Competition as a structuring force in leaf miner communities

The role of competition in structuring communities of herbivorous insects is still debated. Despite this, few studies have simultaneously investigated the strength of various forms of competition and their effect on community composition. In this study, we examine the extent to which different types of competition will affect the presence and abundance of individual leaf miner species in local communities on oak trees Quercus robur. We first use a laboratory experiment to quantify the strength of intra‐ and interspecific competition. We then conduct a large‐scale field experiment to determine whether competition occurring in one year extends to the next. Finally, we use observational field data to examine the extent to which mechanisms of competition uncovered in the two experiments actually reflect into patterns of co‐occurrence in nature. In our experiment, we found direct competition at the leaf‐level to be stronger among conspecific than among heterospecific individuals. Indirect competition among conspecifics lowered the survival and weight of larvae of T. ekebladella, both at the branch and the tree‐level. In contrast, indirect competition among heterospecifics was only detected in one out of three species pairs examined. In the field experiment, the presence of a given moth species in one year affected the relative abundance of leaf miner species in the next year. Nevertheless, patterns of competition observed in these experiments did not translate into repulsion among free‐ranging leaf miners: conspecific larvae of four leaf‐mining species were aggregated on the same trees, shoots and leaves. In contrast, heterospecific larvae were only aggregated at the tree‐level. We propose that despite the fact that leaf miners do compete and that such effects extend through time, the incidence and strength of competition is relatively small at realistic densities. Hence, competition will likely be of minor importance in shaping the distribution of leaf miners in a natural setting.     

Echinoid grazing as a structuring force in coral communities: Whole reef manipulations

To examine the effects of echinoid grazing on shallow water coral community structure, the entire Diadema antillarum Philippi population (> 3000 individuals) was eliminated from a patch reef in Discovery Bay, Jamaica W.I. in January 1974. All remaining regular echinoids, notably including Echinometra viridis A. Agassiz (> 7000 individuals), were removed from one-half of the same reef 6 months later.Where Echinometra was present, its grazing was highly patchy, even at densities of up to 50/m². On the other hand, the effects of grazing by Diadema were more uniformly distributed at equivalent or lower densities.Percent-cover of adult corals was enhanced in the presence of Echinometra viridis, however, it was greatly reduced in the absence of all echinoid grazing as a result of massive overgrowth by algae. Success of coral recruitment (density of coral spat) increased in the absence of Diadema due to the alleviation of biological disturbance imposed by this urchin's feeding activities. The presence of Echinometra viridis, even at the high densities naturally present on the reef, did not deter coral settlement.Coral diversity was highest in the presence of all echinoids, intermediate in the presence of E. viridis (without Diadema), and lowest in the absence of all echinoids. This was due to the disproportionately successful recruitment and resultant high relative abundance of Agaricia at low echinoid densities. Favia, Millepora, Helioseris and Acropora all exhibited universally low recruitment levels. Predation by Diadema and Echinometra is responsible for damaging larger coral colonies, particularly Porites.As echinoid species composition and density was altered, the species composition of benthic algae and associated invertebrates shifted. In this way, the array of species competing for space with coral spat shifted as did their competitive relationships. Major epifaunal competitors included spirorbid polychaetes, various foraminifera (particularly Gypsina), and sponges. Algal competitors included filamentous chlorophytes, corallines (e.g. Jania), and numerous other red algae; the species composition of algal competitors shifted through time. Competitive success in corals varied as echinoid density changed and was species-specific with respect to coral genus. Interspecific competition between coral spat (i.e., interspecific aggression via extracoelenteric digestion) was negligible under all treatments.The presence of Echinometra viridis in high densities (in the absence of Diadema) created conditions where growth and fusion in Agaricia spat were optimized. Under these conditions, fusion allows a young coral colony to attain a large enough size to survive damage incurred from grazing or from competitive overgrowth, decreasing the probability of whole-colony mortality during the early stages of development.     

Organism–quartz interactions in structuring benthic communities: towards a marine bio-mineralogy?

Abiotic and biotic factors determine the distribution and structure of marine benthic communities but the processes invoked to explain such patterns are often inadequate. We demonstrate that the presence of quartz grains in sediments inhibits animal colonization on marine soft-bottoms. We suggest that this phenomenon may be related to the oxidant properties of the quartz crystal surface derived by the generation of silicon-based radicals due to water movement. The interaction between organisms and the crystallographic structure of substrata might play a neglected but important role in structuring coastal benthic communities.     

Interaction between isopod grazing and wave action: a structuring force in macroalgal communities in the southern Baltic Sea

The macroalgal belt in the southern Baltic Sea may be partly structured by the interaction of physical and biological factors. A field study, spanning the 1990s, describes a rapid decline of the Fucus spp. stands along the wave-exposed Swedish southeast coast. During this period, a relative dominance of Fucus vesiculosus L. shifted to a relative dominance of Fucus serratus L. The decline of F. vesiculosus coincided with observations of large numbers of the grazing isopods Idotea baltica (Pallas) and Idotea granulosa Rathke, or with field observations of frequent grazing marks on Fucus fronds. I. baltica, but not I. granulosa, tended to aggregate in the declining Fucus spp. stands, indicating a strong preference for Fucus spp. In a mesocosm experiment I. baltica, when given a choice, grazed both Fucus species at weak water motion. At strong water motion grazing was concentrated on F. vesiculosus. It is hypothesized that one of the reasons I. baltica preferred F. vesiculosus to F. serratus at strong water motion may have been differences in habitat quality, like width of thallus, influencing the ability to cling to the plant. Smaller thallus, as in F. vesiculosus, thus is the preferred habitat for grazing of I. blatica. We postulate that the existence of F. serratus in the area may be favoured by strong wave action and moderate but not strong grazing by I. baltica, relaxing the interspecific competition from F. vesiculosus.     

Occurrence and diversity of naphthalene dioxygenase genes in soil microbial communities from the Maritime Antarctic

The diversity of naphthalene dioxygenase genes ( ndo ) in soil environments from the Maritime Antarctic was assessed, dissecting as well the influence of the two vascular plants that grow in the Antarctic : Deschampsia antarctica and Colobanthus quitensis . Total community DNA was extracted from bulk and rhizosphere soil samples from Jubany station and Potter Peninsula, South Shetland Islands. ndo genes were amplified by a nested PCR and analysed by denaturant gradient gel electrophoresis approach (PCR-DGGE) and cloning and sequencing. The ndo- DGGE fingerprints of oil-contaminated soil samples showed even and reproducible patterns, composed of four dominant bands. The presence of vascular plants did not change the relative abundance of ndo genotypes compared with bulk soil. For non-contaminated sites, amplicons were not obtained for all replicates and the variability among the fingerprints was comparatively higher, likely reflecting a lower abundance of ndo genes. The phylogenetic analyses showed that all sequences were affiliated to the nahAc genes closely related to those described for Pseudomonas species and related mobile genetic elements. This study revealed that a microdiversity of nahAc -like genes exists in microbial communities of Antarctic soils and quantitative PCR indicated that their relative abundance was increased in response to anthropogenic sources of pollution.     

Evaluating the role of biotic interactions in structuring communities using a gradient analysis of multiple interacting guilds

The extent to which ecological communities are coherent entities as opposed to mere intersections of individual species distributions has long been one of the fundamental questions of ecology. Gradient analysis is one commonly used tool for addressing this question; however, all such studies have used organisms from a single taxon or guild. This risks missing important connections due to non‐competitive interactions, which should be more likely to occur between members of different guilds. Such organisms are unlikely to compete for resources and can have complementary niches that promote non‐competitive interactions. We examined the abundances of taxa in four interacting guilds along an elevation gradient in a forest in the southern Appalachian mountains. A causal discovery algorithm was used to investigate the relative frequencies of interguild and intraguild interactions. These were approximately equally common once taxonomic richness was taken into account. We used elements of metacommunity structure analysis to study the extent to which species distributions are non‐independent and tested the hypothesis that combinations of two or more interacting guilds exhibit more coherence than single guilds. In this analysis, all guilds other than collembola were classified as Clementsian or quasi‐Clementsian. (Collembola were classified as random.) When sets of multiple guilds were examined, Clementsian and quasi‐Clementsian structures predominated. We also compared boundary conjunction, measured as Morisita’s index (MI) for these sets of guilds to the weighted average of the guilds’ MI values. Only sets of directly interacting guilds had higher‐than‐baseline boundary conjunction values, and such boundary conjunction values are found in all but one set of directly interacting guilds. Our results highlight the importance of inter‐guild interactions in structuring patterns of cooccurrence. Trophic interactions and plant–fungus symbioses (mutualistic and/or pathogen–host) appear particularly important.     

Temperature adaptation of soil bacterial communities along an Antarctic climate gradient: predicting responses to climate warming

Soil microorganisms, the central drivers of terrestrial Antarctic ecosystems, are being confronted with increasing temperatures as parts of the continent experience considerable warming. Here we determined short‐term temperature dependencies of Antarctic soil bacterial community growth rates, using the leucine incorporation technique, in order to predict future changes in temperature sensitivity of resident soil bacterial communities. Soil samples were collected along a climate gradient consisting of locations on the Antarctic Peninsula (Anchorage Island, 67 °34′S, 68 °08′W), Signy Island (60 °43′S, 45 °38′W) and the Falkland Islands (51 °76′S 59 °03′W). At each location, experimental plots were subjected to warming by open top chambers (OTCs) and paired with control plots on vegetated and fell‐field habitats. The bacterial communities were adapted to the mean annual temperature of their environment, as shown by a significant correlation between the mean annual soil temperature and the minimum temperature for bacterial growth (T_min). Every 1 °C rise in soil temperature was estimated to increase T_min by 0.24–0.38 °C. The optimum temperature for bacterial growth varied less and did not have as clear a relationship with soil temperature. Temperature sensitivity, indicated by Q₁₀ values, increased with mean annual soil temperature, suggesting that bacterial communities from colder regions were less temperature sensitive than those from the warmer regions. The OTC warming (generally <1 °C temperature increases) over 3 years had no effects on temperature relationship of the soil bacterial community. We estimate that the predicted temperature increase of 2.6 °C for the Antarctic Peninsula would increase T_min by 0.6–1 °C and Q₁₀ (0–10 °C) by 0.5 units.     

Identification of actinomycete communities in Antarctic soil from Barrientos Island using PCR-denaturing gradient gel electrophoresis

The diversity of specific bacteria taxa, such as the actinomycetes, has not been reported from the Antarctic island of Barrientos. The diversity of actinomycetes was estimated with two different strategies that use PCR-denaturing gradient gel electrophoresis. First, a PCR was applied, using a group-specific primer that allows selective amplification of actinomycete sequences. Second, a nested-PCR approach was used that allows the estimation of the relative abundance of actinomycetes within the bacterial community. Molecular identification, which was based on 16S rDNA sequence analysis, revealed eight genera of actinomycetes, Actinobacterium, Actinomyces, an uncultured Actinomycete, Streptomyces, Leifsonia, Frankineae, Rhodococcus, and Mycobacterium. The uncultured Actinomyces sp and Rhodococcus sp appear to be the prominent genera of actinomycetes in Barrientos Island soil. PCR-denaturing gradient gel electrophoresis patterns were used to look for correlations between actinomycete abundance and environmental characteristics, such as type of rookery and vegetation. There was a significant positive correlation between type of rookery and abundance of actinomycetes; soil samples collected from active chinstrap penguin rookeries had the highest actinomycete abundance. Vegetation type, such as moss, which could provide a microhabitat for bacteria, did not correlate significantly with actinomycete abundance.     

Disentangling the role of soil in structuring tropical tree communities at Tarap Hill Reserve of Bangladesh

Tarap Hill Reserve, the largest upland reserve of Bangladesh, is situated along the Indo-Burma Biodiversity Hotspot. It encompasses the last remaining patches of natural vegetation in the Northeastern Tarap Mountain System and harbors 87 % of the nationally declared red-listed vascular plant species. Despite requiring high conservation priority, this is one of the least studied reserves in the tropics. In this study, we collected vegetation and soil (eight variables) data from 68 sample plots. We identified the tree communities by cluster analysis and verified them using the multi-response permutation procedure and detrended correspondence analysis. Species richness, diversity, and compositional similarity between the communities were also estimated. In total, 116 tree species representing 69 genera were recorded within the four identified tree community types. Finally, canonical correspondence analysis with associated Monte Carlo permutation tests (499 permutations) was performed to explore the patterns of variation in tree species distribution explained by the soil variables. Soil phosphorus, organic matter content, and pH were most closely correlated with tree compositional variation. Thus, conservation strategies that take into account variations in these influential soil factors may aid in the conservation of trees in the reserve.     

Xenopus as an experimental model for studying evolution of hsp--immune system interactions

The frog Xenopus provides a unique model system for studying the evolutionary conservation of the immunological properties of heat shock proteins (hsps). General methods for maintaining and immunizing isogenetic clones of defined MHC genotypes are presented together with more recently developed protocols for exploring hsp-mediated immune responses in vitro (proliferative and cytotoxic assays) and in vivo (adoptive cell transfer and antibody treatment) in adults and in naturally MHC class I-deficient larvae. Finally, techniques to study modalities of expression of the endoplasmic reticulum resident gp96 at the cell surface of tumor and normal lymphocytes are considered.     

Proximity of krill and salps in an Antarctic coastal ecosystem: evidence from penguin-mounted cameras

Antarctic krill (Euphausia superba) and salps (mainly Salpa thompsoni) are main components of Southern Ocean ecosystem, but little is known about their coastal distribution at a fine scale (<1 km). We deployed miniaturised cameras on breeding chinstrap (n = 9 birds) and gentoo penguins (n = 9 birds) in the Antarctic Peninsula region and obtained 2,333 krill images, 93 salp images and 609 sea floor images from 1,843 dives. 51.2 % of penguin dives that had salps present in the images occurred near the dives with krill images (within 5 min). The vertical distribution of salp images showed overlap with the upper depth zone of krill images. While 16.3 % of dives with krill images were associated in time with the sea floor, only 1.2 % of dives with salp images did. These results revealed close proximity between krill and salps within the penguin’s foraging range in an Antarctic coastal ecosystem. These results also imply that krill patches were common in both pelagic and benthic habitat, whereas salps were common mainly in pelagic habitat. If the effects of deployments are similar between the years or regions, inter-annual or regional comparison using the penguin-mounted camera will be valid for characterising prey environment in the penguin foraging area.     

Role of non-indigenous species in structuring benthic communities after fragmentation events: an experimental approach

Biological Invasions - Habitat loss and fragmentation, and biological invasions are widely considered the most significant threats to global biodiversity. While marine invasions have already shown...     

Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource

Background

Physcomitrella patens, a haploid dominant plant, is fast becoming a useful molecular genetics and bioinformatics tool due to its key phylogenetic position as a bryophyte in the post-genomic era. Genome sequences from select reference species were compared bioinformatically to Physcomitrella patens using reciprocal blasts with the InParanoid software package. A reference protein interaction database assembled using MySQL by compiling BioGrid, BIND, DIP, and Intact databases was queried for moss orthologs existing for both interacting partners. This method has been used to successfully predict interactions for a number of angiosperm plants.

Results

The first predicted protein-protein interactome for a bryophyte based on the interolog method contains 67,740 unique interactions from 5,695 different Physcomitrella patens proteins. Most conserved interactions among proteins were those associated with metabolic processes. Over-represented Gene Ontology categories are reported here.

Conclusion

Addition of moss, a plant representative 200 million years diverged from angiosperms to interactomic research greatly expands the possibility of conducting comparative analyses giving tremendous insight into network evolution of land plants. This work helps demonstrate the utility of “guilt-by-association” models for predicting protein interactions, providing provisional roadmaps that can be explored using experimental approaches. Included with this dataset is a method for characterizing subnetworks and investigating specific processes, such as the Calvin-Benson-Bassham cycle.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0524-1) contains supplementary material, which is available to authorized users.     

Salinity gradient and nutrients as major structuring factors of the phytoplankton communities in salt marshes

This study investigated the major environmental factors structuring, for a year, phytoplankton assemblages in the Sfax saltern (Tunisia): salinity and nutrients. A STATICO analysis based on 11 environmental variables and the abundances of 64 phytoplanktonic species was conducted. STATICO is used to analyze the stable part of the relationships between the environment and species, and then to determine how these relationships change over time. The analysis confirmed that the salinity gradient had a considerable influence on the composition of the phytoplanktonic communities. Bacillariophyceae and Dinophyceae dominated in the least salty ponds, whereas Chlorophyceae and Cyanophyceae dominated in the saltiest ponds, in accordance with the halotolerance level estimated for each species by calculating the optimum salinity and salt tolerance. Nitrogen (N) and phosphorus (P) ions could have a secondary influence on the phytoplankton distribution and its dynamics. Dinophyceae seem to be favored by high ammonium (NH₄ ⁺) concentrations, whereas diatoms seem to be favored by high orthophosphates (PO₄ ^3?) and nitrates (NO₃ ^?) values. The Chlorophyceae Dunalliela salina thrived in the saltiest ponds when the NO₃ ^? concentrations increased.     

Calanoid–cyclopoid interactions: evidence from an 11-year field study in a eutrophic lake

1. The interactions between calanoid and cyclopoid copepods were examined in an 11-year field study of a eutrophic lake (Heiligensee, Berlin, Germany).
2. A diminishing ratio of calanoids to cyclopoids was observed. The responses, however, were species specific. While two cyclopoid species responded with increased populations ( Cyclops vicinus, Thermocyclops oithonoides ), one species exhibited marked declines ( C. kolensis ). Other species extended the duration of their pelagic phase ( Mesocyclops leuckarti, Diacyclops bicuspidatus, T. oithonoides, C. vicinus ), leading to higher population overlaps. Eudiaptomus graciloides and E. gracilis, which used to be present throughout the year, were more frequently absent.
3. These changes coincided with a series of mild winters during which prey availability (algae and rotifers) was high.
4. Enhanced prey availability, in conjunction with a flexible diapausing strategy, are hypothesized to underly the increased success of C. vicinus . Predatory losses due to early occurrence and enhanced abundances of C. vicinus, rather than competition for the same food resources, are hypothesized to be responsible for the declines of C. kolensis and Eudiaptomus .
5. Summer species tended to develop higher abundances early in the season, which led to enhanced seasonal means during spring. These changes cannot be explained by the interaction between calanoids and cyclopoids alone, but were probably a result of changes in fish predation.     

Proteasome-cytochrome c interactions: a model system for investigation of proteasome host-guest interactions

Owing to its high thermal stability and structural simplicity, the archaebacterium Thermoplasma Acidophilum 20S proteasome was selected for mechanistic studies in this work. This oligomeric enzyme complex consists of a barrel-shaped 20S core (approximately 700kDa) comprised of four stacked seven-membered rings with a alpha(7)beta(7)beta(7)alpha(7) subunit structure situated around a 7-fold symmetry axis. The hollow interior of the proteasome has three large interconnected chambers with narrow (13 A diameter) entrances from solution located at either end of the barrel. The 14 beta-subunit proteolytic sites are located on the inner surface of the central chamber. Herein, we demonstrate that unfolded horse heart ferricytochrome c (Cyt c) is a novel chromophoric probe for investigation of the mechanism of proteasome action. Under conditions of temperature and denaturant which unfold Cyt c but do not alter the thermophilic proteasome, Cyt c is extensively cleaved by the proteasome. Ten peptides were isolated and sequenced from the proteasome digest. Analysis of the cleavage products established that unfolded Cyt c and its covalently attached heme prosthetic group are translocated to the central chamber where proteolysis occurs. In the presence of site-specific inhibitors of the proteasome, we demonstrate that unfolded cytochrome c can be sequestered inside the proteasome complex. Upon cooling, a quasistable host-guest complex is formed. Analysis of the complex via UV/visible spectroscopy and mass spectrometry gave evidence that the sequestered Cyt c is essentially intact within the inhibited proteasome. High-performance liquid chromatography data show that (1) complexes with an apparent stoichiometry of approximately one Cyt c per proteasome can be formed and (2) when inhibition is removed from the complex, a rapid turnover of the sequestered Cyt c occurs.