Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: March 16, 2024

Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance of Patescibacteria due to low coverage commonly used PCR primers highly divergent bacterial phylum. Therefore, our current understanding global diversity, distribution, ecological role WWTPs very incomplete. This particularly relevant as considered be associated with microbial host cells can therefore influence temporal variability other groups that important WWTP functioning.

Language: Английский

---

Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system

Microbiome, Journal Year: 2023, Volume and Issue: 11(1)

Published: March 22, 2023

Abstract Background Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution complex associations bacterial hosts, genetic biological features of CPR in low-nutrient environments have received increasing attention. However, wastewater treatment systems remain poorly understood. We utilized genome-centric metagenomics to answer how communities shift over 11 years what kind ecological roles they act an activated sludge system. Results found that approximately 9% (135) the 1,526 non-redundant archaeal metagenome-assembled genomes were affiliated CPR. consistently abundant a relative abundance up 7.5% studied The observed striking fluctuations community compositions limited metabolic biosynthetic capabilities collectively revealed nature dynamics may be directly determined by available hosts. Similarity-based network analysis further confirmed broad hosts lineages. proteome contents sludge-associated had higher similarity those environmental-associated than human-associated ones. Comparative genomic significant enrichment genes for oxygen stress resistance bacteria. Furthermore, carbon cycling horizontal gene transfer extensively identified genomes. Conclusions These findings highlight presence specific host interactions among lineages systems. Despite lack key pathways, these small, yet involvements biogeochemical evolution

Language: Английский

---

Adaptive genetic traits in pelagic freshwater microbes

Environmental Microbiology, Journal Year: 2022, Volume and Issue: 25(3), P. 606 - 641

Published: Dec. 14, 2022

Abstract Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans can be broadly categorized in two groups: free‐living, specialized oligotrophs patch‐associated generalists or copiotrophs. In this review, we aim identify genomic traits that enable pelagic freshwater thrive their habitat. To do so, discuss main genetic differences marine are both dominated by difference sediment microbes, where copiotrophs more prevalent. We phylogenomically analysed a collection >7700 metagenome‐assembled genomes, classified habitat preferences on different taxonomic levels, compared metabolic freshwater, marine, microbes. Metabolic mainly associated with transport functions, environmental information processing, components electron chain, osmoregulation isoelectric point proteins. Several lineages known transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) underlying mechanisms process discussed review. Additionally, distribution, ecology make‐up most abundant prokaryotes described details separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, ‘ Ca . Patescibacteria’.

Language: Английский

---

Flexible genomic island conservation across freshwater and marine Methylophilaceae

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to and marine pelagial that resulted in genome reduction (genome-streamlining) the pelagic taxa. However, extent genetic similarities genomic structure microdiversity two genome-streamlined lineages (freshwater “Ca. Methylopumilus” OM43 lineage) has so far never been compared. Here, we analyzed complete genomes 91 strains isolated 14 lakes Central Europe 12 coastal strains. showed a remarkable niche differentiation with clear species-specific differences preference seasonal distribution. On other hand, observed synteny preservation their by having similar locations types flexible islands (fGIs). Three main fGIs were identified: replacement fGI acting as phage defense, an additive harboring metabolic resistance-related functions, tycheposon containing nitrogen-, thiamine-, heme-related functions. differed relative abundances metagenomic datasets suggesting different levels variability ranging strain-specific population-level adaptations. Moreover, variations one gene seemed be responsible for growth at low substrate concentrations potential biogeographic separation within species. Our study provides first insight into closely related taxa family revealed remarkably dynamics involving mobile elements recombination between members.

Language: Английский

---

Heat‐tolerant intertidal rock pool coral Porites lutea can potentially adapt to future warming

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(5)

Published: Jan. 24, 2024

Abstract The growing threat of global warming on coral reefs underscores the urgency identifying heat‐tolerant corals and discovering their adaptation mechanisms to high temperatures. Corals in intertidal rock pools that vary markedly daily temperature may have improved heat tolerance. In this study, stress experiments were performed scleractinian Porites lutea from subtidal habitat pool Weizhou Island northern South China Sea. Thermotolerance differences two habitats explored through phenotype, physiological indicators, ITS2, 16S rRNA, RNA sequencing. At extremely 34°C, P. had a stronger tolerance than those habitat. strong antioxidant capacity host its microbial partners was important resistance at 34°C immune apoptotic regulation, downregulated metabolism disease‐infection‐related pathways compared , habitat, upregulated Cladocopium C15 (Symbiodiniaceae) photosynthetic efficiency photoprotection, significantly increased bacterial diversity probiotics, including ABY1, Ruegeria Alteromonas . These findings indicate can tolerate temperatures integrated response holobionts. be ‘touchstones’ for future warming. Our research provides new insights into complex by which resist theoretical basis reef ecosystem restoration selection stress‐resistant populations.

Language: Английский

---

Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes

mSystems, Journal Year: 2022, Volume and Issue: 7(4)

Published: Aug. 8, 2022

Reconstruction of metagenome-assembled genomes (MAGs) has become a fundamental approach in microbial ecology. However, MAG is hardly complete and overlooks genomic microdiversity because metagenomic assembly fails to resolve microvariants among closely related genotypes. Aiming at understanding the universal factors that drive or constrain prokaryotic genome diversification, we performed an ecosystem-wide high-resolution exploration by combining spatiotemporal (2 depths × 12 months) sampling from pelagic freshwater system, high-quality reconstruction using long- short-read sequences, profiling single nucleotide variants (SNVs) structural (SVs) through mapping short long reads MAGs, respectively. We reconstructed 575 including 29 circular assemblies, providing reference bacterioplankton. Read against these MAGs identified 100 101,781 SNVs/Mb 0 305 insertions, 467 deletions, 41 duplications, 6 inversions for each MAG. Nonsynonymous SNVs were accumulated genes potentially involved cell surface modification evade phage recognition. Most (80.2%) deletions overlapped with gene coding region, defense systems most frequently (>8% genes) deletion. Some such exhibited monthly shift their allele frequency, suggesting rapid turnover genotypes response predation. extremely low either rare opportunistic bloomers, population persistency key diversification. The results concluded diversification driven primarily viral load constrained bottleneck.

Language: Английский

---

Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 9, 2023

form a highly diverse and widespread superphylum of uncultured microorganisms representing third the global microbial diversity. Most our knowledge on

Language: Английский

---

Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: March 27, 2024

Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centers. Despite substantial contribution to bacterial biomass, microbial food webs, and carbon cycle, phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance community composition biweekly across 3 years a temperate, meso-oligotrophic lake. displayed clear trend spring maximum following the bloom phytoplankton secondary autumn. As represent highly diverse assemblage species, followed succession using amplicon sequencing pufM marker gene. To enhance accuracy taxonomic assignment, developed new primers generate longer amplicons compiled currently largest database genes, comprising 3633 reference sequences spanning all phyla known contain species. With this novel resource, demonstrated majority species appeared during specific phases less than 2% detected whole year. presented an indigenous nature characterized high resilience heterogenic adaptations varying conditions environment. Our findings highlight flow ecological dynamics unveil recurrent dynamic community. By integrating information indicator primary production (Chlorophyll-a) existing models, show play pivotal role recycling dissolved organic matter released bloom. We suggest potential within context PEG model consideration further models.

Language: Английский

---

Genome streamlining in Parcubacteria transitioning from soil to groundwater

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: June 20, 2024

Abstract Background To better understand the influence of habitat on genetic content bacteria, with a focus members Candidate Phyla Radiation (CPR) we studied effects transitioning from soil via seepage waters to groundwater genomic composition ultra-small Parcubacteria , dominating CPR class in waters, using genome resolved metagenomics. Results Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 ) were generated and compared directly counterparts. The estimated average sizes major phyla Proteobacteria Bacteroidota Cand . Patescibacteria (Candidate – bacteria) significantly higher soil-seepage water as their Seepage ( Paceibacteria exhibited 1.18-fold greater mean size 2-fold lower proportion pseudogenes than those groundwater. also showed similar trend reduced seepage. While exploring gene loss adaptive gains closely related lineages groundwater, identified membrane protein, lipoglycopeptide resistance unique Parcubacterium genome. A nitrite reductase was genomes, likely acquired other planktonic microbes horizontal transfer. Conclusions Overall, our data suggest that bacteria including have larger metabolic enrichment counterparts, highlighting possible streamlining latter response selection an oligotrophic environment.

Language: Английский

---

Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique

ISME Communications, Journal Year: 2024, Volume and Issue: 4(1)

Published: Jan. 1, 2024

Abstract The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes major portion of the tree life. Extensive efforts have focused on deciphering functional diversity its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing low-volume filtration approach, successfully harvested microbiome resembling original microbial community. We assessed enrichment aqueous bulk for 30 days novel CPR-specific primer rapidly track fraction through attempts. combination soil extract microbial-derived necromass provided most supportive conditions enrichment. Employing these supplemented conditions, proved superior cultivation, resulting up 13-fold compared 1- 2-fold increase cultivation. Amplicon sequencing revealed 10 significantly enriched orders. highest CPRs was observed some unknown members Parcubacteria order, Cand. Jorgensenbacteria, unclassified UBA9983. Furthermore, identified co-enriched putative host taxa, which may guide more targeted isolation approaches subsequent investigations.

Language: Английский

---