An improved nonparametric lower bound of species richness via a modified good-turing frequency formula

Fine-scale characterization of the soybean rhizosphere microbiome via synthetic long reads and avidity sequencing

BACKGROUND

The rhizosphere microbiome displays structural and functional dynamism driven by plant, microbial, and environmental factors. While such plasticity is a well-evidenced determinant of host health, individual and community-level microbial activity within the rhizosphere remain poorly understood, due in part to the insufficient taxonomic resolution achieved through traditional marker gene amplicon sequencing. This limitation necessitates more advanced approaches (e.g., long-read sequencing) to derive ecological inferences with practical application. To this end, the present study coupled synthetic long-read technology with avidity sequencing to investigate eukaryotic and prokaryotic microbiome dynamics within the soybean (Glycine max) rhizosphere under field conditions.

RESULTS

Synthetic long-read sequencing permitted de novo reconstruction of the entire 18S-ITS1-ITS2 region of the eukaryotic rRNA operon as well as all nine hypervariable regions of the 16S rRNA gene. All full-length, mapped eukaryotic amplicon sequence variants displayed genus-level classification, and 44.77% achieved species-level classification. The resultant eukaryotic microbiome encompassed five kingdoms (19 genera) of protists in addition to fungi - a depth unattainable with conventional short-read methods. In the prokaryotic fraction, every full-length, mapped amplicon sequence variant was resolved at the species level, and 23.13% at the strain level. Thirteen species of Bradyrhizobium were thereby distinguished in the prokaryotic microbiome, with strain-level identification of the two Bradyrhizobium species most reported to nodulate soybean. Moreover, the applied methodology delineated structural and compositional dynamism in response to experimental parameters (i.e., growth stage, cultivar, and biostimulant application), unveiled a saprotroph-rich core microbiome, provided empirical evidence for host selection of mutualistic taxa, and identified key microbial co-occurrence network members likely associated with edaphic and agronomic properties.

CONCLUSIONS

This study is the first to combine synthetic long-read technology and avidity sequencing to profile both eukaryotic and prokaryotic fractions of a plant-associated microbiome. Findings herein provide an unparalleled taxonomic resolution of the soybean rhizosphere microbiota and represent significant biological and technological advancements in crop microbiome research.

A gene with a thousand alleles: The hyper-variable effectors of plant-parasitic nematodes

Pathogens are engaged in a fierce evolutionary arms race with their host. The genes at the forefront of the engagement between kingdoms are often part of diverse and highly mutable gene families. Even in this context, we discovered unprecedented variation in the hyper-variable (HYP) effectors of plant-parasitic nematodes. HYP effectors are single-gene loci that potentially harbor thousands of alleles. Alleles vary in the organization, as well as the number, of motifs within a central hyper-variable domain (HVD). We dramatically expand the HYP repertoire of two plant-parasitic nematodes and define distinct species-specific "rules" underlying the apparently flawless genetic rearrangements. Finally, by analyzing the HYPs in 68 individual nematodes, we unexpectedly found that despite the huge number of alleles, most individuals are germline homozygous. These data support a mechanism of programmed genetic variation, termed HVD editing, where alterations are locus specific, strictly governed by rules, and theoretically produce thousands of variants without errors.

Zygosity-based sex determination in a butterfly drives hypervariability of Masculinizer

Nature has devised many ways of producing males and females. Here, we report on a previously undescribed mechanism for Lepidoptera that functions without a female-specific gene. The number of alleles or allele heterozygosity in a single Z-linked gene (BaMasc) is the primary sex-determining switch in Bicyclus anynana butterflies. Embryos carrying a single BaMasc allele develop into WZ (or Z0) females, those carrying two distinct alleles develop into ZZ males, while (ZZ) homozygotes initiate female development, have mismatched dosage compensation, and die as embryos. Consequently, selection against homozygotes has favored the evolution of spectacular allelic diversity: 205 different coding sequences of BaMasc were detected in a sample of 246 females. The structural similarity of a hypervariable region (HVR) in BaMasc to the HVR in Apis mellifera csd suggests molecular convergence between deeply diverged insect lineages. Our discovery of this primary switch highlights the fascinating diversity of sex-determining mechanisms and underlying evolutionary drivers.

Environmental stress mediates groundwater microbial community assembly

Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.

Comprehensive characterization and database construction of immune repertoire in the largest Chinese glioma cohort

Immune receptor repertoire is valuable for developing immunotherapeutic interventions, but remains poorly understood across glioma subtypes including IDH wild type, IDH mutation without 1p/19q codeletion (IDHmut-noncodel) and IDH mutation with 1p/19q codeletion (IDHmut-codel). We assembled over 320,000 TCR/BCR clonotypes from the largest glioma cohort of 913 RNA sequencing samples in the Chinese population, finding that immune repertoire diversity was more prominent in the IDH wild type (the most aggressive glioma). Fewer clonotypes were shared within each glioma subtype, indicating high heterogeneity of the immune repertoire. The TRA-CDR3 was longer in private than in public clonotypes in IDH wild type. CDR3 variable motifs had higher proportions of hydrophobic residues in private than in public clonotypes, suggesting private CDR3 sequences have greater potential for tumor antigen recognition. Finally, we developed GTABdb, a web-based database designed for hosting, exploring, visualizing, and analyzing glioma immune repertoire. Our study will facilitate developing glioma immunotherapy.

Understory vegetation diversity patterns of Platycladus orientalis and Pinus elliottii communities in Central and Southern China

As a vital component of arbor forests, understory vegetation serves as an essential buffer zone for storing carbon due to its strong capacity for community regeneration. This study aimed to identify the diversity pattern and construction mechanism of Platycladus orientalis and Pinus elliottii understory vegetation based on large-scale sample surveys. The Bayesian Information Criterion value of species abundance distribution (SAD) indicated that the Zipf and Zipf-Mandelbrot models were the best-fitting models. The SAD and gambin fitting results suggested that the Pi. elliottii community had a more balanced structure, with most species being relatively abundant. The multiple regression tree model detected four and six indicator species in P. orientalis and Pi. elliottii communities, respectively. The α-diversity index increased with a rise in altitude and showed a wavy curve with latitude. Linear regression between the β diversity and environmental and geographic distance indicated that the P. orientalis and Pi. elliottii understory communities tended to be dominated by different ecological processes. The partition of β diversity indicated that both communities were dominated by turnover processes, which were caused by environmental classification or spatial constraints. This study helped to understand the diversity maintenance in the P. orientalis and Pi. elliottii understory vegetation communities, and will benefit for diversity restoration and conservation of pure conifer forests.

Biodiversity survey and estimation for line-transect sampling

Conducting biodiversity surveys using a fully randomised design can be difficult due to budgetary constraints (e.g., the cost of labour), site accessibility, and other constraints. To this end, ecologists usually select representative line transects or quadrats from a studied area to collect individuals of a given species and use this information to estimate the levels of biodiversity over an entire region. However, commonly used biodiversity estimators such as Rao's quadratic diversity index (and especially the Gini-Simpson index) were developed based on the assumption of independent sampling of individuals. Therefore, their performance can be compromised or even misleading when applied to species abundance datasets that are collected from non-independent sampling. In this study, we utilise a Markov chain model and derive an associated parameter estimator to account for non-independence in sequential sampling. Empirical tests on two forest plots in tropical (Barro Colorado, Island of Panama) and subtropical (Heishiding Nature Reserve of Guangdong, China) regions and the continental-scale spatial distribution of Acacia species in Australia showed that our estimators performed reasonably well. The estimated parameter measuring the degree of non-independence of subsequent sampling showed that a non-independent effect is very likely to occur when using line transects to sample organisms in subtropical regions at both local and regional spatial scales. In summary, based on a first-order Markov sampling model and using Rao's quadratic diversity index as an example, our study provides an improvement in diversity estimation while simultaneously accounting for the non-independence of sampling in field biodiversity surveys. Our study presents one possible solution for addressing the non-independent sampling of individuals in biodiversity surveys.

Variation in a Darwin Wasp (Hymenoptera: Ichneumonidae) Community along an Elevation Gradient in a Tropical Biodiversity Hotspot: Implications for Ecology and Conservation

Understanding how biodiversity varies from place to place is a fundamental goal of ecology and an important tool for halting biodiversity loss. Parasitic wasps (Hymenoptera) are a diverse and functionally important animal group, but spatial variation in their diversity is poorly understood. We survey a community of parasitic wasps (Ichneumonidae: Pimplinae) using Malaise traps up a mountain in the Brazilian Atlantic Rainforest, and relate the catch to biotic and abiotic habitat characteristics. We find high species richness compared with previous similar studies, with abundance, richness, and diversity peaking at low to intermediate elevation. There is a marked change in community composition with elevation. Habitat factors strongly correlated with elevation also strongly predict changes in the pimpline community, including temperature as well as the density of bamboo, lianas, epiphytes, small trees, and herbs. These results identify several possible surrogates of pimpline communities in tropical forests, which could be used as a tool in conservation. They also contribute to the growing evidence for a typical latitudinal gradient in ichneumonid species richness, and suggest that low to medium elevations in tropical regions will sometimes conserve the greatest number of species locally, but to conserve maximal biodiversity, a wider range of elevations should also be targeted.

Multivalent antigen display on nanoparticle immunogens increases B cell clonotype diversity and neutralization breadth to pneumoviruses

Nanoparticles for multivalent display and delivery of vaccine antigens have emerged as a promising avenue for enhancing B cell responses to protein subunit vaccines. Here, we evaluated B cell responses in rhesus macaques immunized with prefusion-stabilized respiratory syncytial virus (RSV) F glycoprotein trimer compared with nanoparticles displaying 10 or 20 copies of the same antigen. We show that multivalent display skews antibody specificities and drives epitope-focusing of responding B cells. Antibody cloning and repertoire sequencing revealed that focusing was driven by the expansion of clonally distinct B cells through recruitment of diverse precursors. We identified two antibody lineages that developed either ultrapotent neutralization or pneumovirus cross-neutralization from precursor B cells with low initial affinity for the RSV-F immunogen. This suggests that increased avidity by multivalent display facilitates the activation and recruitment of these cells. Diversification of the B cell response by multivalent nanoparticle immunogens has broad implications for vaccine design.

Immunosequencing and Profiling of T Cells at the Maternal-Fetal Interface of Women with Preterm Labor and Chronic Chorioamnionitis

T cells are implicated in the pathophysiology of preterm labor and birth, the leading cause of neonatal morbidity and mortality worldwide. Specifically, maternal decidual T cells infiltrate the chorioamniotic membranes in chronic chorioamnionitis (CCA), a placental lesion considered to reflect maternal anti-fetal rejection, leading to preterm labor and birth. However, the phenotype and TCR repertoire of decidual T cells in women with preterm labor and CCA have not been investigated. In this study, we used phenotyping, TCR sequencing, and functional assays to elucidate the molecular characteristics and Ag specificity of T cells infiltrating the chorioamniotic membranes in women with CCA who underwent term or preterm labor. Phenotyping indicated distinct enrichment of human decidual effector memory T cell subsets in cases of preterm labor with CCA without altered regulatory T cell proportions. TCR sequencing revealed that the T cell repertoire of CCA is characterized by increased TCR richness and decreased clonal expansion in women with preterm labor. We identified 15 clones associated with CCA and compared these against established TCR databases, reporting that infiltrating T cells may possess specificity for maternal and fetal Ags, but not common viral Ags. Functional assays demonstrated that choriodecidual T cells can respond to maternal and fetal Ags. Collectively, our findings provide, to our knowledge, novel insight into the complex processes underlying chronic placental inflammation and further support a role for effector T cells in the mechanisms of disease for preterm labor and birth. Moreover, this work further strengthens the contribution of adaptive immunity to the syndromic nature of preterm labor and birth.

Mathematical Characterization of Private and Public Immune Receptor Sequences

Diverse T and B cell repertoires play an important role in mounting effective immune responses against a wide range of pathogens and malignant cells. The number of unique T and B cell clones is characterized by T and B cell receptors (TCRs and BCRs), respectively. Although receptor sequences are generated probabilistically by recombination processes, clinical studies found a high degree of sharing of TCRs and BCRs among different individuals. In this work, we use a general probabilistic model for T/B cell receptor clone abundances to define "publicness" or "privateness" and information-theoretic measures for comparing the frequency of sampled sequences observed across different individuals. We derive mathematical formulae to quantify the mean and the variances of clone richness and overlap. Our results can be used to evaluate the effect of different sampling protocols on abundances of clones within an individual as well as the commonality of clones across individuals. Using synthetic and empirical TCR amino acid sequence data, we perform simulations to study expected clonal commonalities across multiple individuals. Based on our formulae, we compare these simulated results with the analytically predicted mean and variances of the repertoire overlap. Complementing the results on simulated repertoires, we derive explicit expressions for the richness and its uncertainty for specific, single-parameter truncated power-law probability distributions. Finally, the information loss associated with grouping together certain receptor sequences, as is done in spectratyping, is also evaluated. Our approach can be, in principle, applied under more general and mechanistically realistic clone generation models.

Effects of habitat perturbation on lizard assemblages in the center-west of the Arid Chaco region, Argentina

Several human disturbances contribute to the decrease of vertebrate species' richness and abundance, altering the processes of an ecosystem. We evaluate richness, diversity and relative abundance of species for lizard assemblages at sites with different degrees of perturbation in the center-west of the Arid Chaco region in Argentina. Between 2015 and 2018, six lizard assemblages were sampled monthly -using pitfall traps- in three areas of the Chaco, with a perturbed and an unperturbed (control) replica at each of the areas: (1) Chaco Mountain plain, (2) Chaco Mountain slope, and (3) Chaco Plains, and habitat characteristics of each study site were recorded. We captured 1446 lizards, belonging to 12 species. The perturbed area at the Chaco Mountain plain showed the greatest richness, diversity and abundance of species. In the perturbed Chaco Plains, species abundance decreased by about 50% with respect to the control site. Liolaemus chacoensis was the dominant species at all sites. Some species could be negatively affected by a total loss of arboreal strata, tree trunks and fallen leaves. Structural parameters of lizard assemblages were related to the habitat characteristics; therefore, these results provide information for the conservation and management of lands and lizard assemblages in the Arid Chaco.

Elevational surveys of Sulawesi herpetofauna 1: Gunung Galang, Gunung Dako Nature Reserve

The Indonesian island of Sulawesi has a unique geology and geography, which have produced an astoundingly diverse and endemic flora and fauna and a fascinating biogeographic history. Much biodiversity research has focused on the regional endemism in the island's Central Core and on its four peninsulas, but the biodiversity of the island's many upland regions is still poorly understood for most taxa, including amphibians and reptiles. Here, we report the first of several planned full-mountain checklists from a series of herpetological surveys of Sulawesi's mountains conducted by our team. In more than 3 weeks of work on Gunung Galang, a 2,254 m peak west of the city of Tolitoli, Sulawesi Tengah Province, on Sulawesi's Northern Peninsula, we recovered nearly fifty species of reptiles and amphibians, more than a dozen of which are either new to science or known but undescribed. The incompleteness of our sampling suggests that many more species remain to be discovered on and around this mountain.

Urban biogeography of fungal endophytes across San Francisco

In natural and agricultural systems, the plant microbiome-the microbial organisms associated with plant tissues and rhizosphere soils-has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue to transition out of rural areas and into cities, understanding the factors that shape environmental microbial communities in urban ecosystems stands to become increasingly important.

Assessing Onchocerca volvulus Intensity of Infection and Genetic Diversity Using Mitochondrial Genome Sequencing of Single Microfilariae Obtained before and after Ivermectin Treatment

Onchocerciasis is a neglected tropical disease targeted for elimination using ivermectin mass administration. Ivermectin kills the microfilariae and temporarily arrests microfilariae production by the macrofilariae. We genotyped 436 microfilariae from 10 people each in Ituri, Democratic Republic of the Congo (DRC), and Maridi County, South Sudan, collected before and 4-5 months after ivermectin treatment. Population genetic analyses identified 52 and 103 mitochondrial DNA haplotypes among the microfilariae from DRC and South Sudan, respectively, with few haplotypes shared between people. The percentage of genotype-based correct assignment to person within DRC was ~88% and within South Sudan ~64%. Rarefaction and extrapolation analysis showed that the genetic diversity in DRC, and even more so in South Sudan, was captured incompletely. The results indicate that the per-person adult worm burden is likely higher in South Sudan than DRC. Analyses of haplotype data from a subsample (n = 4) did not discriminate genetically between pre- and post-treatment microfilariae, confirming that post-treatment microfilariae are not the result of new infections. With appropriate sampling, mitochondrial haplotype analysis could help monitor changes in the number of macrofilariae in a population as a result of treatment, identify cases of potential treatment failure, and detect new infections as an indicator of continuing transmission.

The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton

Metabarcoding using high throughput sequencing of amplicons of the 18S rRNA gene is one of the widely used methods for assessing the diversity of microeukaryotes in various ecosystems. We investigated the effectiveness of the V4 and V8-V9 regions of the 18S rRNA gene by comparing the results of metabarcoding microeukaryotic communities using the DADA2 (ASV), USEARCH-UNOISE3 (ZOTU), and USEARCH-UPARSE (OTU with 97% similarity) algorithms. Both regions showed similar levels of genetic variability and taxa identification accuracy. Richness for DADA2 datasets of both regions was lower than for UNOISE3 and UPARSE datasets, which is due to more accurate error correction in amplicons. Microeukaryotic communities (autotrophs and heterotrophs) structure identified using both regions showed a significant relationship with phytoplankton (autotrophs) communities structure based on microscopy in a seasonal freshwater sample series. The strongest relationship was found between the phytoplankton species and V8-V9 ASVs produced by DADA2.

Seagrass macrobenthic biodiversity does not vary in conformity with a leaky-lagoonal confinement gradient

Coastal lagoon ecology often changes on progression from the open, well-flushed mouth region to the depositional zone furthest from the open sea. This is generally considered consequent on increasing 'confinement' and associated features, rather than on the often co-occurringly decreasing salinity. The 12 km Rainbow Channel connecting part of Moreton Bay, a microtidal leaky lagoon, to the adjacent Pacific provides a gradient of increasing confinement without any significant salinity change, i.e. a tenfold increase in water residence time for a salinity decrease of <1. Macrobenthic faunal assemblages characterising intertidal Zostera seagrass at strategic points along its length were compared to test whether their nature changed in conformity with confinement models. Results suggest that it does not; faunal abundance, species richness, evenness and composition remaining effectively unchanged along the gradient. Seagrass systems may constitute a special case because they decouple renewal times of the overlying water and local organic enrichment/decomposition; as may leaky lagoons because of their high tidal velocities.

A TLR7-nanoparticle adjuvant promotes a broad immune response against heterologous strains of influenza and SARS-CoV-2

The ideal vaccine against viruses such as influenza and SARS-CoV-2 must provide a robust, durable and broad immune protection against multiple viral variants. However, antibody responses to current vaccines often lack robust cross-reactivity. Here we describe a polymeric Toll-like receptor 7 agonist nanoparticle (TLR7-NP) adjuvant, which enhances lymph node targeting, and leads to persistent activation of immune cells and broad immune responses. When mixed with alum-adsorbed antigens, this TLR7-NP adjuvant elicits cross-reactive antibodies for both dominant and subdominant epitopes and antigen-specific CD8+ T-cell responses in mice. This TLR7-NP-adjuvanted influenza subunit vaccine successfully protects mice against viral challenge of a different strain. This strategy also enhances the antibody response to a SARS-CoV-2 subunit vaccine against multiple viral variants that have emerged. Moreover, this TLR7-NP augments antigen-specific responses in human tonsil organoids. Overall, we describe a nanoparticle adjuvant to improve immune responses to viral antigens, with promising implications for developing broadly protective vaccines.

Five times over: 42 new Angustopila species highlight Southeast Asia’s rich biodiversity (Gastropoda, Stylommatophora, Hypselostomatidae)

The Southeast Asian genus Angustopila, currently comprising 13 nominal species, encompasses the world’s tiniest land snails. This work shows that there are far more species than previously suspected, and that this genus is in fact, a very speciose group of tiny snails widely distributed in Southeast Asia. Angustopila is revised based on type material of known species as well as 211 samples newly collected in China, Laos, Myanmar, Thailand and Vietnam. Altogether, 53 species and one subspecies are recognised, of which 42 species and subspecies are new to science: A. akrodon Páll-Gergely & Hunyadi, sp. nov., A. apiaria Páll-Gergely & Hunyadi, sp. nov., A. apiostoma Páll-Gergely & Vermeulen, sp. nov., A. apokritodon Páll-Gergely & Hunyadi, sp. nov., A. antidomedon Páll-Gergely & Hunyadi, sp. nov., A. babel Páll-Gergely & Vermeulen, sp. nov., A. bathyodon Páll-Gergely & Hunyadi, sp. nov., A. bidentata Páll-Gergely & Jochum, sp. nov., A. cavicola Páll-Gergely & Dumrongrojwattana, sp. nov., A. cicatricosa Páll-Gergely & Vermeulen, sp. nov., A. coprologos uninodus Páll-Gergely & Grego, ssp. nov., A. erawanica Páll-Gergely & Dumrongrojwattana, sp. nov., A. fratermajor Páll-Gergely & Vermeulen, sp. nov., A. fraterminor Páll-Gergely & Vermeulen, sp. nov., A. gracilis Páll-Gergely & Hunyadi, sp. nov., A. halongensis Páll-Gergely & Vermeulen, sp. nov., A. hyron Páll-Gergely & Vermeulen, sp. nov., A. maasseni Páll-Gergely & Vermeulen, sp. nov., A. majuscula Páll-Gergely & Hunyadi, sp. nov., A. margaritarion Páll-Gergely & Hunyadi, sp. nov., A. megastoma Páll-Gergely & Vermeulen, sp. nov., A. occidentalis Páll-Gergely & Hunyadi, sp. nov., A. oostoma Páll-Gergely & Vermeulen, sp. nov., A. papaver Páll-Gergely & Hunyadi, sp. nov., A. parallela Páll-Gergely & Hunyadi, sp. nov., A. prolixa Páll-Gergely & Hunyadi, sp. nov., A. pusilla Páll-Gergely & Hunyadi, sp. nov., A. pustulata Páll-Gergely & Hunyadi, sp. nov., A. quadridens Páll-Gergely & Vermeulen, sp. nov., A. rara Páll-Gergely & Hunyadi, sp. nov., A. reticulata Páll-Gergely & Hunyadi, sp. nov., A. somsaki Páll-Gergely & Hunyadi, sp. nov., A. steffeki Páll-Gergely & Grego, sp. nov., A. tetradon Páll-Gergely & Hunyadi, sp. nov., A. thersites Páll-Gergely & Vermeulen, sp. nov., A. tonkinospiroides Páll-Gergely & Vermeulen, sp. nov., A. tridentata Páll-Gergely & Hunyadi, sp. nov., A. tweediei Páll-Gergely & Hunyadi, sp. nov., A. uvula Páll-Gergely & Hunyadi, sp. nov., A. vandevenderi Páll-Gergely & Jochum, sp. nov., A. vitrina Páll-Gergely & Hunyadi, sp. nov., A. vomer Páll-Gergely & Hunyadi, sp. nov., A. werneri Páll-Gergely & Hunyadi, sp. nov.

Angustopila subelevata Páll-Gergely & Hunyadi, 2015 is moved to the synonymy of Angustopila elevata (F. G. Thompson & Upatham, 1997), and A. singuladentis Inkhavilay & Panha, 2016 is a junior synonym of A. fabella Páll-Gergely & Hunyadi, 2015. Three species, namely A. elevata, A. fabella and A. szekeresi, are widespread over several hundred kilometres while some other species (A. huoyani, A. parallelasp. nov., A. cavicolasp. nov.) are known from just two sites a few hundred kilometres apart. All others are small range or single-site endemics. The reproductive anatomy of A. erawanicasp. nov. is described.

Bladder cancer is associated with decreased urinary microbiota diversity and alterations in microbial community composition

INTRODUCTION

Human urine microbiota (UM) research has uncovered associations between composition of microbial communities of the lower urinary tract and various disease states including several reports on the putative link between UM and bladder cancer (BC). The aim of this study was to investigate male UM in patients with BC and controls using catheterised urine specimens unlike in previous studies.

METHODS

Urine samples were obtained in theatre after surgical prepping and draping using aseptic catheterisation. DNA was extracted and hypervariable region V4 of the 16S rRNA gene was amplified using 515F and 806R primers. Sequencing was performed on Illumina MiSeq platform. Sequencing data were processed using appropriate software tools. Alpha diversity measures were calculated and compared between groups. Prevalence Interval for Microbiome Evaluation was used to test differences in beta diversity.

RESULTS

A total of 63 samples were included in the analysis. Mean age of study subjects was 65.1 years (SD 12.5). Thirty-four men had bladder cancer and 29 participants were undergoing interventions for benign conditions (benign prostate hyperplasia or upper urinary tract stone disease). BC patients had lower UM richness and diversity than controls (83 vs. 139 operational taxonomic units, P = 0.015; Shannon index: 2.46 vs. 2.94, P = 0.049). There were specific taxa enriched in cancer (Veillonella, Varibaculum, Methylobacterium-Methylorubrum) and control groups (Pasteurella, Corynebacterium, Acinetobacter), respectively.

CONCLUSION

BC patients had lower bladder microbiota richness and diversity than controls. Specific genera were enriched in cancer and control groups, respectively. These results corroborate some of previous reports while contradicting others. Future microbiota research would benefit from parallel transcriptomic/metabolomic analysis.

Unaltered fungal community after fire prevention treatments over widespread Mediterranean rockroses (Halimium lasianthum)

Mediterranean ecosystems are frequently invaded by pyrophytic scrubs such as Halimium lasianthum that colonize areas traditionally used by livestock. A diverse fungal community is associated with this kind of vegetation, playing an important ecological role in these ecosystems. However, uncontrolled expansion of these shrubs considerably increases the risk of wildfires in these stands and, hence, fire-prevention treatments are needed. To investigate the long-term effects of two different forest-fire-prevention treatments on the soil fungal community, we analyzed these communities 9 years after prescribed burning or mechanical shredding were carried out in scrubland dominated by H. lasianthum. Neither of the fire-prevention treatments had a negative long-term effect on the abundance or richness of ectomycorrhizal fungi. However, saprotrophs and lichenized fungi experienced negative effects. Soil fertility significantly affected the distribution of fungi according to their functional groups, and pH was the most influential variable in terms of the distribution of edible species. Our findings indicate that forest management practices to prevent forest fires does not negatively affect the fungal community in the long-term, but for lichens and decomposers. Moreover, prescribed burning is suggested as a more economical way of reducing the risk of wildfires without affecting the ecology of the fungal community.

A more reliable species richness estimator based on the Gamma-Poisson model

Background

Accurately estimating the true richness of a target community is still a statistical challenge, particularly in highly diverse communities. Due to sampling limitations or limited resources, undetected species are present in many surveys and observed richness is an underestimate of true richness. In the literature, methods for estimating the undetected richness of a sample are generally divided into two categories: parametric and nonparametric estimators. Imposing no assumptions on species detection rates, nonparametric methods demonstrate robust statistical performance and are widely used in ecological studies. However, nonparametric estimators may seriously underestimate richness when species composition has a high degree of heterogeneity. Parametric approaches, which reduce the number of parameters by assuming that species-specific detection probabilities follow a given statistical distribution, use traditional statistical inference to calculate species richness estimates. When species detection rates meet the model assumption, the parametric approach could supply a nearly unbiased estimator. However, the infeasibility and inefficiency of solving maximum likelihood functions limit the application of parametric methods in ecological studies when the model assumption is violated, or the collected data is sparse.

Method

To overcome these estimating challenges associated with parametric methods, an estimator employing the moment estimation method instead of the maximum likelihood estimation method is proposed to estimate parameters based on a Gamma-Poisson mixture model. Drawing on the concept of the Good-Turing frequency formula, the proposed estimator only uses the number of singletons, doubletons, and tripletons in a sample for undetected richness estimation.

Results

The statistical behavior of the new estimator was evaluated by using real and simulated data sets from various species abundance models. Simulation results indicated that the new estimator reduces the bias presented in traditional nonparametric estimators, presents more robust statistical behavior compared to other parametric estimators, and provides confidence intervals with better coverage among the discussed estimators, especially in assemblages with high species composition heterogeneity.

One-step PCR amplicon sequencing libraries perform better than two-step when assessing soil microbial diversity and community profiles

Despite adoption of high-throughput sequencing of PCR-amplified microbial taxonomic markers for ecological analyses, distinct approaches for preparing amplicon libraries exist. One approach utilises long fusion primers and a single PCR (one-step) while another utilises shorter primers in a first reaction, before transferring diluted amplicons to a second reaction for barcode index incorporation (two-step). We investigated whether transferring diluted amplicons risked creating artificially simplified, poorly diverse communities. In soils from three sites with paired cropland and forest, one-step yielded higher alpha-diversity indices, including detection of two-four times more unique taxa. Modelling expected taxa per sequence observation predicted that one-step reaches full coverage by 104 sequences per sample while two-step needs 105-109. Comparisons of rank abundance demonstrated that two-step covered only 38-69% of distributions. Beta-diversity showed better separation of communities in response to land use change under one-step, although both approaches showed a significant effect. Driving differences was underestimation of relatively minor taxa with the two-step procedure. These taxa were low in abundance, yet play important roles in carbon cycling, secondary metabolite production, anaerobic metabolism, and bacterial predation. We conclude that one-step amplicon libraries are advisable for studies focussed on diversity or relatively minor yet functionally important taxa.

The Role of Habitat Amount and Vegetation Density for Explaining Loss of Small-Mammal Diversity in a South American Woodland Savanna

The focus of research and conservation in tropical regions is mainly devoted to forest ecosystems, usually neglecting the processes underlying widespread, more open biomes, like savannas. Here we test a wide range of sampled woodland sites across the South American savanna for the direct and indirect effects of habitat loss and vegetation density on the diversity of small-mammal species. We quantify the direction and magnitude of the effects of habitat amount (habitat loss), vegetation density (tree or foliage density), and patch size (species-area effect) on species composition and richness. We also test whether the relative effect sizes of landscape and patch-related metrics predict a persistence gradient from habitat specialist to generalist species across 54 sites. We used structural equation models (SEM) to test our predictions. After 22,032 trap-nights considering all sampled sites and 20 small-mammal species identified, the structural equation model explained 23.5% of the variance in the richness of small-mammal species. Overall, we found that landscape-level metrics were more important in explaining species richness, with a secondary role of patch-level metrics such as vegetation density. The direct effect of local landscape was significant for explaining species richness variation, but a strong positive association between regional and local landscapes was also present. Furthermore, considering the direct and indirect paths, SEM explained 46.2% of the species composition gradient. In contrast to species richness, we recorded that the combined landscape-level and patch-level metrics are crucial to determining small-mammal species composition at savanna patches. The small mammals from the South American woodland savanna exhibit clear ecological gradients on their species composition and richness, driven by habitat specialist (e.g., Thrichomys fosteri, Monodelphis domestica, and Thylamys macrurus) and generalist (e.g., Didelphis albiventris, Rhipidomys macrurus, and Calomys callosus) species’ responses to habitat amount and/or vegetation density, as seen in dense-forest Neotropical biomes.

Patterns and Driving Factors of Diversity in the Shrub Community in Central and Southern China

Climate, topography, and human activities are known to influence plant diversity. In the present study, species-abundance distribution (SAD) patterns of the shrub community were fitted, and the mechanism of contribution of 22 driving factors was assessed. The results showed that the α-diversity index exhibited no significant differences between artificial disturbance and the natural community. The Zipf and Zipf–Mandelbrot models were found to exhibit a good SAD fitting of the communities, thereby exhibiting a different diversity structure. It was observed that the SAD followed more than one rule, and the Zipf–Mandelbrot model was better than other models. The gradient boosting model indicated that precipitation in the wettest month, annual precipitation, and slope direction showed the strongest impact on plant richness. The indicator species of the artificial disturbance and natural community were identified from a multiple regression tree. Furthermore, an increase in species diversity was observed with a rise in latitude, exhibiting a single-peaked curve with increased altitude. β-diversity analysis indicated that both habitat filtering and the neutral effect influenced the establishment of the natural community, while the establishment of the artificial disturbance community was only affected by habitat filtering. Our study provides a better understanding of the ecological process of the maintenance of shrub-community diversity.

Post-extinction recovery of the Phanerozoic oceans and biodiversity hotspots

The fossil record of marine invertebrates has long fuelled the debate as to whether or not there are limits to global diversity in the sea1-5. Ecological theory states that, as diversity grows and ecological niches are filled, the strengthening of biological interactions imposes limits on diversity6,7. However, the extent to which biological interactions have constrained the growth of diversity over evolutionary time remains an open question1-5,8-11. Here we present a regional diversification model that reproduces the main Phanerozoic eon trends in the global diversity of marine invertebrates after imposing mass extinctions. We find that the dynamics of global diversity are best described by a diversification model that operates widely within the exponential growth regime of a logistic function. A spatially resolved analysis of the ratio of diversity to carrying capacity reveals that less than 2% of the global flooded continental area throughout the Phanerozoic exhibits diversity levels approaching ecological saturation. We attribute the overall increase in global diversity during the Late Mesozoic and Cenozoic eras to the development of diversity hotspots under prolonged conditions of Earth system stability and maximum continental fragmentation. We call this the 'diversity hotspots hypothesis', which we propose as a non-mutually exclusive alternative to the hypothesis that the Mesozoic marine revolution led this macroevolutionary trend12,13.

Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations

The majority of microalgal species reproduce asexually, yet population genetic studies rarely find identical multi-locus genotypes (MLG) in microalgal blooms. Instead, population genetic studies identify large genotypic diversity in most microalgal species. This paradox of frequent asexual reproduction but low number of identical genotypes hampers interpretations of microalgal genotypic diversity. We present a computer model for estimating, for the first time, the number of distinct MLGs by simulating microalgal population composition after defined exponential growth periods. The simulations highlighted the effects of initial genotypic diversity, sample size and intraspecific differences in growth rates on the probability of isolating identical genotypes. We estimated the genotypic richness for five natural microalgal species with available high-resolution population genetic data and monitoring-based growth rates, indicating 500 000 to 2 000 000 distinct genotypes for species with few observed clonal replicates (<5%). Furthermore, our simulations indicated high variability in genotypic richness over time and among microalgal species. Genotypic richness was also strongly impacted by intraspecific variability in growth rates. The probability of finding identical MLGs and sampling a representative fraction of genotypes decreased noticeably with smaller sample sizes, challenging the detection of differences in genotypic diversity with typical isolate numbers in the field.

Sand Flies (Diptera: Psychodidae): Fauna and Ecology in the Northeast of Algeria

Sand flies (Diptera: Psychodidae) transmit several Leishmania (Kinetoplastida: Trypanosomatidae) species, which cause leishmaniasis, a significant public health concern in Algeria. We compared sand fly species abundance and composition among different biotopes (urban, peri-urban, rural areas), bioclimatic zones (humid, sub-humid, semi-arid), and elevation ranges. We also used the additive partitioning of beta diversity to test whether the variation in sand fly composition among biotopes, bioclimatic zones, and elevation ranges is due to species turnover or community subsetting. In total, 7,478 specimens were captured; of which, 7,162 (51.5% males vs. 48.5% females) belong to eight species: Phlebotomus perniciosus Newstead, 1911 (77.4% of the total captured specimens), Phlebotomus perfiliewi Parrot, 1930 (14.6%), Phlebotomus longicuspis Nitzulescu, 1911 (5.9%), Phlebotomus papatasi Scopoli, 1786 (<1%), Phlebotomus sergenti Parrot, 1917 (<1%) and Phlebotomus chadlii Rioux, Juminer et Gibily 1966 (<1%), Sergentomyia minuta Adler et Theodor, 1927 (1%), and Sergentomyia fallax Parrot, 1921 (<1%). Sand fly total abundance showed negative correlations with altitude and was significantly higher in rural areas. Sandfly community composition was significantly different between rural and urban/peri-urban areas. The additive partitioning of beta diversity showed that 71.4% of the compositional dissimilarity among elevation ranges and bioclimates was due to sand fly species turnover, and 28.6% resulted from nestedness. However, the variation in sand fly composition among different biotopes was mainly due to community nestedness. Findings from this study help define the risk of Leishmania transmission and develop methods for vector control in Mila province and Algeria as a whole.

Bladder Microbiota Are Associated with Clinical Conditions That Extend beyond the Urinary Tract

Background. Since the discovery of the human urinary microbiota (UM), alterations in microbial community composition have been associated with various genitourinary conditions. The aim of this exploratory study was to examine possible associations of UM with clinical conditions beyond the urinary tract and to test some of the conclusions from previous studies on UM. Methods. Catheterised urine samples from 87 men were collected prior to endoscopic urological interventions under anaesthesia. The composition of the bacterial community in urine was characterized using the hypervariable V4 region of the 16S rRNA gene. Samples from 58 patients yielded a sufficient amount of bacterial DNA for analysis. Alpha diversity measures (number of operational taxonomic units, ACE, iChao2, Shannon and Simpson indices) were compared with the Kruskal–Wallis test. Beta diversity (differences in microbial community composition) was assessed using non-metric dimensional scaling in combination with the Prevalence in Microbiome Analysis algorithm. Results. Differences in bacterial richness and diversity were observed for the following variables: age, diabetes mellitus, dyslipidemia, smoking status and single-dose preoperative antibiotics. Differences in microbial community composition were observed in the presence of chronic kidney disease, lower urinary tract symptoms and antibiotic prophylaxis. Conclusions. UM appears to be associated with certain clinical conditions, including those unrelated to the urinary tract. Further investigation is needed before conclusions can be drawn for diagnostics and treatment.

Prognostic Value of Early Fluorodeoxyglucose-Positron Emission Tomography Response Imaging and Peripheral Immunologic Biomarkers: Substudy of a Phase II Trial of Risk-Adaptive Chemoradiation for Unresectable Non-Small Cell Lung Cancer

Purpose

We sought to examine the prognostic value of fluorodeoxyglucose-positron emission tomography (PET) imaging during chemoradiation for unresectable non-small cell lung cancer for survival and hypothesized that tumor PET response is correlated with peripheral T-cell function.

Methods and Materials

Forty-five patients with American Joint Committee on Cancer version 7 stage IIB-IIIB non-small cell lung cancer enrolled in a phase II trial and received platinum-doublet chemotherapy concurrent with 6 weeks of radiation (NCT02773238). Fluorodeoxyglucose-PET was performed before treatment start and after 24 Gy of radiation (week 3). PET response status was prospectively defined by multifactorial radiologic interpretation. PET responders received 60 Gy in 30 fractions, while nonresponders received concomitant boosts to 74 Gy in 30 fractions. Peripheral blood was drawn synchronously with PET imaging, from which germline DNA sequencing, T-cell receptor sequencing, and plasma cytokine analysis were performed.

Results

Median follow-up was 18.8 months, 1-year overall survival (OS) 82%, 1-year progression-free survival 53%, and 1-year locoregional control 88%. Higher midtreatment PET total lesion glycolysis was detrimental to OS (1 year 87% vs 63%, P < .001), progression-free survival (1 year 60% vs 26%, P = .044), and locoregional control (1 year 94% vs 65%, P = .012), even after adjustment for clinical/treatment factors. Twenty-nine of 45 patients (64%) were classified as PET responders based on a priori definition. Higher tumor programmed death-ligand 1 expression was correlated with response on PET (P = .017). Higher T-cell receptor richness and clone distribution slope were associated with improved OS (P = .018-0.035); clone distribution slope was correlated with PET response (P = .031).

Conclusions

Midchemoradiation PET imaging is prognostic for survival; PET response may be linked to tumor and peripheral T-cell biomarkers.

Analysis of the fecal and oral microbiota in chronic recurrent multifocal osteomyelitis

BACKGROUND

Chronic recurrent multifocal osteomyelitis (CRMO) is a rare autoinflammatory bone disease for which a lack of bacterial involvement is a key diagnostic feature to distinguish it from other symptomatically related diseases. However, the growing evidence suggesting an involvement of the host-associated microbiota in rheumatic disorders together with the now wide accessibility of modern culture-independent methods warrant a closer examination of CRMO.

METHODS

In this study, we show through bacterial 16S rRNA gene profiling that numerous features of the oral- and fecal microbial communities differentiate children with and without CRMO.

RESULTS

Notably, communities in diseased children are characterized by a lack of potential probiotic bacteria in the fecal community and an overabundance of known pathobionts in the oral microbial communities. Of special interest is the HACEK group, a set of commonly known oral pathogens that are implicated in the development of several acute and chronic diseases such as osteitis and rheumatoid arthritis. Furthermore, we observe that gut bacterial communities in the diseased children appear to reflect an altered host physiology more strongly than the oral community, which could suggest an oral disease origin followed by propagation and/or responses beyond the oral cavity.

CONCLUSIONS

Bacterial communities, in particular the oral microbiota, may serve as an indicator of underlying susceptibility to CRMO, or play a yet undefined role in its development.

Forgotten books: The application of unseen species models to the survival of culture

The study of ancient cultures is hindered by the incomplete survival of material artifacts, so we commonly underestimate the diversity of cultural production in historic societies. To correct this survivorship bias, we applied unseen species models from ecology to gauge the loss of narratives from medieval Europe, such as the romances about King Arthur. The estimates obtained are compatible with the scant historic evidence. In addition to events such as library fires, we identified the original evenness of cultural populations as an overlooked factor in these assemblages' stability in the face of immaterial loss. We link the elevated evenness in island literatures to analogous accounts of ecological and cultural diversity in insular communities. These analyses call for a wider application of these methods across the heritage sciences.

The number of tree species on Earth

One of the most fundamental questions in ecology is how many species inhabit the Earth. However, due to massive logistical and financial challenges and taxonomic difficulties connected to the species concept definition, the global numbers of species, including those of important and well-studied life forms such as trees, still remain largely unknown. Here, based on global ground-sourced data, we estimate the total tree species richness at global, continental, and biome levels. Our results indicate that there are ∼73,000 tree species globally, among which ∼9,000 tree species are yet to be discovered. Roughly 40% of undiscovered tree species are in South America. Moreover, almost one-third of all tree species to be discovered may be rare, with very low populations and limited spatial distribution (likely in remote tropical lowlands and mountains). These findings highlight the vulnerability of global forest biodiversity to anthropogenic changes in land use and climate, which disproportionately threaten rare species and thus, global tree richness.

The structure of tropical bat-plant interaction networks during an extreme El Niño-Southern Oscillation event

Interaction network structure reflects the ecological mechanisms acting within biological communities, which are affected by environmental conditions. In tropical forests, higher precipitation usually increases fruit production, which may lead frugivores to increase specialization, resulting in more modular and less nested animal–plant networks. In these ecosystems, El Niño is a major driver of precipitation, but we still lack knowledge of how species interactions change under this influence. To understand bat–plant network structure during an extreme El Niño‐Southern Oscillation event, we determined the links between plantivorous bat species and the plants they consume by DNA barcoding seeds and pulp in bat faeces. These interactions were recorded in the dry forest and rainforest of Costa Rica, during the dry and the wet seasons of an extreme El Niño year. From these we constructed seasonal and whole‐year bat–plant networks and analysed their structures and dissimilarities. In general, networks had low nestedness, had high modularity, and were dominated by one large compartment which included most species and interactions. Contrary to our expectations, networks were less nested and more modular in drier conditions, both in the comparison between forest types and between seasons. We suggest that increased competition, when resources are scarce during drier seasons and habitats, lead to higher resource partitioning among bats and thus higher modularity. Moreover, we have found similar network structures between dry and rainforests during El Niño and non‐El Niño years. Finally, most interaction dissimilarity among networks occurred due to interaction rewiring among species, potentially driven by seasonal changes in resource availability.

Bacterial Abundance, Diversity and Activity During Long-Term Colonization of Non-biodegradable and Biodegradable Plastics in Seawater

The microorganisms living on plastics called "plastisphere" have been classically described as very abundant, highly diverse, and very specific when compared to the surrounding environments, but their potential ability to biodegrade various plastic types in natural conditions have been poorly investigated. Here, we follow the successive phases of biofilm development and maturation after long-term immersion in seawater (7 months) on conventional [fossil-based polyethylene (PE) and polystyrene (PS)] and biodegradable plastics [biobased polylactic acid (PLA) and polyhydroxybutyrate-co-hydroxyvalerate (PHBV), or fossil-based polycaprolactone (PCL)], as well as on artificially aged or non-aged PE without or with prooxidant additives [oxobiodegradable (OXO)]. First, we confirmed that the classical primo-colonization and growth phases of the biofilms that occurred during the first 10 days of immersion in seawater were more or less independent of the plastic type. After only 1 month, we found congruent signs of biodegradation for some bio-based and also fossil-based materials. A continuous growth of the biofilm during the 7 months of observation (measured by epifluorescence microscopy and flow cytometry) was found on PHBV, PCL, and artificially aged OXO, together with a continuous increase in intracellular (³H-leucine incorporation) and extracellular activities (lipase, aminopeptidase, and β-glucosidase) as well as subsequent changes in biofilm diversity that became specific to each polymer type (16S rRNA metabarcoding). No sign of biodegradation was visible for PE, PS, and PLA under our experimental conditions. We also provide a list of operational taxonomic units (OTUs) potentially involved in the biodegradation of these polymers under natural seawater conditions, such as Pseudohongiella sp. and Marinobacter sp. on PCL, Marinicella litoralis and Celeribacter sp. on PHBV, or Myxococcales on artificially aged OXO. This study opens new routes for a deeper understanding of the polymers' biodegradability in seawaters, especially when considering an alternative to conventional fossil-based plastics.

Intrathymic differentiation of natural antibody-producing plasma cells in human neonates

The thymus is a central lymphoid organ primarily responsible for the development of T cells. A small proportion of B cells, however, also reside in the thymus to assist negative selection of self-reactive T cells. Here we show that the thymus of human neonates contains a consistent contingent of CD138⁺ plasma cells, producing all classes and subclasses of immunoglobulins with the exception of IgD. These antibody-secreting cells are part of a larger subset of B cells that share the expression of signature genes defining mouse B1 cells, yet lack the expression of complement receptors CD21 and CD35. Data from single-cell transcriptomic, clonal correspondence and in vitro differentiation assays support the notion of intrathymic CD138⁺ plasma cell differentiation, alongside other B cell subsets with distinctive molecular phenotypes. Lastly, neonatal thymic plasma cells also include clones reactive to commensal and pathogenic bacteria that commonly infect children born with antibody deficiency. Thus, our findings point to the thymus as a source of innate humoral immunity in human neonates.

Antigen-driven clonal selection shapes the persistence of HIV-1-infected CD4+ T cells in vivo

Clonal expansion of infected CD4+ T cells is a major mechanism of HIV-1 persistence and a barrier to achieving a cure. Potential causes are homeostatic proliferation, effects of HIV-1 integration, and interaction with antigens. Here, we show that it is possible to link antigen responsiveness, the full proviral sequence, the integration site, and the T cell receptor β-chain (TCRβ) sequence to examine the role of recurrent antigenic exposure in maintaining the HIV-1 reservoir. We isolated CMV- and Gag-responding CD4+ T cells from 10 treated individuals. Proviral populations in CMV-responding cells were dominated by large clones, including clones harboring replication-competent proviruses. TCRβ repertoires showed high clonality driven by converging adaptive responses. Although some proviruses were in genes linked to HIV-1 persistence (BACH2, STAT5B, MKL1), the proliferation of infected cells under antigenic stimulation occurred regardless of the site of integration. Paired TCRβ and integration site analysis showed that infection could occur early or late in the course of a clone's response to antigen and could generate infected cell populations too large to be explained solely by homeostatic proliferation. Together, these findings implicate antigen-driven clonal selection as a major factor in HIV-1 persistence, a finding that will be a difficult challenge to eradication efforts.

Effects of Fire on Ground-Dwelling Spider (Araneae) Assemblages in Central Indiana Forests

Fire is a natural disturbance that occurs in many temperate and tropical ecosystems worldwide. As ubiquitous members of these ecosystems, spiders (Araneae) are often affected by fire, and their response to this disturbance has been shown to be dependent on taxonomy, functional diversity, seasonality, and a variety of environmental factors. We examined the effect of fire on ground-dwelling spider assemblages in temperate forests in central Indiana over 5 yr and found that spider assemblages were significantly affected by fire disturbance. Overall spider abundance decreased, whereas species richness and diversity remained unaffected. We also found that spider response depended heavily on the family and/or guild to which the spider belonged. We suspect that altered habitat heterogeneity, the patchy nature of fire's effect on leaf litter, and the high rate of recolonization by spiders all played important roles in these observed patterns.

Biological richness of Gunung Slamet, Central Java, and the need for its protection

Designating protected areas remains a core strategy in biodiversity conservation. Despite high endemism, montane forests across the island of Java are under-represented in Indonesia's protected area network. Here, we document the montane biodiversity of Gunung Slamet, an isolated volcano in Central Java, and provide evidence to support its increased protection. During September–December 2018, we surveyed multiple sites for birds, primates, terrestrial mammals, reptiles, amphibians and vegetation. Survey methods included transects, camera traps and targeted searches at six sites, at altitudes of 970–2,512 m. We used species distribution models for birds and mammals of conservation concern to identify priority areas for protection. We recorded 99 bird species (13 globally threatened), 15 mammals (five globally threatened) and 17 reptiles and amphibians (two endemic). Our species distribution models showed considerable cross-taxon congruence between important areas on Slamet's upper slopes, generally above 1,800 m. Particularly important were records of the endemic subspecies of the Endangered Javan laughingthrush Garrulax rufifrons slamatensis, not recorded in the wild since 1925, the Endangered Javan gibbon Hylobates moloch and Javan surili Presbytis comata, and the Vulnerable Javan lutung Trachypithecus auratus and Javan leopard Panthera pardus melas. Recent forest loss has been modest, at least 280 km2 of continuous forest remain above 800 m, and our surveys show that forest habitats are in good condition. However, the mountain is widely used by trappers and hunters. Given its importance for biodiversity conservation, we discuss different options for improving the protection status of Gunung Slamet, including designation as a National Park or Essential Ecosystem.

Empirical abundance distributions are more uneven than expected given their statistical baseline

Exploring and accounting for the emergent properties of ecosystems as complex systems is a promising horizon in the search for general processes to explain common ecological patterns. For example the ubiquitous hollow-curve form of the species abundance distribution is frequently assumed to reflect ecological processes structuring communities, but can also emerge as a statistical phenomenon from the mathematical definition of an abundance distribution. Although the hollow curve may be a statistical artefact, ecological processes may induce subtle deviations between empirical species abundance distributions and their statistically most probable forms. These deviations may reflect biological processes operating on top of mathematical constraints and provide new avenues for advancing ecological theory. Examining ~22,000 communities, we found that empirical SADs are highly uneven and dominated by rare species compared to their statistical baselines. Efforts to detect deviations may be less informative in small communities-those with few species or individuals-because these communities have poorly resolved statistical baselines. The uneven nature of many empirical SADs demonstrates a path forward for leveraging complexity to understand ecological processes governing the distribution of abundance, while the issues posed by small communities illustrate the limitations of using this approach to study ecological patterns in small samples.