. Together, these data demonstrate the potential of these primers to elucidate the diversity of Arcellinida communities in diverse habitats.     

Life histories predict coral community disassembly under multiple stressors

Climate change is reshaping biological communities against a background of existing human pressure. Evaluating the impacts of multiple stressors on community dynamics can be particularly challenging in species‐rich ecosystems, such as coral reefs. Here, we investigate whether life‐history strategies and cotolerance to different stressors can predict community responses to fishing and temperature‐driven bleaching using a 20‐year time series of coral assemblages in Kenya. We found that the initial life‐history composition of coral taxa largely determined the impacts of bleaching and coral loss. Prior to the 1998 bleaching event, coral assemblages within no‐take marine reserves were composed of three distinct life histories – competitive, stress‐tolerant and weedy– and exhibited strong declines following bleaching with limited subsequent recovery. In contrast, fished reefs had lower coral cover, fewer genera and were composed of stress‐tolerant and weedy corals that were less affected by bleaching over the long term. Despite these general patterns, we found limited evidence for cotolerance as coral genera and life histories were variable in their sensitivities to fishing and bleaching. Overall, fishing and bleaching have reduced coral diversity and led to altered coral communities of ‘survivor’ species with stress‐tolerant and weedy life histories. Our findings are consistent with expectations that climate change interacting with existing human pressure will result in the loss of coral diversity and critical reef habitat.     

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.     

Life on Mars

Abstract

There is evidence that at one time Mars had liquid water habitats on its surface. Studies of microbial communities in cold and dry environments on the Earth provide a basis for discussion of the possible nature of any life that may have existed on Mars during that time. Of particular relevance are the cyanobacterial communities found in hypolithic and endolithic habitats in deserts. Microbial mats found under ice-covered lakes provide an additional possible Martian system. Results obtained from these field studies can be used to guide the search for fossil evidence of life on Mars. It is possible that in the future life will be reintroduced on Mars in an effort to restore that planet to habitable conditions. In this case the organisms under study as exemplars of past life may provide the hardy stock of pioneering Martian organisms. These first organisms must be followed by plants. The feasibility of reviving Mars will depend on the ability of plants to grow in an abundance of CO₂ but at extremely low pressures, temperatures, O₂, and N₂ levels. On Mars, biology was, and is, destiny.     

Biodiversity Effects on Biomass Production and Invasion Resistance in Annual versus Perennial Plant Communities

In a field experiment we constructed two different communities using both annual and perennial plant species, in which species diversity is experimentally manipulated. We want to test the relationships between species diversity and biomass production and invasibility and the possible mechanisms driving this relationships, especially, whether the identical mechanisms drive both diversity-production and diversity-invasibility relationships. Our results indicated that a positive diversity-production relationship and negative diversity-invasibility and production-invasibility relationships emerged in two different communities. However, the mechanisms underlying are different in two communities. In the annual communities, the observed positive diversity-production and negative diversity-invasibility relationships are linked by the sampling effect. In the perennial communities, however, the mechanism responsible for these observed relationships are the complementarity effect. Our results also found that, in addition to species diversity, species composition also play an important role in governing the observed relationship. The results of our study suggest that because species in different communities may differ in their life history, biological and physiological traits, mechanisms responsible for the observed relationship between diversity and biomass production and invasibiltiy are likely different.     

The negative effects of pathogen‐infected prey on predators: a meta‐analysis

Intra‐guild predation (IGP) – where a top predator (IG_Pred) consumes both a basal resource and a competitor for that resource (IG_Prey) – has become a fundamental part of understanding species interactions and community dynamics. IGP communities composed of intraguild predators and prey have been well studied; however, we know less about IGP communities composed of predators, pathogens, and resources. Resource quality plays an important role in community dynamics and may influence IGP dynamics as well. We conducted a meta‐analysis on predator–pathogen–resource communities to determine whether resource quality mediated by the pathogen affected predator life‐history traits and if these effects met the theoretical constraints of IGP communities. To do this, we summarized results from studies that investigated the use of predators and pathogens to control insect pests. In these systems, the predators are the IG_Pred and pathogens are the IG_Prey. We found that consumer longevity, fecundity, and survival decreased by 26%, 31% and 13% respectively, when predators consumed pathogen‐infected prey, making the infected prey a low quality resource. Predators also significantly preferred healthy prey over infected prey. When we divided consumers by enemy type, strict predators (e.g. wolf spiders) had no preference while parasitoids preferred healthy prey. Our results suggest that communities containing parasitoids and pathogens may rarely exhibit intraguild predation; whereas, communities composed of strict predators and pathogens are more likely dominated by IGP dynamics. In these latter communities, the consumption of low and high quality resources suggests that IGP communities composed of strict predators, pathogens and prey should naturally persist, supporting IGP theory. Synthesis We investigated how consuming pathogen‐infected prey influence important life‐history parameters of insect predators. Pathogens are used in a variety of biocontrol programs, especially to control crop pests. We found that true predators (i.e. wolf spiders) have no preference for healthy or infected prey and have reduced fecundity, survival and longevity consuming infected prey. However, parasitoids avoided infected prey when possible. In biocontrol programs with multiple control agents, parasitoids and pathogens would do a better job controlling pests as predators would reduce the amount of pathogen available and have reduced fitness from consuming infected prey. However, theory suggests that true predators, prey and pathogens may coexist long term.     

Spatial and resource factors influencing high microbial diversity in soil.

To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant. Two diversity indices, the reciprocal of Simpson's index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns. For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities. In a site richer in organic carbon, microbial communities consistently exhibited the uniform distribution pattern regardless of soil water content and depth. The uniform distribution implies that competition does not shape the structure of these microbial communities. Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone. Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity. Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility.     

Gut microbiota of dung beetles correspond to dietary specializations of adults and larvae

Vertebrate dung is central to the dung beetle life cycle, constituting food for adults and a protective and nutritive refuge for their offspring. Adult dung beetles have soft mandibles and feed primarily on nutritionally rich dung particles, while larvae have sclerotized mandibles and consume coarser dung particles with a higher C/N ratio. Here, using the dung beetles Euoniticellus intermedius and E. triangulatus, we show that these morphological adaptations in mandibular structure are also correlated with differences in basic gut structure and gut bacterial communities between dung beetle life stages. Metagenome functional predictions based on 16S rDNA characterization further indicated that larval gut communities are enriched in genes involved in cellulose degradation and nitrogen fixation compared to adult guts. Larval gut communities are more similar to female gut communities than they are to those of males, and bacteria present in maternally provisioned brood balls and maternal ‘gifts’ (secretions deposited in the brood ball along with the egg) are also more similar to larval gut communities than to those of males. Maternal secretions and maternally provisioned brood balls, as well as dung, were important factors shaping the larval gut community. Differences between gut microbiota in the adults and larvae are likely to contribute to differences in nutrient assimilation from ingested dung at different life history stages.     

野生五唇兰根部内生真菌多样性研究

兰科植物根部的内生真菌在兰科植物的整个生活史中起着重要的作用, 为了解不同生境不同类型的兰科植物内生真菌菌群的多样性, 作者于2004年7月至2005年10月, 以海南岛霸王岭自然保护区内的野生五唇兰(Doritis pulcherrima)作为实验材料, 对不同生境、不同形态的五唇兰植株根部的内生真菌群落多样性进行了研究。从附生于石上及生于杂木林或灌丛中、叶背绿色及叶背紫红色的五唇兰植株新鲜营养根段中共分离出83株内生真菌, 鉴定为19个属, 其中包括培养基筛选实验中分离出的30株14属。镰刀菌属(Fusarium)(24.1%)和丝核菌属 (Rhizocto-nia)(14.5%)为优势属。两种叶色的五唇兰内生真菌群落丰富度较为一致; 而两种不同生境中的五唇兰内生真菌群落丰富度则表现出较大的差异: 附生于灌木的五唇兰内生真菌群落Shannon多样性指数远高于附生岩石的。研究结果表明五唇兰内生真菌多样性更多地受生境的影响而不是受植株形态类型的影响。     

The mid-latitude biodiversity ridge in terrestrial cave fauna

The world's obligate cave-dwelling fauna holds considerable promise for biogeographic analysis because it represents a large number of independent evolutionary experiments in isolation in caves and adaptation to subterranean life. We focus on seven north temperate regions of at least 2000 km², utilizing more than 4300 records of obligate cave-dwelling terrestrial invertebrates. In North America, highest diversity was found in northeast Alabama while in Europe highest diversity was found in Ariège, France, and in southeast Slovenia. Based on these regions as well as more qualitative data from 16 other regions, we hypothesize that a ridge (ca 42°–46° in Europe and 34° in North America) of high biodiversity occurs in temperate areas of high productivity and cave density. This may reflect a strong dependence of cave communities on long term surface productivity (as reflected in actual evapotranspiration), because the subterranean fauna relies almost entirely on resources produced outside caves. This dependence may explain the unique biodiversity pattern of terrestrial cave invertebrates.     

Microbial community composition and function in permanently cold seawater and sediments from an arctic fjord of svalbard

Heterotrophic microbial communities in seawater and sediments metabolize much of the organic carbon produced in the ocean. Although carbon cycling and preservation depend critically on the capabilities of these microbial communities, their compositions and capabilities have seldom been examined simultaneously at the same site. To compare the abilities of seawater and sedimentary microbial communities to initiate organic matter degradation, we measured the extracellular enzymatic hydrolysis rates of 10 substrates (polysaccharides and algal extracts) in surface seawater and bottom water as well as in surface and anoxic sediments of an Arctic fjord. Patterns of enzyme activities differed between seawater and sediments, not just quantitatively, in accordance with higher cell numbers in sediments, but also in their more diversified enzyme spectrum. Sedimentary microbial communities hydrolyzed all of the fluorescently labeled polysaccharide and algal extracts, in most cases at higher rates in subsurface than surface sediments. In seawater, in contrast, only 5 of the 7 polysaccharides and 2 of the 3 algal extracts were hydrolyzed, and hydrolysis rates in surface and deepwater were virtually identical. To compare bacterial communities, 16S rRNA gene clone libraries were constructed from the same seawater and sediment samples; they diverged strongly in composition. Thus, the broader enzymatic capabilities of the sedimentary microbial communities may result from the compositional differences between seawater and sedimentary microbial communities, rather than from gene expression differences among compositionally similar communities. The greater number of phylum- and subphylum-level lineages and operational taxonomic units in sediments than in seawater samples may reflect the necessity of a wider range of enzymatic capabilities and strategies to access organic matter that has already been degraded during passage through the water column. When transformations of marine organic matter are considered, differences in community composition and their different abilities to access organic matter should be taken into account.     

Competition between encrusters on marine hard substrates and its fossil record

Many animals and plants that colonize hard surfaces in the sea are sessile and either bore into, or cement themselves permanently to the substrate surface. Because they retain their life positions after fossilization, these sclerobionts offer scope for studying biotic interactions in the fossil record. Encrusting sclerobionts compete actively for living space, with dominant competitors overgrowing the edges of subordinates. In addition to such marginal overgrowths, spatial competition may also occur through fouling in which larvae recruit directly onto the living surfaces of established sclerobionts. Spatial competition has been studied extensively in modern marine communities but there has been little research on competition between encrusters in ancient communities. This reflects poor knowledge of the taxonomy of the sclerobionts involved, as well as problems in distinguishing between overgrowth in vivo and post‐mortem. Nevertheless, if carefully interpreted, the fossil record of sclerobionts can provide an as yet largely unexploited resource for studying the long‐term ecological and evolutionary dynamics of competition.     

Hypolithic microbial communities: between a rock and a hard place

Drylands are the largest terrestrial biome on Earth and a ubiquitous feature is desert pavement terrain, comprising rocks embedded in the mineral soil surface. Quartz and other translucent rocks are common and microbial communities termed hypoliths develop as biofilms on their ventral surfaces. In extreme deserts these represent major concentrations of biomass, and are emerging as key to geobiological processes and soil stabilization. These highly specialized communities are dominated by cyanobacteria that support diverse heterotrophic assemblages. Here we identify global-scale trends in the ecology of hypoliths that are strongly related to climate, particularly with regard to shifts in cyanobacterial assemblages. A synthesis of available data revealed a linear trend for colonization with regard to climate, and we suggest potential application for hypoliths as 'biomarkers' of aridity on a landscape scale. The potential to exploit the soil-stabilizing properties of hypolithic colonization in environmental engineering on dryland soils is also discussed.