The termite group I phylum is highly diverse and widespread in the environment

The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of "Endomicrobia," which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to "Endomicrobia." Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.     

“Endomicrobia”: Cytoplasmic Symbionts of Termite Gut Protozoa Form a Separate Phylum of Prokaryotes

Lignocellulose digestion by wood-feeding termites depends on the mutualistic interaction of unusual, flagellate protists located in their hindgut. Most of the flagellates harbor numerous prokaryotic endosymbionts of so-far-unknown identity and function. Using a full-cycle molecular approach, we show here that the endosymbionts of the larger gut flagellates of Reticulitermes santonensis belong to the so-called termite group 1 (TG-1) bacteria, a group of clones previously obtained exclusively from gut homogenates of Reticulitermes speratus that are only distantly related to other bacteria and are considered a novel bacterial phylum based on their 16S rRNA gene sequences. Fluorescence in situ hybridization with specifically designed oligonucleotide probes confirmed that TG-1 bacteria are indeed located within the flagellate cells and demonstrated that Trichonympha agilis (Hypermastigida) and Pyrsonympha vertens (Oxymonadida) harbor phylogenetically distinct populations of symbionts (<95% sequence similarity). Transmission electron microscopy revealed that the symbionts are small, spindle-shaped cells (0.6 μm in length and 0.3 μm in diameter) surrounded by two membranes and located within the cytoplasm of their hosts. The symbionts of the two flagellates are described as candidate species in the candidate genus “Endomicrobium.” Moreover, we provide evidence that the members of the TG-1 phylum, for which we propose the candidate name “Endomicrobia,” are phylogenetically extremely diverse and are present in and also restricted to the guts of all lower termites and wood-feeding cockroaches of the genus Cryptocercus, the only insects that are in an exclusive, obligately mutualistic association with such unique cellulose-fermenting protists.     

Source-Sink Colonization as a Possible Strategy of Insects Living in Temporary Habitats

Continuous colonization and re-colonization is critical for survival of insect species living in temporary habitats. When insect populations in temporary habitats are depleted, some species may escape extinction by surviving in permanent, but less suitable habitats, in which long-term population survival can be maintained only by immigration from other populations. Such situation has been repeatedly described in nature, but conditions when and how this occurs and how important this phenomenon is for insect metapopulation survival are still poorly known, mainly because it is difficult to study experimentally. Therefore, we used a simulation model to investigate, how environmental stochasticity, growth rate and the incidence of dispersal affect the positive effect of permanent but poor (“sink”) habitats on the likelihood of metapopulation persistence in a network of high quality but temporary (“source”) habitats. This model revealed that permanent habitats substantially increase the probability of metapopulation persistence of insect species with poor dispersal ability if the availability of temporary habitats is spatio-temporally synchronized. Addition of permanent habitats to a system sometimes enabled metapopulation persistence even in cases in which the metapopulation would otherwise go extinct, especially for species with high growth rates. For insect species with low growth rates the probability of a metapopulation persistence strongly depended on the proportions of “source” to “source” and “sink” to “source” dispersal rates.     

"Endomicrobia": cytoplasmic symbionts of termite gut protozoa form a separate phylum of prokaryotes

Lignocellulose digestion by wood-feeding termites depends on the mutualistic interaction of unusual, flagellate protists located in their hindgut. Most of the flagellates harbor numerous prokaryotic endosymbionts of so-far-unknown identity and function. Using a full-cycle molecular approach, we show here that the endosymbionts of the larger gut flagellates of Reticulitermes santonensis belong to the so-called termite group 1 (TG-1) bacteria, a group of clones previously obtained exclusively from gut homogenates of Reticulitermes speratus that are only distantly related to other bacteria and are considered a novel bacterial phylum based on their 16S rRNA gene sequences. Fluorescence in situ hybridization with specifically designed oligonucleotide probes confirmed that TG-1 bacteria are indeed located within the flagellate cells and demonstrated that Trichonympha agilis (Hypermastigida) and Pyrsonympha vertens (Oxymonadida) harbor phylogenetically distinct populations of symbionts (<95% sequence similarity). Transmission electron microscopy revealed that the symbionts are small, spindle-shaped cells (0.6 microm in length and 0.3 microm in diameter) surrounded by two membranes and located within the cytoplasm of their hosts. The symbionts of the two flagellates are described as candidate species in the candidate genus "Endomicrobium." Moreover, we provide evidence that the members of the TG-1 phylum, for which we propose the candidate name "Endomicrobia," are phylogenetically extremely diverse and are present in and also restricted to the guts of all lower termites and wood-feeding cockroaches of the genus Cryptocercus, the only insects that are in an exclusive, obligately mutualistic association with such unique cellulose-fermenting protists.     

The Fate of Threatened Coastal Dune Habitats in Italy under Climate Change Scenarios

Coastal dunes worldwide harbor threatened habitats characterized by high diversity in terms of plant communities. In Italy, recent assessments have highlighted the insufficient state of conservation of these habitats as defined by the EU Habitats Directive. The effects of predicted climate change could have dramatic consequences for coastal environments in the near future. An assessment of the efficacy of protection measures under climate change is thus a priority. Here, we have developed environmental envelope models for the most widespread dune habitats in Italy, following two complementary approaches: an “indirect” plant-species-based one and a simple “direct” one. We analyzed how habitats distribution will be altered under the effects of two climate change scenarios and evaluated if the current Italian network of protected areas will be effective in the future after distribution shifts. While modeling dune habitats with the “direct” approach was unsatisfactory, “indirect” models had a good predictive performance, highlighting the importance of using species’ responses to climate change for modeling these habitats. The results showed that habitats closer to the sea may even increase their geographical distribution in the near future. The transition dune habitat is projected to remain stable, although mobile and fixed dune habitats are projected to lose most of their actual geographical distribution, the latter being more sensitive to climate change effects. Gap analysis highlighted that the habitats’ distribution is currently adequately covered by protected areas, achieving the conservation target. However, according to predictions, protection level for mobile and fixed dune habitats is predicted to drop drastically under the climate change scenarios which we examined. Our results provide useful insights for setting management priorities and better addressing conservation efforts to preserve these threatened habitats in future.     

Enrichment and Genome Sequence of the Group I.1a Ammonia-Oxidizing Archaeon “Ca. Nitrosotenuis uzonensis” Representing a Clade Globally Distributed in Thermal Habitats

The discovery of ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called “marine” group I.1a) thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as “Candidatus Nitrosotenuis uzonensis”, is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold) of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F₄₂₀ and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, “Candidatus N. uzonensis” also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in “Ca. N. uzonensis”, which potentially include genetic determinants of ecological niche differentiation.     

Categorizing Ideas about Trees: A Tree of Trees

The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a “tree of trees.” Then, we categorize schools of tree-representations. Classical schools like “cladists” and “pheneticists” are recovered but others are not: “gradists” are separated into two blocks, one of them being called here “grade theoreticians.” We propose new interesting categories like the “buffonian school,” the “metaphoricians,” and those using “strictly genealogical classifications.” We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization.     

The Motility Symbiont of the Termite Gut Flagellate Caduceia versatilis Is a Member of the “Synergistes” Group

The flagellate Caduceia versatilis in the gut of the termite Cryptotermes cavifrons reportedly propels itself not by its own flagella but solely by the flagella of ectosymbiotic bacteria. Previous microscopic observations have revealed that the motility symbionts are flagellated rods partially embedded in the host cell surface and that, together with a fusiform type of ectosymbiotic bacteria without flagella, they cover almost the entire surface. To identify these ectosymbionts, we conducted 16S rRNA clone analyses of bacteria physically associated with the Caduceia cells. Two phylotypes were found to predominate in the clone library and were phylogenetically affiliated with the “Synergistes” phylum and the order Bacteroidales in the Bacteroidetes phylum. Probes specifically targeting 16S rRNAs of the respective phylotypes were designed, and fluorescence in situ hybridization (FISH) was performed. As a result, the “Synergistes” phylotype was identified as the motility symbiont; the Bacteroidales phylotype was the fusiform ectobiont. The “Synergistes” phylotype was a member of a cluster comprising exclusively uncultured clones from the guts of various termite species. Interestingly, four other phylotypes in this cluster, including the one sharing 95% sequence identity with the motility symbiont, were identified as nonectosymbiotic, or free-living, gut bacteria by FISH. We thus suggest that the motility ectosymbiont has evolved from a free-living gut bacterium within this termite-specific cluster. Based on these molecular and previous morphological data, we here propose a novel genus and species, “Candidatus Tammella caduceiae,” for this unique motility ectosymbiont of Caducaia versatilis.     

The Ultramicrobacterium “Elusimicrobium minutum” gen. nov., sp. nov., the First Cultivated Representative of the Termite Group 1 Phylum

Insect intestinal tracts harbor several novel, deep-rooting clades of as-yet-uncultivated bacteria whose biology is typically completely unknown. Here, we report the isolation of the first representative of the termite group 1 (TG1) phylum from sterile-filtered gut homogenates of a humivorous scarab beetle larva. Strain Pei191^T is a mesophilic, obligately anaerobic ultramicrobacterium with a gram-negative cell envelope. Cells are typically rod shaped, but cultures are pleomorphic in all growth phases (0.3 to 2.5 μm long and 0.17 to 0.3 μm wide). The isolate grows heterotrophically on sugars and ferments d-galactose, d-glucose, d-fructose, d-glucosamine, and N-acetyl-d-glucosamine to acetate, ethanol, hydrogen, and alanine as major products but only if amino acids are present in the medium. PCR-based screening and comparative 16S rRNA gene sequence analysis revealed that strain Pei191^T belongs to the “intestinal cluster,” a lineage of hitherto uncultivated bacteria present in arthropod and mammalian gut systems. It is only distantly related to the previously described so-called “endomicrobia” lineage, which comprises mainly uncultivated endosymbionts of termite gut flagellates. We propose the name “Elusimicrobium minutum” gen. nov., sp. nov. (type strain, Pei191^T = ATCC BAA-1559^T = JCM 14958^T) for the first isolate of this deep-branching lineage and the name “Elusimicrobia” phyl. nov. for the former TG1 phylum.Insect intestinal tracts harbor an enormous diversity of as-yet-uncultivated bacteria that are characterized only by their 16S rRNA gene sequences and whose biology is typically completely obscure (9, 17, 49). As in other environments (45), many of these sequences form deep-branching phylogenetic lineages that do not contain a single isolate (18, 28). One of these lineages is the termite group 1 (TG1), which was originally discovered by Ohkuma and Kudo (37) and recognized as a phylum-level group (candidate division) by Hugenholtz et al. (20). TG1 bacteria form a major proportion of the microbial community in the hindgut of lower termites (17, 69), where they inhabit the cytoplasm of the intestinal flagellates (38, 53). These so-called “endomicrobia” are specific for the respective flagellate species (21) and, at least in the case of “Candidatus Endomicrobium trichonymphae,” are cospeciating with their flagellate host (22).However, the TG1 phylum also comprises several other deep-rooting lineages (>15% 16S rRNA gene sequence divergence). They are present in a variety of environments, including soils, sediments, and intestinal tracts (14). One of these lineages, the “intestinal cluster,” comprises sequences originating exclusively from intestinal habitats, including the termite gut, but is only distantly related to the lineage comprising the “endomicrobia” (14). Here, we report the isolation of a member of the intestinal cluster from the hindgut of a humivorous scarab beetle larva and its physiological and ultrastructural characterization. We propose a new species, “Elusimicrobium minutum” gen. nov. sp. nov., and define the phylogenetic framework for the first cultivated representative of the TG1 phylum.     

Oxidative stress in cancer associated fibroblasts drives tumor-stroma co-evolution: A new paradigm for understanding tumor metabolism,the field effect and genomic instability in cancer cells

Loss of stromal fibroblast caveolin-1 (Cav-1) is a powerful single independent predictor of poor prognosis in human breast cancer patients, and is associated with early tumor recurrence, lymph node metastasis and tamoxifen-resistance. We developed a novel co-culture system to understand the mechanism(s) by which a loss of stromal fibroblast Cav-1 induces a “lethal tumor microenvironment.” Here, we propose a new paradigm to explain the powerful prognostic value of stromal Cav-1. In this model, cancer cells induce oxidative stress in cancer-associated fibroblasts, which then acts as a “metabolic” and “mutagenic” motor to drive tumor-stroma co-evolution, DNA damage and aneuploidy in cancer cells. More specifically, we show that an acute loss of Cav-1 expression leads to mitochondrial dysfunction, oxidative stress and aerobic glycolysis in cancer associated fibroblasts. Also, we propose that defective mitochondria are removed from cancer-associated fibroblasts by autophagy/mitophagy that is induced by oxidative stress. As a consequence, cancer associated fibroblasts provide nutrients (such as lactate) to stimulate mitochondrial biogenesis and oxidative metabolism in adjacent cancer cells (the “Reverse Warburg effect”). We provide evidence that oxidative stress in cancer-associated fibroblasts is sufficient to induce genomic instability in adjacent cancer cells, via a bystander effect, potentially increasing their aggressive behavior. Finally, we directly demonstrate that nitric oxide (NO) over-production, secondary to Cav-1 loss, is the root cause for mitochondrial dysfunction in cancer associated fibroblasts. In support of this notion, treatment with anti-oxidants (such as N-acetyl-cysteine, metformin and quercetin) or NO inhibitors (L-NAME) was sufficient to reverse many of the cancer-associated fibroblast phenotypes that we describe. Thus, cancer cells use “oxidative stress” in adjacent fibroblasts (1) as an “engine” to fuel their own survival via the stromal production of nutrients and (ii) to drive their own mutagenic evolution towards a more aggressive phenotype, by promoting genomic instability. We also present evidence that the “field effect” in cancer biology could also be related to the stromal production of ROS and NO species. eNOS-expressing fibroblasts have the ability to downregulate Cav-1 and induce mitochondrial dysfunction in adjacent fibroblasts that do not express eNOS. As such, the effects of stromal oxidative stress can be laterally propagated, amplified and are effectively “contagious”—spread from cell-to-cell like a virus—creating an “oncogenic/mutagenic” field promoting widespread DNA damage.Key words: caveolin-1, cancer associated fibroblasts, oxidative stress, reactive oxygen species (ROS), mitochondrial dysfunction, autophagy, nitric oxide (NO), DNA damage, aneuploidy, genomic instability, anti-oxidant cancer therapy, the “field effect” in cancer biology     

In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3)

The “Latescibacteria” (formerly WS3), member of the Fibrobacteres–Chlorobi–Bacteroidetes (FCB) superphylum, represents a ubiquitous candidate phylum found in terrestrial, aquatic, and marine ecosystems. Recently, single-cell amplified genomes (SAGs) representing the “Latescibacteria” were obtained from the anoxic monimolimnion layers of Sakinaw Lake (British Columbia, Canada), and anoxic sediments of a coastal lagoon (Etoliko lagoon, Western Greece). Here, we present a detailed in-silico analysis of the four SAGs to gain some insights on their metabolic potential and apparent ecological roles. Metabolic reconstruction suggests an anaerobic fermentative mode of metabolism, as well as the capability to degrade multiple polysaccharides and glycoproteins that represent integral components of green (Charophyta and Chlorophyta) and brown (Phaeophycaea) algae cell walls (pectin, alginate, ulvan, fucan, hydroxyproline-rich glycoproteins), storage molecules (starch and trehalose), and extracellular polymeric substances (EPSs). The analyzed SAGs also encode dedicated transporters for the uptake of produced sugars and amino acids/oligopeptides, as well as an extensive machinery for the catabolism of all transported sugars, including the production of a bacterial microcompartment (BMC) to sequester propionaldehyde, a toxic intermediate produced during fucose and rhamnose metabolism. Finally, genes for the formation of gas vesicles, flagella, type IV pili, and oxidative stress response were found, features that could aid in cellular association with algal detritus. Collectively, these results indicate that the analyzed “Latescibacteria” mediate the turnover of multiple complex organic polymers of algal origin that reach deeper anoxic/microoxic habitats in lakes and lagoons. The implications of such process on our understanding of niche specialization in microbial communities mediating organic carbon turnover in stratified water bodies are discussed.     

Lytic Cycle of Toxoplasma gondii

Toxoplasma gondii is an obligate intracellular pathogen within the phylum Apicomplexa. This protozoan parasite is one of the most widespread, with a broad host range including many birds and mammals and a geographic range that is nearly worldwide. While infection of healthy adults is usually relatively mild, serious disease can result in utero or when the host is immunocompromised. This sophisticated eukaryote has many specialized features that make it well suited to its intracellular lifestyle. In this review, we describe the current knowledge of how the asexual tachyzoite stage of Toxoplasma attaches to, invades, replicates in, and exits the host cell. Since this process is closely analogous to the way in which viruses reproduce, we refer to it as the Toxoplasma “lytic cycle.”     

Are We Filling the Data Void? An Assessment of the Amount and Extent of Plant Collection Records and Census Data Available for Tropical South America

Large-scale studies are needed to increase our understanding of how large-scale conservation threats, such as climate change and deforestation, are impacting diverse tropical ecosystems. These types of studies rely fundamentally on access to extensive and representative datasets (i.e., “big data”). In this study, I asses the availability of plant species occurrence records through the Global Biodiversity Information Facility (GBIF) and the distribution of networked vegetation census plots in tropical South America. I analyze how the amount of available data has changed through time and the consequent changes in taxonomic, spatial, habitat, and climatic representativeness. I show that there are large and growing amounts of data available for tropical South America. Specifically, there are almost 2,000,000 unique geo-referenced collection records representing more than 50,000 species of plants in tropical South America and over 1,500 census plots. However, there is still a gaping “data void” such that many species and many habitats remain so poorly represented in either of the databases as to be functionally invisible for most studies. It is important that we support efforts to increase the availability of data, and the representativeness of these data, so that we can better predict and mitigate the impacts of anthropogenic disturbances.     

Characterization of the Upper Respiratory Tract Microbiomes of Patients with Pandemic H1N1 Influenza

The upper respiratory tract microbiome has an important role in respiratory health. Influenza A is a common viral infection that challenges that health, and a well-recognized sequela is bacterial pneumonia. Given this connection, we sought to characterize the upper respiratory tract microbiota of individuals suffering from the pandemic H1N1 influenza A outbreak of 2009 and determine if microbiome profiles could be correlated with patient characteristics. We determined the microbial profiles of 65 samples from H1N1 patients by cpn60 universal target amplification and sequencing. Profiles were examined at the phylum and nearest neighbor “species” levels using the characteristics of patient gender, age, originating health authority, sample type and designation (STAT/non-STAT). At the phylum level, Actinobacteria-, Firmicutes- and Proteobacteria-dominated microbiomes were observed, with none of the patient characteristics showing significant profile composition differences. At the nearest neighbor “species” level, the upper respiratory tract microbiomes were composed of 13-20 “species” and showed a trend towards increasing diversity with patient age. Interestingly, at an individual level, most patients had one to three organisms dominant in their microbiota. A limited number of discrete microbiome profiles were observed, shared among influenza patients regardless of patient status variables. To assess the validity of analyses derived from sequence read abundance, several bacterial species were quantified by quantitative PCR and compared to the abundance of cpn60 sequence read counts obtained in the study. A strong positive correlation between read abundance and absolute bacterial quantification was observed. This study represents the first examination of the upper respiratory tract microbiome using a target other than the 16S rRNA gene and to our knowledge, the first thorough examination of this microbiome during a viral infection.     

A network approach to elucidate and prioritize microbial dark matter in microbial communities

Microbes compose most of the biomass on the planet, yet the majority of taxa remain uncharacterized. These unknown microbes, often referred to as “microbial dark matter,” represent a major challenge for biology. To understand the ecological contributions of these Unknown taxa, it is essential to first understand the relationship between unknown species, neighboring microbes, and their respective environment. Here, we establish a method to study the ecological significance of “microbial dark matter” by building microbial co-occurrence networks from publicly available 16S rRNA gene sequencing data of four extreme aquatic habitats. For each environment, we constructed networks including and excluding unknown organisms at multiple taxonomic levels and used network centrality measures to quantitatively compare networks. When the Unknown taxa were excluded from the networks, a significant reduction in degree and betweenness was observed for all environments. Strikingly, Unknown taxa occurred as top hubs in all environments, suggesting that “microbial dark matter” play necessary ecological roles within their respective communities. In addition, novel adaptation-related genes were detected after using 16S rRNA gene sequences from top-scoring hub taxa as probes to blast metagenome databases. This work demonstrates the broad applicability of network metrics to identify and prioritize key Unknown taxa and improve understanding of ecosystem structure across diverse habitats.Subject terms: Microbial ecology, Metagenomics     

Effects of natural and seminatural elements on the composition and dispersion of carabid beetles inhabiting an agroecosystem in Northern Italy

The natural and seminatural components of agricultural landscapes play a key role in maintaining a high level of biodiversity. Being the Po Valley one of the most human‐dominated and intensively cultivated landscapes in Europe, we investigated the effect of no‐crop habitats on carabid richness and composition and evaluated the role of tree row as corridor for forest carabid dispersion. Carabids were sampled with 70 pitfall traps arranged in 35 sampling plots along three parallel transects (80, 100, and 140 m long) and encompassing five different habitats: tree row, tree row edge, grassland, forest edge, and forest. We found 5,615 individuals belonging to 55 species. Despite the similarity in species richness, all the habitats investigated showed a peculiar and distinct species assemblage. The main distinction was between the "open habitat" cluster composed of grassland and tree row edge and the “forest" cluster composed of forest, tree row, and forest edge. We found that forest species are able to penetrate the grassland matrix up to 30 m from the forest edge and that a distance of no more than 60 m between tree row and forest can allow the passage of up to 50% of the forest species. Beyond this distance, the grassland matrix becomes a barrier, preventing them from reaching other suitable habitats. Our findings confirm the importance of maintaining different types of natural habitats to significantly increase biodiversity in an intensively cultivated agroecosystem and demonstrated the role of linear elements as a corridor and “stepping stones” for many forest species.     

Living with Aliens: Effects of Invasive Shrub Honeysuckles on Avian Nesting

Invasive species have come to the forefront of conservation biology as a major threat to native biodiversity. Habitats dominated by shrub honeysuckles (Lonicera spp.) in the United States have been characterized as “ecological traps” by ecologists. Here we tested this hypothesis by investigating the effects of shrub honeysuckles on the nesting ecology of native birds in seven study sites in central Pennsylvania, USA. We examined how the abundance of shrub honeysuckles influenced the selection of nesting substrates and habitat for a community of common songbirds, and the parental-care behavior and nestling development of gray catbirds (Dumetella carolinensis). We found that birds had a strong bias towards nesting in honeysuckle shrubs, but not necessarily for nesting in honeysuckle-dominated habitats. Nest predation rates were affected by the density of nests in a habitat, but not by the overall abundance of honeysuckles in such habitats. Honeysuckle abundance in the habitat did show significant effects on some parental-care behavioral parameters: catbirds had higher nest visitation rates and shorter visit lengths in areas of high honeysuckle density. On average, Gray catbirds fed fruit 12%±0.31 s.e. of their nestling-feeding bouts, mostly fruits of shrub honeysuckles. Nestlings in sites with high honeysuckle density also showed higher mass:tarsus ratios, suggesting a good (possibly better) physiological condition of catbird nestlings at the time of fledging. Our study shows that honeysuckle-dominated habitats could have equivocal effects on nesting parameters of common species of native birds. We advise more caution in the widespread denomination of novel plant communities with high densities of honeysuckle as “ecological traps” as effects can be null or positive on native birds in certain localities.