Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities DOI
Alexa M. Nicolas, Alexander L. Jaffe, Erin Nuccio

et al.

mSystems, Journal Year: 2021, Volume and Issue: 6(4)

Published: Aug. 17, 2021

Here, we investigated overlooked microbes in soil, candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota (DPANN) archaea, by size fractionating small particles from an approach typically used for the recovery of viral metagenomes. Concentration these cells (<0.2 μm) allowed us to identify organisms as part rare soil biosphere sample genomes that were absent non-size-fractionated

Language: Английский

The microbial dimension of submarine groundwater discharge: current challenges and future directions DOI Creative Commons
Clara Ruiz‐González, Valentí Rodellas, Jordi García-Orellana

et al.

FEMS Microbiology Reviews, Journal Year: 2021, Volume and Issue: 45(5)

Published: Jan. 28, 2021

ABSTRACT Despite the relevance of submarine groundwater discharge (SGD) for ocean biogeochemistry, microbial dimension SGD remains poorly understood. can influence marine communities through supplying chemical compounds and microorganisms, in turn, microbes at land–ocean transition zone determine chemistry reaching ocean. However, compared with inland groundwater, little is known about coastal aquifers. Here, we review state art SGD, emphasis on prokaryotes, identify current challenges future directions. Main include improving diversity description microbiota, characterized by ultrasmall, inactive novel taxa, high ratios sediment-attached versus free-living cells. Studies should explore dynamics their role cycles aquifers, bidirectional dispersal seawater bacterioplankton responses to SGD. This will require not only combining sequencing methods, visualization linking taxonomy activity but also considering entire groundwater–marine continuum. Interactions between traditionally independent disciplines (e.g. hydrogeology, ecology) are needed frame study terrestrial aquatic microorganisms beyond limits presumed habitats, foster our understanding processes biogeochemical cycles.

Language: Английский

Citations

56
Acquisition of the arginine deiminase system benefits epiparasitic Saccharibacteria and their host bacteria in a mammalian niche environment DOI Creative Commons
Jing Tian, Daniel R. Utter, Lujia Cen

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(2)

Published: Jan. 6, 2022

Significance The Candidate Phyla Radiation (CPR) is a large monophyletic lineage with poorly understood biology. Saccharibacteria are ultrasmall parasitic CPR bacteria highly reduced genomes that have made the transition from an environmental origin to mammals. We tested function and impact of arginine deiminase system (ADS), catabolism pathway likely acquired by mammal-associated during their environment-to-mammal niche transition. showed ADS not only helped facilitate Saccharibacterial adaptation mammals but also contributed establishment cooperative episymbiotic interaction bacterial hosts within mammalian microbiomes. Our study provides experimental evidence demonstrating importance in facilitating environment niche.

Language: Английский

Citations

46
Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR DOI Creative Commons
Cecilia Chiriac, Paul‐Adrian Bulzu, Adrian‐Ştefan Andrei

et al.

Microbiome, Journal Year: 2022, Volume and Issue: 10(1)

Published: June 4, 2022

The increased use of metagenomics and single-cell genomics led to the discovery organisms from phyla with no cultivated representatives proposed new microbial lineages such as candidate radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, cell sizes, a general host-associated lifestyle was for radiation. So far, most CPR genomes were obtained groundwaters; however, their diversity, abundance, role in surface freshwaters is largely unexplored. Here, we attempt close these knowledge gaps by deep metagenomic sequencing 119 samples 17 different freshwater lakes located Europe Asia. Moreover, applied Fluorescence situ Hybridization followed Catalyzed Reporter Deposition (CARD-FISH) first visualization distinct samples.A total 174 dereplicated metagenome-assembled (MAGs) diverse recovered investigated lakes, higher prevalence hypolimnion (162 MAGs). They (median size 1 Mbp) generally found low abundances (0.02-14.36 coverage/Gb) estimated slow replication rates. analysis genomic traits CARD-FISH results showed that an eclectic group terms capabilities potential lifestyles, ranging what appear be free-living host- particle-associated groups. Although some complexes electron transport chain present MAGs, together ion-pumping rhodopsins heliorhodopsins, believe they probably adopt fermentative metabolism. Terminal oxidases might function O2 scavenging, while heliorhodopsins could involved mitigation against oxidative stress.A high diversity MAGs recovered, did not seem limited specific trophic states. Their capacities resemble ones described groundwater animal-associated samples, apart Gracilibacteria possesses more complete pathways. Even though this mostly host-associated, also observed clades (ABY1, Paceibacteria, Saccharimonadia) unattached any other associated 'lake snow' particles Gracilibacteria), suggesting broad range life-strategies phylum. Video Abstract.

Language: Английский

Citations

44
Role of Sedum alfredii and soil microbes in the remediation of ultra-high content heavy metals contaminated soil DOI
Zhenjun Tian, Guowen Li, Wenzhong Tang

et al.

Agriculture Ecosystems & Environment, Journal Year: 2022, Volume and Issue: 339, P. 108090 - 108090

Published: July 21, 2022

Language: Английский

Citations

44
Chemolithoautotroph distributions across the subsurface of a convergent margin DOI
Timothy J. Rogers, Joy Buongiorno, Gerdhard L Jessen

et al.

The ISME Journal, Journal Year: 2022, Volume and Issue: 17(1), P. 140 - 150

Published: Oct. 18, 2022

Language: Английский

Citations

40
Carbon fixation pathways across the bacterial and archaeal tree of life DOI Creative Commons
Alessandro N Garritano, Weizhi Song, Torsten Thomas

et al.

PNAS Nexus, Journal Year: 2022, Volume and Issue: 1(5)

Published: Oct. 4, 2022

Carbon fixation is a critical process for our planet; however, its distribution across the bacterial and archaeal domains of life has not been comprehensively studied. Here, we performed an analysis 52,515 metagenome-assembled genomes discover carbon pathways in 1,007 bacteria archaea. We reveal genomic potential through reverse tricarboxylic acid cycle previously unrecognized phyla (i.e. Thermoplasmatota Elusimicrobiota) show that 3-hydroxypropionate bi-cycle not, as thought, restricted to phylum Chloroflexota. The data also substantially expand phylogenetic breadth autotrophy dicarboxylate/4-hydroxybutyrate Calvin-Benson-Bassham cycle. Finally, 3-hydroxypropionate/4-hydroxybutyrate cycle, exclusively found Archaea, was detected Bacteria. thus appears be much more widespread than known, this study lays foundation better understand role archaea global primary production how they contribute microbial sinks.

Language: Английский

Citations

38
A genome catalogue of lake bacterial diversity and its drivers at continental scale DOI
Rebecca E. Garner, Susanne A. Kraemer, Vera E. Onana

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(10), P. 1920 - 1934

Published: July 31, 2023

Language: Английский

Citations

28
Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system DOI Creative Commons
Yulin Wang, Yulin Zhang, Yu Hu

et al.

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

Citations

24
BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis DOI Creative Commons
Zhiguang Qiu,

Li Yuan,

Chun-Ang Lian

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 11, 2024

Abstract Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency tools adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT ( B inning A cross a S eries ssemb l ies T oolkit) and refinement short- long-read sequencing data. employs multiple binners with thresholds to produce initial bins, then utilizes neural networks identify core sequences remove redundant bins refine non-redundant bins. Using same assemblies generated from Critical Assessment Metagenome Interpretation (CAMI) datasets, produces up twice as many MAGs VAMB, DASTool, or metaWRAP. Processing lake sediment dataset, ~30% more than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that can retrieve 47.6% opening-reading frames These results highlight robust handling metagenomic data BASALT.

Language: Английский

Citations

14
Contamination Status of Novel Organophosphate Esters Derived from Organophosphite Antioxidants in Soil and the Effects on Soil Bacterial Communities DOI
Meng Gao, Qiuyue Zhang,

Shanxing Wu

et al.

Environmental Science & Technology, Journal Year: 2024, Volume and Issue: 58(24), P. 10740 - 10751

Published: May 21, 2024

The contamination status of novel organophosphate esters (NOPEs) and their precursors organophosphite antioxidants (OPAs) hydroxylated/diester transformation products (OH-OPEs/di-OPEs) in soils across a large-scale area China were investigated. total concentrations the three test NOPEs soil 82.4–716 ng g–1, which considerably higher than those traditional OPEs (4.50–430 g–1), OPAs (n.d.–30.8 OH-OPEs (n.d.–0.49 di-OPEs (0.57–21.1 g–1). One NOPE compound, i.e., tris(2,4-di-tert-butylphenyl) phosphate (AO168 = O) contributed over 65% studied OPE-associated contaminants. A 30-day incubation experiment was performed to confirm influence AO168 O on bacterial communities. Specific genera belonging Proteobacteria, such as Lysobacter Ensifer, enriched O-contaminated soils. Moreover, ecological function methylotrophy observed be significantly enhanced (t-test, p < 0.01) treated with O, while nitrogen fixation inhibited 0.01). These findings comprehensively revealed contaminants environment provided first evidence effects microbial

Language: Английский

Citations

12