Community Diversity Metrics Research Articles

Clinical Investigation of Bacteriome in Primary Endodontic Infections With Apical Periodontitis Using High-Throughput Sequencing Analysis

IntroductionThis study characterized the bacteriome in primary endodontic infection (PEI) with apical periodontitis (AP), identified core and rare bacteriome species and community diversity metrics, and analyzed the relationship between the bacteriome composition, diversity and features, and patient variables. MethodsTwenty-seven patients with PEI and AP were sampled. The DNA was extracted and quantified using quantitative polymerase chain reaction. Raw V3-V4 amplicon sequencing data were processed with the DADA2 pipeline to generate amplicon sequence variants, and taxonomic assignment of the amplicon sequence variants up to the species level was done against the Human Oral Microbiome Database. Core bacteriome and differential abundance analyses were performed using ANCOM. Alpha diversity was determined using Chao1, Shannon, and Simpson indexes. LeFse analysis was used to identify abundant taxa. Sparse Estimation of Correlations among Microbiomes analysis estimated linear and nonlinear relationships among bacteria. ResultsOf 27, 24 root canal samples were analyzed, and 3 root canal sampling were filtered out with a low read count. The bacterial phyla with top mean relative abundance were Bacteroidetes, Firmicutes, Synergistetes, Fusobacteria, and Actinobacteria. A total of 113 genera and 215 species were identified. The samples were gathered into 3 clusters. LefSe analysis identified differences in abundant taxa between distinct age, gender, symptomatology, and lesion size groups. Sparse Estimation of Correlations among Microbiomes distance analysis indicated Slackia exigua as the node with the highest degree. ConclusionsThe bacteriome in PEI with AP among the patients in this study was complex and displayed high microbial heterogeneity. Moreover, age, gender, symptomatology, and lesion size were associated with differences in bacteriome features in PEI with AP.

VAMPirus: A versatile amplicon processing and analysis program for studying viruses.

Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user-friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide- and amino acid-based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies and community diversity metrics. The vAMPirus analytical framework leverages 16 different opensource tools and provides optional approaches that can increase the ratio of biological signal-to-noise and thereby reveal patterns that would have otherwise been masked. Here, we validate the vAMPirus analytical framework and illustrate its implementation as a general virus amplicon sequencing workflow by recapitulating findings from two previously published double-stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef-associated RNA virus. vAMPirus is streamlined within Nextflow, offering straightforward scalability, standardization and communication of virus lineage-specific analyses. The vAMPirus framework is designed to be adaptable; community-driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability.

Multisite Field Evaluation of Bacteriophages for Fire Blight Management: Incorporation of Ultraviolet Radiation Protectants and Impact on the Apple Flower Microbiome.

Fire blight, a disease of pome fruits caused by the bacterium Erwinia amylovora, has become increasingly difficult to manage after the emergence of streptomycin-resistant strains. Alternative antibiotics and copper are available; however, these chemicals have use restrictions in some countries and also can carry risks of phytotoxicity. Therefore, there is growing interest in biological-based management options, with bacteriophage (phages) showing promise, as these naturally occurring pathogens of bacteria are easy to isolate and grow. However, there are several technical challenges regarding the implementation of phage biocontrol in the field, as the viral molecules suffer from ultraviolet radiation (UVR) degradation and can die off rapidly in the absence of the host bacterium. In this work, we assessed the efficacy of Erwinia phages and a commercial phage product for blossom blight control in the field across multiple locations in the eastern United States. In these tests, disease control ranged from 0.0 to 82.7%, and addition of a UVR protectant only resulted in significantly increased disease control in 2 of 12 tests. We also analyzed microbial community population changes in response to phage application. Changes in bacterial community diversity metrics over time were not detected; however, relative abundances of target taxa were temporarily reduced after phage applications, indicating that these phage applications did not have deleterious effects on the flower microbiome. We have demonstrated that biological control of fire blight with phages is achievable, but a better understanding of phage-pathogen dynamics is required to optimize disease control efficacy.

Shotgun metagenomics captures more microbial diversity than targeted 16S rRNA gene sequencing for field specimens and preserved museum specimens.

The use of museum specimens for research in microbial evolutionary ecology remains an under-utilized investigative dimension with important potential. Despite this potential, there remain barriers in methodology and analysis to the wide-spread adoption of museum specimens for such studies. Here, we hypothesized that there would be significant differences in taxonomic prediction and related diversity among sample type (museum or fresh) and sequencing strategy (medium-depth shotgun metagenomic or 16S rRNA gene). We found dramatically higher predicted diversity from shotgun metagenomics when compared to 16S rRNA gene sequencing in museum and fresh samples, with this differential being larger in museum specimens. Broadly confirming these hypotheses, the highest diversity found in fresh samples was with shotgun sequencing using the Rep200 reference inclusive of viruses and microeukaryotes, followed by the WoL reference database. In museum-specimens, community diversity metrics also differed significantly between sequencing strategies, with the alpha-diversity ACE differential being significantly greater than the same comparisons made for fresh specimens. Beta diversity results were more variable, with significance dependent on reference databases used. Taken together, these findings demonstrate important differences in diversity results and prompt important considerations for future experiments and downstream analyses aiming to incorporate microbiome datasets from museum specimens.

Marine protected areas ineffectively protect seagrass and coral reef fish communities in the Phu Quoc and An Thoi archipelago, Vietnam

Abstract The Phu Quoc marine protected area (MPA) is a multiple‐use MPA that was established in 2007 and is a component of Vietnam’s National MPA System. The MPA is divided into two spatially separated zones based on habitat type: a seagrass zone and a coral reef zone. In this study, visual census data were collected in 2018–2019 and were used to derive fish biomass and community diversity metrics as proxies for ecosystem condition and function (trophic and mobility). The effectiveness of the MPA in protecting fish communities in the seagrass and coral reef zones was evaluated. An updated characterization of the Phu Quoc fish communities, and an assessment of fish community variation among regions and between habitat types, is provided. In total, 125 species representing 74 genera of 40 families were recorded. Omnivores were the most abundant (38%), followed by planktivores (24%), whereas piscivores (2%) were scarce. There was an especially low density of high‐value fishery target species such as Haemulidae (<0.01%), Carangidae (<0.2%), Lethrinidae (<0.3%), Lutjanidae (<0.4%), Serranidae (<2%), and Chaetodontidae (<3%). Alarmingly, fishes with a total length of >20 cm only accounted for 1% of the total individuals. Species and functional composition were similar between protected and unprotected areas but differed among regions and between habitats. These results suggest that the protection of fishes provided by Phu Quoc MPA at the time of this study was ineffective. The taxonomic composition of fish communities has remained relatively unchanged over the last approximately 25 years, with the density of large fishes and commercial species remaining low. There is capacity to improve MPA performance by providing adequate resources for threat management and using evidence‐based decision‐making in management. The 2020 rezoning and expansion of the Phu Quoc MPA is discussed with regards to prioritizing biodiversity and coverage targets.

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

BackgroundThe 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82].ResultsAt both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690 ± 110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1–27). At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% — 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%).ConclusionsRamifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated — for example, with popular approaches such as Faith’s phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics.4mzDXUb8zk-Zv1MEqYqhctVideo

Resiliency and Recovery of Aquatic Vegetation Following Scouring Floods in Two First-Magnitude Springs, Missouri, USA

This study quantifies the loss of vegetative cover in Alley and Big springs, Missouri, following a catastrophic, ‘100 year’ flood, and documents their subsequent recovery. Foliar cover of aquatic vegetation was measured in each spring along six transects, each having three sample cells (1 m2, N = 18). Species diversity analyses included taxa richness, Shannon’s diversity index, and Simpson’s diversity index, which were expressed as the effective number of species (S, He, and De). Species metrics were calculated as individual species frequency (ISF), percent foliar cover (PFC), and species importance value (SIV). Post-flood community diversity metrics (S, He, and De) for the springs were largely not significant for most measures (Epps–Singleton test p > 0.05). This suggests that they may not be sufficiently sensitive for detecting change in springs when the sample size is small. Bare substrate increased significantly at Big Spring post-flood (mean = 87.50%; Epps–Singleton test, p = 0.02), but not at Alley Spring (Epps–Singleton test, p = 0.42). Various alga taxa generally exhibited increased frequency and abundance following the flood, which is reflected in their overall higher SIVs. Most hydrophyte species at Alley Spring showed a marked decline compared to the pre-flood average, only to substantially increase in the last year of sampling, thus maintaining their approximate species important values relative to their pre-flood averages. Several hydrophyte species at Big Spring showed significant decreases (Epps–Singleton test p < 0.05) in their respective community metrics, and recovery had not returned to pre-flood levels on the last sampling date. This study showed that loss and recovery of aquatic vegetation in high-magnitude Ozark springs following flooding are a function of flood intensity as well as substrate size and retention, and proximity to the receiving stream.

Nested analysis of macroinvertebrate diversity along a river continuum: Identifying relevant spatial scales for stream communities

AbstractBenthic macroinvertebrates are important for stream ecosystem function and are considerable food resources for vertebrate consumers such as fish. The diversity, composition, and distribution of stream macroinvertebrate taxa are affected by factors that act at different spatial scales, from microhabitat to watershed‐level effects. While comparative studies of watershed‐level and between stream influences on benthic diversity are common, the effects of scale are less investigated within individual river segments. Benthic macroinvertebrates were systematically sampled across nested spatial scales along a 2.2‐km near‐pristine stretch of the Upper Black River (MI, USA), and analyzed in relation to near‐bed flow and substrate features. Responses of community diversity metrics to near‐bed conditions were quantified, and diversity was modeled to determine the contribution of each spatial scale to total diversity. Near‐bed conditions, especially Froude number and substrate size, were positively associated with macroinvertebrate diversity and abundance. Larger (e.g., 100 m stream reach) and finer scales (e.g., individual samples) accounted for a greater proportion of variation in taxon richness and abundance, respectively. Longitudinal variation in environmental conditions was an important driver of macroinvertebrate diversity, with replacement between sites (i.e., turnover) contributing a considerably greater proportion of variation in total diversity than nestedness. Results demonstrate that macroinvertebrate communities were shaped by both local flow and substrate conditions as well as taxa replacement over larger spatial scales. This emphasizes the importance of maintaining the hydro‐morphological integrity along stream courses as a requisite condition to further watershed and fisheries conservation and management.

Natural fire does not affect the structure and beta diversity of plant-pollinator networks, but diminishes floral-visitor specialization in Cerrado

Fire acts as an ecological filter determining species diversity and composition of communities. In tropical savannas in Central Brazil, natural fire happens through lightning, but anthropogenic fire is also common, either controlled fire prescribed for management of vegetation and to promote grass growth or accidental and intentional fires related to deforestation and land use changes. Frequent fire events can have a negative effect on biodiversity by causing deaths of susceptible organisms, as well as through the homogenization of vegetation. Besides the composition of plant and animal species, fire also modifies biotic interactions, such as pollination, which impact ecosystem functioning. Here, we evaluated how time since the last fire event (hereafter postfire time interval) affects the structure, beta diversity of interactions and specialization of plants and floral visitors in a naturally burned Cerrado area. Postfire time interval had no effect on the structure of interaction networks and community diversity metrics, including beta-diversity of interactions. We did, however, find a positive relationship between flower abundance and postfire time intervals, and a negative effect of postfire time intervals on floral visitor species-level specialization. Thus, the negative effect of postfire time intervals on floral visitor specialization may be explained by the lower resource availability in areas recently burnt. The lack of strong and consistent effect of time interval since the last fire on plant-pollinator interactions from the Cerrado probably results from the resilience of these interactions to natural fires, which is a common element in this ecosystem. Increased frequency of more intense anthropogenic fires, however, may have stronger effects on biodiversity, and deserves further investigation in this biodiversity hotspot.

Weed Community in a Conventionally-Grown Olive Orchard Vs. Weed Community in Consociation with Pyrethrum (Tanacetum cinerariifolium (Trevir.) Sch. Bip.)

On the experimental plots of the Institute of Agriculture and Tourism in Poreč, weed communities were analyzed in a conventionally‐grown olive orchard and in consociation with pyrethrum. Phytocenological surveys were conducted in March, June, and September using the Braun-Blanquet Cover Abundance Scale. Altogether, 54 species of vascular plants were recognized in both orchards. However, in a conventionally‐grown olive orchard, 27 were identified, whereas 42 weed species were identified in consociation with pyrethrum. Only 15 weeds were common to both orchards. Between both olive orchards, significant differences existed regarding the floristic and community diversity metrics. In consociation with pyrethrum as a cover crop, olive orchard had a more stable weed community during the season, while two weed species, Mercurialis annuua L. and Medicago arabica (L.) Huds., dominated in a conventionally‐grown orchard in the fall. The weed communities in both orchards significantly differ considering the appearance season (spring, summer, and fall). An autumnal weed community in a conventionally‐grown olive orchard was more diverse, more abundant, and with a more distinct floristic composition than a weed community in the spring and summer periods. However, an olive‐orchard weed community in consociation with pyrethrum also differed regarding the season, but a Canonical Correspondence Analysis (CCA) demonstrated a clear separation of a more diverse estival weed community than the one observed in the spring and summer.

Community diversity metrics, interactions, and metabolic functions of bacteria associated with municipal solid waste landfills at different maturation stages.

Municipal landfills are hot spots of dynamic bioprocesses facilitated by complex interactions of a multifaceted microbiome, whose functioning in municipal landfills at different maturing stages is poorly understood. This study determined bacterial community composition, interaction conetworks, metabolic functions, and controlling physicochemical properties in two landfills aged 14 and 36 years. High throughput sequencing revealed a similar distribution of bacterial diversity, evenness, and richness in the 14‐ and 36‐year‐old landfills in the 0–90 cm depth. At deeper layers (120–150 cm), the 14‐year‐old landfill had significantly greater bacterial diversity and richness indicating that it is a more active microcosm than the 36‐year‐old landfill, where phylum Epsilonbacteraeota was overwhelmingly dominant. The taxonomic and functional diversity in the 14‐year‐old landfill was further reflected by the abundant presence of indicator genera Pseudomonas,Lutispora,Hydrogenspora, and Sulfurimonas coupled with the presence of biomarker enzymes associated with carbon (C), nitrogen (N), and sulfur (S) metabolism. Furthermore, canonical correspondence analysis revealed that bacteria in the 14‐year‐old landfill were positively correlated with high C, N, S, and phosphorus resulting in positive cooccurrence interactions. In the 36‐year‐old landfill, negative coexclusion interactions populated by members of N fixing Rhizobiales were dominant, with metabolic functions and biomarker enzymes predicting significant N fixation that, as indicated by interaction network, potentially inhibited ammonia‐intolerant bacteria. Overall, our findings show that diverse bacterial community in the 14‐year‐old landfill was dominated by copiotrophs associated with positive conetworks, whereas the 36‐year‐old landfill was dominated by lithotrophs linked to coexclusion interactions that greatly reduced bacterial diversity and richness.

Fish assemblages and size-spectra variation among rivers of Lake Victoria Basin, Kenya

Riverine ecosystems are some of the most biologically diverse on earth, but are also among the most threatened by anthropogenic actions. Lack of local-scale studies monitoring changes in riverine populations makes it difficult to determine how communities respond to region-specific anthropogenic threats. In this study, we compared fish assemblage structure in six rivers in the Lake Victoria Basin (LVB), Kenya. Data collected during different periods between 2004 and 2018 were used to derive abundance size-spectra parameters and community diversity metrics as proxies for ecosystem condition and function. Species dominance in the rivers was high with only five species accounting for >72% of cumulative relative abundance while, 33 species contributed <10% of all individuals sampled. One-way analysis of similarity test (ANOSIM) indicated significant dissimilarity in fish composition between the rivers (Global R = 0.405, p = 0.0187) while, similarity percentage analysis (SIMPER) partitioned differences to variations in relative abundance of mainly two species (Labeobarbus altianalis, and Labeo victorianus). Eight species were restricted to single river basins suggesting presence of local endemism. Abundance size-spectra parameters (intercepts and slopes) used as proxies for food-web capacity and ecological efficiency fluctuated over time with periods of relative stability, indicating spatial (among rivers) and temporal (yearly) variations in ecological processes in the rivers. The food-web capacity and ecological efficiency indices showed basin-specific relationships with community metrics (dominance, richness, evenness, Shannon-Weiner and Simpson diversity indices) and catch per unit effort (CPUE), suggesting their potential use as indicators of ecosystem structure. The findings of this study show promise in the use of size-spectra parameters as proxies for riverine ecosystem structure and functioning under a gradient of perturbation.

Predicting the structure of turtle assemblages along a megatransect in West Africa

AbstractUnderstanding large- and small-scale patterns and the determinants of species richness is central for the study of evolutionary mechanisms. The extent to which species richness in local communities is related to larger-scale processes is a pre-eminent topic in ecological and evolutionary research. To investigate how local and regional species richness are related, we sampled freshwater turtle assemblages in seven localities to represent the variation in ecological conditions along a 90 km south–north megatransect in Benin, West Africa. In each locality, all turtles captured were identified and measured, and the microhabitat in which individual turtles were observed was classified. Based on these data, we used community diversity metrics to compare turtle assemblages. Spatial autocorrelation did not affect our data. For all localities pooled, two species (Pelusios castaneus and Pelomedusa olivacea) were the most common and one species (Trionyx triunguis) was the rarest. Analyses of the commonest and more numerous species showed that the abundance of Pelusios castaneus declined with an increase in latitude and longitude, but the opposite was true for Pelomedusa olivacea. We showed that various characteristics of the microhabitat were significantly correlated with the abundance of the two common species. We found significant but variable south–north gradients in microhabitat use for different turtle species. Our results highlight the importance of studying interactions between local environments, the ecological requirements of each species and their synecological relationships.

Symbiont community diversity is more variable in corals that respond poorly to stress.

Coral reefs are declining globally as climate change and local water quality press environmental conditions beyond the physiological tolerances of holobionts-the collective of the host and its microbial symbionts. To assess the relationship between symbiont composition and holobiont stress tolerance, community diversity metrics were quantified for dinoflagellate endosymbionts (Family: Symbiodiniaceae) from eight Acropora millepora genets that thrived under or responded poorly to various stressors. These eight selected genets represent the upper and lower tails of the response distribution of 40 coral genets that were exposed to four stress treatments (and control conditions) in a 10-day experiment. Specifically, four 'best performer' coral genets were analyzed at the end of the experiment because they survived high temperature, high pCO2 , bacterial exposure, or combined stressors, whereas four 'worst performer' genets were characterized because they experienced substantial mortality under these stressors. At the end of the experiment, seven of eight coral genets mainly hosted Cladocopium symbionts, whereas the eighth genet was dominated by both Cladocopium and Durusdinium symbionts. Symbiodiniaceae alpha and beta diversity were higher in worst performing genets than in best performing genets. Symbiont communities in worst performers also differed more after stress exposure relative to their controls (based on normalized proportional differences in beta diversity), than did best performers. A generalized joint attribute model estimated the influence of host genet and treatment on Symbiodiniaceae community composition and identified strong associations among particular symbionts and host genet performance, as well as weaker associations with treatment. Although dominant symbiont physiology and function contribute to host performance, these findings emphasize the importance of symbiont community diversity and stochasticity as components of host performance. Our findings also suggest that symbiont community diversity metrics may function as indicators of resilience and have potential applications in diverse disciplines from climate change adaptation to agriculture and medicine.

Urbanization alters belowground invertebrate community structure in semi-arid regions: A comparison of lawns, biofilters and sage scrub

As the proportion of the human population living in cities continues to increase, understanding the factors affecting urban biodiversity is crucial to enhancing conservation efforts, urban ecosystem function, and human wellbeing. Here we present the results of the first comparative study of belowground invertebrate communities in urban soils (lawns and biofilters) and remnant patches of native coastal sage scrub (CSS) in a semi-arid urban environment. Among 12 sites sampled in La Jolla, California, USA, invertebrate community composition was most homogeneous among lawns, which differed significantly in composition from both biofilters and CSS. In almost all other aspects of invertebrate community diversity metrics (richness, evenness, diversity) as well as environmental factors (moisture, organic matter, plant cover and richness), lawns differed significantly from native CSS habitats, but biofilters were intermediate and not significantly different from other habitat types. Lawn soil invertebrate evenness and diversity were significantly lower, but density was highest in lawns, with higher densities of oligochaetes (Megadrilacea, Enchytraeidae), fly larvae (Sciaridae, Chironomidae), mites (Oribatida, Mesostigmata), and springtails (Poduromorpha, Symphypleona) in lawns relative to CSS. Differences in soil moisture, organic matter, and plant, tree, and building cover explained 40–62% of the variability in invertebrate density, richness, diversity, and evenness among sites. These findings suggest a shift in belowground invertebrate community structure that may be common among urbanizing semi-arid environments. The amendment of urban dryland soils with organic matter and moisture alters the presence and population density of several invertebrate taxa, and may cause a transition toward dominance by desiccation-intolerant litter transformers.

The Composition of Midgut Bacteria in Aedes aegypti (Diptera: Culicidae) That Are Naturally Susceptible or Refractory to Dengue Viruses.

The composition, abundance, and diversity of midgut bacteria in mosquitoes can influence pathogen transmission. We used 16S rRNA microbiome profiling to survey midgut microbial diversity in pooled samples of laboratory colonized dengue-refractory, Cali-MIB, and dengue-susceptible, Cali-S Aedes aegypti (Linnaeus). The 16S rRNA sequences from the sugar-fed midguts of adult females clustered to 63 amplicon sequence variants (ASVs), primarily from Proteobacteria, Firmicutes, Flavobacteria, and Actinobacteria. An average of five ASVs dominated the midguts, and most ASVs were present in both Cali-MIB and Cali-S midguts. No differences in abundance were noted at any phylogenetic level (Phylum, Class, Order, Family, Genus) by analysis of composition of microbiome (w = 0). No community diversity metrics were significantly different between refractory and susceptible mosquitoes. These data suggest that phenotypic differences in the susceptibility to dengue virus between Cali-MIB and Cali-S are not likely due to major differences in midgut bacterial communities.

Abiotic and biotic predictors of macroecological patterns in bird and butterfly coloration

AbstractAnimal color phenotypes are invariably influenced by both their biotic community and the abiotic environments. A host of hypotheses have been proposed for how variables such as solar radiation, habitat shadiness, primary productivity, temperature, rainfall, and community diversity might affect animal color traits. However, while individual factors have been linked to coloration in specific contexts, little is known about which factors are most important across broad taxonomic and geographic scales. Using data collected from 570 species of birds and 424 species of butterflies from Australia, which inhabit an area spanning a latitudinal range of 35° and covering deserts, tropical and temperate forests, savannas, and heathlands, we test multiple hypotheses from the coloration literature and assess their relative importance. We show that bird and butterfly species exhibit more reflective and less saturated colors in better‐lit environments, a pattern that is robust across an array of variables expected to influence the intensity or quality of ambient light in an environment. Both taxa display more diverse colors in regions with greater net primary production and longer growing seasons. Models that included variables related to energy inputs and resources in ecosystems have better explanatory power for bird and butterfly coloration overall than do models that included community diversity metrics. However, the diversity of the bird community in an environment was the single most powerful predictor of color pattern variation in both birds and butterflies. We observed strong similarities across taxa in the covariance between color and environmental factors, suggesting the presence of fundamental macroecological drivers of visual appearance across disparate taxa.

Quantitative Genetics of the Maize Leaf Microbiome

The degree to which the genotype of an organism can affect the composition of its associated microbial communities (“microbiome”) varies by organism and habitat, and in many cases is unknown. We analyzed the metabolically active bacteria of maize leaves across 300 diverse maize lines growing in a common environment. We performed comprehensive heritability analysis for 49 community diversity metrics, 380 bacterial clades, and 9,042 predicted metagenomic functions. We find that only a few bacterial clades (5) and diversity metrics (2) are significantly heritable, while a much larger number of metabolic functions (200) are. Many of these associations appear to be driven by the Methylobacteria in each sample. Among these heritable metabolic traits, Fisher’s exact test identifies significant overrepresentation of traits relating to short-chain carbon metabolism, secretion, and nitrotoluene degradation. Genome-wide association analysis identified a small number of associated loci for these heritable traits, including two that affect multiple traits. Our results indicate that while most of the maize leaf microbiome composition is driven by environmental factors and/or stochastic founder events, a subset of bacterial taxa and metabolic functions is nonetheless significantly impacted by host genetics. Additional work will be needed to identify the exact nature of these interactions and what effects they may have on their host. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Brachiopod morphology, life mode, and crushing predation in the Ordovician Arnheim Formation, Kentucky, USA

Predation on ancient shelled prey is an often-studied topic in paleoecology, but the early Paleozoic and the brachiopods that dominated the seafloor at that time are relatively underrepresented in the predation literature. We assessed predatory repair scar frequencies among the brachiopod genera from the Early Richmondian (Late Ordovician) Oregonia Member (Arnheim Formation) near Flemingsburg, Kentucky. We found higher repair frequencies on the concavo-convex Rafinesquina and Leptaena relative to the bi-convex genera. There were no trends in repair frequency through the stratigraphic section and no relationships between repair frequency and community diversity metrics. It is possible that concavo-convex brachiopods’ flat shape, thin shell profile, and free-lying (no pedicle attachment) lifestyle made them more likely or appealing targets of Ordovician crushing predators. It is also possible that concavo-convex brachiopods were better suited to survive crushing attacks than biconvex taxa. We also found differences in shell ornament that may influence the visibility of repair scars.

Building biodiversity: drivers of bird and butterfly diversity on tropical urban roof gardens

AbstractConservation of faunal diversity in highly urbanized landscapes is facilitated through the integration of anthropogenic and natural elements in urban green spaces. Roof gardens have the potential to provide resources for urban wildlife populations, yet they typically offer marginal ecological conditions relative to ground‐level habitat so it is necessary to identify the factors associated with focal taxa diversity and abundance to better inform their planning, design, and management. We conducted 20 monthly surveys of diurnal bird and butterfly visitors to 30 urban roof gardens in the tropical city‐state of Singapore. Sixty‐five site variables were evaluated for their relative importance to four community diversity metrics (species richness, Simpson's diversity, abundance, and functional dispersion) using a conceptual framework relevant to key stakeholders involved in roof garden planning, design, and management. Surveys from a total of 80 observation hours per site recorded more than 23,000 independent bird and butterfly encounters, comprising 53 bird and 57 butterfly species, which represents 13% and 18% of the avifauna and butterfly fauna in Singapore, respectively. Twenty‐four species (12 birds, 12 butterflies) were considered uncommon or rare. Reproductive behaviors (courtship, mating, or nesting) were noted in 35 species (20 birds, 15 butterflies). Understory birds were under‐represented, whereas understory butterflies were over‐represented compared to the overall Singapore fauna. Early morning noise showed strong negative linear correlations with diversity of both taxa, but this variable was also negatively associated with planted area, perhaps indicating proxy effects. Faunal diversity decreased asymptotically with height. Both managed and spontaneous floral diversity had clear positive effects on bird and butterfly diversity. Our results provide clear indication that tropical urban roof gardens can support a diverse subset of the bird and butterfly species assemblages. Site height, site area, and plant selection are suggested to play dominant roles in determining the attractiveness of roof gardens for wildlife. To a first approximation, roof gardens should be built lower than 50 m in height and contain planted areas larger than 1100 m2, as well as shrubs for birds and both managed and spontaneous nectar plant species for butterflies.