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Efremova J, Mazzella V, Mirasole A, Teixidó N, Núñez-Pons L. Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO 2 vents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170171. [PMID: 38246375 DOI: 10.1016/j.scitotenv.2024.170171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/23/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3-V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.
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Affiliation(s)
- Jana Efremova
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
| | - Valerio Mazzella
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Alice Mirasole
- Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy.
| | - Núria Teixidó
- NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy; Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Ischia Marine Centre, Ischia 80077, Naples, Italy; Laboratoire d'Océanographie de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-mer, France.
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy; NBFC, National Biodiversity Future Center, Piazza Marina 61, 90133 Palermo, Italy.
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Valentin-Alvarado LE, Fakra SC, Probst AJ, Giska JR, Jaffe AL, Oltrogge LM, West-Roberts J, Rowland J, Manga M, Savage DF, Greening C, Baker BJ, Banfield JF. Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism. MICROBIOME 2024; 12:15. [PMID: 38273328 PMCID: PMC10811913 DOI: 10.1186/s40168-023-01704-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 10/18/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling. RESULTS Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix. Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems. CONCLUSIONS Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract.
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Affiliation(s)
- Luis E Valentin-Alvarado
- Graduate Group in Microbiology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Sirine C Fakra
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexander J Probst
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry,, University of Duisburg-Essen, Essen, Essen, Germany
| | - Jonathan R Giska
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- Cleaner Air Oregon Program, Oregon Department of Environmental Quality, Portland, USA
| | - Alexander L Jaffe
- Graduate Group in Microbiology, University of California, Berkeley, CA, USA
| | - Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Jacob West-Roberts
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Joel Rowland
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- Earth and Env. Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Michael Manga
- Earth and Planetary Science, University of California, Berkeley, CA, USA
- University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Brett J Baker
- Department of Integrative Biology, University of Texas, Austin, USA
- Department of Marine Science, University of Texas, Austin, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Marine Science, University of Texas, Austin, USA.
- Energy Geoscience Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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Abstract
Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal microbiomes. Here, we review the literature concerning habitat transitions among a variety of bacterial and archaeal lineages, considering the frequency of migration events, potential environmental barriers, and mechanisms of adaptation to new physicochemical conditions, including the modification of protein inventories and other genomic characteristics. Cells dependent on microbial hosts, particularly bacteria from the Candidate Phyla Radiation, have undergone repeated habitat transitions from environmental sources into animal microbiomes. We compare their trajectories to those of both free-living cells-including the Melainabacteria, Elusimicrobia, and methanogenic archaea-and cellular endosymbionts and bacteriophages, which have made similar transitions. We conclude by highlighting major related topics that may be worthy of future study.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Cindy J Castelle
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
| | - Jillian F Banfield
- Innovative Genomics Institute and Department of Earth and Planetary Science, University of California, Berkeley, California, USA;
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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4
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Riley R, Bowers RM, Camargo AP, Campbell A, Egan R, Eloe-Fadrosh EA, Foster B, Hofmeyr S, Huntemann M, Kellom M, Kimbrel JA, Oliker L, Yelick K, Pett-Ridge J, Salamov A, Varghese NJ, Clum A. Terabase-Scale Coassembly of a Tropical Soil Microbiome. Microbiol Spectr 2023; 11:e0020023. [PMID: 37310219 PMCID: PMC10434106 DOI: 10.1128/spectrum.00200-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023] Open
Abstract
Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes' sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete, <5% contaminated, with predicted 23S, 16S, and 5S rRNA genes and ≥18 tRNAs) metagenome-assembled genomes (MAGs), including two from the candidate phylum Eremiobacterota. Another 268 medium-quality (≥50% complete, <10% contaminated) MAGs were extracted, including the candidate phyla Dependentiae, Dormibacterota, and Methylomirabilota. In total, 307 medium- or higher-quality MAGs were assigned to 23 phyla, compared to 294 MAGs assigned to nine phyla in the same samples individually assembled. The low-quality (<50% complete, <10% contaminated) MAGs from the coassembly revealed a 49% complete rare biosphere microbe from the candidate phylum FCPU426 among other low-abundance microbes, an 81% complete fungal genome from the phylum Ascomycota, and 30 partial eukaryotic MAGs with ≥10% completeness, possibly representing protist lineages. A total of 22,254 viruses, many of them low abundance, were identified. Estimation of metagenome coverage and diversity indicates that we may have characterized ≥87.5% of the sequence diversity in this humid tropical soil and indicates the value of future terabase-scale sequencing and coassembly of complex environments. IMPORTANCE Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is metagenome assembly, the computational reconstruction of genome sequences from microbial communities. "Coassembly" of metagenomic sequence data, in which multiple samples are assembled together, enables more complete detection of microbial genomes in an environment than "multiassembly," in which samples are assembled individually. To demonstrate the potential for coassembling terabases of metagenome data to drive biological discovery, we applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 Tbp of reads from a humid tropical soil environment. The resulting coassembly, its functional annotation, and analysis are presented here. The coassembly yielded more, and phylogenetically more diverse, microbial, eukaryotic, and viral genomes than the multiassembly of the same data. Our resource may facilitate the discovery of novel microbial biology in tropical soils and demonstrates the value of terabase-scale metagenome sequencing.
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Affiliation(s)
- Robert Riley
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Robert M. Bowers
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Antonio Pedro Camargo
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Ashley Campbell
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Rob Egan
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | | | - Brian Foster
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Steven Hofmeyr
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marcel Huntemann
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Matthew Kellom
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Jeffrey A. Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Leonid Oliker
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Katherine Yelick
- Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, California, USA
| | - Asaf Salamov
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Neha J. Varghese
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
| | - Alicia Clum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA
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Maatouk M, Merhej V, Pontarotti P, Ibrahim A, Rolain JM, Bittar F. Metallo-Beta-Lactamase-like Encoding Genes in Candidate Phyla Radiation: Widespread and Highly Divergent Proteins with Potential Multifunctionality. Microorganisms 2023; 11:1933. [PMID: 37630493 PMCID: PMC10459063 DOI: 10.3390/microorganisms11081933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/22/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
The Candidate Phyla Radiation (CPR) was found to harbor a vast repertoire of genes encoding for enzymes with potential antibiotic resistance activity. Among these, as many as 3349 genes were predicted in silico to contain a metallo-beta-lactamase-like (MBL-like) fold. These proteins were subject to an in silico functional characterization by comparing their protein profiles (presence/absence of conserved protein domains) to other MBLs, including 24 already expressed in vitro, along with those of the beta-lactamase database (BLDB) (n = 761). The sequence similarity network (SSN) was then used to predict the functional clusters of CPR MBL-like sequences. Our findings showed that CPR MBL-like sequences were longer and more diverse than bacterial MBL sequences, with a high content of functional domains. Most CPR MBL-like sequences did not show any SSN connectivity with expressed MBLs, indicating the presence of many potential, yet unidentified, functions in CPR. In conclusion, CPR was shown to have many protein functions and a large sequence variability of MBL-like folds, exceeding all known MBLs. Further experimental and evolutionary studies of this superfamily of hydrolyzing enzymes are necessary to illustrate their functional annotation, origin, and expansion for adaptation or specialization within a given niche or compared to a specific substrate.
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Affiliation(s)
- Mohamad Maatouk
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Vicky Merhej
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Pierre Pontarotti
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), 13009 Marseille, France
| | - Ahmad Ibrahim
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
| | - Fadi Bittar
- Microbes, Evolution, Phylogénie et Infection (MEPHI), Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (M.M.); (P.P.); (A.I.); (J.-M.R.)
- Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France
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6
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Santana-Pereira ALR, Moen FS, Severance B, Liles MR. Influence of soil nutrients on the presence and distribution of CPR bacteria in a long-term crop rotation experiment. Front Microbiol 2023; 14:1114548. [PMID: 37577441 PMCID: PMC10413278 DOI: 10.3389/fmicb.2023.1114548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Bacteria affiliated with the Candidate Phyla Radiation (CPR) are a hyper-diverse group of ultra-small bacteria with versatile yet sparse metabolisms. However, most insights into this group come from a surprisingly small number of environments, and recovery of CPR bacteria from soils has been hindered due to their extremely low abundance within complex microbial assemblages. In this study we enriched soil samples from 14 different soil fertility treatments for ultra-small (<0.45 μm) bacteria in order to study rare soil CPR. 42 samples were sequenced, enabling the reconstruction of 27 quality CPR metagenome-assembled genomes (MAGs) further classified as Parcubacteria/Paceibacteria, Saccharibacteria/Saccharimonadia and ABY1, in addition to representative genomes from Gemmatimonadetes, Dependentiae and Chlamydae phyla. These genomes were fully annotated and used to reconstruct the CPR community across all 14 plots. Additionally, for five of these plots, the entire microbiota was reconstructed using 16S amplification, showing that specific soil CPR may form symbiotic relationships with a varied and circumstantial range of hosts. Cullars CPR had a prevalence of enzymes predicted to degrade plant-derived carbohydrates, which suggests they have a role in plant biomass degradation. Parcubacteria appear to be more apt at microfauna necromass degradation. Cullars Saccharibacteria and a Parcubacteria group were shown to carry a possible aerotolerance mechanism coupled with potential for aerobic respiration, which appear to be a unique adaptation to the oxic soil environment. Reconstruction of CPR communities across treatment plots showed that they were not impacted by changes in nutrient levels or microbiota composition, being only impacted by extreme conditions, causing some CPR to dominate the community. These findings corroborate the understanding that soil-dwelling CPR bacteria have a very broad symbiont range and have metabolic capabilities associated to soil environments which allows them to scavenge resources and form resilient communities. The contributions of these microbial dark matter species to soil ecology and plant interactions will be of significant interest in future studies.
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Affiliation(s)
| | | | | | - Mark R. Liles
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
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7
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Maatouk M, Rolain JM, Bittar F. Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation. Microorganisms 2023; 11:1231. [PMID: 37317205 DOI: 10.3390/microorganisms11051231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial ecology is a critical field for understanding the composition, diversity, and functions of microorganisms in various environmental and health-related processes. The discovery of Candidate Phyla Radiation (CPR) through culture-independent methods has introduced a new division of microbes characterized by a symbiotic/parasitic lifestyle, small cell size, and small genome. Despite being poorly understood, CPRs have garnered significant attention in recent years due to their widespread detection in a variety of environmental and clinical samples. These microorganisms have been found to exhibit a high degree of genetic diversity compared to other microbes. Several studies have shed light on their potential importance in global biogeochemical cycles and their impact on various human activities. In this review, we provide a systematic overview of the discovery of CPRs. We then focus on describing how the genomic characteristics of CPRs have helped them interact with and adapt to other microbes in different ecological niches. Future works should focus on discovering the metabolic capacities of CPRs and, if possible, isolating them to obtain a better understanding of these microorganisms.
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Affiliation(s)
- Mohamad Maatouk
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Fadi Bittar
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
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8
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Oren A, Göker M. Candidatus List. Lists of names of prokaryotic Candidatus phyla. Int J Syst Evol Microbiol 2023; 73. [PMID: 37159402 DOI: 10.1099/ijsem.0.005821] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
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9
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Smith WPJ, Wucher BR, Nadell CD, Foster KR. Bacterial defences: mechanisms, evolution and antimicrobial resistance. Nat Rev Microbiol 2023:10.1038/s41579-023-00877-3. [PMID: 37095190 DOI: 10.1038/s41579-023-00877-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 04/26/2023]
Abstract
Throughout their evolutionary history, bacteria have faced diverse threats from other microorganisms, including competing bacteria, bacteriophages and predators. In response to these threats, they have evolved sophisticated defence mechanisms that today also protect bacteria against antibiotics and other therapies. In this Review, we explore the protective strategies of bacteria, including the mechanisms, evolution and clinical implications of these ancient defences. We also review the countermeasures that attackers have evolved to overcome bacterial defences. We argue that understanding how bacteria defend themselves in nature is important for the development of new therapies and for minimizing resistance evolution.
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Affiliation(s)
- William P J Smith
- Division of Genomics, Infection and Evolution, University of Manchester, Manchester, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Benjamin R Wucher
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Carey D Nadell
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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10
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Pellegrinetti TA, Cotta SR, Sarmento H, Costa JS, Delbaje E, Montes CR, Camargo PB, Barbiero L, Rezende-Filho AT, Fiore MF. Bacterial Communities Along Environmental Gradients in Tropical Soda Lakes. MICROBIAL ECOLOGY 2023; 85:892-903. [PMID: 35916937 DOI: 10.1007/s00248-022-02086-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 07/25/2022] [Indexed: 05/04/2023]
Abstract
Soda lake environments are known to be variable and can have distinct differences according to geographical location. In this study, we investigated the effects of different environmental conditions of six adjacent soda lakes in the Pantanal biome (Mato Grosso do Sul state, Brazil) on bacterial communities and their functioning using a metagenomic approach combined with flow cytometry and chemical analyses. Ordination analysis using flow cytometry and water chemistry data from two sampling periods (wet and dry) clustered soda lakes into three different profiles: eutrophic turbid (ET), oligotrophic turbid (OT), and clear vegetated oligotrophic (CVO). Analysis of bacterial community composition and functioning corroborated this ordination; the exception was one ET lake, which was similar to one OT lake during the wet season, indicating drastic shifts between seasons. Microbial abundance and diversity increased during the dry period, along with a considerable number of limnological variables, all indicative of a strong effect of the precipitation-evaporation balance in these systems. Cyanobacteria were associated with high electric conductivity, pH, and nutrient availability, whereas Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were correlated with landscape morphology variability (surface water, surface perimeter, and lake volume) and with lower salinity and pH levels. Stress response metabolism was enhanced in OT and ET lakes and underrepresented in CVO lakes. The microbiome dataset of this study can serve as a baseline for restoring impacted soda lakes. Altogether, the results of this study demonstrate the sensitivity of tropical soda lakes to climate change, as slight changes in hydrological regimes might produce drastic shifts in community diversity.
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Affiliation(s)
- Thierry A Pellegrinetti
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Simone R Cotta
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Hugo Sarmento
- Department of Hydrobiology, Federal University of São Carlos (UFSCar), São Carlos, São Paulo, 13565-905, Brazil
| | - Juliana S Costa
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Endrews Delbaje
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Celia R Montes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Plinio B Camargo
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil
| | - Laurent Barbiero
- The Observatory Midi-Pyrénées, Geoscience Environment Toulouse, Research Institute for Development, The National Center for Research Scientific, Paul Sabatier University, 31400, Toulouse, France
| | - Ary T Rezende-Filho
- Faculty of Engineering, Architecture and Urbanism and Geography, Federal University of Mato Grosso do Sul, Mato Grosso do Sul, Campo Grande, 79070-900, Brazil
| | - Marli F Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba, São Paulo, 13416-000, Brazil.
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11
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Wang Y, Zhang Y, Hu Y, Liu L, Liu SJ, Zhang T. Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system. MICROBIOME 2023; 11:56. [PMID: 36945052 PMCID: PMC10031880 DOI: 10.1186/s40168-023-01494-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/14/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution and complex associations with bacterial hosts, genetic and biological features of CPR bacteria in low-nutrient environments have received increasing attention. However, CPR bacteria in wastewater treatment systems remain poorly understood. We utilized genome-centric metagenomics to answer how CPR communities shift over 11 years and what kind of ecological roles they act in an activated sludge system. RESULTS We found that approximately 9% (135) of the 1,526 non-redundant bacterial and archaeal metagenome-assembled genomes were affiliated with CPR. CPR bacteria were consistently abundant with a relative abundance of up to 7.5% in the studied activated sludge system. The observed striking fluctuations in CPR community compositions and the limited metabolic and biosynthetic capabilities in CPR bacteria collectively revealed the nature that CPR dynamics may be directly determined by the available hosts. Similarity-based network analysis further confirmed the broad bacterial hosts of CPR lineages. The proteome contents of activated sludge-associated CPR had a higher similarity to those of environmental-associated CPR than to those of human-associated ones. Comparative genomic analysis observed significant enrichment of genes for oxygen stress resistance in activated sludge-associated CPR bacteria. Furthermore, genes for carbon cycling and horizontal gene transfer were extensively identified in activated sludge-associated CPR genomes. CONCLUSIONS These findings highlight the presence of specific host interactions among CPR lineages in activated sludge systems. Despite the lack of key metabolic pathways, these small, yet abundant bacteria may have significant involvements in biogeochemical cycling and bacterial evolution in activated sludge systems. Video Abstract.
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Affiliation(s)
- Yulin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000 People’s Republic of China
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong, People’s Republic of China
| | - Yulin Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong, People’s Republic of China
| | - Yu Hu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000 People’s Republic of China
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong, People’s Republic of China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000 People’s Republic of China
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong, People’s Republic of China
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12
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Chiriac MC, Haber M, Salcher MM. Adaptive genetic traits in pelagic freshwater microbes. Environ Microbiol 2023; 25:606-641. [PMID: 36513610 DOI: 10.1111/1462-2920.16313] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.
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Affiliation(s)
| | - Markus Haber
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, Ceske Budejovice, Czechia
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13
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Barbosa FAS, Brait LAS, Coutinho FH, Ferreira CM, Moreira EF, de Queiroz Salles L, Meirelles PM. Ecological landscape explains aquifers microbial structure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160822. [PMID: 36526191 DOI: 10.1016/j.scitotenv.2022.160822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Aquifers have significant social, economic, and ecological importance. They supply 30 % of the freshwater for human consumption worldwide, including agricultural and industrial use. Despite aquifers' importance, the relationships between aquifer categories and their inhabiting microbial communities are still unknown. Characterizing variations within microbial communities' function and taxonomy structure at different aquifers could give a panoramic view of patterns that may enable the detection and prediction of environmental impact caused by multiple sources. Using publicly available shotgun metagenomic datasets, we examined whether soil properties, land use, and climate variables would have a more significant influence on the taxonomy and functional structure of the microbial communities than the ecological landscapes of the aquifer (i.e., Karst, Porous, Saline, Geyser, and Porous Contaminated). We found that these categories are stronger predictors of microbial communities' structure than geographical localization. In addition, our results show that microbial richness and dominance patterns are the opposite of those found in multicellular life, where extreme habitats harbour richer functional and taxonomic microbial communities. We found that low-abundant and recently described candidate taxa, such as the chemolithoautotrophic genus Candidatus Altiarcheum and the Candidate phylum Parcubacteria, are the main contributors to aquifer microbial communities' dissimilarities. Genes related to gram-negative bacteria proteins, cell wall structures, and phage activity were the primary contributors to aquifer microbial communities' dissimilarities among the aquifers' ecological landscapes. The results reported in the present study highlight the utility of using ecological landscapes for investigating aquifer microbial communities. In addition, we suggest that functions played by recently described and low abundant bacterial groups need further investigation once they might affect water quality, geochemical cycles, and the effects of anthropogenic disturbances such as pollution and climatic events on aquifers.
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Affiliation(s)
| | | | - Felipe Hernandes Coutinho
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Camilo M Ferreira
- Institute of Biology, Federal University of Bahia, Salvador, Brazil; National Institute of Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (IN-TREE), Brazil
| | | | | | - Pedro Milet Meirelles
- Institute of Biology, Federal University of Bahia, Salvador, Brazil; National Institute of Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (IN-TREE), Brazil.
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14
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Gios E, Mosley OE, Weaver L, Close M, Daughney C, Handley KM. Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles. ISME COMMUNICATIONS 2023; 3:13. [PMID: 36808147 PMCID: PMC9938205 DOI: 10.1038/s43705-023-00223-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 06/16/2023]
Abstract
Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.
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Affiliation(s)
- Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- NINA, Norwegian Institute for Nature Research, Trondheim, Norway
| | - Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- NatureMetrics Ltd, Surrey Research Park, Guildford, UK
| | - Louise Weaver
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Murray Close
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Chris Daughney
- GNS Science, Lower Hutt, New Zealand
- NIWA, National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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15
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Jaffe AL, Bardot C, Le Jeune AH, Liu J, Colombet J, Perrière F, Billard H, Castelle CJ, Lehours AC, Banfield JF. Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified Lac Pavin. MICROBIOME 2023; 11:14. [PMID: 36694212 PMCID: PMC9875498 DOI: 10.1186/s40168-022-01416-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Permanently stratified lakes contain diverse microbial communities that vary with depth and so serve as useful models for studying the relationships between microbial community structure and geochemistry. Recent work has shown that these lakes can also harbor numerous bacteria and archaea from novel lineages, including those from the Candidate Phyla Radiation (CPR). However, the extent to which geochemical stratification differentially impacts carbon metabolism and overall genetic potential in CPR bacteria compared to other organisms is not well defined. RESULTS Here, we determine the distribution of microbial lineages along an oxygen gradient in Lac Pavin, a deep, stratified lake in central France, and examine the influence of this gradient on their metabolism. Genome-based analyses revealed an enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and anoxic zone/sediments, suggesting that oxygen likely plays a role in structuring metabolic strategies in non-CPR bacteria and archaea. Notably, we find that the oxidation of methane and its byproducts is largely spatially separated from methane production, which is mediated by diverse communities of sediment methanogens that vary on the centimeter scale. In contrast, we detected evidence for RuBisCO throughout the water column and sediments, including form II/III and form III-related enzymes encoded by CPR bacteria in the water column and DPANN archaea in the sediments. On the whole, though, CPR bacteria and phages did not show strong signals of gene content differentiation by depth, despite the fact that distinct species groups populate different lake and sediment compartments. CONCLUSIONS Overall, our analyses suggest that environmental gradients in Lac Pavin select for capacities of CPR bacteria and phages to a lesser extent than for other bacteria and archaea. This may be due to the fact that selection in the former groups is indirect and depends primarily on host characteristics. Video Abstract.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Corinne Bardot
- Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Clermont-Auvergne, F-63000, Clermont-Ferrand, France
| | - Anne-Hélène Le Jeune
- Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Clermont-Auvergne, F-63000, Clermont-Ferrand, France
| | - Jett Liu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jonathan Colombet
- Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Clermont-Auvergne, F-63000, Clermont-Ferrand, France
| | - Fanny Perrière
- Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Clermont-Auvergne, F-63000, Clermont-Ferrand, France
| | - Hermine Billard
- Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Clermont-Auvergne, F-63000, Clermont-Ferrand, France
| | - Cindy J Castelle
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Anne-Catherine Lehours
- Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Clermont-Auvergne, F-63000, Clermont-Ferrand, France
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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16
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Vigneron A, Cruaud P, Guyoneaud R, Goñi-Urriza M. Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations. Front Microbiol 2023; 13:1073483. [PMID: 36699594 PMCID: PMC9868632 DOI: 10.3389/fmicb.2022.1073483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023] Open
Abstract
Patescibacteria form a highly diverse and widespread superphylum of uncultured microorganisms representing a third of the global microbial diversity. Most of our knowledge on Patescibacteria putative physiology relies on metagenomic mining and metagenome-assembled genomes, but the in situ activities and the ecophysiology of these microorganisms have been rarely explored, leaving the role of Patescibacteria in ecosystems elusive. Using a genome-centric metatranscriptomic approach, we analyzed the diel and seasonal gene transcription profiles of 18 Patescibacteria populations in brackish microbial mats to test whether our understanding of Patescibacteria metabolism allows the extrapolation of their in situ activities. Although our results revealed a circadian cycle in Patescibacteria activities, a strong streamlined genetic expression characterized the Patescibacteria populations. This result has a major consequence for the extrapolation of their physiology and environmental function since most transcribed genes were uncharacterized, indicating that the ecophysiology of Patescibacteria cannot be yet reliably predicted from genomic data.
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Affiliation(s)
- Adrien Vigneron
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Rémy Guyoneaud
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Marisol Goñi-Urriza
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
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17
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Occurrence, Diversity, and Genomes of " Candidatus Patescibacteria" along the Early Diagenesis of Marine Sediments. Appl Environ Microbiol 2022; 88:e0140922. [PMID: 36468881 PMCID: PMC9765117 DOI: 10.1128/aem.01409-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
The phylum "Candidatus Patescibacteria" (or Candidate Phyla Radiation [CPR]) accounts for roughly one-quarter of microbial diversity on Earth, but the presence and diversity of these bacteria in marine sediments have been rarely charted. Here, we investigate the abundance, diversity, and metabolic capacities of CPR bacteria in three sediment sites (Mohns Ridge, North Pond, and Costa Rica Margin) with samples covering a wide range of redox zones formed during the early diagenesis of organic matter. Through metagenome sequencing, we found that all investigated sediment horizons contain "Ca. Patescibacteria" (0.4 to 28% of the total communities), which are affiliated with the classes "Ca. Paceibacteria," "Ca. Gracilibacteria," "Ca. Microgenomatia," "Ca. Saccharimonadia," "Ca. ABY1," and "Ca. WWE3." However, only a subset of the diversity of marine sediment "Ca. Patescibacteria," especially the classes "Ca. Paceibacteria" and "Ca. Gracilibacteria," can be captured by 16S rRNA gene amplicon sequencing with commonly used universal primers. We recovered 11 metagenome-assembled genomes (MAGs) of CPR from these sediments, most of which are novel at the family or genus level in the "Ca. Paceibacteria" class and are missed by the amplicon sequencing. While individual MAGs are confined to specific anoxic niches, the lack of capacities to utilize the prevailing terminal electron acceptors indicates that they may not be directly selected by the local redox conditions. These CPR bacteria lack essential biosynthesis pathways and may use a truncated glycolysis pathway to conserve energy as fermentative organotrophs. Our findings suggest that marine sediments harbor some novel yet widespread CPR bacteria during the early diagenesis of organic matter, which needs to be considered in population dynamics assessments in this vast environment. IMPORTANCE Ultrasmall-celled "Ca. Patescibacteria" have been estimated to account for one-quarter of the total microbial diversity on Earth, the parasitic lifestyle of which may exert a profound control on the overall microbial population size of the local ecosystems. However, their diversity and metabolic functions in marine sediments, one of the largest yet understudied ecosystems on Earth, remain virtually uncharacterized. By applying cultivation-independent approaches to a range of sediment redox zones, we reveal that "Ca. Patescibacteria" members are rare but widespread regardless of the prevailing geochemical conditions. These bacteria are affiliated with novel branches of "Ca. Patescibacteria" and have been largely missed in marker gene-based surveys. They do not have respiration capacity but may conserve energy by fermenting organic compounds from their episymbiotic hosts. Our findings suggest that these novel "Ca. Patescibacteria" are among the previously overlooked microbes in diverse marine sediments.
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18
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Ji Y, Zhang P, Zhou S, Gao P, Wang B, Jiang J. Widespread but Poorly Understood Bacteria: Candidate Phyla Radiation. Microorganisms 2022; 10:2232. [PMID: 36422302 PMCID: PMC9698310 DOI: 10.3390/microorganisms10112232] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 08/15/2023] Open
Abstract
Candidate Phyla Radiation (CPR) bacteria is a bacterial division composed mainly of candidate phyla bacteria with ultra-small cell sizes, streamlined genomes, and limited metabolic capacity, which are generally considered to survive in a parasitic or symbiotic manner. Despite their wide distribution and rich diversity, CPR bacteria have received little attention until recent years, and are therefore poorly understood. This review systematically summarizes the history of CPR research, the parasitic/symbiotic lifestyle, and the ecological distribution and unique metabolic features of CPR bacteria, hoping to provide guidance for future ecological and physiological research on CPR bacteria.
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Affiliation(s)
| | | | | | | | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
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19
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Marghoob MU, Rodriguez-Sanchez A, Imran A, Mubeen F, Hoagland L. Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan. Front Microbiol 2022; 13:1020175. [PMID: 36419426 PMCID: PMC9676371 DOI: 10.3389/fmicb.2022.1020175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/10/2022] [Indexed: 08/27/2023] Open
Abstract
Soil salinization and heavy metal (HM) contamination are major challenges facing agricultural systems worldwide. Determining how soil microbial communities respond to these stress factors and identifying individual phylotypes with potential to tolerate these conditions while promoting plant growth could help prevent negative impacts on crop productivity. This study used amplicon sequencing and several bioinformatic programs to characterize differences in the composition and potential functional capabilities of soil bacterial, fungal, and archaeal communities in five agricultural fields that varied in salinity and HM concentrations within the Indus basin region of Pakistan. The composition of bacteria with the potential to fix atmospheric nitrogen (N) and produce the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase were also determined. Microbial communities were dominated by: Euryarchaeota (archaea), Actinobacteria, Proteobacteria, Planctomycetota, Firimicutes, Patescibacteria and Acidobacteria (bacteria), and Ascomycota (fungi), and all soils contained phylotypes capable of N-fixation and ACC-deaminase production. Salinity influenced bacterial, but not archaeal or fungal communities. Both salinity and HM altered the relative abundance of many phylotypes that could potentially promote or harm plant growth. These stress factors also appeared to influence the potential functional capabilities of the microbial communities, especially in their capacity to cycle phosphorous, produce siderophores, and act as symbiotrophs or pathotrophs. Results of this study confirm that farms in this region are at risk due to salinization and excessive levels of some toxic heavy metals, which could negatively impact crop and human health. Changes in soil microbial communities and their potential functional capabilities are also likely to affect several critical agroecosystem services related to nutrient cycling, pathogen suppression, and plant stress tolerance. Many potentially beneficial phylotypes were identified that appear to be salt and HM tolerant and could possibly be exploited to promote these services within this agroecosystem. Future efforts to isolate these phylotypes and determine whether they can indeed promote plant growth and/or carry out other important soil processes are recommended. At the same time, identifying ways to promote the abundance of these unique phylotypes either through modifying soil and crop management practices, or developing and applying them as inoculants, would be helpful for improving crop productivity in this region.
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Affiliation(s)
- Muhammad Usama Marghoob
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | | | - Asma Imran
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Fathia Mubeen
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Constituent College of Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Lori Hoagland
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
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20
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Galal A, Abou Elhassan S, Saleh AH, Ahmed AI, Abdelrahman MM, Kamal MM, Khalel RS, Ziko L. A survey of the biosynthetic potential and specialized metabolites of Archaea and understudied Bacteria. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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21
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Mosley OE, Gios E, Close M, Weaver L, Daughney C, Handley KM. Nitrogen cycling and microbial cooperation in the terrestrial subsurface. THE ISME JOURNAL 2022; 16:2561-2573. [PMID: 35941171 PMCID: PMC9562985 DOI: 10.1038/s41396-022-01300-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022]
Abstract
The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding N2O reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.
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22
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Tsurumaki M, Saito M, Tomita M, Kanai A. Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis. RNA (NEW YORK, N.Y.) 2022; 28:1041-1057. [PMID: 35688647 PMCID: PMC9297842 DOI: 10.1261/rna.079103.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/06/2022] [Indexed: 06/01/2023]
Abstract
The candidate phyla radiation (CPR) is a large bacterial group consisting mainly of uncultured lineages. They have small cells and small genomes, and they often lack ribosomal proteins uL1, bL9, and/or uL30, which are basically ubiquitous in non-CPR bacteria. Here, we comprehensively analyzed the genomic information on CPR bacteria and identified their unique properties. The distribution of protein lengths in CPR bacteria peaks at around 100-150 amino acids, whereas the position of the peak varies in the range of 100-300 amino acids in free-living non-CPR bacteria, and at around 100-200 amino acids in most symbiotic non-CPR bacteria. These results show that the proteins of CPR bacteria are smaller, on average, than those of free-living non-CPR bacteria, like those of symbiotic non-CPR bacteria. We found that ribosomal proteins bL28, uL29, bL32, and bL33 have been lost in CPR bacteria in a taxonomic lineage-specific manner. Moreover, the sequences of approximately half of all ribosomal proteins of CPR differ, in part, from those of non-CPR bacteria, with missing regions or specifically added regions. We also found that several regions in the 16S, 23S, and 5S rRNAs of CPR bacteria are lacking, which presumably caused the total predicted lengths of the three rRNAs of CPR bacteria to be smaller than those of non-CPR bacteria. The regions missing in the CPR ribosomal proteins and rRNAs are located near the surface of the ribosome, and some are close to one another. These observations suggest that ribosomes are smaller in CPR bacteria than those in free-living non-CPR bacteria, with simplified surface structures.
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Affiliation(s)
- Megumi Tsurumaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Motofumi Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan
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Fujii N, Kuroda K, Narihiro T, Aoi Y, Ozaki N, Ohashi A, Kindaichi T. Metabolic Potential of the Superphylum Patescibacteria Reconstructed from Activated Sludge Samples from a Municipal Wastewater Treatment Plant. Microbes Environ 2022; 37. [PMID: 35768268 PMCID: PMC9530719 DOI: 10.1264/jsme2.me22012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Patescibacteria are widely distributed in various environments and often detected in activated sludge. However, limited information is currently available on their phylogeny, morphology, and ecophysiological role in activated sludge or interactions with other microorganisms. In the present study, we identified microorganisms that interacted with Patescibacteria in activated sludge via a correlation ana-lysis using the 16S rRNA gene, and predicted the metabolic potential of Patescibacteria using a metagenomic ana-lysis. The metagenome-assembled genomes of Patescibacteria consisted of three Saccharimonadia, three Parcubacteria, and one Gracilibacteria, and showed a strong positive correlation of relative abundance with Chitinophagales. Metabolic predictions from ten recovered patescibacterial and five Chitinophagales metagenome-assembled genomes supported mutualistic interactions between a member of Saccharimonadia and Chitinophagales via N-acetylglucosamine, between a member of Parcubacteria and Chitinophagales via nitrogen compounds related to denitrification, and between Gracilibacteria and Chitinophagales via phospholipids in activated sludge. The present results indicate that various interactions between Patescibacteria and Chitinophagales are important for the survival of Patescibacteria in activated sludge ecosystems.
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Affiliation(s)
- Naoki Fujii
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yoshiteru Aoi
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University
| | - Noriatsu Ozaki
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Akiyoshi Ohashi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
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Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease. Clin Microbiol Rev 2022; 35:e0014021. [PMID: 35658516 DOI: 10.1128/cmr.00140-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as "ultramicrobacteria" with a cell volume under 0.1 μm3 and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.
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Chiriac MC, Bulzu PA, Andrei AS, Okazaki Y, Nakano SI, Haber M, Kavagutti VS, Layoun P, Ghai R, Salcher MM. Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR. MICROBIOME 2022; 10:84. [PMID: 35659305 PMCID: PMC9166423 DOI: 10.1186/s40168-022-01274-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, and cell sizes, and a general host-associated lifestyle was proposed for the radiation. So far, most CPR genomes were obtained from groundwaters; however, their diversity, abundance, and role in surface freshwaters is largely unexplored. Here, we attempt to close these knowledge gaps by deep metagenomic sequencing of 119 samples of 17 different freshwater lakes located in Europe and Asia. Moreover, we applied Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) for a first visualization of distinct CPR lineages in freshwater samples. RESULTS A total of 174 dereplicated metagenome-assembled genomes (MAGs) of diverse CPR lineages were recovered from the investigated lakes, with a higher prevalence from hypolimnion samples (162 MAGs). They have reduced genomes (median size 1 Mbp) and were generally found in low abundances (0.02-14.36 coverage/Gb) and with estimated slow replication rates. The analysis of genomic traits and CARD-FISH results showed that the radiation is an eclectic group in terms of metabolic capabilities and potential lifestyles, ranging from what appear to be free-living lineages to host- or particle-associated groups. Although some complexes of the electron transport chain were present in the CPR MAGs, together with ion-pumping rhodopsins and heliorhodopsins, we believe that they most probably adopt a fermentative metabolism. Terminal oxidases might function in O2 scavenging, while heliorhodopsins could be involved in mitigation against oxidative stress. CONCLUSIONS A high diversity of CPR MAGs was recovered, and distinct CPR lineages did not seem to be limited to lakes with specific trophic states. Their reduced metabolic capacities resemble the ones described for genomes in groundwater and animal-associated samples, apart from Gracilibacteria that possesses more complete metabolic pathways. Even though this radiation is mostly host-associated, we also observed organisms from different clades (ABY1, Paceibacteria, Saccharimonadia) that appear to be unattached to any other organisms or were associated with 'lake snow' particles (ABY1, Gracilibacteria), suggesting a broad range of potential life-strategies in this phylum. Video Abstract.
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Affiliation(s)
- Maria-Cecilia Chiriac
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Adrian-Stefan Andrei
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Yusuke Okazaki
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Shin-ichi Nakano
- Center of Ecological Research, Kyoto University, 2-509-3 Hirano, Otsu, Shiga Japan
| | - Markus Haber
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Vinicius Silva Kavagutti
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, Czech Republic
| | - Paul Layoun
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, Czech Republic
| | - Rohit Ghai
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Michaela M. Salcher
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
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Bell E, Lamminmäki T, Alneberg J, Qian C, Xiong W, Hettich RL, Frutschi M, Bernier-Latmani R. Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface. THE ISME JOURNAL 2022; 16:1583-1593. [PMID: 35173296 PMCID: PMC9123182 DOI: 10.1038/s41396-022-01207-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/19/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Microbial life is widespread in the terrestrial subsurface and present down to several kilometers depth, but the energy sources that fuel metabolism in deep oligotrophic and anoxic environments remain unclear. In the deep crystalline bedrock of the Fennoscandian Shield at Olkiluoto, Finland, opposing gradients of abiotic methane and ancient seawater-derived sulfate create a terrestrial sulfate-methane transition zone (SMTZ). We used chemical and isotopic data coupled to genome-resolved metaproteogenomics to demonstrate active life and, for the first time, provide direct evidence of active anaerobic oxidation of methane (AOM) in a deep terrestrial bedrock. Proteins from Methanoperedens (formerly ANME-2d) are readily identifiable despite the low abundance (≤1%) of this genus and confirm the occurrence of AOM. This finding is supported by 13C-depleted dissolved inorganic carbon. Proteins from Desulfocapsaceae and Desulfurivibrionaceae, in addition to 34S-enriched sulfate, suggest that these organisms use inorganic sulfur compounds as both electron donor and acceptor. Zerovalent sulfur in the groundwater may derive from abiotic rock interactions, or from a non-obligate syntrophy with Methanoperedens, potentially linking methane and sulfur cycles in Olkiluoto groundwater. Finally, putative episymbionts from the candidate phyla radiation (CPR) and DPANN archaea represented a significant diversity in the groundwater (26/84 genomes) with roles in sulfur and carbon cycling. Our results highlight AOM and sulfur disproportionation as active metabolisms and show that methane and sulfur fuel microbial activity in the deep terrestrial subsurface.
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Affiliation(s)
- Emma Bell
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland.
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
| | | | - Johannes Alneberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, SE-17121, Sweden
| | - Chen Qian
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Weili Xiong
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Manon Frutschi
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland.
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27
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Potential for Natural Attenuation of Domestic and Agricultural Pollution in Karst Groundwater Environments. WATER 2022. [DOI: 10.3390/w14101597] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In karst areas, anthropogenic contaminants reach the subsurface with detrimental effects on the groundwater ecosystem and downstream springs, which often serve as drinking water sources for the local human communities. We analyzed the water chemistry and microbial community composition in upstream and downstream locations of five hydrokarst systems (HKS) during four seasons. Conductivity and nitrates were higher in the downstream springs than in the pre-karst waters, whereas the concentration of organic matter, considered here as a pollution indicator, was lower. The microbial community composition varied largely between upstream and downstream locations, with multiple species of potentially pathogenic bacteria decreasing in the HKS. Bacteria indicative of pollution decreased as well when passing through the HKS, but potential biodegraders increased. This suggests that the HKS can filter out part of the polluting organic matter and, with it, part of the associated microorganisms. Nevertheless, the water quality, including the presence of pathogens in downstream springs, must be further monitored to control whether the water is appropriate for consumption. In parallel, the human populations located upstream must be advised of the risks resulting from their daily activities, improper stocking of their various wastes and dumping of their refuse in surface streams.
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28
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New Beta-lactamases in Candidate Phyla Radiation: Owning Pleiotropic Enzymes Is a Smart Paradigm for Microorganisms with a Reduced Genome. Int J Mol Sci 2022; 23:ijms23105446. [PMID: 35628255 PMCID: PMC9145738 DOI: 10.3390/ijms23105446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 01/08/2023] Open
Abstract
The increased exploitation of microbial sequencing methods has shed light on the high diversity of new microorganisms named Candidate Phyla Radiation (CPR). CPR are mainly detected via 16S rRNA/metabarcoding analyses or metagenomics and are found to be abundant in all environments and present in different human microbiomes. These microbes, characterized by their symbiotic/epiparasitic lifestyle with bacteria, are directly exposed to competition with other microorganisms sharing the same ecological niche. Recently, a rich repertoire of enzymes with antibiotic resistance activity has been found in CPR genomes by using an in silico adapted screening strategy. This reservoir has shown a high prevalence of putative beta-lactamase-encoding genes. We expressed and purified five putative beta-lactamase sequences having the essential domains and functional motifs from class A and class B beta-lactamase. Their enzymatic activities were tested against various beta-lactam substrates using liquid chromatography-mass spectrometry (LC-MS) and showed some beta-lactamase activity even in the presence of a beta-lactamase inhibitor. In addition, ribonuclease activity was demonstrated against RNA that was not inhibited by sulbactam and EDTA. None of these proteins could degrade single- and double-stranded-DNA. This study is the first to express and test putative CPR beta-lactamase protein sequences in vitro. Our findings highlight that the reduced genomes of CPR members harbor sequences encoding for beta-lactamases known to be multifunction hydrolase enzymes.
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29
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Alberdi A, Andersen SB, Limborg MT, Dunn RR, Gilbert MTP. Disentangling host-microbiota complexity through hologenomics. Nat Rev Genet 2022; 23:281-297. [PMID: 34675394 DOI: 10.1038/s41576-021-00421-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 02/07/2023]
Abstract
Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.
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Affiliation(s)
- Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Sandra B Andersen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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30
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Dataset for Genome Sequencing and De Novo Assembly of the Candidate Phyla Radiation in Supragingival Plaque. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:4899824. [PMID: 35345870 PMCID: PMC8957474 DOI: 10.1155/2022/4899824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 01/26/2022] [Indexed: 11/17/2022]
Abstract
The Candidate Phyla Radiation (CPR), as a newly discovered and difficult-to-culture bacterium, accounts for the majority of the bacterial domain, which may be related to various oral diseases, including dental caries. Restricted by laboratory culture conditions, there is limited knowledge about oral CPR. Advances in metagenomics provide a new way to study CPR through molecular biology. Here, we used metagenomic assembly and binning to reconstruct more and higher quality metagenome-assembled genomes (MAGs) of CPR from oral dental plaque. These MAGs represent novel CPR species, which differed from all known CPR organisms. Relative abundance of different CPR MAGs in the caries and caries-free group was estimated by mapping metagenomic reads to newly constructed MAGs. The relative abundance of two CPR MAGs was significantly increased in the caries group, indicating that there might be a relationship with caries activity. The detection of a large number of unclassified CPR MAGs in the dataset implies that the phylogenetic diversity of CPR is enormous. The results provide a reference value for exploring the ecological distribution and function of uncultured or difficult-to-culture microorganisms.
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Long-Term Incubation of Lake Water Enables Genomic Sampling of Consortia Involving Planctomycetes and Candidate Phyla Radiation Bacteria. mSystems 2022; 7:e0022322. [PMID: 35353011 PMCID: PMC9040852 DOI: 10.1128/msystems.00223-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Microbial communities in lakes can profoundly impact biogeochemical processes through their individual activities and collective interactions. However, the complexity of these communities poses challenges, particularly for studying rare organisms such as Candidate Phyla Radiation bacteria (CPR) and enigmatic entities such as aster-like nanoparticles (ALNs). Here, a reactor was inoculated with water from Lake Fargette, France, and maintained under dark conditions at 4°C for 31 months and enriched for ALNs, diverse Planctomycetes, and CPR bacteria. We reconstructed draft genomes and predicted metabolic traits for 12 diverse Planctomycetes and 9 CPR bacteria, some of which are likely representatives of undescribed families or genera. One CPR genome representing the little-studied lineage “Candidatus Peribacter” was curated to completion (1.239 Mbp) and unexpectedly encodes the full gluconeogenesis pathway. Metatranscriptomic data indicate that some planctomycetes and CPR bacteria were active under the culture conditions, accounting for ∼30% and ∼1% of RNA reads mapping to the genome set, respectively. We also reconstructed genomes and obtained transmission electron microscope images for numerous viruses, including one with a >300-kbp genome and several predicted to infect Planctomycetes. Together, our analyses suggest that freshwater Planctomycetes are central players in a subsystem that includes ALNs, symbiotic CPR bacteria, and viruses. IMPORTANCE Laboratory incubations of natural microbial communities can aid in the study of member organisms and their networks of interaction. This is particularly important for understudied lineages for which key elements of basic biology are still emerging. Using genomics and microscopy, we found that members of the bacterial lineage Planctomycetes may be central players in a subset of a freshwater lake microbiome that includes other bacteria, archaea, viruses, and mysterious entities, called aster-like nanoparticles (ALNs), whose origin is unknown. Our results help constrain the possible origins of ALNs and provide insight into possible interactions within a complex lake ecosystem.
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32
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Danczak RE, Sengupta A, Fansler SJ, Chu RK, Garayburu-Caruso VA, Renteria L, Toyoda J, Wells J, Stegen JC. Inferring the Contribution of Microbial Taxa and Organic Matter Molecular Formulas to Ecological Assembly. Front Microbiol 2022; 13:803420. [PMID: 35250925 PMCID: PMC8894727 DOI: 10.3389/fmicb.2022.803420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/14/2022] [Indexed: 11/23/2022] Open
Abstract
Understanding the mechanisms underlying the assembly of communities has long been the goal of many ecological studies. While several studies have evaluated community wide ecological assembly, fewer have focused on investigating the impacts of individual members within a community or assemblage on ecological assembly. Here, we adapted a previous null model β-nearest taxon index (βNTI) to measure the contribution of individual features within an ecological community to overall assembly. This new metric, called feature-level βNTI (βNTIfeat), enables researchers to determine whether ecological features (e.g., individual microbial taxa) contribute to divergence, convergence, or have insignificant impacts across spatiotemporally resolved metacommunities or meta-assemblages. Using βNTIfeat, we revealed that unclassified microbial lineages often contributed to community divergence while diverse groups (e.g., Crenarchaeota, Alphaproteobacteria, and Gammaproteobacteria) contributed to convergence. We also demonstrate that βNTIfeat can be extended to other ecological assemblages such as organic molecules comprising organic matter (OM) pools. OM had more inconsistent trends compared to the microbial community though CHO-containing molecular formulas often contributed to convergence, while nitrogen and phosphorus-containing formulas contributed to both convergence and divergence. A network analysis was used to relate βNTIfeat values from the putatively active microbial community and the OM assemblage and examine potentially common contributions to ecological assembly across different communities/assemblages. This analysis revealed that P-containing formulas often contributed to convergence/divergence separately from other ecological features and N-containing formulas often contributed to assembly in coordination with microorganisms. Additionally, members of Family Geobacteraceae were often observed to contribute to convergence/divergence in conjunction with both N- and P-containing formulas, suggesting a coordinated ecological role for family members and the nitrogen/phosphorus cycle. Overall, we show that βNTIfeat offers opportunities to investigate the community or assemblage members, which shape the phylogenetic or functional landscape, and demonstrate the potential to evaluate potential points of coordination across various community types.
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Affiliation(s)
- Robert E. Danczak
- Ecosystem Sciences, Pacific Northwest National Laboratory, Richland, WA, United States
- *Correspondence: Robert E. Danczak,
| | - Aditi Sengupta
- Department of Biology, California Lutheran University, Thousand Oaks, CA, United States
| | - Sarah J. Fansler
- Ecosystem Sciences, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Rosalie K. Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | | | - Lupita Renteria
- Ecosystem Sciences, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jason Toyoda
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jacqueline Wells
- Ecosystem Sciences, Pacific Northwest National Laboratory, Richland, WA, United States
| | - James C. Stegen
- Ecosystem Sciences, Pacific Northwest National Laboratory, Richland, WA, United States
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33
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Maatouk M, Ibrahim A, Rolain JM, Merhej V, Bittar F. Small and Equipped: the Rich Repertoire of Antibiotic Resistance Genes in Candidate Phyla Radiation Genomes. mSystems 2021; 6:e0089821. [PMID: 34874773 PMCID: PMC8651080 DOI: 10.1128/msystems.00898-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/10/2021] [Indexed: 11/20/2022] Open
Abstract
Microbes belonging to Candidate Phyla Radiation (CPR) have joined the tree of life as a new branch, thanks to the intensive application of metagenomics and sequencing technologies. CPR have been eventually identified by 16S rRNA analysis, and they represent more than 26% of microbial diversity. Despite their ultrasmall size, reduced genome, and metabolic pathways which mainly depend on exosymbiotic or exoparasitic relationships with the bacterial host, CPR microbes were found to be abundant in almost all environments. They can be considered survivors in highly competitive circumstances within microbial communities. However, their defense mechanisms and phenotypic characteristic remain poorly explored. Here, we conducted a thorough in silico analysis on 4,062 CPR genomes to search for antibiotic resistance (AR)-like enzymes using BLASTp and functional domain predictions against an exhaustive consensus AR database and conserved domain database (CDD), respectively. Our findings showed that a rich reservoir of divergent AR-like genes (n = 30,545 hits, mean = 7.5 hits/genome [0 to 41]) were distributed across the 13 CPR superphyla. These AR-like genes encode 89 different enzymes that are associated with 14 different chemical classes of antimicrobials. Most hits found (93.6%) were linked to glycopeptide, beta-lactam, macrolide-lincosamide-streptogramin (MLS), tetracycline, and aminoglycoside resistance. Moreover, two AR profiles were discerned for the Microgenomates group and "Candidatus Parcubacteria," which were distinct between them and differed from all other CPR superphyla. CPR cells seem to be active players during microbial competitive interactions; they are well equipped for microbial combat in different habitats, which ensures their natural survival and continued existence. IMPORTANCE To our knowledge, this study is one of the few studies that characterize the defense systems in the CPR group and describes the first repertoire of antibiotic resistance (AR) genes. The use of a BLAST approach with lenient criteria followed by a careful examination of the functional domains has yielded a variety of enzymes that mainly give three different mechanisms of action of resistance. Our genome analysis showed the existence of a rich reservoir of CPR resistome, which is associated with different antibiotic families. Moreover, this analysis revealed the hidden face of the reduced-genome CPR, particularly their weaponry with AR genes. These data suggest that CPR are competitive players in the microbial war, and they can be distinguished by specific AR profiles.
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Affiliation(s)
- Mohamad Maatouk
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ahmad Ibrahim
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Vicky Merhej
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Fadi Bittar
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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Chaudhari NM, Overholt WA, Figueroa-Gonzalez PA, Taubert M, Bornemann TLV, Probst AJ, Hölzer M, Marz M, Küsel K. The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers. ENVIRONMENTAL MICROBIOME 2021; 16:24. [PMID: 34906246 PMCID: PMC8672522 DOI: 10.1186/s40793-021-00395-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/03/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges. RESULTS Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1 µm filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1 µm fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2 µm fractions. On average, Patescibacteria enriched in the smaller 0.1 µm filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2 µm fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota). CONCLUSION Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to attach multiple hosts just long enough to loot or exchange supplies.
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Affiliation(s)
- Narendrakumar M. Chaudhari
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Will A. Overholt
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Perla Abigail Figueroa-Gonzalez
- Department for Chemistry, Environmental Microbiology and Biotechnology, Group for Aquatic Microbial Ecology (GAME), University Duisburg-Essen, Essen, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Till L. V. Bornemann
- Department for Chemistry, Environmental Microbiology and Biotechnology, Group for Aquatic Microbial Ecology (GAME), University Duisburg-Essen, Essen, Germany
| | - Alexander J. Probst
- Department for Chemistry, Environmental Microbiology and Biotechnology, Group for Aquatic Microbial Ecology (GAME), University Duisburg-Essen, Essen, Germany
| | - Martin Hölzer
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena, Germany
- European Virus Bioinformatics Center, Friedrich Schiller University, Jena, Germany
- Present Address: Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Manja Marz
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena, Germany
- European Virus Bioinformatics Center, Friedrich Schiller University, Jena, Germany
- FLI Leibniz Institute for Age Research, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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Degenhardt J, Merder J, Heyerhoff B, Simon H, Engelen B, Waska H. Cross-Shore and Depth Zonations in Bacterial Diversity Are Linked to Age and Source of Dissolved Organic Matter across the Intertidal Area of a Sandy Beach. Microorganisms 2021; 9:1720. [PMID: 34442799 PMCID: PMC8399146 DOI: 10.3390/microorganisms9081720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
Microbial communities and dissolved organic matter (DOM) are intrinsically linked within the global carbon cycle. Demonstrating this link on a molecular level is hampered by the complexity of both counterparts. We have now investigated this connection within intertidal beach sediments, characterized by a runnel-ridge system and subterranean groundwater discharge. Using datasets generated by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and Ilumina-sequencing of 16S rRNA genes, we predicted metabolic functions and determined links between bacterial communities and DOM composition. Four bacterial clusters were defined, reflecting differences within the community compositions. Those were attributed to distinct areas, depths, or metabolic niches. Cluster I was found throughout all surface sediments, probably involved in algal-polymer degradation. In ridge and low water line samples, cluster III became prominent. Associated porewaters indicated an influence of terrestrial DOM and the release of aromatic compounds from reactive iron oxides. Cluster IV showed the highest seasonality and was associated with species previously reported from a subsurface bloom. Interestingly, Cluster II harbored several members of the candidate phyla radiation (CPR) and was related to highly degraded DOM. This may be one of the first geochemical proofs for the role of candidate phyla in the degradation of highly refractory DOM.
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Affiliation(s)
- Julius Degenhardt
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Julian Merder
- Department of Global Ecology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Benedikt Heyerhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Heike Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Bert Engelen
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
| | - Hannelore Waska
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany
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Reconstruction of Metagenome-Assembled Genomes from Aquaria. Microbiol Resour Announc 2021; 10:e0055721. [PMID: 34351234 PMCID: PMC8340870 DOI: 10.1128/mra.00557-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Here, we report 11 metagenome-assembled genomes (MAGs) reconstructed from freshwater and saltwater aquaria, including representatives of Polynucleobacter, Anaerolinea, Roseobacter, Flavobacteriia, Octadecabacter, Mycobacterium, and Candidate Phyla Radiation (CPR) members. These MAGs can serve as a resource for aquatic research and elucidating the role of CPR taxa in the built environment.
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Koirala A, Brözel VS. Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea. Microorganisms 2021; 9:microorganisms9081662. [PMID: 34442741 PMCID: PMC8399215 DOI: 10.3390/microorganisms9081662] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/16/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022] Open
Abstract
The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico prediction of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocumented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes are currently supported by biochemical evidence of diazotrophy. In addition, this work provides reference for any inter-phyla comparison of Nif sequences and a quality database of Nif proteins that can be used for identifying new Nif sequences.
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Affiliation(s)
- Amrit Koirala
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA;
| | - Volker S. Brözel
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA;
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa
- Correspondence: ; Tel.: +1-605-688-6144
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Wiegand S, Dam HT, Riba J, Vollmers J, Kaster AK. Printing Microbial Dark Matter: Using Single Cell Dispensing and Genomics to Investigate the Patescibacteria/Candidate Phyla Radiation. Front Microbiol 2021; 12:635506. [PMID: 34220732 PMCID: PMC8241940 DOI: 10.3389/fmicb.2021.635506] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
As of today, the majority of environmental microorganisms remain uncultured. They are therefore referred to as "microbial dark matter." In the recent past, cultivation-independent methods like single-cell genomics (SCG) enabled the discovery of many previously unknown microorganisms, among them the Patescibacteria/Candidate Phyla Radiation (CPR). This approach was shown to be complementary to metagenomics, however, the development of additional and refined sorting techniques beyond the most commonly used fluorescence-activated cell sorting (FACS) is still desirable to enable additional downstream applications. Adding image information on the number and morphology of sorted cells would be beneficial, as would be minimizing cell stress caused by sorting conditions such as staining or pressure. Recently, a novel cell sorting technique has been developed, a microfluidic single-cell dispenser, which assesses the number and morphology of the cell in each droplet by automated light microscopic processing. Here, we report for the first time the successful application of the newly developed single-cell dispensing system for label-free isolation of individual bacteria from a complex sample retrieved from a wastewater treatment plant, demonstrating the potential of this technique for single cell genomics and other alternative downstream applications. Genome recovery success rated above 80% with this technique-out of 880 sorted cells 717 were successfully amplified. For 50.1% of these, analysis of the 16S rRNA gene was feasible and led to the sequencing of 50 sorted cells identified as Patescibacteria/CPR members. Subsequentially, 27 single amplified genomes (SAGs) of 15 novel and distinct Patescibacteria/CPR members, representing yet unseen species, genera and families could be captured and reconstructed. This phylogenetic distinctness of the recovered SAGs from available metagenome-assembled genomes (MAGs) is accompanied by the finding that these lineages-in whole or in part-have not been accessed by genome-resolved metagenomics of the same sample, thereby emphasizing the importance and opportunities of SCGs.
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Affiliation(s)
- Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Hang T. Dam
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Julian Riba
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - John Vollmers
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Institute for Applied Biosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Co R, Hug LA. Prediction, enrichment and isolation identify a responsive, competitive community of cellulolytic microorganisms from a municipal landfill. FEMS Microbiol Ecol 2021; 97:6261183. [PMID: 33930130 DOI: 10.1093/femsec/fiab065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/27/2021] [Indexed: 01/04/2023] Open
Abstract
Landfills are engineered, heterogeneously contaminated sites containing large reservoirs of paper waste. Cellulose degradation is an important process within landfill microbial ecology, and these anoxic, saturated environments are prime locations for discovery of cellulases that may offer improvements on industrial cellulose degradation efforts. We sampled leachate from three locations within a municipal landfill, a leachate collection cistern, and groundwater from an adjacent aquifer to identify cellulolytic populations and their associated cellulases. Metagenomic sequencing identified wide-spread and taxonomically diverse cellulolytic potential, with a notable scarcity of predicted exocellulases. 16S rRNA amplicon sequencing detected nine landfill microorganisms enriched in a customized leachate medium amended with microcrystalline cellulose or common paper stocks. Paper-enrichment cultures showed competition dynamics in response to the specific composition (lignin: hemi-cellulose: cellulose) of the different paper stocks. From leachate biomass, four novel cellulolytic bacteria were isolated, including two with the capacity for cellulolysis at industrially relevant temperatures. None of the isolates demonstrated exocellulase activity, consistent with the metagenome-based predictions. However, there was very little overlap between metagenome-derived predicted cellulolytic organisms, organisms enriched on paper sources, or the isolates, suggesting the landfill cellulolytic community is at low abundance but able to rapidly respond to introduced substrates.
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Affiliation(s)
- Rebecca Co
- Dapartment of Biology, University of Waterloo, 200 University Ave, Waterloo, ON, N2L3G1, Canada
| | - Laura A Hug
- Dapartment of Biology, University of Waterloo, 200 University Ave, Waterloo, ON, N2L3G1, Canada
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40
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Patil PK, Baskaran V, Vinay TN, Avunje S, Leo-Antony M, Shekhar MS, Alavandi SV, Vijayan KK. Abundance, community structure and diversity of nitrifying bacterial enrichments from low and high saline brackishwater environments. Lett Appl Microbiol 2021; 73:96-106. [PMID: 33780023 DOI: 10.1111/lam.13480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022]
Abstract
The study reports diversity in nitrifying microbial enrichments from low (0·5-5‰) and high (18-35‰) saline ecosystems. Microbial community profiling of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) enrichments was analysed by sequencing 16S rRNA and was processed using Mothur pipeline. The α-diversity indices showed the richness of nitrifying bacterial consortia from the high saline environment and were clustering based on the source of the sample. AOB and NOB enrichments from both the environments showed diverse lineages of phyla distributed in both groups with 38 and 34 phyla from low saline and 53 and 40 phyla in high saline sources, respectively. At class level, α- and γ-proteobacteria were found to be more dominant in both the enrichments. AOBs and NOBs in enrichments from low saline environments were dominated by Nitrosomonadaceae, Gallionellaceae (Nitrotoga sp.) and Ectothiorhodospiraceae and Nitrospira, respectively. Though Chromatiaceae were present in both AOB and NOB enrichments, Nitrosoglobus and Nitrosococcus dominated the AOBs while NOBs were dominated by uncultured genera, whereas Rhizobiales were found in both the enrichments. AOBs and NOBs in enrichments from high saline environments were dominated by Nitrospira-like AOBs, Nitrosomonas and Nitrosococcus genera, whereas ammonia-oxidizing archaea (AOA) group included Nitrosopumilus and Nitrososphaera genera comprising and Nitrospirae, respectively. The majority of the genera obtained in both the salinities were found to be either uncultured or unclassified groups. Results of the study suggest that the AOB and NOB consortia have unique and diverse microbes in each of the enrichments, capable of functioning in aquaculture systems practised at different salinities (0-60 ppt).
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Affiliation(s)
- P K Patil
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - V Baskaran
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - T-N Vinay
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - S Avunje
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - M Leo-Antony
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - M S Shekhar
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - S V Alavandi
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
| | - K K Vijayan
- Central Institute of Brackishwater Aquaculture, ICAR, Chennai, India
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David GM, López-García P, Moreira D, Alric B, Deschamps P, Bertolino P, Restoux G, Rochelle-Newall E, Thébault E, Simon M, Jardillier L. Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns. Mol Ecol 2021; 30:2162-2177. [PMID: 33639035 DOI: 10.1111/mec.15864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/27/2022]
Abstract
Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.
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Affiliation(s)
- Gwendoline M David
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | | | - David Moreira
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Benjamin Alric
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, Villeurbanne, France
| | - Philippe Deschamps
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Paola Bertolino
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Gwendal Restoux
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Emma Rochelle-Newall
- Sorbonne Université, UPEC, CNRS, IRD, INRAE, Institute d'Ecologie de des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
| | - Elisa Thébault
- Sorbonne Université, UPEC, CNRS, IRD, INRAE, Institute d'Ecologie de des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
| | - Marianne Simon
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Ludwig Jardillier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
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García-Rodríguez F, Piccini C, Carrizo D, Sánchez-García L, Pérez L, Crisci C, Oaquim ABJ, Evangelista H, Soutullo A, Azcune G, Lüning S. Centennial glacier retreat increases sedimentation and eutrophication in Subantarctic periglacial lakes: A study case of Lake Uruguay. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 754:142066. [PMID: 33254911 DOI: 10.1016/j.scitotenv.2020.142066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/04/2020] [Accepted: 08/27/2020] [Indexed: 06/12/2023]
Abstract
High resolution XRF scanning documented inter-annual paleolimnological changes of a Subantarctic periglacial lake, during a process of centennial glacier retreat in King George Island, Antarctica. Two major paleoenvironmental stages were inferred from the combined analysis of elemental, molecular and isotopic biomarkers, with a boundary or transition set at about 3200 yr BP. The first stage was characterized by a relatively low allochthonous organic content, reduced productivity and nitrogen levels. Such paleoenvironmental conditions are interpreted as a terrestrial system under periglacial influence, where material influx was related to erosion process from the melt water discharge, because of the proximity to the Collins Glacier ice cap. After the major Holocene glacier advance dated at about 3500 yr BP, the ice cap retreat led to the formation of Lake Uruguay, which involved in filling processes leading to moraine deposits, proglacial meltwater channels, and lakes next to the land glacier. During the second stage, with the onset of the Current Warm Period, prior to 1900 CE the stabilization of the Zr/Rb ratio within the laminated sediments documented the origin of the lacustrine sedimentation system, with subsequent increases in the sedimentation rate and biomass content (total nitrogen and organic carbon). Time series analyses revealed that the lake displayed variability cycles related to El Niño Southern Oscillation (ENSO), as reflected by high resolution sedimentological proxies for grain size, weathering, allochthonous inputs from the watershed, increase of biomass and productivity, and changes in redox conditions, all of which displayed similar oscillation cycles from 2 to 6 yr. During this periglacial recession and associated eutrophication process, we detected a striking loss in both bacterial specific richness and diversity as inferred from preliminary selected ancient DNA analyses. Thus, the Antarctic warming scenario leading to glacier depletion appears to exert deterioration consequences on the Subantarctic microbial web.
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Affiliation(s)
- F García-Rodríguez
- Universidad de la República, Centro Universitario Regional Este, CURE Rocha y Maldonado, Uruguay; Universidade Federal de Rio Grande, Instituto de Oceanografia, Programa de Pós-Graduação em Oceanología, Rio Grande, Brazil.
| | - C Piccini
- Instituto de Investigaciones Biológicas Clemente Estable, Departamento de Microbiología, Av. Italia 3318, Montevideo 11600, Uruguay
| | - D Carrizo
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | | | - L Pérez
- Universidad de la República, Centro Universitario Regional Este, CURE Rocha y Maldonado, Uruguay
| | - C Crisci
- Universidad de la República, Centro Universitario Regional Este, CURE Rocha y Maldonado, Uruguay
| | - A B J Oaquim
- LARAMG/Universidade do Estado do Rio de Janeiro - UERJ, Departamento de Biofísica, Maracanã 0550900, RJ, Brazil
| | - H Evangelista
- LARAMG/Universidade do Estado do Rio de Janeiro - UERJ, Departamento de Biofísica, Maracanã 0550900, RJ, Brazil
| | - A Soutullo
- Universidad de la República, Centro Universitario Regional Este, CURE Rocha y Maldonado, Uruguay; Instituto Antártico Uruguayo, Montevideo, Uruguay
| | - G Azcune
- Universidad de la República, Centro Universitario Regional Este, CURE Rocha y Maldonado, Uruguay
| | - S Lüning
- Institute for Hydrography, Geoecology and Climate Sciences, Hauptstraße 47, 6315 Ägeri, Switzerland
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Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems. Nat Microbiol 2021; 6:354-365. [PMID: 33495623 PMCID: PMC7906910 DOI: 10.1038/s41564-020-00840-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022]
Abstract
Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health. Metagenomics and electron microscopy are combined to analyse the diversity of episymbiotic CPR bacteria and DPANN archaea in eight groundwater communities.
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Alexyuk M, Bogoyavlenskiy A, Alexyuk P, Moldakhanov Y, Berezin V, Digel I. Epipelagic microbiome of the Small Aral Sea: Metagenomic structure and ecological diversity. Microbiologyopen 2021; 10:e1142. [PMID: 33305509 PMCID: PMC7882900 DOI: 10.1002/mbo3.1142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/04/2020] [Accepted: 11/07/2020] [Indexed: 11/11/2022] Open
Abstract
Microbial diversity studies regarding the aquatic communities that experienced or are experiencing environmental problems are essential for the comprehension of the remediation dynamics. In this pilot study, we present data on the phylogenetic and ecological structure of microorganisms from epipelagic water samples collected in the Small Aral Sea (SAS). The raw data were generated by massive parallel sequencing using the shotgun approach. As expected, most of the identified DNA sequences belonged to Terrabacteria and Actinobacteria (40% and 37% of the total reads, respectively). The occurrence of Deinococcus-Thermus, Armatimonadetes, Chloroflexi in the epipelagic SAS waters was less anticipated. Surprising was also the detection of sequences, which are characteristic for strict anaerobes-Ignavibacteria, hydrogen-oxidizing bacteria, and archaeal methanogenic species. We suppose that the observed very broad range of phylogenetic and ecological features displayed by the SAS reads demonstrates a more intensive mixing of water masses originating from diverse ecological niches of the Aral-Syr Darya River basin than presumed before.
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Affiliation(s)
- Madina Alexyuk
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | | | - Pavel Alexyuk
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Yergali Moldakhanov
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Vladimir Berezin
- Research and Production Center for Microbiology and VirologyAlmatyKazakhstan
| | - Ilya Digel
- Institute for BioengineeringAachen University of Applied SciencesJülichGermany
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Abstract
Ultra-small microorganisms are ubiquitous in Earth’s environments. Ultramicrobacteria, which are defined as having a cell volume of <0.1 μm3, are often numerically dominant in aqueous environments. Cultivated representatives among these bacteria, such as members of the marine SAR11 clade (e.g., “Candidatus Pelagibacter ubique”) and freshwater Actinobacteria and Betaproteobacteria, possess highly streamlined, small genomes and unique ecophysiological traits. Many ultramicrobacteria may pass through a 0.2-μm-pore-sized filter, which is commonly used for filter sterilization in various fields and processes. Cultivation efforts focusing on filterable small microorganisms revealed that filtered fractions contained not only ultramicrocells (i.e., miniaturized cells because of external factors) and ultramicrobacteria, but also slender filamentous bacteria sometimes with pleomorphic cells, including a special reference to members of Oligoflexia, the eighth class of the phylum Proteobacteria. Furthermore, the advent of culture-independent “omics” approaches to filterable microorganisms yielded the existence of candidate phyla radiation (CPR) bacteria (also referred to as “Ca. Patescibacteria”) and ultra-small members of DPANN (an acronym of the names of the first phyla included in this superphyla) archaea. Notably, certain groups in CPR and DPANN are predicted to have minimal or few biosynthetic capacities, as reflected by their extremely small genome sizes, or possess no known function. Therefore, filtered fractions contain a greater variety and complexity of microorganisms than previously expected. This review summarizes the broad diversity of overlooked filterable agents remaining in “sterile” (<0.2-μm filtered) environmental samples.
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Affiliation(s)
- Ryosuke Nakai
- Applied Molecular Microbiology Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
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46
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A Need for Improved Cellulase Identification from Metagenomic Sequence Data. Appl Environ Microbiol 2020; 87:AEM.01928-20. [PMID: 33067195 DOI: 10.1128/aem.01928-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Improved sequencing technologies and the maturation of metagenomic approaches allow the identification of gene variants with potential industrial applications, including cellulases. Cellulase identification from metagenomic environmental surveys is complicated by inconsistent nomenclature and multiple categorization systems. Here, we summarize the current classification and nomenclature systems, with recommendations for improvements to these systems. Addressing the issues described will strengthen the annotation of cellulose-active enzymes from environmental sequence data sets-a rapidly growing resource in environmental and applied microbiology.
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47
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Gagen EJ, Levett A, Paz A, Bostelmann H, Valadares RBDS, Bitencourt JAP, Gastauer M, Nunes GL, Oliveira G, Vasconcelos PM, Tyson GW, Southam G. Accelerating microbial iron cycling promotes re-cementation of surface crusts in iron ore regions. Microb Biotechnol 2020; 13:1960-1971. [PMID: 32812342 PMCID: PMC7533318 DOI: 10.1111/1751-7915.13646] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/18/2020] [Accepted: 07/19/2020] [Indexed: 12/02/2022] Open
Abstract
Accelerating microbial iron cycling is an innovative environmentally responsible strategy for mine remediation. In the present study, we extend the application of microbial iron cycling in environmental remediation, to include biocementation for the aggregation and stabilization of mine wastes. Microbial iron reduction was promoted monthly for 10 months in crushed canga (a by-product from iron ore mining, dominated by crystalline iron oxides) in 1 m3 containers. Ferrous iron concentrations reached 445 ppm in treatments and diverse lineages of the candidate phyla radiation dominated pore waters, implicating them in fermentation and/or metal cycling in this system. After a 6-month evaporation period, iron-rich cements had formed between grains and 20-cm aggregates were recoverable from treatments throughout the 1-m depth profile, while material from untreated and water-only controls remained unconsolidated. Canga-adapted plants seeded into one of the treatments germinated and grew well. Therefore, application of this geobiotechnology offers promise for stabilization of mine wastes, as well as re-formation of surface crusts that underpin unique and threatened plant ecosystems in iron ore regions.
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Affiliation(s)
- Emma J. Gagen
- School of Earth and Environmental SciencesThe University of QueenslandSt LuciaQLD4072Australia
- Australian Centre for EcogenomicsSchool of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLD4072Australia
| | - Alan Levett
- School of Earth and Environmental SciencesThe University of QueenslandSt LuciaQLD4072Australia
- Present address:
GFZ German Research Centre for GeosciencesPotsdam14473Germany
| | - Anat Paz
- School of Earth and Environmental SciencesThe University of QueenslandSt LuciaQLD4072Australia
| | - Heike Bostelmann
- School of Earth and Environmental SciencesThe University of QueenslandSt LuciaQLD4072Australia
| | | | | | | | | | | | - Paulo M. Vasconcelos
- School of Earth and Environmental SciencesThe University of QueenslandSt LuciaQLD4072Australia
| | - Gene W. Tyson
- Australian Centre for EcogenomicsSchool of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLD4072Australia
- Present address:
School of Biomedical SciencesQueensland University of TechnologyBrisbaneQLD4001Australia
| | - Gordon Southam
- School of Earth and Environmental SciencesThe University of QueenslandSt LuciaQLD4072Australia
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48
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Nelson WC, Tully BJ, Mobberley JM. Biases in genome reconstruction from metagenomic data. PeerJ 2020; 8:e10119. [PMID: 33194386 PMCID: PMC7605220 DOI: 10.7717/peerj.10119] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 09/16/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Advances in sequencing, assembly, and assortment of contigs into species-specific bins has enabled the reconstruction of genomes from metagenomic data (MAGs). Though a powerful technique, it is difficult to determine whether assembly and binning techniques are accurate when applied to environmental metagenomes due to a lack of complete reference genome sequences against which to check the resulting MAGs. METHODS We compared MAGs derived from an enrichment culture containing ~20 organisms to complete genome sequences of 10 organisms isolated from the enrichment culture. Factors commonly considered in binning software-nucleotide composition and sequence repetitiveness-were calculated for both the correctly binned and not-binned regions. This direct comparison revealed biases in sequence characteristics and gene content in the not-binned regions. Additionally, the composition of three public data sets representing MAGs reconstructed from the Tara Oceans metagenomic data was compared to a set of representative genomes available through NCBI RefSeq to verify that the biases identified were observable in more complex data sets and using three contemporary binning software packages. RESULTS Repeat sequences were frequently not binned in the genome reconstruction processes, as were sequence regions with variant nucleotide composition. Genes encoded on the not-binned regions were strongly biased towards ribosomal RNAs, transfer RNAs, mobile element functions and genes of unknown function. Our results support genome reconstruction as a robust process and suggest that reconstructions determined to be >90% complete are likely to effectively represent organismal function; however, population-level genotypic heterogeneity in natural populations, such as uneven distribution of plasmids, can lead to incorrect inferences.
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Affiliation(s)
- William C. Nelson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Benjamin J. Tully
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
- Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
| | - Jennifer M. Mobberley
- Chemical and Biological Signature Science Group, Pacific Northwest National Laboratory, Richland, WA, USA
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Wong HL, MacLeod FI, White RA, Visscher PT, Burns BP. Microbial dark matter filling the niche in hypersaline microbial mats. MICROBIOME 2020; 8:135. [PMID: 32938503 PMCID: PMC7495880 DOI: 10.1186/s40168-020-00910-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/19/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been shown to possess a substantial abundance of uncultivable microorganisms. These enigmatic microbes, jointly coined as 'microbial dark matter' (MDM), are hypothesised to play key roles in modern microbial mats. RESULTS We reconstructed 115 metagenome-assembled genomes (MAGs) affiliated to MDM, spanning 42 phyla. This study reports for the first time novel microorganisms (Zixibacterial order GN15) putatively taking part in dissimilatory sulfate reduction in surface hypersaline settings, as well as novel eukaryote signature proteins in the Asgard archaea. Despite possessing reduced-size genomes, the MDM MAGs are capable of fermenting and degrading organic carbon, suggesting a role in recycling organic carbon. Several forms of RuBisCo were identified, allowing putative CO2 incorporation into nucleotide salvaging pathways, which may act as an alternative carbon and phosphorus source. High capacity of hydrogen production was found among Shark Bay MDM. Putative schizorhodopsins were also identified in Parcubacteria, Asgard archaea, DPANN archaea, and Bathyarchaeota, allowing these members to potentially capture light energy. Diversity-generating retroelements were prominent in DPANN archaea that likely facilitate the adaptation to a dynamic, host-dependent lifestyle. CONCLUSIONS This is the first study to reconstruct and describe in detail metagenome-assembled genomes (MAGs) affiliated with microbial dark matter in hypersaline microbial mats. Our data suggests that these microbial groups are major players in these systems. In light of our findings, we propose H2, ribose and CO/CO2 as the main energy currencies of the MDM community in these mat systems. Video Abstract.
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Affiliation(s)
- Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Fraser I MacLeod
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
| | - Richard Allen White
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
- RAW Molecular Systems LLC, Spokane, WA, USA
- Department of Bioinformatics and Genomics, The University of North Carolina, Charlotte, NC, USA
| | - Pieter T Visscher
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia
- Department of Marine Sciences, University of Connecticut, Mansfield, USA
- Biogeosciences, the Université de Bourgogne Franche-Comté, Dijon, France
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, Australia.
- Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia.
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50
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Jaffe AL, Castelle CJ, Matheus Carnevali PB, Gribaldo S, Banfield JF. The rise of diversity in metabolic platforms across the Candidate Phyla Radiation. BMC Biol 2020; 18:69. [PMID: 32560683 PMCID: PMC7304191 DOI: 10.1186/s12915-020-00804-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/01/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A unifying feature of the bacterial Candidate Phyla Radiation (CPR) is a limited and highly variable repertoire of biosynthetic capabilities. However, the distribution of metabolic traits across the CPR and the evolutionary processes underlying them are incompletely resolved. RESULTS Here, we selected ~ 1000 genomes of CPR bacteria from diverse environments to construct a robust internal phylogeny that was consistent across two unlinked marker sets. Mapping of glycolysis, the pentose phosphate pathway, and pyruvate metabolism onto the tree showed that some components of these pathways are sparsely distributed and that similarity between metabolic platforms is only partially predicted by phylogenetic relationships. To evaluate the extent to which gene loss and lateral gene transfer have shaped trait distribution, we analyzed the patchiness of gene presence in a phylogenetic context, examined the phylogenetic depth of clades with shared traits, and compared the reference tree topology with those of specific metabolic proteins. While the central glycolytic pathway in CPR is widely conserved and has likely been shaped primarily by vertical transmission, there is evidence for both gene loss and transfer especially in steps that convert glucose into fructose 1,6-bisphosphate and glycerate 3P into pyruvate. Additionally, the distribution of Group 3 and Group 4-related NiFe hydrogenases is patchy and suggests multiple events of ancient gene transfer. CONCLUSIONS We infer that patterns of gene gain and loss in CPR, including acquisition of accessory traits in independent transfer events, could have been driven by shifts in host-derived resources and led to sparse but varied genetic inventories.
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Affiliation(s)
- Alexander L Jaffe
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Simonetta Gribaldo
- Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
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