Global Ecological Pattern of Ammonia-Oxidizing Archaea

<div><p>Background</p><p>The global distribution of ammonia-oxidizing archaea (AOA), which play a pivotal role in the nitrification process, has been confirmed through numerous ecological studies. Though newly available <i>amoA</i> (ammonia monooxygenase subunit A) gene sequences from new environments are accumulating rapidly in public repositories, a lack of information on the ecological and evolutionary factors shaping community assembly of AOA on the global scale is apparent.</p> <p>Methodology and Results</p><p>We conducted a meta-analysis on uncultured AOA using over ca. 6,200 archaeal <i>amoA</i> gene sequences, so as to reveal their community distribution patterns along a wide spectrum of physicochemical conditions and habitat types. The sequences were dereplicated at 95% identity level resulting in a dataset containing 1,476 archaeal <i>amoA</i> gene sequences from eight habitat types: namely soil, freshwater, freshwater sediment, estuarine sediment, marine water, marine sediment, geothermal system, and symbiosis. The updated comprehensive <i>amoA</i> phylogeny was composed of three major monophyletic clusters (i.e. <i>Nitrosopumilus</i>, <i>Nitrosotalea</i>, <i>Nitrosocaldus</i>) and a non-monophyletic cluster constituted mostly by soil and sediment sequences that we named <i>Nitrososphaera</i>. Diversity measurements indicated that marine and estuarine sediments as well as symbionts might be the largest reservoirs of AOA diversity. Phylogenetic analyses were further carried out using macroevolutionary analyses to explore the diversification pattern and rates of nitrifying archaea. In contrast to other habitats that displayed constant diversification rates, marine planktonic AOA interestingly exhibit a very recent and accelerating diversification rate congruent with the lowest phylogenetic diversity observed in their habitats. This result suggested the existence of AOA communities with different evolutionary history in the different habitats.</p> <p>Conclusion and Significance</p><p>Based on an up-to-date <i>amoA</i> phylogeny, this analysis provided insights into the possible evolutionary mechanisms and environmental parameters that shape AOA community assembly at global scale.</p> </div

Principal coordinate analysis (PCoA) plot for archaeal <i>amoA</i> gene assemblages based on the eight types of habitats deduced from the online Fast UniFrac software (a).

<p>Hierarchical clustering analysis (UPGMA algorithm with 100 replicates Jackknife supporting test) for the all archaeal <i>amoA</i> gene sequences represent of eight types of habitats according to the online Fast UniFrac software. The number of sequence (n), number of libraries (Nlib), phylogenetic diversity with s.d. (PD±s.d.) and phylogenetic species variability (PSV) in each habitat is given. S.d. for PSV index was less than 0.001 for all habitats (b).</p

Diversification rates plotted as lineage through-time (ltt) plots based on ultrametric trees (penalized likelihood method).

<p>Bar plot in the upper left corner indicates the values γ (i.e. rate of cladogenesis) for each habitat.</p

Phylogenetic tree based on archaeal <i>amoA</i> gene sequences from the variable samples on the global level using the maximum likelihood (ML) criterion.

<p>The credible support over 70% for each node was indicated with round circle on the node. The outer color circle around the phylogenetic tree suggested the different habitats.</p

PCoA analyses for archaeal <i>amoA</i> gene assemblages based on the different environmental factors calculated by the online Fast UniFrac software (A, living style; B, oxygen; C, salinity; D, temperature).

<p>PCoA analyses for archaeal <i>amoA</i> gene assemblages based on the different environmental factors calculated by the online Fast UniFrac software (A, living style; B, oxygen; C, salinity; D, temperature).</p

Additional file 2: of Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment

List of PTMs. (XLSX 696 kb

Image_2_Prevalence and molecular characteristics of polymyxin-resistant Enterobacterales in a Chinese tertiary teaching hospital.tif

IntroductionPolymyxin-resistant Enterobacterales poses a significant threat to public health globally, but its prevalence and genomic diversity within a sole hospital is less well known. In this study, the prevalence of polymyxin-resistant Enterobacterales in a Chinese teaching hospital was investigated with deciphering of their genetic determinants of drug resistance.MethodsPolymyxin-resistant Enterobacterales isolates identified by matrix-assisted laser desorption were collected in Ruijin Hospital from May to December in 2021. Both the VITEK 2 Compact and broth dilution methods were used to determine polymyxin B (PMB) susceptibility. Polymyxin-resistant isolates were further characterized by molecular typing using PCR, multi-locus sequence typing, and sequencing of the whole genome.ResultsOf the 1,216 isolates collected, 32 (2.6%) across 12 wards were polymyxin-resistant (minimum inhibitory concentration (MIC) range, PMB 4–256 mg/ml, and colistin 4 ≥ 16 mg/ ml). A total of 28 (87.5%) of the polymyxin-resistant isolates had reduced susceptibility to imipenem and meropenem (MIC ≥ 16 mg/ml). Of the 32 patients, 15 patients received PMB treatment and 20 survived before discharge. The phylogenetic tree of these isolates showed they belonged to different clones and had multiple origins. The polymyxin-resistant Klebsiella pneumoniae isolates belonged to ST-11 (85.72%), ST-15 (10.71%), and ST-65 (3.57%), and the polymyxin-resistant Escherichia coli belonged to four different sequence types, namely, ST-69 (25.00%), ST-38 (25.00%), ST-648 (25.00%), and ST-1193 (25.00%). In addition, six mgrB specific mutations (snp_ALT c.323T>C and amino acid change p.Val8Ala) were identified in 15.6% (5/32) of the isolates. mcr-1, a plasmid-mediated polymyxin-resistant gene, was found in three isolates, and non-synonymous mutations including T157P, A246T, G53V, and I44L were also observed.DiscussionIn our study, a low prevalence of polymyxin-resistant Enterobacterales was observed, but these isolates were also identified as multidrug resistant. Therefore, efficient infection control measures should be implemented to prevent the further spread of resistance to last-line polymyxin therapy.</p

Additional file 1: Table S1. of Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment

Features of the assembled metagenomes and binned draft genomes. Table S2. Conserved single-copy protein-coding genes for the estimation of genome completeness. The numbers of the 139 single copy genes in Nitrospirae bacterium sp. nov were compared with that in closely related genomes. Table S3. Numbers of genes involved in carbohydrate metabolism, nitrogen metabolism, and sulfur metabolism in Nitrospirae bacterium sp. nov and the reference genomes. Figure S1. Work flow of the present study. Three samples were collected decimeters apart: one for the metagenomic sequencing, protein database construction, and genome binning and two for the metaproteomic and PTM analyses. Figure S2. A Venn diagram showing the overlaps between identified proteins (a) and PTMs (b) in the two metaproteomic samples. Figure S3. Alignments of partial F-type-ATPase protein sequences to show the PTM sites. Figure S4. Phylogenetic organization of the Nitrospirae bacterium sp. nov strain and closely related Nitrospirae strains based on 16S rRNA sequences (~1400 bp). Figure S5. Phylogenetic organization of the Nitrospirae bacterium sp. nov strain and Nitrospirae strains based on concatenated single-copy genes. (DOC 1298 kb

Table_1_Prevalence and molecular characteristics of polymyxin-resistant Enterobacterales in a Chinese tertiary teaching hospital.xlsx

IntroductionPolymyxin-resistant Enterobacterales poses a significant threat to public health globally, but its prevalence and genomic diversity within a sole hospital is less well known. In this study, the prevalence of polymyxin-resistant Enterobacterales in a Chinese teaching hospital was investigated with deciphering of their genetic determinants of drug resistance.MethodsPolymyxin-resistant Enterobacterales isolates identified by matrix-assisted laser desorption were collected in Ruijin Hospital from May to December in 2021. Both the VITEK 2 Compact and broth dilution methods were used to determine polymyxin B (PMB) susceptibility. Polymyxin-resistant isolates were further characterized by molecular typing using PCR, multi-locus sequence typing, and sequencing of the whole genome.ResultsOf the 1,216 isolates collected, 32 (2.6%) across 12 wards were polymyxin-resistant (minimum inhibitory concentration (MIC) range, PMB 4–256 mg/ml, and colistin 4 ≥ 16 mg/ ml). A total of 28 (87.5%) of the polymyxin-resistant isolates had reduced susceptibility to imipenem and meropenem (MIC ≥ 16 mg/ml). Of the 32 patients, 15 patients received PMB treatment and 20 survived before discharge. The phylogenetic tree of these isolates showed they belonged to different clones and had multiple origins. The polymyxin-resistant Klebsiella pneumoniae isolates belonged to ST-11 (85.72%), ST-15 (10.71%), and ST-65 (3.57%), and the polymyxin-resistant Escherichia coli belonged to four different sequence types, namely, ST-69 (25.00%), ST-38 (25.00%), ST-648 (25.00%), and ST-1193 (25.00%). In addition, six mgrB specific mutations (snp_ALT c.323T>C and amino acid change p.Val8Ala) were identified in 15.6% (5/32) of the isolates. mcr-1, a plasmid-mediated polymyxin-resistant gene, was found in three isolates, and non-synonymous mutations including T157P, A246T, G53V, and I44L were also observed.DiscussionIn our study, a low prevalence of polymyxin-resistant Enterobacterales was observed, but these isolates were also identified as multidrug resistant. Therefore, efficient infection control measures should be implemented to prevent the further spread of resistance to last-line polymyxin therapy.</p

Image_1_Prevalence and molecular characteristics of polymyxin-resistant Enterobacterales in a Chinese tertiary teaching hospital.jpeg

IntroductionPolymyxin-resistant Enterobacterales poses a significant threat to public health globally, but its prevalence and genomic diversity within a sole hospital is less well known. In this study, the prevalence of polymyxin-resistant Enterobacterales in a Chinese teaching hospital was investigated with deciphering of their genetic determinants of drug resistance.MethodsPolymyxin-resistant Enterobacterales isolates identified by matrix-assisted laser desorption were collected in Ruijin Hospital from May to December in 2021. Both the VITEK 2 Compact and broth dilution methods were used to determine polymyxin B (PMB) susceptibility. Polymyxin-resistant isolates were further characterized by molecular typing using PCR, multi-locus sequence typing, and sequencing of the whole genome.ResultsOf the 1,216 isolates collected, 32 (2.6%) across 12 wards were polymyxin-resistant (minimum inhibitory concentration (MIC) range, PMB 4–256 mg/ml, and colistin 4 ≥ 16 mg/ ml). A total of 28 (87.5%) of the polymyxin-resistant isolates had reduced susceptibility to imipenem and meropenem (MIC ≥ 16 mg/ml). Of the 32 patients, 15 patients received PMB treatment and 20 survived before discharge. The phylogenetic tree of these isolates showed they belonged to different clones and had multiple origins. The polymyxin-resistant Klebsiella pneumoniae isolates belonged to ST-11 (85.72%), ST-15 (10.71%), and ST-65 (3.57%), and the polymyxin-resistant Escherichia coli belonged to four different sequence types, namely, ST-69 (25.00%), ST-38 (25.00%), ST-648 (25.00%), and ST-1193 (25.00%). In addition, six mgrB specific mutations (snp_ALT c.323T>C and amino acid change p.Val8Ala) were identified in 15.6% (5/32) of the isolates. mcr-1, a plasmid-mediated polymyxin-resistant gene, was found in three isolates, and non-synonymous mutations including T157P, A246T, G53V, and I44L were also observed.DiscussionIn our study, a low prevalence of polymyxin-resistant Enterobacterales was observed, but these isolates were also identified as multidrug resistant. Therefore, efficient infection control measures should be implemented to prevent the further spread of resistance to last-line polymyxin therapy.</p