Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the ...corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments.
Soil plant-pathogenic (PF) and mycorrhizal fungi (MF) are both important in maintaining plant diversity, for example via host-specialized effects. However, empirical knowledge on the degree of host ...specificity and possible factors affecting the fungal assemblages is lacking.
We identified PF and MF in fine roots of 519 individuals across 45 subtropical tree species in southern China in order to quantify the importance of host phylogeny (including via its effects on functional traits), habitat and space in determining fungal communities. We also compared host specificity in PF and MF at different host-phylogenetic scales.
In both PF and MF, host phylogeny independently accounted for > 19% of the variation in fungal richness and composition, whereas environmental and spatial factors each explained no more than 4% of the variation. Over 77% of the variation explained by phylogeny was attributable to covariation in plant functional traits. Host specificity was phylogenetically scale-dependent, being stronger in PF than in MF at low host-phylogenetic scales (e.g. within genus) but similar at larger scales.
Our study suggests that host-phylogenetic effects dominate the assembly of both PF and MF communities, resulting from phylogenetically clustered plant traits. The scale-dependent host specificity implies that PF were specialized at lower-level and MF at higher-level host taxa.
The accumulation and transfer of Pb, Zn, Cu, and Cd along a soil-plant-insect-chicken food chain at contaminated sites were investigated. The study site nearing the Pb/Zn mine had been contaminated ...by heavy metals severely. Cadmium and Pb concentrations steadily declined with increasing trophic level (
p < 0.01), but concentrations of Zn and Cu slightly increased from plant to insect larva (
p > 0.05). The concentrations of heavy metals were the highest in chicken muscle, with lower values in liver and blood. The bioaccumulation of Pb was observed in chicken livers. The eliminations of Pb, Zn, Cu, and Cd via insect and chicken feces avoid metal bioaccumulation in insect and chicken body. These results suggest that the accumulation of heavy metals in specific animal organ of tissues could not be neglected, although transfer of metals to chicken from plant and insect was limited.
Root aeration, arsenic (As) accumulation, and speciation in rice of 20 different genotypes with regular irrigation of water containing 0.4 mg As l -1 were investigated. Different genotypes had ...different root anatomy demonstrated by entire root porosity (ranging from 12.43% to 33.21%), which was significantly correlated with radial oxygen loss (ROL) (R=0.64, P<0.01). Arsenic accumulation differed between genotypes, but there were no significant differences between Indica and Japonica subspecies, as well as paddy and upland rice. Total ROL from entire roots was correlated with metal tolerance (expressed as percentage mean of control straw biomass, R=0.69, P<0.01) among the 20 genotypes; total As concentration (R=-0.67, P<0.01) and inorganic As concentration (R=-0.47, P<0.05) in rice grains of different genotypes were negatively correlated with ROL. There were also significant genotype effects in percentage inorganic As (F=15.8, P<0.001) and percentage cacodylic acid (F=22.1, P<0.001), respectively. Root aeration of different genotypes and variation of genotypes on As accumulation and speciation would be useful for selecting genotypes to grow in areas contaminated by As.
Bacterial evolution is characterized by strong purifying selection as well as rapid adaptive evolution in changing environments. In this context, the genomic GC content (genomic GC) varies greatly ...but presents some level of phylogenetic stability, making it challenging to explain based on current hypotheses. To illuminate the evolutionary mechanisms of the genomic GC, we analyzed the base composition and functional inventory of 11,083 representative genomes. A phylogenetically constrained bimodal distribution of the genomic GC, which mainly originated from parallel divergences in the early evolution, was demonstrated. Such variation of the genomic GC can be well explained by DNA replication and repair (DRR), in which multiple pathways correlate with the genomic GC. Furthermore, the biased conservation of various stress-related genes, especially the DRR-related ones, implies distinct adaptive processes in the ancestral lineages of high- or low-GC clades which are likely induced by major environmental changes. Our findings support that the mutational biases resulting from these legacies of ancient adaptation have changed the course of adaptive evolution and generated great variation in the genomic GC. This highlights the importance of indirect effects of natural selection, which indicates a new model for bacterial evolution.
GC content has been shown to be an important factor in microbial ecology and evolution, and the genomic GC of bacteria can be characterized by great intergenomic heterogeneity, high intragenomic homogeneity, and strong phylogenetic inertia, as well as being associated with the environment. Current hypotheses concerning direct selection or mutational biases cannot well explain these features simultaneously. Our findings of the genomic GC showing that ancient adaptations have transformed the DRR system and that the resulting mutational biases further contributed to a bimodal distribution of it offer a more reasonable scenario for the mechanism. This would imply that, when thinking about the evolution of life, diverse processes of adaptation exist, and combined effects of natural selection should be considered.
Autophagy involves massive degradation of intracellular components and functions as a conserved system that helps cells to adapt to adverse conditions. In mammals, hypoxia rapidly stimulates ...autophagy as a cell survival response. Here, we examine the function of autophagy in the regulation of the plant response to submergence, an abiotic stress that leads to hypoxia and anaerobic respiration in plant cells. In Arabidopsis thaliana, submergence induces the transcription of autophagy-related (ATG) genes and the formation of autophagosomes. Consistent with this, the autophagy-defective (atg) mutants are hypersensitive to submergence stress and treatment with ethanol, the end product of anaerobic respiration. Upon submergence, the atg mutants have increased levels of transcripts of anaerobic respiration genes (alcohol dehydrogenase 1, ADH1 and pyruvate decarboxylase 1, PDC1), but reduced levels of transcripts of other hypoxia- and ethylene-responsive genes. Both submergence and ethanol treatments induce the accumulation of reactive oxygen species (ROS) in the rosettes of atg mutants more than in the wild type. Moreover, the production of ROS by the nicotinamide adenine dinucleotide phosphate (NADPH) oxidases is necessary for plant tolerance to submergence and ethanol, submergence-induced expression of ADH1 and PDC1, and activation of autophagy. The submergence- and ethanol-sensitive phenotypes in the atg mutants depend on a complete salicylic acid (SA) signaling pathway. Together, our findings demonstrate that submergence-induced autophagy functions in the hypoxia response in Arabidopsis by modulating SA-mediated cellular homeostasis.
•Ten strains of ACC-utilizing or N2-fixing bacteria were isolated and identified.•The isolated PGPB strongly promoted the growth of plants on sterilized tailings.•A consortium of 10 strains did not ...further increase the growth-promoting efficiency.•Plant growth-promoting effects of the PGPB were weaker in non-sterilized tailings.
Ten strains of Cu-tolerant bacteria with potential plant growth-promoting ability were isolated by selecting strains with the ability to use 1-aminocyclopropane-1-carboxylate as a sole nitrogen source (designated ACC-B) or fix nitrogen (designated FLN-B) originating from the rhizosphere of plants growing on copper tailings. All 10 strains proved to have intrinsic ability to produce indole acetic acid and siderophores, and most of them could mobilize insoluble phosphate. In addition, a greenhouse study showed that ACC-B, FLN-B and a mixture of both had similar, potent ability to stimulate growth of Pennisetum purpureum, Medicago sativa and Oenothera erythrosepala plants grown on sterilized tailings. For instance, above-ground biomass of P. purpureum was 278–357% greater after 60d growth on sterilized tailings in their presence. They could also significantly promote the growth of the plants grown on non-sterilized tailings, though the growth-promoting effects were much weaker. So, strategies for using of the plant growth-promoting bacteria in the practice of phytoremediation deserve further studies to get higher growth-promoting efficiency.
Microorganisms play an important role in weathering sulfide minerals worldwide and thrive in metal-rich and extremely acidic environments in acid mine drainage (AMD). Advanced molecular methods ...provide in-depth information on the microbial diversity and community dynamics in the AMD-generating environment. Although the diversity is relatively low and in general inversely correlated with the acidity, a considerable number of microbial species have been detected and described in AMD ecosystems. The acidophilic microbial communities dominated by iron/sulfur-oxidizing microbes vary widely in their composition and structure across diverse environmental gradients. Environmental conditions affect the microbial community assembly via direct and indirect interactions with microbes, resulting in an environmentally dependent biogeographic pattern. This article summarizes the latest studies to provide a better understanding of the microbial biodiversity and community assembly in AMD environments.
Bioaccumulation of arsenic (As) in rice (
) increases human exposure to this toxic, carcinogenic element. Recent studies identified several As transporters, but the regulation of these transporters ...remains unclear. Here, we show that the rice R2R3 MYB transcription factor OsARM1 (ARSENITE-RESPONSIVE MYB1) regulates As-associated transporters genes. Treatment with As(III) induced
transcript accumulation and an OsARM1-GFP fusion localized to the nucleus. Histochemical analysis of
lines indicated that
was expressed in the phloem of vascular bundles in basal and upper nodes. Knockout of
(
CRISPR/Cas9-generated mutants) improved tolerance to As(III) and overexpression of
(
lines) increased sensitivity to As(III). Measurement of As in As(III)-treated plants showed that under low As(III) conditions (2 μM), more As was transported from the roots to the shoots in
. By contrast, more As accumulated in the roots in
in response to high As(III) exposure (25 μM). In particular, the As(III) levels in node I were significantly higher in
, but significantly lower in
, compared to wild-type plants, implying that OsARM1 is important for the regulation of root-to-shoot translocation of As. Moreover,
, and
, which encode key As transporters, were significantly downregulated in
and upregulated in
compared to wild type. Chromatin immunoprecipitation-quantitative PCR of
indicated that OsARM1 binds to the conserved MYB-binding sites in the promoters or genomic regions of
, and
in rice. Our findings suggest that the OsARM1 transcription factor has essential functions in regulating As uptake and root-to-shoot translocation in rice.
Little is known about the underlying airway microbiome diversity in chronic obstructive pulmonary disease (COPD) at in-depth taxonomic levels. Here we present the first insights on the COPD airway ...microbiome at species and strain-levels. The full-length 16S rRNA gene was characterized from sputum in 98 COPD patients and 27 age-matched healthy controls, using the Pacific Biosciences sequencing platform. Individual species within the same genus exhibited reciprocal relationships with COPD and disease severity. Species dominant in health can be taken over by another species within the same genus but with potentially increasing pathogenicity in severe COPD patients.
, an opportunistic pathogen, was significantly increased in frequent exacerbators (fold-change = 4.94, FDR
= 0.005). There were distinct patterns of interaction between bacterial species and host inflammatory mediators according to neutrophilic or eosinophilic inflammations, two major airway inflammatory phenotypes in COPD.
e,
, and
were associated with enhanced Th1, Th17 and pro-inflammatory mediators, while a group of seven species including
were specifically associated with Th2 mediators related to eosinophilia. We developed an automated pipeline to assign strain-level taxonomy leveraging bacterial intra-genomic 16S allele frequency. Using this pipeline we further resolved three non-typeable
strains PittEE, PittGG and 86-028NP with reasonable precision and uncovered strain-level variation related to airway inflammation. In particular, 86-028NP and PittGG strains exhibited inverse associations with Th2 chemokines CCL17 and CCL13, suggesting their abundances may inversely predict eosinophilic inflammation. A systematic comparison of 16S hypervariable regions indicated V1V3 instead of the commonly used V4 region was the best surrogate for airway microbiome. The full-length 16S data augmented the power of functional inference, which slightly better recapitulated the actual metagenomes. This led to the unique identification of butyrate-producing and nitrate reduction pathways as depleted in COPD. Our analysis uncovered finer-scale airway microbial diversity that was previously underappreciated, thus enabled a refined view of the airway microbiome in COPD.
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