Quantitative metagenomic analyses based on average genome size normalization

Over the past quarter-century, microbiologists have used DNA sequence information to aid in the characterization of microbial communities. During the last decade, this has expanded from single genes to microbial community genomics, or metagenomics, in which the gene content of an environment can provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data by estimating average genome sizes. This normalization can relieve comparative biases introduced by differences in community structure, number of sequencing reads, and sequencing read lengths between different metagenomes. We demonstrate the utility of this approach by comparing metagenomes from two different marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how differences in environment affect their abundances, we characterize three different types of autotrophic organisms: aerobic, photosynthetic carbon fixers (the Cyanobacteria); anaerobic, photosynthetic carbon fixers (the Chlorobi); and anaerobic, nonphotosynthetic carbon fixers (the Desulfobacteraceae). These analyses demonstrate how genome proportionality compares to SSU rRNA gene relative abundance and how factors such as average genome size and SSU rRNA gene copy number affect sampling probability and therefore both types of community analysis.     

“Who’s the face?”: communication and white identity in a Texas business community

This article examines the relationship between whiteness and communication through analysing how white business community members acknowledge their own, usually invisible, white identity. Discourse analysis of interactions in a Texas organization shows how white members construct white identity as intersecting with Texan, masculine, age and professional identity categories. Members mark the overt construction of white identity as a dispreferred action through using disclaimers, formulations, pauses, humour and non-racial terms. Analysis of minority business member talk illustrates how minorities orient to white members’ talk as exclusive towards minorities because they do not overtly and directly discuss race and because they orient to regional identity in a way that ignores racial diversity among Texans. Thus while white members attempt to acknowledge their raced position in the Texas business community, their communicative actions repeatedly index white identities and reproduce the hegemonic position of white, male, Texan professional identities in this community.     

Community Completeness: Linking Local and Dark Diversity within the Species Pool Concept

Biodiversity of ecological communities has been examined widely. However, comparisons of observed species richness are limited because they fail to reveal what part of the differences are caused by natural variation in species pool size and what part is due to dark diversity – the absence of suitable species from a species pool. In other words, conventional biodiversity inventories do not convey information about how complete local plant communities are. We therefore propose the community completeness concept – a new perspective on the species pool framework. In order to ascertain community completeness, we need to estimate the extent of dark diversity, for which several methods are under development. We recommend the Community Completeness Index based on a log-ratio (or logistic) expression: ln(observed richness/dark diversity). This metric offers statistical advantages over other methods (e.g. the proportion of observed richness from the species pool). We discuss how community completeness can be related to long-term and successional community stability, landscape properties and disturbance patterns as well as to a variety of biotic interactions within and among trophic levels. The community completeness concept is related to but distinctive from the alpha-beta-gamma diversity approach and the community saturation phenomenon. The Community Completeness Index is a valuable metric for comparing biodiversity of different ecosystems for nature conservation. It can be used to measure the success of ecological restoration and vulnerability to invasion by alien species. In summary, community completeness is an interface between observed local observed species richness and dark diversity, which can be useful both in theoretical and applied biodiversity research.     

Structure and use of distance calls in wild bonobos (Pan paniscus)

We report the physical structure and use of a distance call (high-hoot) by wild bonobos (Pan paniscus).Although spectrographic analyses reveal high structural variability, the total sample can be subdivided according to the composition of units—the presence or absence of an initial segment—and the range of the lowest harmonic. Analyses of samples from male—female pairs,vocalizing simultaneously and in close proximity, reveal that both animals utter calls in more or less precise temporal alternation but with different spectral ranges. Whether these differences are gender-specific or related to other factors, such as age or the social relations between particular individuals, is not clear. We suggest that (a) individuals of the same party may coordinate their vocal activity on both the temporal and the spectral level and (b) high hootings stimulate emission of equal vocalizations by members of other parties and may increase cohesion among community members. Comparison of a restricted number of spectrograms from known individuals indicates that bonobos may be able to adjust spectral parameters of one type of distance calls (high- hoot) according to corresponding calls of conspecifics.     

Mutualistic Interactions Drive Ecological Niche Convergence in a Diverse Butterfly Community

Ecological communities are structured in part by evolutionary interactions among their members. A number of recent studies incorporating phylogenetics into community ecology have upheld the paradigm that competition drives ecological divergence among species of the same guild. However, the role of other interspecific interactions, in particular positive interactions such as mutualism, remains poorly explored. We characterized the ecological niche and inferred phylogenetic relationships among members of a diverse community of neotropical Müllerian mimetic butterflies. Müllerian mimicry is one of the best studied examples of mutualism, in which unpalatable species converge in wing pattern locally to advertize their toxicity to predators. We provide evidence that mutualistic interactions can drive convergence along multiple ecological axes, outweighing both phylogeny and competition in shaping community structure. Our findings imply that ecological communities are adaptively assembled to a much greater degree than commonly suspected. In addition, our results show that phenotype and ecology are strongly linked and support the idea that mimicry can cause ecological speciation through multiple cascading effects on species' biology.     

Focus: Vaccines: Embracing the Diversity of Latinx Communities to Promote Vaccinations

While vaccine hesitancy is well documented in the literature among the Latinx community, little attention or effort is given to the nuances among the members of individual communities, such as country of origin, immigration status, generational status, primary language, race, age, sex, gender, or rural residence and how these complexities affect vaccine messaging and uptake. We have evidence that this heterogeneity causes differences in access to healthcare, attitudes towards vaccines, and degree of health disparities. In this review we will describe their impact on vaccination rates in the Latinx community, highlighting missed opportunities for public health outreach, and how targeted messaging could improve vaccine uptake.     

Characterization of Bacterial,Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem

Sponge-associated microbial communities include members from the three domains of life. In the case of bacteria, they are diverse, host specific and different from the surrounding seawater. However, little is known about the diversity and specificity of Eukarya and Archaea living in association with marine sponges. This knowledge gap is even greater regarding sponges from regions other than temperate and tropical environments. In Antarctica, marine sponges are abundant and important members of the benthos, structuring the Antarctic marine ecosystem. In this study, we used high throughput ribosomal gene sequencing to investigate the three-domain diversity and community composition from eight different Antarctic sponges. Taxonomic identification reveals that they belong to families Acarnidae, Chalinidae, Hymedesmiidae, Hymeniacidonidae, Leucettidae, Microcionidae, and Myxillidae. Our study indicates that there are different diversity and similarity patterns between bacterial/archaeal and eukaryote microbial symbionts from these Antarctic marine sponges, indicating inherent differences in how organisms from different domains establish symbiotic relationships. In general, when considering diversity indices and number of phyla detected, sponge-associated communities are more diverse than the planktonic communities. We conclude that three-domain microbial communities from Antarctic sponges are different from surrounding planktonic communities, expanding previous observations for Bacteria and including the Antarctic environment. Furthermore, we reveal differences in the composition of the sponge associated bacterial assemblages between Antarctic and tropical-temperate environments and the presence of a highly complex microbial eukaryote community, suggesting a particular signature for Antarctic sponges, different to that reported from other ecosystems.     

The impact of interactions on invasion and colonization resistance in microbial communities

In human microbiota, the prevention or promotion of invasions can be crucial to human health. Invasion outcomes, in turn, are impacted by the composition of resident communities and interactions of resident members with the invader. Here we study how interactions influence invasion outcomes in microbial communities, when interactions are primarily mediated by chemicals that are released into or consumed from the environment. We use a previously developed dynamic model which explicitly includes species abundances and the concentrations of chemicals that mediate species interaction. Using this model, we assessed how species interactions impact invasion by simulating a new species being introduced into an existing resident community. We classified invasion outcomes as resistance, augmentation, displacement, or disruption depending on whether the richness of the resident community was maintained or decreased and whether the invader was maintained in the community or went extinct. We found that as the number of invaders introduced into the resident community increased, disruption rather than augmentation became more prevalent. With more facilitation of the invader by the resident community, resistance outcomes were replaced by displacement and augmentation. By contrast, with more facilitation among residents, displacement outcomes shifted to resistance. When facilitation of the resident community by the invader was eliminated, the majority of augmentation outcomes turned into displacement, while when inhibition of residents by invaders was eliminated, invasion outcomes were largely unaffected. Our results suggest that a better understanding of interactions within resident communities and between residents and invaders is crucial to predicting the success of invasions into microbial communities.     

Bonding or bridging? Professional network organizations of second-generation Turks in the Netherlands and France

ABSTRACT

This article analyses network organizations founded by descendants of Turkish migrants in the Netherlands and France. By surveying members of two such organizations and interviewing several of their board members, we learn how these organizations function, their success in building and extending social networks, and their efficacy at improving labour market prospects for young second-generation professionals of Turkish descent. Our findings reveal a hybrid structure, whereby the organizations gear many of their activities towards mainstream society. In comparison to traditional immigrant organizations, their attitude is more open to other social groups, yet they still have a clear stronghold in the ethnic immigrant community. We conclude that ethnicity is not the main element in the successful second generation’s organizing process. Factors such as educational trajectories, professional ambitions, feelings of responsibility for other members and newly acquired socioeconomic status are the main reasons for this group to organize.     

The ecology of the planktonic diatom Cyclotella and its implications for global environmental change studies

The fossil record of diatoms in lake sediments can be used to assess the effects of climate variability on lake ecosystems if ecological relationships between diatom community structure and environmental parameters are well understood. Cyclotella sensu lato taxa are a key group of diatoms that are frequently dominant members of phytoplankton communities in low‐ to moderate‐productivity lakes. Their relative abundances have fluctuated significantly in palaeolimnological records spanning over a century in arctic, alpine, boreal and temperate lakes. This suggests that these species are sensitive to environmental change and may serve as early indicators of ecosystem effects of global change. Yet patterns of change in Cyclotella species are not synchronous or unidirectional across, or even within, regions, raising the question of how to interpret these widespread changes in diatom community structure. We suggest that the path forward in resolving seemingly disparate records is to identify clearly the autecology of Cyclotella species, notably the role of nutrients, dissolved organic carbon and light, coupled with better consideration of both the mechanisms controlling lake thermal stratification processes and the resulting effects of changing lake thermal regimes on light and nutrients. Here we begin by reviewing the literature on the resource requirements of common Cyclotella taxa, illustrating that many studies reveal the importance of light, nitrogen, phosphorus, and interactions among these resources in controlling relative abundances. We then discuss how these resource requirements can be linked to shifts in limnological processes driven by environmental change, including climate‐driven change in lakewater temperature, thermal stratification and nutrient loading, as well as acidification‐driven shifts in nutrients and water clarity. We examine three case studies, each involving two lakes from the same region that have disparate trends in the relative abundances of the same species, and illustrate how the mechanisms by which these species abundances are changing can be deciphered. Ultimately, changes in resource availability and water clarity are key factors leading to shifts in Cyclotella abundances. Tighter integration of the autecology of this important group of diatoms with environmental change and subsequent alterations in limnological processes will improve interpretations of palaeolimnological records, and clarify the drivers of seemingly disparate patterns in fossil records showing widespread and rapid changes across the northern hemisphere.     

The microbiome of pest insects: it is not just bacteria

Insects are associated with multiple microbes that have been reported to influence various aspects of their biology. Most studies in insects, including pest species, focus on the bacterial communities of the microbiome even though the microbiome consists of members of many more kingdoms, which can also have large influence on the life history of insects. In this review, we present some key examples of how the different members of the microbiome, such as bacteria, fungi, viruses, archaea, and protozoa, affect the fitness and behavior of pest insects. Moreover, we argue that interactions within and among microbial groups are abundant and of great importance, necessitating the use of a community approach to study microbial–host interactions. We propose that the restricted focus on bacteria very likely hampers our understanding of the functioning and impact of the microbiome on the biology of pest insects. We close our review by highlighting a few open questions that can provide an in‐depth understanding of how other components of the microbiome, in addition to bacteria, might influence host performance, thus contributing to pest insect ecology.     

Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants

Ruminants are unique among livestock due to their ability to efficiently convert plant cell wall carbohydrates into meat and milk. This ability is a result of the evolution of an essential symbiotic association with a complex microbial community in the rumen that includes vast numbers of bacteria, methanogenic archaea, anaerobic fungi and protozoa. These microbes produce a diverse array of enzymes that convert ingested feedstuffs into volatile fatty acids and microbial protein which are used by the animal for growth. Recent advances in high-throughput sequencing and bioinformatic analyses have helped to reveal how the composition of the rumen microbiome varies significantly during the development of the ruminant host, and with changes in diet. These sequencing efforts are also beginning to explain how shifts in the microbiome affect feed efficiency. In this review, we provide an overview of how meta-omics technologies have been applied to understanding the rumen microbiome, and the impact that diet has on the rumen microbial community.     

Community Perceptions of Hospitals and Shared Physical Space: A Qualitative Study

In addition to providing critical medical services to communities, hospitals are also forces of broader change when seen from the perspective of neighborhood development. Over the past few decades the obligation on the part of U.S. nonprofit hospitals to positively impact the communities in which they are located has become entrenched in both U.S. tax law and the practices of many hospitals. This article presents findings from a grounded theory qualitative study of the relationship between a non-profit children’s hospital in Columbus, Ohio, and the neighborhood in which it is located. Based on in-depth interviews with local residents and community leaders, findings suggest that community members often interpret distance, safety, and transportation in different, and often counter-intuitive ways. Drawing upon literature from medical geography and sociology, the authors argue that hospitals may benefit from working closely with community members to determine how space is understood and constructed when planning community health interventions.     

Optimizing the analysis of human intestinal microbiota with phylogenetic microarray

Phylogenetic microarrays present an attractive strategy to high-throughput interrogation of complex microbial communities. In this work, we present several approaches to optimize the analysis of intestinal microbiota with the recently developed Microbiota Array. First, we determined how 16S rDNA-specific PCR amplification influenced bacterial detection and the consistency of measured abundance values. Bacterial detection improved with an increase in the number of PCR amplification cycles, but 25 cycles were sufficient to achieve the maximum possible detection. A PCR-caused deviation in the measured abundance values was also observed. We also developed two mathematical algorithms that aimed to account for a predicted cross-hybridization of 16S rDNA fragments among different species, and to adjust the measured hybridization signal based on the number of 16S rRNA gene copies per species genome. The 16S rRNA gene copy adjustment indicated that the presence of members of the class Clostridia might be overestimated in some 16S rDNA-based studies. Finally, we show that the examination of total community RNA with phylogenetic microarray can provide estimates of the relative metabolic activity of individual community members. Complementary profiling of genomic DNA and total RNA isolated from the same sample presents an opportunity to assess population structure and activity in the same microbial community.     

Microbial Community Profiling to Investigate Transmission of Bacteria Between Life Stages of the Wood-Boring Beetle, Anoplophora glabripennis

Many insects harbor specific bacteria in their digestive tract, and these gut microbiota often play important roles in digestion and nutrient provisioning. While it is common for a given insect species to harbor a representative gut microbial community as a population, how this community is acquired and maintained from generation to generation is not known for most xylophagous insects, except termites. In this study, we examined acquisition of gut microbiota by the wood-feeding beetle, Anoplophora glabripennis, by identifying and comparing microbial community members among different life stages of the insect and with microbes it encounters in the environment. Automated ribosomal intergenic spacer analysis was employed to compare bacterial communities present in the egg and larval stages of A. glabripennis as well as with microbes found in the oviposition site and the surrounding woody tissue. Multivariate analyses were used to identify relationships between sample type and specific bacterial types (operational taxonomic units). From this analysis, bacteria that were derived from the environment, the oviposition site, and/or the egg were identified and compared with taxa found in larvae. Results showed that while some larval microbes were derived from environmental sources, other members of the larval microbial community appear to be vertically transmitted. These findings could lead to a better understanding of which microbial species are critical for the survival of this insect and to development of techniques that could be used to alter this community to disrupt the digestive physiology of the host insect as a biological control measure.     

Self-organization, layered structure, and aggregation enhance persistence of a synthetic biofilm consortium

Microbial consortia constitute a majority of the earth's biomass, but little is known about how these cooperating communities persist despite competition among community members. Theory suggests that non-random spatial structures contribute to the persistence of mixed communities; when particular structures form, they may provide associated community members with a growth advantage over unassociated members. If true, this has implications for the rise and persistence of multi-cellular organisms. However, this theory is difficult to study because we rarely observe initial instances of non-random physical structure in natural populations. Using two engineered strains of Escherichia coli that constitute a synthetic symbiotic microbial consortium, we fortuitously observed such spatial self-organization. This consortium forms a biofilm and, after several days, adopts a defined layered structure that is associated with two unexpected, measurable growth advantages. First, the consortium cannot successfully colonize a new, downstream environment until it self-organizes in the initial environment; in other words, the structure enhances the ability of the consortium to survive environmental disruptions. Second, when the layered structure forms in downstream environments the consortium accumulates significantly more biomass than it did in the initial environment; in other words, the structure enhances the global productivity of the consortium. We also observed that the layered structure only assembles in downstream environments that are colonized by aggregates from a previous, structured community. These results demonstrate roles for self-organization and aggregation in persistence of multi-cellular communities, and also illustrate a role for the techniques of synthetic biology in elucidating fundamental biological principles.     

Estimating Virus Production Rates in Aquatic Systems

Viruses are pervasive components of marine and freshwater systems, and are known to be significant agents of microbial mortality. Developing quantitative estimates of this process is critical as we can then develop better models of microbial community structure and function as well as advance our understanding of how viruses work to alter aquatic biogeochemical cycles. The virus reduction technique allows researchers to estimate the rate at which virus particles are released from the endemic microbial community. In brief, the abundance of free (extracellular) viruses is reduced in a sample while the microbial community is maintained at near ambient concentration. The microbial community is then incubated in the absence of free viruses and the rate at which viruses reoccur in the sample (through the lysis of already infected members of the community) can be quantified by epifluorescence microscopy or, in the case of specific viruses, quantitative PCR. These rates can then be used to estimate the rate of microbial mortality due to virus-mediated cell lysis.     

Biodiversity effects on ecosystem functioning respond unimodally to environmental stress

Understanding how biodiversity (B) affects ecosystem functioning (EF) is essential for assessing the consequences of ongoing biodiversity changes. An increasing number of studies, however, show that environmental conditions affect the shape of BEF relationships. Here, we first use a game‐theoretic community model to reveal that a unimodal response of the BEF slope can be expected along environmental stress gradients, but also how the ecological mechanisms underlying this response may vary depending on how stress affects species interactions. Next, we analysed a global dataset of 44 experiments that crossed biodiversity with environmental conditions. Confirming our main model prediction, the effect of biodiversity on ecosystem functioning tends to be greater at intermediate levels of environmental stress, but varies among studies corresponding to differences in stress‐effects on species interactions. Together, these results suggest that increases in stress from ongoing global environmental changes may amplify the consequences of biodiversity changes.     

Inferring Social Status and Rich Club Effects in Enterprise Communication Networks

Social status, defined as the relative rank or position that an individual holds in a social hierarchy, is known to be among the most important motivating forces in social behaviors. In this paper, we consider the notion of status from the perspective of a position or title held by a person in an enterprise. We study the intersection of social status and social networks in an enterprise. We study whether enterprise communication logs can help reveal how social interactions and individual status manifest themselves in social networks. To that end, we use two enterprise datasets with three communication channels — voice call, short message, and email — to demonstrate the social-behavioral differences among individuals with different status. We have several interesting findings and based on these findings we also develop a model to predict social status. On the individual level, high-status individuals are more likely to be spanned as structural holes by linking to people in parts of the enterprise networks that are otherwise not well connected to one another. On the community level, the principle of homophily, social balance and clique theory generally indicate a “rich club” maintained by high-status individuals, in the sense that this community is much more connected, balanced and dense. Our model can predict social status of individuals with 93% accuracy.