Widespread but Poorly Understood Bacteria: Candidate Phyla Radiation

Microorganisms, Journal Year: 2022, Volume and Issue: 10(11), P. 2232 - 2232

Published: Nov. 11, 2022

Candidate Phyla Radiation (CPR) bacteria is a bacterial division composed mainly of candidate phyla with ultra-small cell sizes, streamlined genomes, and limited metabolic capacity, which are generally considered to survive in parasitic or symbiotic manner. Despite their wide distribution rich diversity, CPR have received little attention until recent years, therefore poorly understood. This review systematically summarizes the history research, parasitic/symbiotic lifestyle, ecological unique features bacteria, hoping provide guidance for future physiological research on bacteria.

Language: Английский

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Single‐amplified genomes reveal most streamlined free‐living marine bacteria

Environmental Microbiology, Journal Year: 2023, Volume and Issue: 25(6), P. 1136 - 1154

Published: Feb. 9, 2023

Evolutionary adaptations of prokaryotes to the environment sometimes result in genome reduction. Our knowledge this phenomenon among free-living bacteria remains scarce. We address dynamics and limits reduction by examining one most abundant ocean, SAR86 clade. Despite its abundance, comparative genomics has been limited absence pure cultures poor representation metagenome-assembled genomes. co-assembled multiple previously available single-amplified genomes obtain first complete from members four families. All families showed a convergent evolutionary trajectory with characteristic features streamlined genomes, pronounced TMED112 family. This family size ca. 1 Mb only bp as median intergenic distance, exceeding values found other microbes such SAR11, OM43 Prochlorococcus. genomic simplification led biosynthesis essential molecules, DNA repair-related genes, ability sense respond environmental factors, which could suggest an dependence on co-occurring for survival (Black Queen hypothesis). Therefore, these reconstructed within clade provide new insights into marine bacteria.

Language: Английский

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Microbial community structure and water quality performance in local scrubber reclaim system for water reclamation of the semiconductor industry: a case study of a semiconductor plant in Beijing.

Environmental Research, Journal Year: 2025, Volume and Issue: unknown, P. 120905 - 120905

Published: Jan. 1, 2025

Language: Английский

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Interstitial microbial communities of coastal sediments are dominated by Nanoarchaeota

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 18, 2025

Microbial communities in subsurface coastal sediments are highly diverse and play an important role nutrient cycling. While the major fraction of microorganisms sandy lives as epipsammon (attached to sand grains), only a small thrives interstitial porewaters. So far, little is known about composition these free-living microbial communities. In beach, investigated this study, we compared archaeal bacterial community structures within corresponding porewaters applying 16S rRNA gene sequencing. We found that prokaryotes had proportion 0.2-2.3% bulk communities, depending on pore space. The showed overlap with attached 4-7% ASVs, comprised unique 75-81% ASVs exclusively They were more than respective sediment-attached much higher archaea-to-bacteria ratio. archaea mainly affiliated Nanoarchaeota DPANN superphylum, relative abundance up 50% included several species related Candidate Phyla Radiation (CPR). Both prokaryotic lineages have cell sizes, comprising not-yet cultured unidentified metabolic functions. Our findings supported by investigation adjacent tidal flat, showing similar trend. Thus, our results indicate presence distinct sediments. This natural enrichment members CPR provides opportunity for targeted metagenomic analyses or even isolating groups further characterization.

Language: Английский

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An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov

Microbial Ecology, Journal Year: 2025, Volume and Issue: 88(1)

Published: March 14, 2025

Abstract The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales Chlamydiae ). Here, we provide detailed comprehensive account on the current knowledge . First, acknowledging up-to-date phylogenetic reconstructions recent nomenclatural proposals, reevaluate their taxonomy, thus re-ranking them as suborder, i.e. Holosporineae , within Rhodospirillales Then, examine diversity presenting 20 described genera many yet undescribed sub-lineages, well variety respective environments provenance which belong several different supergroups. Noteworthy representatives are infectious intranuclear Holospora host manipulator ‘ Caedimonas ’, farmed shrimp pathogen Candidatus Hepatobacter’. Next, put these in context whole by comparing available data least studied representatives, including genome sequences. Accordingly, reason most probable trajectories for interactions, specificity, emergence potential pathogens aquaculture possibly humans, future research directions investigate those open points

Language: Английский

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Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: April 7, 2025

Abstract Background Candidate Phyla Radiation (CPR) represents a unique superphylum characterized by ultra-small cell size and symbiotic lifestyle. Although CPR bacteria have been identified in varied environments, their broader distribution, associations with hosts, ecological roles remain largely unexplored. To address these knowledge gaps, serpentinite-like environment was selected as simplified model system to investigate the communities hyperalkaline environments association hosts extreme conditions. Additionally, enzymatic activity, global evolution of CPR-derived genes encoding essential metabolites (e.g., folate or vitamin B 9 ) were analyzed assessed. Results In highly alkaline ecosystem (pH = 10.9–12.4), metagenomic analyses water sediment samples revealed that constituted 1.93–34.8% microbial communities. Metabolic reconstruction 12 high-quality metagenome-assembled genomes (MAGs) affiliated novel taxa from orders UBA6257, UBA9973, Paceibacterales suggests lack complete biosynthetic pathways for amino acids, lipids, nucleotides. Notably, commonly harbored associated cofactor biosynthesis metabolism, including dihydrofolate reductase ( folA ), serine hydroxymethyltransferase glyA methylenetetrahydrofolate folD ). two presumed auxotrophic incapable forming tetrahydrofolate (THF) due absence , potential some harboring genes. The functionality experimentally verified heterologous expression -deletion mutant Escherichia coli MG1655 Δ . Further assessment available n 4,581) proteins synthesis bioactive derivatives and/or genes) present 90.8% examined. It widespread metabolic complementarity between hosts. Conclusions This finding deepens our understanding mechanisms CPR-host symbiosis, providing insight into cofactor-dependent mutualistic interactions. Our observations suggest may contribute organisms indirectly influence biogeochemical processes.

Language: Английский

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Multi-Metagenome Analysis Unravels Community Collapse After Sampling and Hints the Cultivation Strategy of CPR Bacteria in Groundwater

Microorganisms, Journal Year: 2025, Volume and Issue: 13(5), P. 972 - 972

Published: April 24, 2025

Groundwater harbors phylogenetically diverse Candidate Phyla Radiation (CPR) bacteria, representing an ideal ecosystem for studying this microbial dark matter. However, no CPR strains have been successfully isolated from groundwater, severely limiting further research. This study employed a multi-metagenome approach, integrating time-resolved sampling, antibiotic/nutrient interventions, and correlation networks to unravel ecological roles in groundwater provide insights into their subsequent cultivation. Through 36 metagenomes system containing at least 68 phyla, we revealed the time-sensitive collapse of communities: total abundance plummeted 7.9% 0.15% within 48 h post-sampling, driven by competition with rapidly dividing non-CPR such as members Pseudomonadota. Ampicillin (100 mg/L) stabilized communities suppressing competitors, whereas low-nutrient conditions paradoxically reversed effect. Long-term enrichment (14 months) recovered 63 phyla (0.35% abundance), revealing survival resilience despite nutrient deprivation. Correlation prioritized Actinomyces, novel Acidimicrobiaceae genus, Aestuariivirga, Baekduia Caedimonadaceae potential partners, providing actionable targets co-culture trials. Here, propose recommendations spanning activation status, identification symbiotic optimization culture conditions, which bypass traditional blind cultivation are critical future efforts cultivate bacterial groundwater. Cultivating bacteria will contribute clarifying diversity, roles, evolutionary mechanisms, metabolic pathways, genetic potential.

Language: Английский

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Comparative assessment of novel nematicide trifluenfuronate and fosthiazate on soil ecosystem: from microbial community structure to KEGG functional pathways

Journal of Environmental Sciences, Journal Year: 2025, Volume and Issue: unknown

Published: May 1, 2025

Language: Английский

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Growth of Candidate Phyla Radiation bacteria in groundwater incubations reveals widespread adaptations to oxic conditions

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: May 20, 2025

Background: The Candidate Phyla Radiation (CPR) comprises a widespread but poorly understood group of bacteria with limited cultured representatives, largely due to their metabolic dependencies on microbial hosts. In laboratory incubations, CPR often decline sharply in relative abundance, even when samples originate from natural environments where they dominate, such as groundwater, can represent over 50% the microbiome. Suitable enrichment conditions and host interactions remain defined. Results: Here, we analyzed 16S rRNA gene amplicon data 397 groundwater incubation across 31 treatments, including 22 under oxic conditions, identify factors that promote survival growth. Despite an initial decline, abundances recovered longer times, reaching up 11-30% community. total, detected 1,410 sequence variants (ASVs), spanning six major classes commonly found groundwater. Enrichment success was treatment-specific: Cand.Saccharimonadia dominated incubations polysaccharides (up 31.4%), while Cand. Parcubacteria were enriched (>23%) treatments stimulating methylotrophs autotrophs. ASV-specific growth rates based quantitative PCR showed some doubled within 1-2 days, comparable faster-growing non-CPR bacteria, most had doubling times around 15 days. Strikingly, reached higher absolute than anoxic conditions. Metabolic network analysis metagenome-assembled genomes revealed 62% annotated genes associated functions linked fact, 25 encoded enzymes directly utilize oxygen, challenging long-standing view strictly anaerobic, fermentative organisms. Conclusions: Our findings demonstrate diverse lineages not only survive actively grow discovery for oxygen-dependent reactions substantial reveals unexpected flexibility, helping explain persistence ecological wide range environments.

Language: Английский

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A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics

Environmental Microbiome, Journal Year: 2023, Volume and Issue: 18(1)

Published: Feb. 23, 2023

Abstract Background Lake Baikal, the world’s deepest freshwater lake, contains important numbers of Candidatus Patescibacteria (formerly CPR) in its reaches. However, previously obtained CPR metagenome-assembled genomes recruited very poorly indicating potential other groups being present. Here, we have applied for first time a long-read (PacBio CCS) metagenomic approach to analyze depth Ca. living bathypelagic water column Baikal at 1600 m. Results The retrieval nearly complete 16S rRNA genes before assembly has allowed us detect presence novel and likely endemic group inhabiting Baikal. This seems possess extremely high intra-clade diversity, precluding genomes' assembly. read binning scaffolding indicate that these microbes are similar (i.e. parasites or symbionts), although they seem carry more anabolic pathways, reflecting oligotrophic habitat inhabit. bins not been found anywhere, but one appears small amounts an deep alpine Thun. We propose this be named Baikalibacteria. Conclusion recovery via metagenomics plus use uncover highly diverse “hidden” prokaryotes key strategies move forward ecogenomic microbiology. possesses enormous intraclade diversity akin what happens with interclade level, which is remarkable environment changed little last 25 million years.

Language: Английский

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