Joint spatiotemporal modelling reveals seasonally dynamic patterns of Japanese encephalitis vector abundance across India

Predicting vector abundance and seasonality, key components of mosquito-borne disease (MBD) hazard, is essential to determine hotspots of MBD risk and target interventions effectively. Japanese encephalitis (JE), an important MBD, is a leading cause of viral encephalopathy in Asia with 100,000 cases estimated annually, but data on the principal vector Culex tritaeniorhynchus is lacking. We developed a Bayesian joint-likelihood model that combined information from available vector occurrence and abundance data to predict seasonal vector abundance for C. tritaeniorhynchus (a constituent of JE hazard) across India, as well as examining the environmental drivers of these patterns. Using data collated from 57 locations from 24 studies, we find distinct seasonal and spatial patterns of JE vector abundance influenced by climatic and land use factors. Lagged precipitation, temperature and land use intensity metrics for rice crop cultivation were the main drivers of vector abundance, independent of seasonal, or spatial variation. The inclusion of environmental factors and a seasonal term improved model prediction accuracy (mean absolute error [MAE] for random cross validation = 0.48) compared to a baseline model representative of static hazard predictions (MAE = 0.95), signalling the importance of seasonal environmental conditions in predicting JE vector abundance. Vector abundance varied widely across India with high abundance predicted in northern, north-eastern, eastern, and southern regions, although this ranged from seasonal (e.g., Uttar Pradesh, West Bengal) to perennial (e.g., Assam, Tamil Nadu). One-month lagged predicted vector abundance was a significant predictor of JE outbreaks (odds ratio 2.45, 95% confidence interval: 1.52–4.08), highlighting the possible development of vector abundance as a proxy for JE hazard. We demonstrate a novel approach that leverages information from sparse vector surveillance data to predict seasonal vector abundance–a key component of JE hazard–over large spatial scales, providing decision-makers with better guidance for targeting vector surveillance and control efforts.     

Metagenomic sequencing reveals viral abundance and diversity in mosquitoes from the Shaanxi-Gansu-Ningxia region,China

BackgroundMosquitoes host and transmit numerous arthropod-borne viruses (arboviruses) that cause disease in both humans and animals. Effective surveillance of virome profiles in mosquitoes is vital to the prevention and control of mosquito-borne diseases in northwestern China, where epidemics occur frequently.MethodsMosquitoes were collected in the Shaanxi-Gansu-Ningxia region (Shaanxi Province, Gansu Province, and Ningxia Hui Autonomous Region) of China from June to August 2019. Morphological methods were used for taxonomic identification of mosquito species. High-throughput sequencing and metagenomic analysis were used to characterize mosquito viromes.ResultsA total of 22,959 mosquitoes were collected, including Culex pipiens (45.7%), Culex tritaeniorhynchus (40.6%), Anopheles sinensis (8.4%), Aedes (5.2%), and Armigeres subalbatus (0.1%). In total, 3,014,183 (0.95% of clean reads) viral sequences were identified and assigned to 116 viral species (including pathogens such as Japanese encephalitis virus and Getah virus) in 31 viral families, including Flaviviridae, Togaviridae, Phasmaviridae, Phenuiviridae, and some unclassified viruses. Mosquitoes collected in July (86 species in 26 families) showed greater viral diversity than those from June and August. Culex pipiens (69 species in 25 families) and Culex tritaeniorhynchus (73 species in 24 families) carried more viral species than Anopheles sinensis (50 species in 19 families) or Aedes (38 species in 20 families) mosquitoes.ConclusionViral diversity and abundance were affected by mosquito species and collection time. The present study elucidates the virome compositions of various mosquito species in northwestern China, improving the understanding of virus transmission dynamics for comparison with those of disease outbreaks.     

Species patterns in foliar nitrogen concentration, nitrogen content and 13C abundance for understory saplings across light gradients

Soil nitrogen (N) supply and uptake by regenerating trees is an important ecosystem attribute but difficult to quantify in partial-cut forests where light availability varies. The foliar attributes of N concentration (N_%) and N per unit area (N_a) may help characterize the influence of soil nutrition, but ideally the relationship between soils and foliage would be tested separately by species across well-defined light gradients. To do this, we examined foliar attributes of four tree species across gradients of light availability in 12 year-old partially-cut forests in northwest British Columbia, Canada. There were no differences in forest floor or mineral soil N mineralization rates across the light gradients, and for western hemlock (Tsuga heterophylla) and hybrid white spruce (Picea glauca x sitchensis), this consistent level of soil N supply corresponded with unchanging foliar N_%. In contrast, foliar N_% of Betula papyrifera (paper birch) and Thuja plicata (western redcedar) declined with shading, perhaps due to shifts in root-shoot biomass allocation for B. papyrifera, and climatic constraints on shade tolerance for T. plicata. Leaf δ¹³C approached an asymptote at approx. 40% full light for the coniferous species, but increased linearly with light for B. papyrifera. Foliar N_a was linearly correlated with leaf δ¹³C for three species, reflecting the dual effect of light and nutrition on photosynthesis processes, and suggesting that foliar N_a may be a simple parameter to integrate both resource constraints on regenerating saplings. These results demonstrate both support for and limits to foliar attributes among species in isolating soil N effects against light constraints in partial-cut forests.     

Single-cell analysis of murine long-term hematopoietic stem cells reveals distinct patterns of gene expression during fetal migration

Background

Long-term hematopoietic stem cells (LT-HSCs) migrate from the fetal liver (FL) to the fetal bone marrow (FBM) during development. Various adhesion and chemotactic receptor genes have been implicated in the migration of adult LT-HSCs. However, their role in the migration of fetal LT-HSCs is not clearly understood due, in part, to the rare number of these cells in fetal tissues, which preclude classical gene expression analysis. The aim of this study is to characterize the expression of migration related genes in fetal LT-HSC across different anatomical locations during development.

Methodology/Principal Findings

We isolated fetal LT-HSC from different developmental stages, as well as different anatomical locations, and performed single-cell multiplex RT-qPCR and flow cytometry analysis of eight molecules involved in adult LT-HSC migration. Our results show that the gene expression of the chemokine receptor Cxcr4 in LT-HSC varies across developmental microenvironments and times, while the cadherin Cdh2 (Ncad) and the calcium receptor Casr show higher gene expression and variability only in FBM at 17.5 days post coitum (dpc). The cadherin Cdh5 (Vecad) maintains high expression variability only during fetal development, while the integrin subunit Itga5 (α5) increases its variability after 14.5 dpc. The integrin subunits Itga4 (α4) and Itgal (Lfa1), as well as the selectin ligand Selplg (Psgl1), did not show differences in their expression in single LT-HSCs irrespective of the developmental times or anatomical microenvironments studied.

Conclusions/Significance

Our data demonstrate that the expression pattern of phenotypically identical, single LT-HSCs fluctuates as a function of developmental stage and anatomical microenvironment. This is the first exhaustive gene expression comparison of migration-related molecules in fetal tissues across developmental times, enhancing the understanding of LT-HSC migration fate decisions during development.     

The shape of abundance distributions across temperature gradients in reef fishes

Improving predictions of ecological responses to climate change requires understanding how local abundance relates to temperature gradients, yet many factors influence local abundance in wild populations. We evaluated the shape of thermal‐abundance distributions using 98 422 abundance estimates of 702 reef fish species worldwide. We found that curved ceilings in local abundance related to sea temperatures for most species, where local abundance declined from realised thermal ‘optima’ towards warmer and cooler environments. Although generally supporting the abundant‐centre hypothesis, many species also displayed asymmetrical thermal‐abundance distributions. For many tropical species, abundances did not decline at warm distribution edges due to an unavailability of warmer environments at the equator. Habitat transitions from coral to macroalgal dominance in subtropical zones also influenced abundance distribution shapes. By quantifying the factors constraining species’ abundance, we provide an important empirical basis for improving predictions of community re‐structuring in a warmer world.     

Metagenomic analysis of Streptomyces lividans reveals host-dependent functional expression

Most functional metagenomic studies have been limited by the poor expression of many genes derived from metagenomic DNA in Escherichia coli, which has been the predominant surrogate host to date. To expand the range of expressed genes, we developed tools for construction and functional screening of metagenomic libraries in Streptomyces lividans. We expanded on previously published protocols by constructing a system that enables retrieval and characterization of the metagenomic DNA from biologically active clones. To test the functionality of these methods, we constructed and screened two metagenomic libraries in S. lividans. One was constructed with pooled DNA from 14 bacterial isolates cultured from Alaskan soil and the second with DNA directly extracted from the same soil. Functional screening of these libraries identified numerous clones with hemolytic activity, one clone that produces melanin by a previously unknown mechanism, and one that induces the overproduction of a secondary metabolite native to S. lividans. All bioactive clones were functional in S. lividans but not in E. coli, demonstrating the advantages of screening metagenomic libraries in more than one host.     

Metagenomic analysis of BTEX-contaminated forest soil microcosm

A microcosmal experiment using a metagenomic technique was designed to assess the effect of BTEX (benzene, toluene, ethylbenzene, and xylenes) on an indigenous bacterial community in a Daejeon forest soil. A compositional shift of bacterial groups in an artificial BTEX-contaminated soil was examined by the 16S rDNA PCR-DGGE method. Phylogenetic analysis of 16S rDNAs in the dominant DGGE bands showed that the number of Actinobacteria and Bacillus populations increased. To confirm these observations, we performed PCR to amplify the 23S rDNA and 16S rDNA against the sample metagenome using Actinobacteria-targeting and Bacilli-specific primer sets, respectively. The result further confirmed that a bacterial community containing Actinobacteria and Bacillus was affected by BTEX.     

Stand composition,proximity to overstory trees and gradients of soil moisture influence patterns of subalpine fir seedling emergence and survival

Background and Aims

We experimentally examined how variability in mixed forest stand composition, spatial relationships to dominant trees and their environmental correlates influence seedling emergence and survival.

Methods

Fir seeds were placed at distances of 1 and 25 cm in each cardinal direction at the base of mature aspen and fir trees and in interspaces in aspen dominant, mixed and conifer dominant stands and in adjacent meadows. Fir seedling emergence, mortality, water relations and foliar nutrition were determined and soil moisture was measured.

Results

Subalpine fir germination was 9 and 13 fold greater, and seedling mortality was lower in aspen stands than mixed and conifer dominated stands. Germination was two-fold greater at the base of aspen trees compared to fir trees and stand interspaces and was significantly greater on the north side of aspen trees. Soil moisture was greatest in aspen dominated stands, with the highest soil moisture conditions occurring at the base of aspen trees and in interspaces. Fir seedlings had better water relations when growing next to aspen trees and had significantly higher foliar N and P in aspen stands.

Conclusions

Aspen appear to facilitate fir establishment by creating favorable soil resource and light conditions that increase germination rates and seedling survival.     

Coordination of photosynthetic traits across soil and climate gradients

“Least-cost theory” posits that C₃ plants should balance rates of photosynthetic water loss and carboxylation in relation to the relative acquisition and maintenance costs of resources required for these activities. Here we investigated the dependency of photosynthetic traits on climate and soil properties using a new Australia-wide trait dataset spanning 528 species from 67 sites. We tested the hypotheses that plants on relatively cold or dry sites, or on relatively more fertile sites, would typically operate at greater CO₂ drawdown (lower ratio of leaf internal to ambient CO₂, C_i:C_a) during light-saturated photosynthesis, and at higher leaf N per area (N_area) and higher carboxylation capacity (V_{cmax 25}) for a given rate of stomatal conductance to water vapour, g_sw. These results would be indicative of plants having relatively higher water costs than nutrient costs. In general, our hypotheses were supported. Soil total phosphorus (P) concentration and (more weakly) soil pH exerted positive effects on the N_area–g_sw and V_{cmax 25}–g_sw slopes, and negative effects on C_i:C_a. The P effect strengthened when the effect of climate was removed via partial regression. We observed similar trends with increasing soil cation exchange capacity and clay content, which affect soil nutrient availability, and found that soil properties explained similar amounts of variation in the focal traits as climate did. Although climate typically explained more trait variation than soil did, together they explained up to 52% of variation in the slope relationships and soil properties explained up to 30% of the variation in individual traits. Soils influenced photosynthetic traits as well as their coordination. In particular, the influence of soil P likely reflects the Australia's geologically ancient low-relief landscapes with highly leached soils. Least-cost theory provides a valuable framework for understanding trade-offs between resource costs and use in plants, including limiting soil nutrients.     

Regular patterns for proteome-wide distribution of protein abundance across species

A proteome of the bio-entity, including cell, tissue, organ, and organism, consists of proteins of diverse abundance. The principle that determines the abundance of different proteins in a proteome is of fundamental significance for an understanding of the building blocks of the bio-entity. Here, we report three regular patterns in the proteome-wide distribution of protein abundance across species such as human, mouse, fly, worm, yeast, and bacteria: in most cases, protein abundance is positively correlated with the protein's origination time or sequence conservation during evolution; it is negatively correlated with the protein's domain number and positively correlated with domain coverage in protein structure, and the correlations became stronger during the course of evolution; protein abundance can be further stratified by the function of the protein, whereby proteins that act on material conversion and transportation (mass category) are more abundant than those that act on information modulation (information category). Thus, protein abundance is intrinsically related to the protein's inherent characters of evolution, structure, and function.     

温度和水分变化对冻土区泥炭地土壤氮循环功能基因丰度的影响

以大兴安岭多年冻土区泥炭地为研究对象,通过室内模拟增温实验,研究温度升高对不同深度（0-150 cm）土壤氮循环功能基因丰度的影响。同时针对0-20 cm和20-40 cm土壤设置两个水分处理,分别为土壤原始含水量和淹水状态,研究水分变化对表层土壤氮循环功能基因丰度的影响。结果表明温度升高显著提高了活动层（0-60 cm）、过渡层（60-80 cm）、永冻层（80-100 cm）中nifH、nirK基因丰度,温度升高显著提高了活动层（0-40 cm）和过渡层（60-80 cm）中nirS基因丰度。温度升高显著提高了过渡层（60-80 cm）NH₄⁺-N和较深永冻层（140-150 cm）NO₃^--N的含量,但降低了过渡层（60-80 cm）NO₃^--N和较深永冻层（120-150 cm）NH₄⁺-N的含量,相关性分析表明,NH₄⁺-N含量与nifH和nirS基因丰度呈显著正相关,NO₃^--N含量与nirK基因丰度呈显著正相关,说明温度升高能够通过改变微生物丰度促进过渡层固氮作用和反硝化作用。在增温条件下,淹水处理使表层土壤nirS和nirK基因丰度及NH₄⁺-N含量降低,但提高了NO₃^--N含量,说明淹水造成了过度还原的条件使反硝化底物浓度降低,降低反硝化微生物活性进而抑制了土壤反硝化作用。该结果对于明确未来气候变化影响下冻土区泥炭地土壤氮循环过程具有重要意义。     

Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community

Advances in DNA extraction and next‐generation sequencing have made a vast number of historical herbarium specimens available for genomic investigation. These specimens contain not only genomic information from the individual plants themselves, but also from associated microorganisms such as bacteria and fungi. These microorganisms may have colonized the living plant (e.g., pathogens or host‐associated commensal taxa) or may result from postmortem colonization that may include decomposition processes or contamination during sample handling. Here we characterize the metagenomic profile from shotgun sequencing data from herbarium specimens of two widespread plant species (Ambrosia artemisiifolia and Arabidopsis thaliana) collected up to 180 years ago. We used blast searching in combination with megan and were able to infer the metagenomic community even from the oldest herbarium sample. Through comparison with contemporary plant collections, we identify three microbial species that are nearly exclusive to herbarium specimens, including the fungus Alternaria alternata, which can comprise up to 7% of the total sequencing reads. This species probably colonizes the herbarium specimens during preparation for mounting or during storage. By removing the probable contaminating taxa, we observe a temporal shift in the metagenomic composition of the invasive weed Am. artemisiifolia. Our findings demonstrate that it is generally possible to use herbarium specimens for metagenomic analyses, but that the results should be treated with caution, as some of the identified species may be herbarium contaminants rather than representing the natural metagenomic community of the host plant.     

Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta

Sponge-associated bacteria are thought to produce many novel bioactive compounds, including polyketides. PCR amplification of ketosynthase domains of type I modular polyketide synthases (PKS) from the microbial community of the marine sponge Discodermia dissoluta revealed great diversity and a novel group of sponge-specific PKS ketosynthase domains. Metagenomic libraries totaling more than four gigabases of bacterial genomes associated with this sponge were screened for type I modular PKS gene clusters. More than 90% of the clones in total sponge DNA libraries represented bacterial DNA inserts, and 0.7% harbored PKS genes. The majority of the PKS hybridizing clones carried small PKS clusters of one to three modules, although some clones encoded large multimodular PKSs (more than five modules). The most abundant large modular PKS appeared to be encoded by a bacterial symbiont that made up < 1% of the sponge community. Sequencing of this PKS revealed 14 modules that, if expressed and active, is predicted to produce a multimethyl-branched fatty acid reminiscent of mycobacterial lipid components. Metagenomic libraries made from fractions enriched for unicellular or filamentous bacteria differed significantly, with the latter containing numerous nonribosomal peptide synthetase (NRPS) and mixed NRPS-PKS gene clusters. The filamentous bacterial community of D. dissoluta consists mainly of Entotheonella spp., an unculturable sponge-specific taxon previously implicated in the biosynthesis of bioactive peptides.     

Dendrochronological analysis of white oak growth patterns across a topographic moisture gradient in southern Ohio

Moisture availability is a key factor that influences white oak (Quercus alba L.) growth and wood production. In unglaciated eastern North America, available soil moisture varies greatly along topographic and edaphic gradients. This study was aimed at determining the effects of soil moisture variability and macroclimate on white oak growth in mixed-oak forests of southern Ohio. Using accurately dated and measured tree rings, we analyzed 119 white oaks growing across an integrated moisture index (IMI), a computer-generated GIS model that simultaneously combines topographic and edaphic features into a moisture index scale. Growth trends varied considerably across the IMI, with trees in mesic sites exhibiting patterns much different from those in either xeric or intermediate sites. BAI growth and biomass increments were higher for trees growing in the intermediate and mesic sites than those from the xeric sites. Correlation and response function analyses, and redundancy analysis revealed significant relations between ring-width indices and climate, with current year May–July PDSI, precipitation and temperature as the most important correlates of white oak growth. Additionally, climatic influences on growth rate were variable across the IMI; trees in xeric sites showed much greater coefficients relative to those from the intermediate and mesic sites. Despite these differences, xeric and intermediate trees exhibited similar growth patterns. The present results provide further evidence of the usefulness of the IMI for identifying and comparing white oak growth patterns across the complex, dissected landscape of southern Ohio.     

Comparative metagenomic,phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.