Unravelling interspecies interactions across heterogeneities in complex biofilm communities

The importance of microbial biofilms has been well-recognized for several decades, and focus is now shifting towards investigating multispecies biofilm communities rather than mono- or dual-species biofilms. Therefore, the demand for techniques that provide a sufficient amount of information at adequate resolution is increasing. One major challenge for multispecies studies is that diversity and spatial organization often lead to a high degree of spatial and chemical heterogeneity. Many current approaches do not account for such heterogeneity and therefore only provide average information (−omics techniques in particular), which could obscure important information about the community. Here, we bring attention to the issues of heterogeneity when analysing synthetic multi-species biofilms, in vitro, and the importance of multi-scale approaches. We provide an overview of current and newer approaches that can be applied to biofilm communities, in order to elucidate interactions at the appropriate scale.     

Soil nematodes mediate positive interactions between legume plants and rhizobium bacteria

Symbiosis between legume species and rhizobia results in the sequestration of atmospheric nitrogen into ammonium, and the early mechanisms involved in this symbiosis have become a model for plant-microbe interactions and thus highly amenable for agricultural applications. The working model for this interaction states that the symbiosis is the outcome of a chemical/molecular dialogue initiated by flavonoids produced by the roots of legumes and released into the soil as exudates, which specifically induce the synthesis of nodulation factors in rhizobia that initiate the nodulation process. Here, we argue that other organisms, such as the soil nematode Caenorhabditis elegans, also mediate the interaction between roots and rhizobia in a positive way, leading to nodulation. We report that C. elegans transfers the rhizobium species Sinorhizobium meliloti to the roots of the legume Medicago truncatula in response to plant-released volatiles that attract the nematode. These findings reveal a biologically-relevant and largely unknown interaction in the rhizosphere that is multitrophic and may control the initiation of the symbiosis.     

Dynamic interactions between cells and their extracellular matrix mediate embryonic development

Cells and their surrounding extracellular matrix microenvironment interact throughout all stages of life. Understanding the continuously changing scope of cell‐matrix interactions in vivo is crucial to garner insights into both congenital birth defects and disease progression. A current challenge in the field of developmental biology is to adapt in vitro tools and rapidly evolving imaging technology to study cell‐matrix interactions in a complex 4‐D environment. In this review, we highlight the dynamic modulation of cell‐matrix interactions during development. We propose that individual cell‐matrix adhesion proteins are best considered as complex proteins that can play multiple, often seemingly contradictory roles, depending upon the context of the microenvironment. In addition, cell‐matrix proteins can also exert different short versus long term effects. It is thus important to consider cell behavior in light of the microenvironment because of the constant and dynamic reciprocal interactions occurring between them. Finally, we suggest that analysis of cell‐matrix interactions at multiple levels (molecules, cells, tissues) in vivo is critical for an integrated understanding because different information can be acquired from all size scales. Mol. Reprod. Dev. 77: 475–488, 2010. © 2010 Wiley‐Liss, Inc.     

Functional diversity across space and time: trends in wader communities on British estuaries

Aim British estuarine ecosystems support large populations of protected migratory waders. Understanding how wader communities vary spatially and how they may be changing temporally can greatly improve the understanding of these dynamic ecosystems. Here, we explore the variation in functional diversity (using a range of morphological and ecological traits) in order to identify the processes shaping wader communities on British estuaries and how these processes may be changing. Location England, Wales and Scotland. Methods We use national survey data (Wetland Bird Survey) from 1980/1981 to 2006/2007 winter to calculate functional diversity (FD) – an index that measures trait dispersion – in wader communities on 100 estuaries. We test for evidence of non‐random patterns of diversity and explore the relative importance of two key processes, environmental filtering and competition, in shaping these communities. Results The observed FD was significantly and positively associated with species richness and to a lesser extent estuary area, followed by longitude. An increase in observed FD was observed since 1980, supported by a small but significant slope. In the majority of cases, changes in FD were mirrored by changes in species richness. Observed FD was on average lower than expected by chance, as indicated by a negative value of observed minus expected FD. However, this difference became less negative over time, with observed minus expected FD values increasing slightly, but significantly, over the study period. Main conclusions Wader FD varies across British estuaries, and the relative influence of the processes by which communities are structured appears to be changing through time. We discuss the potential drivers underlying these patterns and the importance of identifying such drivers for the protection of wader communities.     

Do domatia mediate mutualistic interactions between coffee plants and predatory mites?

Many plant species possess structures on their leaves that often harbour predatory or fungivorous mites. These so‐called domatia are thought to mediate a mutualistic interaction; the plant gains protection because mites decimate plant pathogenic fungi or herbivores, whereas the mites find shelter in the domatia. We tested this hypothesis using two species of coffee (Coffea spp.) plants that posses domatia consisting of small cavities at the underside of the leaves, and which often harbour mites. We assessed densities of domatia, of the predatory mite Iphiseiodes zuluagai Denmark and Muma (Acari: Phytoseiidae) and of herbivorous mites Oligonychus ilicis (McGregor) (Acari: Tetranychidae) and Brevipalpus phoenicis (Geijskes) (Acari: Tenuipalpidae) on Coffea arabica L. (Rubiaceae) and Coffea canephora Pierre in the field. Over a period of 50 days, C. arabica harboured on average 7.5 times more predatory mites and 0.4–0.66 fewer prey mites than C. canephora. Hence, the higher density of predatory mites on C. arabica could not be explained by higher densities of prey. However, the density of domatia on C. arabica was on average 1.65 times higher than on C. canephora, and within each species, leaves with higher densities of domatia also harboured more predators. This suggests a positive effect of domatia on predatory mites. In the laboratory, survival of adult female predatory mites on leaves of C. arabica with open domatia was indeed significantly higher than on leaves with closed domatia. Hence, predatory mites benefited from the domatia. However, plants with higher densities of domatia did not harbour fewer herbivores. Taken together, our study only provides partial evidence for a mutualistic interaction between coffee plants and predatory mites, mediated by domatia.     

Two-component elements mediate interactions between cytokinin and salicylic acid in plant immunity

Recent studies have revealed an important role for hormones in plant immunity. We are now beginning to understand the contribution of crosstalk among different hormone signaling networks to the outcome of plant-pathogen interactions. Cytokinins are plant hormones that regulate development and responses to the environment. Cytokinin signaling involves a phosphorelay circuitry similar to two-component systems used by bacteria and fungi to perceive and react to various environmental stimuli. In this study, we asked whether cytokinin and components of cytokinin signaling contribute to plant immunity. We demonstrate that cytokinin levels in Arabidopsis are important in determining the amplitude of immune responses, ultimately influencing the outcome of plant-pathogen interactions. We show that high concentrations of cytokinin lead to increased defense responses to a virulent oomycete pathogen, through a process that is dependent on salicylic acid (SA) accumulation and activation of defense gene expression. Surprisingly, treatment with lower concentrations of cytokinin results in increased susceptibility. These functions for cytokinin in plant immunity require a host phosphorelay system and are mediated in part by type-A response regulators, which act as negative regulators of basal and pathogen-induced SA-dependent gene expression. Our results support a model in which cytokinin up-regulates plant immunity via an elevation of SA-dependent defense responses and in which SA in turn feedback-inhibits cytokinin signaling. The crosstalk between cytokinin and SA signaling networks may help plants fine-tune defense responses against pathogens.     

The CCAAT binding factor can mediate interactions between CONSTANS-like proteins and DNA

CONSTANS-Like (COL) proteins are plant-specific nuclear regulators of gene expression but do not contain a known DNA-binding motif. We tested whether a common DNA-binding protein can deliver these proteins to specific cis-acting elements. We screened for proteins that interact with two members of a subgroup of COL proteins. These COL proteins were Tomato COL1 (TCOL1), which does not seem to be involved in the control of flowering time, and the Arabidopsis thaliana CONSTANS (AtCO) protein which mediates photoperiodic induction of flowering. We show that the C-terminal plant-specific CCT (CO, CO-like, TIMING OF CAB EXPRESSION 1) domain of both proteins binds the trimeric CCAAT binding factor (CBF) via its HAP5/NF-YC component. Chromatin immunoprecipitation demonstrated that TCOL is recruited to the CCAAT motifs of the yeast CYC1 and HEM1 promoters by HAP5. In Arabidopsis, each of the three CBF components is encoded by several different genes that are highly transcribed. Under warm long days, high levels of expression of a tomato HAP5 (THAP5a) gene can reduce the flowering time of Arabidopsis. A mutation in the CCT domain of TCOL1 disrupts the interaction with THAP5 and the analogous mutation in AtCO impairs its function and delays flowering. CBFs are therefore likely to recruit COL proteins to their DNA target motifs in planta.     

Non-random interactions within and across guilds shape the potential to coexist in multi-trophic ecological communities

Theory posits that the persistence of species in ecological communities is shaped by their interactions within and across trophic guilds. However, we lack empirical evaluations of how the structure, strength and sign of biotic interactions drive the potential to coexist in diverse multi-trophic communities. Here, we model community feasibility domains, a theoretically informed measure of multi-species coexistence probability, from grassland communities comprising more than 45 species on average from three trophic guilds (plants, pollinators and herbivores). Contrary to our hypothesis, increasing community complexity, measured either as the number of guilds or community richness, did not decrease community feasibility. Rather, we observed that high degrees of species self-regulation and niche partitioning allow for maintaining larger levels of community feasibility and higher species persistence in more diverse communities. Our results show that biotic interactions within and across guilds are not random in nature and both structures significantly contribute to maintaining multi-trophic diversity.     

Trans interactions between galactosylceramide and cerebroside sulfate across apposed bilayers

The two glycosphingolipids galactosylceramide (GalC) and its sulfated form, cerebroside sulfate (CBS), are present at high concentrations in the multilayered myelin sheath and are involved in carbohydrate-carbohydrate interactions between the lipid headgroups. In order to study the structure of the complex of these two glycolipids by Fourier transform infrared (FTIR) spectroscopy, GalC dispersions were combined with CBS dispersions in the presence and absence of Ca(2+). The FTIR spectra indicated that a strong interaction occurred between these glycolipids even in the absence of Ca(2+). The interaction resulted in dehydration of the sulfate, changes in the intermolecular hydrogen bonding interactions of the sugar and other oxygens, decreased intermolecular hydrogen bonding of the amide C==O of GalC and dehydration of the amide region of one or both of the lipids in the mixture, and disordering of the hydrocarbon chains of both lipids. The spectra also show that Ca(2+) interacts with the sulfate of CBS. Although they do not reveal which other groups of CBS and GalC interact with Ca(2+) or which groups participate in the interaction between the two lipids, they do show that the sulfate is not directly involved in interaction with GalC, since it can still bind to Ca(2+) in the mixture. The interaction between these two lipids could be either a lateral cis interaction in the same bilayer or a trans interaction between apposed bilayers. The type of interaction between the lipids, cis or trans, was investigated using fluorescent and spin-label probes and anti-glycolipid antibodies. The results confirmed a strong interaction between the GalC and the CBS microstructures. They suggested further that this interaction caused the CBS microstructures to be disrupted so that CBS formed a single bilayer around the GalC multilayered microstructures, thus sequestering GalC from the external aqueous phase. Thus the CBS and GalC interacted via a trans interaction across apposed bilayers, which resulted in dehydration of the headgroup and interface region of both lipid bilayers. The strong interaction between these lipids may be involved in stabilization of the myelin sheath.     

Positive interactions in communities

Current concepts of the role of interspecific interactions in communities have been shaped by a profusion of experimental studies of interspecific competition over the past few decades. Evidence for the importance of positive interactions - facilitations - in community organization and dynamics has accrued to the point where it warrants formal inclusion into community ecology theory, as it has been in evolutionary biology.     

Herbivore-induced plant volatiles mediate behavioral interactions between a leaf-chewing and a phloem-feeding herbivore

Plants respond adaptively to herbivore stress in order to maintain fitness. Upon herbivore attack, plants emit blends of volatile organic compounds (VOCs) that differ from those that are constitutively emitted. These defense responses are typically specific to the identity of the attacking herbivore and often linked to the herbivore's feeding guild (e.g. chewing, phloem-feeding). Herbivores use plant volatiles to locate suitable host plants and changes in volatile emissions can affect host-plant location. Therefore, herbivores from separate feeding guilds can interact indirectly through the modulation of plant responses. In this study we tested how damage by an herbivore from one feeding guild affected the host-plant choice of an herbivore from a separate feeding guild, and vice versa. A chewing herbivore, the Colorado potato beetle (Leptinotarsa decemlineata), and a phloem feeding herbivore, the green peach aphid (Myzus persicae), were assayed in olfactometers to assess behavioral responses to odors emitted by potato plants (Solanum tuberosum) that were damaged by herbivores from the other feeding guild. Leptinotarsa decemlineata oriented more frequently towards undamaged plants compared to M. persicae damaged plants. Surprisingly, M. persicae preferred plants that were damaged by L. decemlineata, although previous studies had shown that they perform worse on these plants. Distinct differences were detected in the volatile profiles of herbivore-damaged and undamaged plants. Leptinotarsa decemlineata induced stronger volatile emissions compared to undamaged control plants, while M. persicae tended to suppress volatile emissions. These herbivores demonstrate contrasting induction of plant volatiles and behavioral responses. Exploring the nature of co-occurring herbivores and how they perceive potential hosts can play a significant role in understanding the ecological functions and community dynamics of plant plasticity and interactions with a variety of herbivores.     

Changes in soil microbial communities modulate interactions between maize and weeds

Plant and Soil - Despite the importance of the soil microbiota to plant growth, the role of soil microorganisms in crop-weed competition remains largely unexplored. Here, we investigated the...     

Dynamics of parasite communities and interactions between wild and domestic ruminants

Dynamics of parasite communities and host-parasite-environment interactions can be influenced by different factors. The present note, by discussing some field experiences in wild and domestic ruminant populations, approaches eco-epidemiology of abomasal nematodes in relation with host health and dynamics. Factors possibly playing a role in the host-parasite relationship are discussed, as well as possible use of macroparasites as ecological and sanitary indicators. The above topics are approached in a management perspective, in particular regarding interactions between domestic and wild ruminant populations.     

Phylogenetic community structure and phylogenetic turnover across space and edaphic gradients in western Amazonian tree communities

Ecological and evolutionary processes influence community assembly at both local and regional scales. Adding a phylogenetic dimension to studies of species turnover allows tests of the extent to which environmental gradients, geographic distance and the historical biogeography of lineages have influenced speciation and dispersal of species throughout a region. We compare measures of beta diversity, phylogenetic community structure and phylobetadiversity (phylogenetic distance among communities) in 34 plots of Amazonian trees across white‐sand and clay terra firme forests in a 60 000 square kilometer area in Loreto, Peru. Dominant taxa in white‐sand forests were phylogenetically clustered, consistent with environmental filtering of conserved traits. Phylobetadiversity measures found significant phylogenetic clustering between terra firme communities separated by geographic distances of <200–300 km, consistent within recent local speciation at the watershed scale in the Miocene‐aged clay‐soil forests near the foothills of the Andes. Although both distance and habitat type yielded statistically significant effects on both species and phylogenetic turnover, the patterns we observed were more consistent with an effect of habitat specialization than dispersal limitation. Our results suggest a role for both broad‐scale biogeographic and evolutionary processes, as well as habitat specialization, influencing community structure in Amazonian forests.     

Museum metabarcoding: A novel method revealing gut helminth communities of small mammals across space and time

Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host and parasite/pathogen dynamics. We developed a new technique to identify intestinal helminth parasites and applied it to shrews (Eulipotyphla: Soricidae) because they are ubiquitous, occupy diverse habitats, and host a diverse and abundant parasite fauna. Notably, we included museum specimens preserved in various ways to explore the efficacy of using metabarcoding analyses that may enable identification of helminth symbiont communities from historical archives. We successfully sequenced the parasite communities (using 12S mtDNA, 16S mtDNA, 28S rDNA) of 23 whole gastrointestinal tracts. All gastrointestinal tracts were obtained from the Museum of Southwestern Biology, USA, and from recent field collections, varying both in time since fixation (ranging from 4?months to 16?years) and preservation method (70% or 95% ethanol stored at room temperature, or flash frozen in liquid nitrogen and stored at ?80?°C). Our proof of concept demonstrates the feasibility of applying next generation DNA sequencing techniques to authoritatively identify the parasite/pathogen communities within whole gastrointestinal tracts from museum specimens of varying age and fixation, and the value of future preservation of host-associated whole gastrointestinal tracts in public research archives. This powerful approach facilitates future comparative examinations of the distributions and interactions among multiple associated groups of organisms through time and space.     

Why wood density varies across communities

Communities are the emergent outcome of individual‐level trait–environment interactions. In this issue of the Journal of Vegetation Science, Ibanez et al. utilize an impressive data set from New Caledonia to demonstrate how the interaction of climatic axes drives the distribution and diversity of wood density in tree communities. Here, we discuss their specific findings and their broader implications for trait‐based ecology.     

植物邻体间的正相互作用

植物间的正负相互作用是构建植被群落的重要因素,也是群落生态学研究的中心内容之一。近20a来,植物间正相互作用的研究得到快速发展。综述了正相互作用的定义,不同植物群落中的直接、间接正相互作用及其发生机制,正相互作用研究的实验和模型方法,正负相互作用随胁迫梯度的变化及正相互作用对群落构建的影响。探讨了正相互作用研究前景:(1)进一步理解正负相互作用的平衡及其对群落构建的影响;(2)加深对全球变暖背景下的正相互作用的认识;(3)需把正相互作用研究同进化联系起来;(4)充分发挥正相互作用在生态系统中的推动力作用,把正相互作用应用到生态恢复中,为恢复退化生态系统服务。