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Shi LD, West-Roberts J, Schoelmerich MC, Penev PI, Chen L, Amano Y, Lei S, Sachdeva R, Banfield JF. Methanotrophic Methanoperedens archaea host diverse and interacting extrachromosomal elements. Nat Microbiol 2024; 9:2422-2433. [PMID: 38918468 DOI: 10.1038/s41564-024-01740-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 05/20/2024] [Indexed: 06/27/2024]
Abstract
Methane emissions are mitigated by anaerobic methane-oxidizing archaea, including Methanoperedens. Some Methanoperedens host huge extrachromosomal genetic elements (ECEs) called Borgs that may modulate their activity, yet the broader diversity of Methanoperedens ECEs is understudied. Here we report small enigmatic linear ECEs, circular viruses and unclassified ECEs that are predicted to replicate within Methanoperedens. Linear ECEs have inverted terminal repeats, tandem repeats and coding patterns that are strongly reminiscent of Borgs, but they are only 52-145 kb in length. As they share proteins with Borgs and Methanoperedens, we refer to them as mini-Borgs. Mini-Borgs are genetically diverse and can be assigned to at least five family-level groups. We identify eight families of Methanoperedens viruses, some of which encode multi-haem cytochromes, and circular ECEs encoding transposon-associated TnpB genes with proximal population-heterogeneous CRISPR arrays. These ECEs exchange genetic information with each other and with Methanoperedens, probably impacting their archaeal host activity and evolution.
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Affiliation(s)
- Ling-Dong Shi
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jacob West-Roberts
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Marie C Schoelmerich
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Environmental Systems Sciences, ETH Zurich, Zurich, Switzerland
| | - Petar I Penev
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - LinXing Chen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Yuki Amano
- Sector of Decommissioning and Radioactive Wastes Management, Japan Atomic Energy Agency, Ibaraki, Japan
| | - Shufei Lei
- Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA.
- Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
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2
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McCain JSP, Britten GL, Hackett SR, Follows MJ, Li GW. Microbial reaction rate estimation using proteins and proteomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.13.607198. [PMID: 39185172 PMCID: PMC11343155 DOI: 10.1101/2024.08.13.607198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Microbes transform their environments using diverse enzymatic reactions. However, it remains challenging to measure microbial reaction rates in natural environments. Despite advances in global quantification of enzyme abundances, the individual relationships between enzyme abundances and their reaction rates have not been systematically examined. Using matched proteomic and reaction rate data from microbial cultures, we show that enzyme abundance is often insufficient to predict its corresponding reaction rate. However, we discovered that global proteomic measurements can be used to make accurate rate predictions of individual reaction rates (median R 2 = 0.78). Accurate rate predictions required only a small number of proteins and they did not need explicit prior mechanistic knowledge or environmental context. These results indicate that proteomes are encoders of cellular reaction rates, potentially enabling proteomic measurements in situ to estimate the rates of microbially mediated reactions in natural systems. Significance One of the most basic phenotypes of a microbe is its set of associated reaction rates, but quantifying these rates in situ remains extremely challenging, especially in natural systems. We used molecular data and statistical models to estimate microbial rates in steady state cultures. We found that many reaction rates are highly predictable using proteomic data, though single proteins are typically not informative for their associated reaction rates. This result suggests that gene expression data from complex microbial communities could be used to estimate in situ reaction rates, providing new clues into the lives and environmental function of microbes.
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Appa CR, Grieshaber NA, Yang H, Omsland A, McCormick S, Chiarelli TJ, Grieshaber SS. The chlamydial transcriptional regulator Euo is a key switch in cell form developmental progression but is not involved in the committed step to the formation of the infectious form. mSphere 2024:e0043724. [PMID: 39140730 DOI: 10.1128/msphere.00437-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/10/2024] [Indexed: 08/15/2024] Open
Abstract
Bacteria in the genus Chlamydia are a significant health burden worldwide. They infect a wide range of vertebrate animals, including humans and domesticated animals. In humans, C. psittaci can cause zoonotic pneumonia, while C. pneumoniae causes a variety of respiratory infections. Infections with C. trachomatis cause ocular or genital infections. All chlamydial species are obligate intracellular bacteria that replicate exclusively inside of eukaryotic host cells. Chlamydial infections are dependent on a complex infection cycle that depends on transitions between specific cell forms. This cycle consists of cell forms specialized for host cell invasion, the elementary body (EB), and a form specialized for intracellular replication, the reticulate body (RB). In addition to the EB and RB, there is a transitionary cell form that mediates the transformation between the RB and the EB, the intermediate body (IB). In this study, we ectopically expressed the regulatory protein Euo and showed that high levels of expression resulted in reversible arrest of the development cycle. The arrested chlamydial cells were trapped phenotypically at an early IB stage of the cycle. These cells had exited the cell cycle but had not shifted gene expression from RB like to IB/EB like. This arrested state was dependent on continued expression of Euo. When ectopic expression was reversed, Euo levels dropped in the arrested cells which led to the repression of native Euo expression and the resumption of the developmental cycle. Our data are consistent with a model where Euo expression levels impact IB maturation to the infectious EB but not the production of the IB form. IMPORTANCE Bacterial species in the Chlamydiales order infect a variety of vertebrate animals and are a global health concern. They cause various diseases in humans, including genital and respiratory infections. The bacteria are obligate intracellular parasites that rely on a complex infectious cycle involving multiple cell forms. All species share the same life cycle, transitioning through different states to form the infectious elementary body (EB) to spread infections to new hosts. The Euo gene, encoding a DNA-binding protein, is involved in regulating this cycle. This study showed that ectopic expression of Euo halted the cycle at an early stage. This arrest depended on continued Euo expression. When Euo expression was reversed, the developmental cycle resumed. Additionally, this study suggests that high levels of Euo expression affect the formation of the infectious EB but not the production of the cell form committed to EB formation.
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Affiliation(s)
- Cody R Appa
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | | | - Hong Yang
- Paul G. Allen School For Global Health, Washington State University, Pullman, Washington, USA
| | - Anders Omsland
- Paul G. Allen School For Global Health, Washington State University, Pullman, Washington, USA
| | - Sean McCormick
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Travis J Chiarelli
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Scott S Grieshaber
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
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4
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Melki R, Litvak Y. From vacant to vivid: The nutritional landscape drives infant gut microbiota establishment. Mol Microbiol 2024. [PMID: 39044538 DOI: 10.1111/mmi.15296] [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: 10/11/2023] [Revised: 06/25/2024] [Accepted: 07/03/2024] [Indexed: 07/25/2024]
Abstract
From the moment of birth, the newborn gastrointestinal tract is infiltrated by various bacteria originating from both maternal and environmental sources. These colonizing bacteria form a complex microbiota community that undergoes continuous changes until adulthood and plays an important role in infant health. The maturation of the infant gut microbiota is driven by many factors and follows a distinct patterned trajectory, with specific bacterial taxa establish in the intestine in accordance with developmental milestones as the infant grows. In this review, we highlight how elements such as diet and host physiology select for specific microbial functions and shape the composition of the bacterial community in the large intestine.
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Affiliation(s)
- Reut Melki
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yael Litvak
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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5
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Sakurai R, Fukuda Y, Tada C. Circular metagenome-assembled genome of Candidatus Cloacimonadota recovered from anaerobic digestion sludge. Microbiol Resour Announc 2024; 13:e0040324. [PMID: 38916296 PMCID: PMC11256810 DOI: 10.1128/mra.00403-24] [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: 04/17/2024] [Accepted: 06/06/2024] [Indexed: 06/26/2024] Open
Abstract
This study reports a circular metagenome-assembled genome (cMAG) of Candidatus Cloacimonadota recovered from a mesophilic full-scale food waste treatment plant. The cMAG spans 2,298,113 bp, with 980× coverage and 1 contig.
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Affiliation(s)
- Riku Sakurai
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, Japan
| | - Yasuhiro Fukuda
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
| | - Chika Tada
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
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6
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Jiao JY, Ma SC, Salam N, Zhou Z, Lian ZH, Fu L, Chen Y, Peng CH, OuYang YT, Fan H, Li L, Yi Y, Zhang JY, Wang JY, Liu L, Gao L, Oren A, Woyke T, Dodsworth JA, Hedlund BP, Li WJ, Cheng L. Cultivation of novel Atribacterota from oil well provides new insight into their diversity, ecology, and evolution in anoxic, carbon-rich environments. MICROBIOME 2024; 12:123. [PMID: 38971798 PMCID: PMC11227167 DOI: 10.1186/s40168-024-01836-7] [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: 11/24/2023] [Accepted: 05/13/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND The Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood. RESULTS We report the isolation of the second member of Atribacterota, Thermatribacter velox gen. nov., sp. nov., within a new family Thermatribacteraceae fam. nov., and the short-term laboratory cultivation of a member of the JS1 lineage, Phoenicimicrobium oleiphilum HX-OS.bin.34TS, both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that Thermatribacter velox B11T and Phoenicimicrobium oleiphilum HX-OS.bin.34TS ferment sugars and n-alkanes, respectively, producing H2, CO2, and acetate as common products. Comparative genomics showed that all members of the Atribacterota lack a complete Wood-Ljungdahl Pathway (WLP), but that the Reductive Glycine Pathway (RGP) is widespread, indicating that the RGP, rather than WLP, is a central hub in Atribacterota metabolism. Ancestral character state reconstructions and phylogenetic analyses showed that key genes encoding the RGP (fdhA, fhs, folD, glyA, gcvT, gcvPAB, pdhD) and other central functions were gained independently in the two classes, Atribacteria (OP9) and Phoenicimicrobiia (JS1), after which they were inherited vertically; these genes included fumarate-adding enzymes (faeA; Phoenicimicrobiia only), the CODH/ACS complex (acsABCDE), and diverse hydrogenases (NiFe group 3b, 4b and FeFe group A3, C). Finally, we present genome-resolved community metabolic models showing the central roles of Atribacteria (OP9) and Phoenicimicrobiia (JS1) in acetate- and hydrocarbon-rich environments. CONCLUSION Our findings expand the knowledge of the diversity, physiology, ecology, and evolution of the phylum Atribacterota. This study is a starting point for promoting more incisive studies of their syntrophic biology and may guide the rational design of strategies to cultivate them in the laboratory. Video Abstract.
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Affiliation(s)
- Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shi-Chun Ma
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
- National Agri-Food Biotechnology Institute, Sector-81 (Knowledge City), Mohali, 140306, Punjab, India
| | - Zhuo Zhou
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Li Fu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Ying Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Cheng-Hui Peng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Yu-Ting OuYang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hui Fan
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Ling Li
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Yue Yi
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Jing-Yi Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jing-Yuan Wang
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lei Gao
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California Merced, Life and Environmental Sciences, Merced, CA, USA
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, 610000, People's Republic of China.
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7
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Schoelmerich MC, Ly L, West-Roberts J, Shi LD, Shen C, Malvankar NS, Taib N, Gribaldo S, Woodcroft BJ, Schadt CW, Al-Shayeb B, Dai X, Mozsary C, Hickey S, He C, Beaulaurier J, Juul S, Sachdeva R, Banfield JF. Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires. Nat Commun 2024; 15:5414. [PMID: 38926353 PMCID: PMC11208441 DOI: 10.1038/s41467-024-49548-8] [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: 04/11/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming "Candidatus Methanoperedens" archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes. 13 complete and four near-complete linear genomes share 40 genes that define a largely syntenous genome backbone. We use these conserved genes to identify new Borgs from peatland soil and to delineate Borg phylogeny, revealing two major clades. Remarkably, Borg genes encoding nanowire-like electron-transferring cytochromes and cell surface proteins are more highly expressed than those of host Methanoperedens, indicating that Borgs augment the Methanoperedens activity in situ. We reconstructed the first complete 4.00 Mbp genome for a Methanoperedens that is inferred to be a Borg host and predicted its methylation motifs, which differ from pervasive TC and CC methylation motifs of the Borgs. Thus, methylation may enable Methanoperedens to distinguish their genomes from those of Borgs. Very high Borg to Methanoperedens ratios and structural predictions suggest that Borgs may be capable of encapsulation. The findings clearly define Borgs as a distinct class of ECE with shared genomic signatures, establish their diversification from a common ancestor with genetic inheritance, and raise the possibility of periodic existence outside of host cells.
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Affiliation(s)
- Marie C Schoelmerich
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Environmental Systems Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Lynn Ly
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | - Jacob West-Roberts
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Ling-Dong Shi
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Deptartment of Molecular Biophysics and Biochemistry, Yale University, West Haven, CT, USA
| | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Deptartment of Molecular Biophysics and Biochemistry, Yale University, West Haven, CT, USA
| | - Najwa Taib
- Institut Pasteur, Université de Paris cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université de Paris cité, Unit Evolutionary Biology of the Microbial Cell, Paris, France
| | - Ben J Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD, Australia
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Basem Al-Shayeb
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | | | | | - Scott Hickey
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | - Christine He
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | | | - Sissel Juul
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
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8
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Chaudhari NM, Pérez-Carrascal OM, Overholt WA, Totsche KU, Küsel K. Genome streamlining in Parcubacteria transitioning from soil to groundwater. ENVIRONMENTAL MICROBIOME 2024; 19:41. [PMID: 38902796 PMCID: PMC11188291 DOI: 10.1186/s40793-024-00581-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/03/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics. RESULTS Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer. CONCLUSIONS Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.
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Affiliation(s)
- Narendrakumar M Chaudhari
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Friedrich-Schiller-Universität, Leipzig, Germany
| | - Olga M Pérez-Carrascal
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Will A Overholt
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany
| | - Kai U Totsche
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Hydrogeology, Institute of Geowissenschaften, Friedrich-Schiller-Universität Jena, Burgweg 11, 07749, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, Germany.
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Friedrich-Schiller-Universität, Leipzig, Germany.
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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9
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Dubois L, Valles-Colomer M, Ponsero A, Helve O, Andersson S, Kolho KL, Asnicar F, Korpela K, Salonen A, Segata N, de Vos WM. Paternal and induced gut microbiota seeding complement mother-to-infant transmission. Cell Host Microbe 2024; 32:1011-1024.e4. [PMID: 38870892 DOI: 10.1016/j.chom.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 04/03/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024]
Abstract
Microbial colonization of the neonatal gut involves maternal seeding, which is partially disrupted in cesarean-born infants and after intrapartum antibiotic prophylaxis. However, other physically close individuals could complement such seeding. To assess the role of both parents and of induced seeding, we analyzed two longitudinal metagenomic datasets (health and early life microbiota [HELMi]: N = 74 infants, 398 samples, and SECFLOR: N = 7 infants, 35 samples) with cesarean-born infants who received maternal fecal microbiota transplantation (FMT). We found that the father constitutes a stable source of strains for the infant independently of the delivery mode, with the cumulative contribution becoming comparable to that of the mother after 1 year. Maternal FMT increased mother-infant strain sharing in cesarean-born infants, raising the average bacterial empirical growth rate while reducing pathogen colonization. Overall, our results indicate that maternal seeding is partly complemented by that of the father and support the potential of induced seeding to restore potential deviations in this process.
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Affiliation(s)
- Léonard Dubois
- Department CIBIO, University of Trento, 38123 Trento, Italy
| | - Mireia Valles-Colomer
- Department CIBIO, University of Trento, 38123 Trento, Italy; MELIS Department, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Alise Ponsero
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Otto Helve
- Children's Hospital, Pediatric Research Center, University of Helsinki, and Helsinki University Hospital, 00014 Helsinki, Finland; Department of Health Security, Finnish Institute for Health and Welfare, 0014 Helsinki, Finland
| | - Sture Andersson
- Children's Hospital, Pediatric Research Center, University of Helsinki, and Helsinki University Hospital, 00014 Helsinki, Finland
| | - Kaija-Leena Kolho
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | | | - Katri Korpela
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Anne Salonen
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Nicola Segata
- Department CIBIO, University of Trento, 38123 Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy.
| | - Willem M de Vos
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland; Laboratory of Microbiology, University of Wageningen, 6703 WE Wageningen, the Netherlands.
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10
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Yang L, Lawhorn S, Bongrand C, Kosmopoulos JC, Kuwabara J, VanNieuwenhze M, Mandel MJ, McFall-Ngai M, Ruby E. Bacterial growth dynamics in a rhythmic symbiosis. Mol Biol Cell 2024; 35:ar79. [PMID: 38598294 PMCID: PMC11238090 DOI: 10.1091/mbc.e24-01-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024] Open
Abstract
The symbiotic relationship between the bioluminescent bacterium Vibrio fischeri and the bobtail squid Euprymna scolopes serves as a valuable system to investigate bacterial growth and peptidoglycan (PG) synthesis within animal tissues. To better understand the growth dynamics of V. fischeri in the crypts of the light-emitting organ of its juvenile host, we showed that, after the daily dawn-triggered expulsion of most of the population, the remaining symbionts rapidly proliferate for ∼6 h. At that point the population enters a period of extremely slow growth that continues throughout the night until the next dawn. Further, we found that PG synthesis by the symbionts decreases as they enter the slow-growing stage. Surprisingly, in contrast to the most mature crypts (i.e., Crypt 1) of juvenile animals, most of the symbiont cells in the least mature crypts (i.e., Crypt 3) were not expelled and, instead, remained in the slow-growing state throughout the day, with almost no cell division. Consistent with this observation, the expression of the gene encoding the PG-remodeling enzyme, L,D-transpeptidase (LdtA), was greatest during the slowly growing stage of Crypt 1 but, in contrast, remained continuously high in Crypt 3. Finally, deletion of the ldtA gene resulted in a symbiont that grew and survived normally in culture, but was increasingly defective in competing against its parent strain in the crypts. This result suggests that remodeling of the PG to generate additional 3-3 linkages contributes to the bacterium's fitness in the symbiosis, possibly in response to stresses encountered during the very slow-growing stage.
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Affiliation(s)
- Liu Yang
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - Susannah Lawhorn
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - Clotilde Bongrand
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | - James C. Kosmopoulos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Jill Kuwabara
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
| | | | - Mark J. Mandel
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53706
| | - Margaret McFall-Ngai
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Edward Ruby
- Carnegie Institution for Science, Pasadena, CA 91101
- Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96848
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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11
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Liao C, Rolling T, Djukovic A, Fei T, Mishra V, Liu H, Lindberg C, Dai L, Zhai B, Peled JU, van den Brink MRM, Hohl TM, Xavier JB. Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes. Nat Microbiol 2024; 9:1555-1565. [PMID: 38698178 PMCID: PMC11152985 DOI: 10.1038/s41564-024-01680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/20/2024] [Indexed: 05/05/2024]
Abstract
The detection of oral bacteria in faecal samples has been associated with inflammation and intestinal diseases. The increased relative abundance of oral bacteria in faeces has two competing explanations: either oral bacteria invade the gut ecosystem and expand (the 'expansion' hypothesis), or oral bacteria transit through the gut and their relative increase marks the depletion of other gut bacteria (the 'marker' hypothesis). Here we collected oral and faecal samples from mouse models of gut dysbiosis (antibiotic treatment and DSS-induced colitis) and used 16S ribosomal RNA sequencing to determine the abundance dynamics of oral bacteria. We found that the relative, but not absolute, abundance of oral bacteria increases, reflecting the 'marker' hypothesis. Faecal microbiome datasets from diverse patient cohorts, including healthy individuals and patients with allogeneic haematopoietic cell transplantation or inflammatory bowel disease, consistently support the 'marker' hypothesis and explain associations between oral bacterial abundance and patient outcomes consistent with depleted gut microbiota. By distinguishing between the two hypotheses, our study guides the interpretation of microbiome compositional data and could potentially identify cases where therapies are needed to rebuild the resident microbiome rather than protect against invading oral bacteria.
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Affiliation(s)
- Chen Liao
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thierry Rolling
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Division of Infectious Diseases, First Department of Medicine, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Ana Djukovic
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Teng Fei
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vishwas Mishra
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Medical College, New York, NY, USA
| | - Hongbin Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chloe Lindberg
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bing Zhai
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jonathan U Peled
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Marcel R M van den Brink
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Tobias M Hohl
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, New York, NY, USA.
| | - Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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12
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García-Lozano M, Henzler C, Porras MÁG, Pons I, Berasategui A, Lanz C, Budde H, Oguchi K, Matsuura Y, Pauchet Y, Goffredi S, Fukatsu T, Windsor D, Salem H. Paleocene origin of a streamlined digestive symbiosis in leaf beetles. Curr Biol 2024; 34:1621-1634.e9. [PMID: 38377997 DOI: 10.1016/j.cub.2024.01.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024]
Abstract
Timing the acquisition of a beneficial microbe relative to the evolutionary history of its host can shed light on the adaptive impact of a partnership. Here, we investigated the onset and molecular evolution of an obligate symbiosis between Cassidinae leaf beetles and Candidatus Stammera capleta, a γ-proteobacterium. Residing extracellularly within foregut symbiotic organs, Stammera upgrades the digestive physiology of its host by supplementing plant cell wall-degrading enzymes. We observe that Stammera is a shared symbiont across tortoise and hispine beetles that collectively comprise the Cassidinae subfamily, despite differences in their folivorous habits. In contrast to its transcriptional profile during vertical transmission, Stammera elevates the expression of genes encoding digestive enzymes while in the foregut symbiotic organs, matching the nutritional requirements of its host. Despite the widespread distribution of Stammera across Cassidinae beetles, symbiont acquisition during the Paleocene (∼62 mya) did not coincide with the origin of the subfamily. Early diverging lineages lack the symbiont and the specialized organs that house it. Reconstructing the ancestral state of host-beneficial factors revealed that Stammera encoded three digestive enzymes at the onset of symbiosis, including polygalacturonase-a pectinase that is universally shared. Although non-symbiotic cassidines encode polygalacturonase endogenously, their repertoire of plant cell wall-degrading enzymes is more limited compared with symbiotic beetles supplemented with digestive enzymes from Stammera. Highlighting the potential impact of a symbiotic condition and an upgraded metabolic potential, Stammera-harboring beetles exploit a greater variety of plants and are more speciose compared with non-symbiotic members of the Cassidinae.
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Affiliation(s)
- Marleny García-Lozano
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Christine Henzler
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | | | - Inès Pons
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Aileen Berasategui
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany; Amsterdam Institute for Life and Environment, Vrije Universiteit, Amsterdam 1081 HV, the Netherlands
| | - Christa Lanz
- Genome Center, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Heike Budde
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Kohei Oguchi
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan; Misaki Marine Biological Station, The University of Tokyo, Miura 238-0225, Japan
| | - Yu Matsuura
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Yannick Pauchet
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Shana Goffredi
- Department of Biology, Occidental College, Los Angeles, CA 90041, USA
| | - Takema Fukatsu
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Donald Windsor
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Hassan Salem
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany; Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama.
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13
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Sullivan GJ, Barquist L, Cain AK. A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria. mSystems 2024; 9:e0066523. [PMID: 38470252 PMCID: PMC11019837 DOI: 10.1128/msystems.00665-23] [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: 07/07/2023] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Functional genomics techniques, such as transposon insertion sequencing and RNA-sequencing, are key to studying relative differences in bacterial mutant fitness or gene expression under selective conditions. However, certain stress conditions, mutations, or antibiotics can directly interfere with DNA synthesis, resulting in systematic changes in local DNA copy numbers along the chromosome. This can lead to artifacts in sequencing-based functional genomics data when comparing antibiotic treatment to an unstressed control. Further, relative differences in gene-wise read counts may result from alterations in chromosomal replication dynamics, rather than selection or direct gene regulation. We term this artifact "chromosomal location bias" and implement a principled statistical approach to correct it by calculating local normalization factors along the chromosome. These normalization factors are then directly incorporated into statistical analyses using standard RNA-sequencing analysis methods without modifying the read counts themselves, preserving important information about the mean-variance relationship in the data. We illustrate the utility of this approach by generating and analyzing a ciprofloxacin-treated transposon insertion sequencing data set in Escherichia coli as a case study. We show that ciprofloxacin treatment generates chromosomal location bias in the resulting data, and we further demonstrate that failing to correct for this bias leads to false predictions of mutant drug sensitivity as measured by minimum inhibitory concentrations. We have developed an R package and user-friendly graphical Shiny application, ChromoCorrect, that detects and corrects for chromosomal bias in read count data, enabling the application of functional genomics technologies to the study of antibiotic stress.IMPORTANCEAltered gene dosage due to changes in DNA replication has been observed under a variety of stresses with a variety of experimental techniques. However, the implications of changes in gene dosage for sequencing-based functional genomics assays are rarely considered. We present a statistically principled approach to correcting for the effect of changes in gene dosage, enabling testing for differences in the fitness effects or regulation of individual genes in the presence of confounding differences in DNA copy number. We show that failing to correct for these effects can lead to incorrect predictions of resistance phenotype when applying functional genomics assays to investigate antibiotic stress, and we provide a user-friendly application to detect and correct for changes in DNA copy number.
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Affiliation(s)
- Geraldine J. Sullivan
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Lars Barquist
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Amy K. Cain
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, Australia
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14
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Sakurai R, Fukuda Y, Tada C. Circular metagenome-assembled genome of Candidatus Patescibacteria recovered from anaerobic digestion sludge. Microbiol Resour Announc 2024; 13:e0008324. [PMID: 38526092 PMCID: PMC11008200 DOI: 10.1128/mra.00083-24] [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: 01/29/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024] Open
Abstract
A single-contig, circular metagenome-assembled genome (cMAG) of Candidatus (Ca.) Patescibacteria was reconstructed from a mesophilic full-scale food waste treatment plant in Japan. The genome is of small size and lacks fundamental biosynthetic pathways. Taxonomic analysis using the Genome Taxonomy Database revealed that this cMAG belonged to the genus JAEZRQ01 (Ca. Parcubacteria).
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Affiliation(s)
- Riku Sakurai
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
- Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, Japan
| | - Yasuhiro Fukuda
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
| | - Chika Tada
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Osaki, Miyagi, Japan
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15
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Chen Z, Shi Z, Zhang Y, Shi Y, Sun M, Cui Y, Zhang S, Luo G. Metagenomic analysis towards understanding the effects of ammonia on chain elongation process for medium chain fatty acids production. BIORESOURCE TECHNOLOGY 2024; 395:130413. [PMID: 38310979 DOI: 10.1016/j.biortech.2024.130413] [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: 12/26/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/06/2024]
Abstract
The production of medium chain fatty acids (MCFAs) through chain elongation (CE) from organic wastes/wastewater has attracted much attention, while the effects of a common inhibitor-ammonia has not been elucidated. The mechanism of ammonia affecting CE was studied by metagenomic. The lag phase duration of caproate production was increased, and the maximum caproate production rate was decreased by 43.4 % at 4 g-N/L, as compared to 0 g-N/L. And hydrochar (HC) alleviated the inhibition of ammonia at 4 g-N/L. Metagenomic analysis indicated that ammonia induced UBA4085 sp.FDU78 as the dominant microorganism, and metabolic reconstruction revealed its potential CE ability. Furthermore, ammonia inhibited the reverse β oxidation pathway and Acetyl-CoA production pathway. The tolerance of UBA4085 sp.FDU78 to ammonia was associated with the uptake of inorganic ions, energy conservation, and synthesis of osmoprotectants. The present study provided a deep-insight on the ammonia tolerance mechanism on the CE process.
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Affiliation(s)
- Zheng Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Zhijian Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Yalei Zhang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; State Key Laboratory of Pollution Control and Resource Reuse, Shanghai 200092, China
| | - Yan Shi
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Meichen Sun
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Yong Cui
- Shanghai Wujiaochang Environmental Technology Co., Ltd, Shanghai 200438, China
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China; Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai 200438, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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16
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Shi Z, Zhang C, Tan X, Xie L, Luo G. Syntrophic microbes involved in the oxidation of short-chain fatty acids in continuous-flow anaerobic digesters treating waste activated sludge with hydrochar. Appl Environ Microbiol 2024; 90:e0204723. [PMID: 38205997 PMCID: PMC10880590 DOI: 10.1128/aem.02047-23] [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: 11/14/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
The rapid degradation of short-chain fatty acids (SCFAs) is an essential issue of anaerobic digestion (AD), in which SCFA oxidizers could generally metabolize in syntrophy with methanogens. The dynamic responses of active metagenome-assembled genomes to low concentrations of propionate and acetate were analyzed to identify specific syntrophic SCFA oxidizers and their metabolic characteristics in continuous-flow AD systems treating waste activated sludge with and without hydrochar. In this study, hydrochar increased methane production by 19%, possibly due to hydrochar enhancing acidification and methanogenesis processes. A putative syntrophic propionate oxidizer and two acetate oxidizers contributed substantially to the syntrophic degradation of SCFAs, and hydrochar positively regulated their functional gene expressions. A significant relationship was established between the replication rate of SCFA oxidizers and their stimulation-related transcriptional activity. Acetate was degraded in the hydrochar group, which might be mainly through the syntrophic acetate oxidizer from the genus Desulfallas and methanogens from the genus Methanosarcina.IMPORTANCEShort-chain fatty acid (SCFA) degradation is an important process in the methanogenic ecosystem. However, current knowledge of this microbial mechanism is mainly based on studies on a few model organisms incubated as mono- or co-cultures or in enrichments, which cannot provide appropriate evidence in complex environments. Here, this study revealed the microbial mechanism of a hydrochar-mediated anaerobic digestion (AD) system promoting SCFA degradation at the species level and identified key SCFA oxidizing bacteria. Our analysis provided new insights into the SCFA oxidizers involved in the AD of waste activated sludge facilitated by hydrochar.
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Affiliation(s)
- Zhijian Shi
- Department of Environmental Science and Engineering, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Fudan University, Shanghai, China
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai, China
| | - Chen Zhang
- Department of Environmental Science and Engineering, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Fudan University, Shanghai, China
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai, China
| | - Xuejun Tan
- Shanghai Municipal Engineering Design Institute (Group) Co., Ltd., Shanghai, China
| | - Li Xie
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, China
| | - Gang Luo
- Department of Environmental Science and Engineering, Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Fudan University, Shanghai, China
- Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
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17
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Zhang M, Zhao B, Yan Y, Cheng Z, Li Z, Han L, Sun Y, Zheng Y, Xia Y. Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169203. [PMID: 38086476 DOI: 10.1016/j.scitotenv.2023.169203] [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: 10/11/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d-1 and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.
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Affiliation(s)
- Miao Zhang
- School of Environment, Harbin Institute of Technology, Harbin 150001, China; School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuxi Yan
- School of Environment, Harbin Institute of Technology, Harbin 150001, China; School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhanwen Cheng
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zengyi Li
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Long Han
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuqin Sun
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yan Zheng
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China; Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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18
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Hessler T, Harrison ST, Banfield JF, Huddy RJ. Harnessing Fermentation May Enhance the Performance of Biological Sulfate-Reducing Bioreactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2830-2846. [PMID: 38301118 PMCID: PMC10867827 DOI: 10.1021/acs.est.3c04187] [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: 06/01/2023] [Revised: 12/28/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Biological sulfate reduction (BSR) represents a promising strategy for bioremediation of sulfate-rich waste streams, yet the impact of metabolic interactions on performance is largely unexplored. Here, genome-resolved metagenomics was used to characterize 17 microbial communities in reactors treating synthetic sulfate-contaminated solutions. Reactors were supplemented with lactate or acetate and a small amount of fermentable substrate. Of the 163 genomes representing all the abundant bacteria, 130 encode 321 NiFe and FeFe hydrogenases and all genomes of the 22 sulfate-reducing microorganisms (SRM) encode genes for H2 uptake. We observed lactate oxidation solely in the first packed bed reactor zone, with propionate and acetate oxidation in the middle and predominantly acetate oxidation in the effluent zone. The energetics of these reactions are very different, yet sulfate reduction kinetics were unaffected by the type of electron donor available. We hypothesize that the comparable rates, despite the typically slow growth of SRM on acetate, are a result of the consumption of H2 generated by fermentation. This is supported by the sustained performance of a predominantly acetate-supplemented stirred tank reactor dominated by diverse fermentative bacteria encoding FeFe hydrogenase genes and SRM capable of acetate and hydrogen consumption and CO2 assimilation. Thus, addition of fermentable substrates to stimulate syntrophic relationships may improve the performance of BSR reactors supplemented with inexpensive acetate.
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Affiliation(s)
- Tomas Hessler
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The
Innovative Genomics Institute at the University of California, Berkeley, California CA94720, United
States
- The
Department of Earth and Planetary Science, University of California, Berkeley, California CA94720, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, Berkeley, California CA94720, United States
| | - Susan T.L. Harrison
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The Future
Water Institute, University of Cape Town, Cape Town 7700, South Africa
| | - Jillian F. Banfield
- The
Innovative Genomics Institute at the University of California, Berkeley, California CA94720, United
States
- The
Department of Earth and Planetary Science, University of California, Berkeley, California CA94720, United States
- The
Department of Environmental Science, Policy and Management, University of California, Berkeley, California CA94720, United States
| | - Robert J. Huddy
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The Future
Water Institute, University of Cape Town, Cape Town 7700, South Africa
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19
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Abstract
Biogeography is the study of species distribution and diversity within an ecosystem and is at the core of how we understand ecosystem dynamics and interactions at the macroscale. In gut microbial communities, a historical reliance on bulk sequencing to probe community composition and dynamics has overlooked critical processes whereby microscale interactions affect systems-level microbiota function and the relationship with the host. In recent years, higher-resolution sequencing and novel single-cell level data have uncovered an incredible heterogeneity in microbial composition and have enabled a more nuanced spatial understanding of the gut microbiota. In an era when spatial transcriptomics and single-cell imaging and analysis have become key tools in mammalian cell and tissue biology, many of these techniques are now being applied to the microbiota. This fresh approach to intestinal biogeography has given important insights that span temporal and spatial scales, from the discovery of mucus encapsulation of the microbiota to the quantification of bacterial species throughout the gut. In this Review, we highlight emerging knowledge surrounding gut biogeography enabled by the observation and quantification of heterogeneity across multiple scales.
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Affiliation(s)
- Giselle McCallum
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carolina Tropini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada.
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20
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Man DKW, Hermans SM, Taubert M, Garcia SL, Hengoju S, Küsel K, Rosenbaum MA. Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique. ISME COMMUNICATIONS 2024; 4:ycae080. [PMID: 38946848 PMCID: PMC11214157 DOI: 10.1093/ismeco/ycae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/24/2024] [Accepted: 06/20/2024] [Indexed: 07/02/2024]
Abstract
The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.
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Affiliation(s)
- DeDe Kwun Wai Man
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
| | - Syrie M Hermans
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Food Science and Microbiology, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, 1142 Auckland, New Zealand
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
| | - Martin Taubert
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, 106 91 Stockholm, Sweden
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany
| | - Sundar Hengoju
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
| | - Kirsten Küsel
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
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21
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Deulofeu-Capo O, Sebastián M, Auladell A, Cardelús C, Ferrera I, Sánchez O, Gasol JM. Growth rates of marine prokaryotes are extremely diverse, even among closely related taxa. ISME COMMUNICATIONS 2024; 4:ycae066. [PMID: 38800126 PMCID: PMC11126302 DOI: 10.1093/ismeco/ycae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/31/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024]
Abstract
Marine prokaryotes play crucial roles in ocean biogeochemical cycles, being their contribution strongly influenced by their growth rates. Hence, elucidating the variability and phylogenetic imprint of marine prokaryotes' growth rates are crucial for better determining the role of individual taxa in biogeochemical cycles. Here, we estimated prokaryotic growth rates at high phylogenetic resolution in manipulation experiments using water from the northwestern Mediterranean Sea. Experiments were run in the four seasons with different treatments that reduced growth limiting factors: predators, nutrient availability, viruses, and light. Single-amplicon sequence variants (ASVs)-based growth rates were calculated from changes in estimated absolute abundances using total prokaryotic abundance and the proportion of each individual ASV. The trends obtained for growth rates in the different experiments were consistent with other estimates based on total cell-counts, catalyzed reporter deposition fluorescence in situ hybridization subcommunity cell-counts or metagenomic-operational taxonomic units (OTUs). Our calculations unveil a broad range of growth rates (0.3-10 d-1) with significant variability even within closely related ASVs. Likewise, the impact of growth limiting factors changed over the year for individual ASVs. High numbers of responsive ASVs were shared between winter and spring seasons, as well as throughout the year in the treatments with reduced nutrient limitation and viral pressure. The most responsive ASVs were rare in the in situ communities, comprising a large pool of taxa with the potential to rapidly respond to environmental changes. Essentially, our results highlight the lack of phylogenetic coherence in the range of growth rates observed, and differential responses to the various limiting factors, even for closely related taxa.
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Affiliation(s)
- Ona Deulofeu-Capo
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya 08003, Spain
| | - Marta Sebastián
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya 08003, Spain
| | - Adrià Auladell
- Institut de Biologia Evolutiva, CSIC-UPF, Barcelona 08003, Catalunya, Spain
| | - Clara Cardelús
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya 08003, Spain
| | - Isabel Ferrera
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, IEO-CSIC, Puerto Pesquero s/n, Fuengirola 29640, Málaga, Spain
| | - Olga Sánchez
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Catalunya 08193, Spain
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Barcelona, Catalunya 08003, Spain
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22
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Sharkey LKR, Guerillot R, Walsh CJ, Turner AM, Lee JYH, Neville SL, Klatt S, Baines SL, Pidot SJ, Rossello FJ, Seemann T, McWilliam HEG, Cho E, Carter GP, Howden BP, McDevitt CA, Hachani A, Stinear TP, Monk IR. The two-component system WalKR provides an essential link between cell wall homeostasis and DNA replication in Staphylococcus aureus. mBio 2023; 14:e0226223. [PMID: 37850732 PMCID: PMC10746227 DOI: 10.1128/mbio.02262-23] [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: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE The opportunistic human pathogen Staphylococcus aureus uses an array of protein sensing systems called two-component systems (TCS) to sense environmental signals and adapt its physiology in response by regulating different genes. This sensory network is key to S. aureus versatility and success as a pathogen. Here, we reveal for the first time the full extent of the regulatory network of WalKR, the only staphylococcal TCS that is indispensable for survival under laboratory conditions. We found that WalKR is a master regulator of cell growth, coordinating the expression of genes from multiple, fundamental S. aureus cellular processes, including those involved in maintaining cell wall metabolism, protein biosynthesis, nucleotide metabolism, and the initiation of DNA replication.
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Affiliation(s)
- Liam K. R. Sharkey
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Romain Guerillot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Calum J. Walsh
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Adrianna M. Turner
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jean Y. H. Lee
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephanie L. Neville
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephan Klatt
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, Parkville, Victoria, Australia
| | - Sarah L. Baines
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Fernando J. Rossello
- University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Hamish E. G. McWilliam
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ellie Cho
- Biological Optical Microscopy Platform, University of Melbourne, Melbourne, Victoria, Australia
| | - Glen P. Carter
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher A. McDevitt
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, Centre for Pathogen Genomics, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
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23
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Simon SA, Schmidt K, Griesdorn L, Soares AR, Bornemann TLV, Probst AJ. Dancing the Nanopore limbo - Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction. BMC Genomics 2023; 24:727. [PMID: 38041056 PMCID: PMC10693096 DOI: 10.1186/s12864-023-09853-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. Here, we evaluated lower-than-recommended DNA quantities for Nanopore library preparation by determining sequencing quality, community composition, assembly quality and recovery of MAGs. RESULTS We generated 27 Nanopore metagenomes using the commercially available ZYMO mock community and varied the amount of input DNA from 1000 ng (the recommended minimum) down to 1 ng in eight steps. The quality of the generated reads remained stable across all input levels. The read mapping accuracy, which reflects how well the reads match a known reference genome, was consistently high across all libraries. The relative abundance of the species in the metagenomes was stable down to input levels of 50 ng. High-quality MAGs (> 95% completeness, ≤ 5% contamination) could be recovered from metagenomes down to 35 ng of input material. When combined with publicly available Illumina reads for the mock community, Nanopore reads from input quantities as low as 1 ng improved the quality of hybrid assemblies. CONCLUSION Our results show that the recommended DNA amount for Nanopore library preparation can be substantially reduced without any adverse effects to genome recovery and still bolster hybrid assemblies when combined with short-read data. We posit that the results presented herein will enable studies to improve genome recovery from low-biomass environments, enhancing microbiome understanding.
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Affiliation(s)
- Sophie A Simon
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany.
| | - Katharina Schmidt
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
| | - Lea Griesdorn
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
| | - André R Soares
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Till L V Bornemann
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany.
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
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24
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Olm MR, Spencer SP, Silva EL, Sonnenburg JL. Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568153. [PMID: 38045399 PMCID: PMC10690254 DOI: 10.1101/2023.11.21.568153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
IgA, the most highly produced human antibody, is continually secreted into the gut to shape the intestinal microbiota. Methodological limitations have critically hindered defining which microbial strains are targeted by IgA and why. Here, we develop a new technique, Metagenomic Immunoglobulin Sequencing (MIG-Seq), and use it to determine IgA coating levels for thousands of gut microbiome strains in healthy humans. We find that microbes associated with both health and disease have higher levels of coating, and that microbial genes are highly predictive of IgA binding levels, with mucus degradation genes especially correlated with high binding. We find a significant reduction in replication rates among microbes bound by IgA, and demonstrate that IgA binding is more correlated with host immune status than traditional microbial abundance measures. This study introduces a powerful technique for assessing strain-level IgA binding in human stool, paving the way for deeper understanding of IgA-based host microbe interactions.
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Affiliation(s)
- Matthew R. Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean P. Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Gastroenterology and Hepatology, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Evelyn Lemus Silva
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin L. Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA, USA
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25
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Li S, Mosier D, Dong X, Kouris A, Ji G, Strous M, Diao M. Frequency of change determines effectiveness of microbial response strategies. THE ISME JOURNAL 2023; 17:2047-2057. [PMID: 37723339 PMCID: PMC10579261 DOI: 10.1038/s41396-023-01515-9] [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: 06/27/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]
Abstract
Nature challenges microbes with change at different frequencies and demands an effective response for survival. Here, we used controlled laboratory experiments to investigate the effectiveness of different response strategies, such as post-translational modification, transcriptional regulation, and specialized versus adaptable metabolisms. For this, we inoculated replicated chemostats with an enrichment culture obtained from sulfidic stream microbiomes 16 weeks prior. The chemostats were submitted to alternatingly oxic and anoxic conditions at three frequencies, with periods of 1, 4 and 16 days. The microbial response was recorded with 16S rRNA gene amplicon sequencing, shotgun metagenomics, transcriptomics and proteomics. Metagenomics resolved provisional genomes of all abundant bacterial populations, mainly affiliated with Proteobacteria and Bacteroidetes. Almost all these populations maintained a steady growth rate under both redox conditions at all three frequencies of change. Our results supported three conclusions: (1) Oscillating oxic/anoxic conditions selected for generalistic species, rather than species specializing in only a single condition. (2) A high frequency of change selected for strong codon usage bias. (3) Alignment of transcriptomes and proteomes required multiple generations and was dependent on a low frequency of change.
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Affiliation(s)
- Shengjie Li
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, 100871, Beijing, China
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Damon Mosier
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Angela Kouris
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, 100871, Beijing, China
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Muhe Diao
- Department of Geoscience, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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26
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Rahlff J, Wietz M, Giebel HA, Bayfield O, Nilsson E, Bergström K, Kieft K, Anantharaman K, Ribas-Ribas M, Schweitzer HD, Wurl O, Hoetzinger M, Antson A, Holmfeldt K. Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick. ISME COMMUNICATIONS 2023; 3:97. [PMID: 37723220 PMCID: PMC10507051 DOI: 10.1038/s43705-023-00307-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]
Abstract
Visible surface films, termed slicks, can extensively cover freshwater and marine ecosystems, with coastal regions being particularly susceptible to their presence. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (herein slick SML) harbors a distinctive bacterial community, but generally little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we characterized viruses and bacteria in a brackish slick SML in comparison to non-slick SML as well as seawater below slick and non-slick areas (subsurface water = SSW). Size-fractionated filtration of all samples distinguished viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. Specific metabolic profiles of bacterial metagenome-assembled genomes and isolates in the slick SML included a prevalence of genes encoding motility and carbohydrate-active enzymes (CAZymes). Several vOTUs were enriched in slick SML, and many virus variants were associated with particles. Nine vOTUs were only found in slick SML, six of them being targeted by slick SML-specific clustered-regularly interspaced short palindromic repeats (CRISPR) spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages for Alishewanella sp. and Pseudoalteromonas tunicata, abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks contributes to biogeochemical cycling in coastal ecosystems.
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Affiliation(s)
- Janina Rahlff
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
| | - Matthias Wietz
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Helge-Ansgar Giebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Center for Marine Sensors (ZfMarS), Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Wilhelmshaven, Germany
| | - Oliver Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Emelie Nilsson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Kristofer Bergström
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Kristopher Kieft
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Mariana Ribas-Ribas
- Center of Marine Sensors (ZfMarS), Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Wilhelmshaven, Germany
| | | | - Oliver Wurl
- Center of Marine Sensors (ZfMarS), Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Wilhelmshaven, Germany
| | - Matthias Hoetzinger
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Alfred Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Karin Holmfeldt
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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27
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Lim JJ, Diener C, Wilson J, Valenzuela JJ, Baliga NS, Gibbons SM. Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes. Nat Commun 2023; 14:5682. [PMID: 37709733 PMCID: PMC10502120 DOI: 10.1038/s41467-023-41424-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/04/2023] [Indexed: 09/16/2023] Open
Abstract
Longitudinal sampling of the stool has yielded important insights into the ecological dynamics of the human gut microbiome. However, human stool samples are available approximately once per day, while commensal population doubling times are likely on the order of minutes-to-hours. Despite this mismatch in timescales, much of the prior work on human gut microbiome time series modeling has assumed that day-to-day fluctuations in taxon abundances are related to population growth or death rates, which is likely not the case. Here, we propose an alternative model of the human gut as a stationary system, where population dynamics occur internally and the bacterial population sizes measured in a bolus of stool represent a steady-state endpoint of these dynamics. We formalize this idea as stochastic logistic growth. We show how this model provides a path toward estimating the growth phases of gut bacterial populations in situ. We validate our model predictions using an in vitro Escherichia coli growth experiment. Finally, we show how this method can be applied to densely-sampled human stool metagenomic time series data. We discuss how these growth phase estimates may be used to better inform metabolic modeling in flow-through ecosystems, like animal guts or industrial bioreactors.
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Affiliation(s)
- Joe J Lim
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, 98105, USA
| | | | - James Wilson
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Departments of Biology and Microbiology, University of Washington, Seattle, WA, 98105, USA
- Lawrence Berkeley National Laboratory, CA, 94720, Berkeley, USA
- Molecular and Cellular Biology Program, University of Washington, WA, 98105, Seattle, USA
- Molecular Engineering Graduate Program, University of Washington, WA, 98105, Seattle, USA
| | - Sean M Gibbons
- Institute for Systems Biology, Seattle, WA, 98109, USA.
- Molecular Engineering Graduate Program, University of Washington, WA, 98105, Seattle, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98105, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, 98105, USA.
- eScience Institute, University of Washington, Seattle, WA, 98105, USA.
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Desdouits M, Reynaud Y, Philippe C, Guyader FSL. A Comprehensive Review for the Surveillance of Human Pathogenic Microorganisms in Shellfish. Microorganisms 2023; 11:2218. [PMID: 37764063 PMCID: PMC10537662 DOI: 10.3390/microorganisms11092218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Bivalve molluscan shellfish have been consumed for centuries. Being filter feeders, they may bioaccumulate some microorganisms present in coastal water, either naturally or through the discharge of human or animal sewage. Despite regulations set up to avoid microbiological contamination in shellfish, human outbreaks still occur. After providing an overview showing their implication in disease, this review aims to highlight the diversity of the bacteria or enteric viruses detected in shellfish species, including emerging pathogens. After a critical discussion of the available methods and their limitations, we address the interest of technological developments using genomics to anticipate the emergence of pathogens. In the coming years, further research needs to be performed and methods need to be developed in order to design the future of surveillance and to help risk assessment studies, with the ultimate objective of protecting consumers and enhancing the microbial safety of bivalve molluscan shellfish as a healthy food.
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Affiliation(s)
| | | | | | - Françoise S. Le Guyader
- Ifremer, Unité Microbiologie Aliment Santé et Environnement, RBE/LSEM, 44311 Nantes, France; (M.D.); (Y.R.); (C.P.)
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White C, Antell E, Schwartz SL, Lawrence JE, Keren R, Zhou L, Yu K, Zhuang W, Alvarez-Cohen L. Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios. Front Microbiol 2023; 14:1243410. [PMID: 37637134 PMCID: PMC10450351 DOI: 10.3389/fmicb.2023.1243410] [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: 06/20/2023] [Accepted: 07/13/2023] [Indexed: 08/29/2023] Open
Abstract
Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4+:NO2-, where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4+:NO2- ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4+:NO2- ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4+:NO2- ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.
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Affiliation(s)
- Christian White
- Department of Civil & Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Edmund Antell
- Department of Civil & Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Sarah L. Schwartz
- Department of Civil & Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States
| | | | - Ray Keren
- Department of Civil & Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Lijie Zhou
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Weiqin Zhuang
- Department of Civil & Environmental Engineering, University of Auckland, Auckland, New Zealand
| | - Lisa Alvarez-Cohen
- Department of Civil & Environmental Engineering, University of California, Berkeley, Berkeley, CA, United States
- Earth and Environmental Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Li S, Diao M, Liao Y, Ji G. Performance, microbial growth and community interactions of iron-dependent denitrification in freshwaters. ENVIRONMENT INTERNATIONAL 2023; 178:108124. [PMID: 37540923 DOI: 10.1016/j.envint.2023.108124] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/21/2023] [Accepted: 07/30/2023] [Indexed: 08/06/2023]
Abstract
Iron-dependent denitrification is a safe and promising technology for nitrogen removal in freshwaters. However, the understanding of microbial physiology and interactions during the process was limited. Denitrifying systems inoculated with freshwater samples were operated with and without iron(II) at a low C/N ratio for 54 days. Iron addition improved nitrogen removal. Batch experiments confirmed that microbially mediated reaction rather than abiotic reaction dominated during the process. Metagenomics recovered genomes of the five most abundant microorganisms, which accounted for over 99% of the community in every triplicate of the iron-based system. Based on codon usage bias, all of them were fast-growing organisms. The total abundance of fast-growing organisms was 38% higher in the system with iron than in the system without iron. Notably, the most abundant organism Diaphorobacter did not have enzymes for asparagine and aspartate biosynthesis, whereas Rhodanobacter could not produce serine and cobalamin. Algoriphagus and Areminomonas lost synthesis enzymes for more amino acids and vitamins. However, they could always obtain these growth-required substances from another microorganism in the community. The two-partner relationship minimized the limitation on microbial reproduction and increased community stability. Our results indicated that iron addition improved nitrogen removal by supplying electron donors, promoting microbial growth, and building up syntrophic interactions among microorganisms with timely communications. The findings provided new insights into the process, with implications for freshwater remediation.
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Affiliation(s)
- Shengjie Li
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China; Department of Geoscience, University of Calgary, Calgary, AB T2N 1N4, Canada; Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Muhe Diao
- Department of Geoscience, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Yinhao Liao
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China
| | - Guodong Ji
- Key Laboratory of Water and Sediment Sciences, Ministry of Education, Department of Environmental Engineering, Peking University, Beijing 100871, China.
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31
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Lee HW, Yoon SR, Dang YM, Kang M, Lee K, Ha JH, Bae JW. Presence of an ultra-small microbiome in fermented cabbages. PeerJ 2023; 11:e15680. [PMID: 37483986 PMCID: PMC10358336 DOI: 10.7717/peerj.15680] [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: 02/14/2023] [Accepted: 06/13/2023] [Indexed: 07/25/2023] Open
Abstract
Background Ultramicrobacteria (UMB), also known as ultra-small bacteria, are tiny bacteria with a size less than 0.1 µm3. They have a high surface-to-volume ratio and are found in various ecosystems, including the human body. UMB can be classified into two types: one formed through cell contraction and the other that maintains a small size. The ultra-small microbiome (USM), which may contain UMB, includes all bacteria less than 0.2 µm in size and is difficult to detect with current methods. However, it poses a potential threat to food hygiene, as it can pass through sterilization filters and exist in a viable but non-culturable (VBNC) state. The data on the USM of foods is limited. Some bacteria, including pathogenic species, are capable of forming UMB under harsh conditions, making it difficult to detect them through conventional culture techniques. Methods The study described above focused on exploring the diversity of USM in fermented cabbage samples from three different countries (South Korea, China, and Germany). The samples of fermented cabbage (kimchi, suancai, and sauerkraut) were purchased and stored in chilled conditions at approximately 4 °C until filtration. The filtration process involved two steps of tangential flow filtration (TFF) using TFF cartridges with different pore sizes (0.2 µm and 100 kDa) to separate normal size bacteria (NM) and USM. The USM and NM isolated via TFF were stored in a refrigerator at 4 °C until DNA extraction. The extracted DNA was then amplified using PCR and the full-length 16S rRNA gene was sequenced using single-molecule-real-time (SMRT) sequencing. The transmission electron microscope (TEM) was used to confirm the presence of microorganisms in the USM of fermented cabbage samples. Results To the best of our knowledge, this is the first study to identify the differences between USM and NM in fermented cabbages. Although the size of the USM (average 2,171,621 bp) was smaller than that of the NM (average 15,727,282 bp), diversity in USM (average H' = 1.32) was not lower than that in NM (average H' = 1.22). In addition, some members in USM probably underwent cell shrinkage due to unfavorable environments, while others maintained their size. Major pathogens were not detected in the USM in fermented cabbages. Nevertheless, several potentially suspicious strains (genera Cellulomonas and Ralstonia) were detected. Our method can be used to screen food materials for the presence of USM undetectable via conventional methods. USM and NM were efficiently separated using tangential flow filtration and analyzed via single-molecule real-time sequencing. The USM of fermented vegetables exhibited differences in size, diversity, and composition compared with the conventional microbiome. This study could provide new insights into the ultra-small ecosystem in fermented foods, including fermented cabbages.
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Affiliation(s)
- Hae-Won Lee
- Hygienic Safety ⋅ Materials Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - So-Ra Yoon
- Hygienic Safety ⋅ Materials Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Yun-Mi Dang
- Hygienic Safety ⋅ Materials Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Miran Kang
- Practical Technology Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Kwangho Lee
- Center for Research Facilities, Chonnam National University, Gwangju, Republic of Korea
| | - Ji-Hyung Ha
- Hygienic Safety ⋅ Materials Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
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32
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Walkup J, Dang C, Mau RL, Hayer M, Schwartz E, Stone BW, Hofmockel KS, Koch BJ, Purcell AM, Pett-Ridge J, Wang C, Hungate BA, Morrissey EM. The predictive power of phylogeny on growth rates in soil bacterial communities. ISME COMMUNICATIONS 2023; 3:73. [PMID: 37454187 PMCID: PMC10349831 DOI: 10.1038/s43705-023-00281-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement of taxon-specific traits within natural microbial communities. There is mounting evidence of a phylogenetic signal in these traits, which may support prediction and microbiome management frameworks. We investigated phylogeny-based trait prediction using bacterial growth rates from soil communities in Arctic, boreal, temperate, and tropical ecosystems. Here we show that phylogeny predicts growth rates of soil bacteria, explaining an average of 31%, and up to 58%, of the variation within ecosystems. Despite limited overlap in community composition across these ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Phylogenetic relationships could explain up to 38% (averaging 14%) of the variation in growth rates across the highly disparate ecosystems studied. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria in the wild, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems.
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Affiliation(s)
- Jeth Walkup
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Chansotheary Dang
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Bram W Stone
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kirsten S Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Alicia M Purcell
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA
- University of California Merced, Life & Environmental Sciences Department, Merced, CA, 95343, USA
| | - Chao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, LN, China
| | - Bruce A Hungate
- Center for Ecosystem Science and Society (Ecoss), Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Ember M Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA.
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Carter MM, Olm MR, Merrill BD, Dahan D, Tripathi S, Spencer SP, Yu FB, Jain S, Neff N, Jha AR, Sonnenburg ED, Sonnenburg JL. Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell 2023; 186:3111-3124.e13. [PMID: 37348505 PMCID: PMC10330870 DOI: 10.1016/j.cell.2023.05.046] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 02/12/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.
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Affiliation(s)
- Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Bryan D Merrill
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Surya Tripathi
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Sean P Spencer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Feiqiao B Yu
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sunit Jain
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aashish R Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Erica D Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA.
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Center for Human Microbiome Studies, Stanford University School of Medicine, Stanford, CA 94304, USA.
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34
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Long GS, Hider J, Duggan AT, Klunk J, Eaton K, Karpinski E, Giuffra V, Ventura L, Prowse TL, Fornaciari A, Fornaciari G, Holmes EC, Golding GB, Poinar HN. A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade. PLoS Pathog 2023; 19:e1011538. [PMID: 37523413 PMCID: PMC10414615 DOI: 10.1371/journal.ppat.1011538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 08/10/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023] Open
Abstract
Brucellosis is a disease caused by the bacterium Brucella and typically transmitted through contact with infected ruminants. It is one of the most common chronic zoonotic diseases and of particular interest to public health agencies. Despite its well-known transmission history and characteristic symptoms, we lack a more complete understanding of the evolutionary history of its best-known species-Brucella melitensis. To address this knowledge gap we fortuitously found, sequenced and assembled a high-quality ancient B. melitensis draft genome from the kidney stone of a 14th-century Italian friar. The ancient strain contained fewer core genes than modern B. melitensis isolates, carried a complete complement of virulence genes, and did not contain any indication of significant antimicrobial resistances. The ancient B. melitensis genome fell as a basal sister lineage to a subgroup of B. melitensis strains within the Western Mediterranean phylogenetic group, with a short branch length indicative of its earlier sampling time, along with a similar gene content. By calibrating the molecular clock we suggest that the speciation event between B. melitensis and B. abortus is contemporaneous with the estimated time frame for the domestication of both sheep and goats. These results confirm the existence of the Western Mediterranean clade as a separate group in the 14th CE and suggest that its divergence was due to human and ruminant co-migration.
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Affiliation(s)
- George S. Long
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Jessica Hider
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Ana T. Duggan
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Jennifer Klunk
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Daicel Arbor Biosciences, Ann Arbor, Michigan, United States of America
| | - Katherine Eaton
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Emil Karpinski
- Department of Biology, McMaster University, Hamilton, Canada
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Luca Ventura
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
- Division of Pathology, San Salvatore Hospital, Coppito, Italy
| | - Tracy L. Prowse
- Department of Anthropology, McMaster University, Hamilton, Canada
| | - Antonio Fornaciari
- Division of Paleopathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, University of Sydney, Sydney, Australia
| | | | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Canada
- Department of Anthropology, McMaster University, Hamilton, Canada
- Department of Biochemistry, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- CIFAR Humans and the Microbiome Program, Toronto, Canada
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Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS. Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization. Nat Commun 2023; 14:3510. [PMID: 37316519 PMCID: PMC10267222 DOI: 10.1038/s41467-023-39121-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial community function depends on both taxonomic composition and spatial organization. While composition of the human gut microbiome has been deeply characterized, less is known about the organization of microbes between regions such as lumen and mucosa and the microbial genes regulating this organization. Using a defined 117 strain community for which we generate high-quality genome assemblies, we model mucosa/lumen organization with in vitro cultures incorporating mucin hydrogel carriers as surfaces for bacterial attachment. Metagenomic tracking of carrier cultures reveals increased diversity and strain-specific spatial organization, with distinct strains enriched on carriers versus liquid supernatant, mirroring mucosa/lumen enrichment in vivo. A comprehensive search for microbial genes associated with this spatial organization identifies candidates with known adhesion-related functions, as well as novel links. These findings demonstrate that carrier cultures of defined communities effectively recapitulate fundamental aspects of gut spatial organization, enabling identification of key microbial strains and genes.
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Affiliation(s)
- Xiaofan Jin
- Gladstone Institutes, San Francisco, CA, USA
| | | | - Jia Yan
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Xiandong Meng
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- University of California San Francisco, San Francisco, CA, USA.
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36
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Bornemann TLV, Esser SP, Stach TL, Burg T, Probst AJ. uBin: A manual refining tool for genomes from metagenomes. Environ Microbiol 2023; 25:1077-1083. [PMID: 36764661 DOI: 10.1111/1462-2920.16351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023]
Abstract
Resolving bacterial and archaeal genomes from metagenomes has revolutionized our understanding of Earth's biomes yet producing high-quality genomes from assembled fragments has been an ever-standing problem. While automated binning software and their combination produce prokaryotic bins in high throughput, their manual refinement has been slow, sometimes difficult or missing entirely facilitating error propagation in public databases. Here, we present uBin, a GUI-based, standalone bin refiner that runs on all major operating platforms and was additionally designed for educational purposes. When applied to the public CAMI dataset, refinement of bins using GC content, coverage and taxonomy was able to improve 78.9% of bins by decreasing their contamination. We also applied the bin refiner as a standalone binner to public metagenomes from the International Space Station and demonstrate the recovery of near-complete genomes, whose replication indices indicate the active proliferation of microbes in Earth's lower orbit. uBin is an easy to instal software for bin refinement, binning of simple metagenomes and communication of metagenomic results to other scientists and in classrooms. The software and its helper scripts are open source and available under https://github.com/ProbstLab/uBin.
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Affiliation(s)
- Till L V Bornemann
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
| | - Sarah P Esser
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
| | - Tom L Stach
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
| | - Tim Burg
- Independent Researcher, Im Acker 59, Koblenz, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Germany
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37
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Zhou Z, Tran PQ, Adams AM, Kieft K, Breier JA, Fortunato CS, Sheik CS, Huber JA, Li M, Dick GJ, Anantharaman K. Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes. THE ISME JOURNAL 2023:10.1038/s41396-023-01421-0. [PMID: 37179442 DOI: 10.1038/s41396-023-01421-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
In globally distributed deep-sea hydrothermal vent plumes, microbiomes are shaped by the redox energy landscapes created by reduced hydrothermal vent fluids mixing with oxidized seawater. Plumes can disperse over thousands of kilometers and their characteristics are determined by geochemical sources from vents, e.g., hydrothermal inputs, nutrients, and trace metals. However, the impacts of plume biogeochemistry on the oceans are poorly constrained due to a lack of integrated understanding of microbiomes, population genetics, and geochemistry. Here, we use microbial genomes to understand links between biogeography, evolution, and metabolic connectivity, and elucidate their impacts on biogeochemical cycling in the deep sea. Using data from 36 diverse plume samples from seven ocean basins, we show that sulfur metabolism defines the core microbiome of plumes and drives metabolic connectivity in the microbial community. Sulfur-dominated geochemistry influences energy landscapes and promotes microbial growth, while other energy sources influence local energy landscapes. We further demonstrated the consistency of links among geochemistry, function, and taxonomy. Amongst all microbial metabolisms, sulfur transformations had the highest MW-score, a measure of metabolic connectivity in microbial communities. Additionally, plume microbial populations have low diversity, short migration history, and gene-specific sweep patterns after migrating from background seawater. Selected functions include nutrient uptake, aerobic oxidation, sulfur oxidation for higher energy yields, and stress responses for adaptation. Our findings provide the ecological and evolutionary bases of change in sulfur-driven microbial communities and their population genetics in adaptation to changing geochemical gradients in the oceans.
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Affiliation(s)
- Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Freshwater and Marine Sciences Graduate Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alyssa M Adams
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kristopher Kieft
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John A Breier
- School of Earth, Environmental, and Marine Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | | | - Cody S Sheik
- Department of Biology and Large Lakes Observatory, University of Minnesota Duluth, Duluth, MN, 55812, USA
| | - Julie A Huber
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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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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39
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Verma AK, Noumani A, Yadav AK, Solanki PR. FRET Based Biosensor: Principle Applications Recent Advances and Challenges. Diagnostics (Basel) 2023; 13:diagnostics13081375. [PMID: 37189476 DOI: 10.3390/diagnostics13081375] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 05/17/2023] Open
Abstract
Förster resonance energy transfer (FRET)-based biosensors are being fabricated for specific detection of biomolecules or changes in the microenvironment. FRET is a non-radiative transfer of energy from an excited donor fluorophore molecule to a nearby acceptor fluorophore molecule. In a FRET-based biosensor, the donor and acceptor molecules are typically fluorescent proteins or fluorescent nanomaterials such as quantum dots (QDs) or small molecules that are engineered to be in close proximity to each other. When the biomolecule of interest is present, it can cause a change in the distance between the donor and acceptor, leading to a change in the efficiency of FRET and a corresponding change in the fluorescence intensity of the acceptor. This change in fluorescence can be used to detect and quantify the biomolecule of interest. FRET-based biosensors have a wide range of applications, including in the fields of biochemistry, cell biology, and drug discovery. This review article provides a substantial approach on the FRET-based biosensor, principle, applications such as point-of-need diagnosis, wearable, single molecular FRET (smFRET), hard water, ions, pH, tissue-based sensors, immunosensors, and aptasensor. Recent advances such as artificial intelligence (AI) and Internet of Things (IoT) are used for this type of sensor and challenges.
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Affiliation(s)
- Awadhesh Kumar Verma
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ashab Noumani
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Amit K Yadav
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pratima R Solanki
- Lab D NanoBiolab, Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067, India
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40
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Stach TL, Sieber G, Shah M, Simon SA, Soares A, Bornemann TLV, Plewka J, Künkel J, Becker C, Meyer F, Boenigk J, Probst AJ. Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater. Microbiologyopen 2023; 12:e1347. [PMID: 37186231 PMCID: PMC10012233 DOI: 10.1002/mbo3.1347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/02/2023] [Accepted: 02/17/2023] [Indexed: 03/15/2023] Open
Abstract
Microbial communities in freshwater streams play an essential role in ecosystem functioning via biogeochemical cycling. Yet, the impacts of treated wastewater influx into stream ecosystems on microbial strain diversity remain mostly unexplored. Here, we coupled full-length 16S ribosomal RNA gene Nanopore sequencing and strain-resolved metagenomics to investigate the impact of treated wastewater on a mesocosm system (AquaFlow) run with restored river water. Over 10 days, community Bray-Curtis dissimilarities between treated and control mesocosm decreased (0.57 ± 0.058 to 0.26 ± 0.046) based on ribosomal protein S3 gene clustering, finally converging to nearly identical communities. Similarly, strain-resolved metagenomics revealed a high diversity of bacteria and viruses after the introduction of treated wastewater; these microbes also decreased over time resulting in the same strain clusters in control and treatment at the end of the experiment. Specifically, 39.2% of viral strains detected in all samples were present after the introduction of treated wastewater only. Although bacteria present at low abundance in the treated wastewater introduced additional antibiotic resistance genes, signals of naturally occurring ARG-encoding organisms resembled the resistome at the endpoint. Our results suggest that the previously stressed freshwater stream and its microbial community are resilient to a substantial introduction of treated wastewater.
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Affiliation(s)
- Tom L. Stach
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | - Guido Sieber
- Department of BiodiversityUniversity of Duisburg‐EssenEssenGermany
| | - Manan Shah
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
- Department of BiodiversityUniversity of Duisburg‐EssenEssenGermany
| | - Sophie A. Simon
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | - André Soares
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | - Till L. V. Bornemann
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | - Julia Plewka
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | - Julian Künkel
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
| | | | - Folker Meyer
- Institute for Artificial IntelligenceUniversity of Duisburg‐EssenEssenGermany
| | - Jens Boenigk
- Department of BiodiversityUniversity of Duisburg‐EssenEssenGermany
- Centre of Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Alexander J. Probst
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of ChemistryUniversity of Duisburg‐EssenEssenGermany
- Centre of Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
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41
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Tan CCS, Ko KKK, Chen H, Liu J, Loh M, Chia M, Nagarajan N. No evidence for a common blood microbiome based on a population study of 9,770 healthy humans. Nat Microbiol 2023; 8:973-985. [PMID: 36997797 PMCID: PMC10159858 DOI: 10.1038/s41564-023-01350-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 03/02/2023] [Indexed: 04/01/2023]
Abstract
Human blood is conventionally considered sterile but recent studies suggest the presence of a blood microbiome in healthy individuals. Here we characterized the DNA signatures of microbes in the blood of 9,770 healthy individuals using sequencing data from multiple cohorts. After filtering for contaminants, we identified 117 microbial species in blood, some of which had DNA signatures of microbial replication. They were primarily commensals associated with the gut (n = 40), mouth (n = 32) and genitourinary tract (n = 18), and were distinct from pathogens detected in hospital blood cultures. No species were detected in 84% of individuals, while the remainder only had a median of one species. Less than 5% of individuals shared the same species, no co-occurrence patterns between different species were observed and no associations between host phenotypes and microbes were found. Overall, these results do not support the hypothesis of a consistent core microbiome endogenous to human blood. Rather, our findings support the transient and sporadic translocation of commensal microbes from other body sites into the bloodstream.
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Affiliation(s)
- Cedric C S Tan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- UCL Genetics Institute, University College London, London, UK.
| | - Karrie K K Ko
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
- Department of Microbiology, Singapore General Hospital, Singapore, Republic of Singapore
- Department of Molecular Pathology, Singapore General Hospital, Singapore, Republic of Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Hui Chen
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Jianjun Liu
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Marie Loh
- Population and Global Health, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore
- Department of Epidemiology and Biostatistics, Imperial College London, South Kensington, London, UK
- National Skin Centre, Singapore, Republic of Singapore
| | - Minghao Chia
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.
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42
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Neumann CJ, Mahnert A, Kumpitsch C, Kiu R, Dalby MJ, Kujawska M, Madl T, Kurath-Koller S, Urlesberger B, Resch B, Hall LJ, Moissl-Eichinger C. Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine. Nat Commun 2023; 14:1349. [PMID: 36906612 PMCID: PMC10008552 DOI: 10.1038/s41467-023-36825-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/13/2023] [Indexed: 03/13/2023] Open
Abstract
Preterm infants with very low birthweight are at serious risk for necrotizing enterocolitis. To functionally analyse the principles of three successful preventive NEC regimens, we characterize fecal samples of 55 infants (<1500 g, n = 383, female = 22) longitudinally (two weeks) with respect to gut microbiome profiles (bacteria, archaea, fungi, viruses; targeted 16S rRNA gene sequencing and shotgun metagenomics), microbial function, virulence factors, antibiotic resistances and metabolic profiles, including human milk oligosaccharides (HMOs) and short-chain fatty acids (German Registry of Clinical Trials, No.: DRKS00009290). Regimens including probiotic Bifidobacterium longum subsp. infantis NCDO 2203 supplementation affect microbiome development globally, pointing toward the genomic potential to convert HMOs. Engraftment of NCDO 2203 is associated with a substantial reduction of microbiome-associated antibiotic resistance as compared to regimens using probiotic Lactobacillus rhamnosus LCR 35 or no supplementation. Crucially, the beneficial effects of Bifidobacterium longum subsp. infantis NCDO 2203 supplementation depends on simultaneous feeding with HMOs. We demonstrate that preventive regimens have the highest impact on development and maturation of the gastrointestinal microbiome, enabling the establishment of a resilient microbial ecosystem that reduces pathogenic threats in at-risk preterm infants.
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Affiliation(s)
- Charlotte J Neumann
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine; Medical University of Graz, Graz, Styria, 8010, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine; Medical University of Graz, Graz, Styria, 8010, Austria
| | - Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine; Medical University of Graz, Graz, Styria, 8010, Austria
| | - Raymond Kiu
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Matthew J Dalby
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Magdalena Kujawska
- Chair of Intestinal Microbiome, School of Life Sciences, ZIEL-Institute for Food & Health; Technical University of Munich, Freising, Bavaria, 85354, Germany
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & Biochemistry, Medical University of Graz, Graz, Styria, 8010, Austria
- BioTechMed, Graz, Styria, 8010, Austria
| | - Stefan Kurath-Koller
- Division of Paediatric Cardiology, Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Graz, Styria, 8036, Austria
| | - Berndt Urlesberger
- Division of Neonatology; Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Graz, Styria, 8036, Austria
- Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Graz, Styria, 8036, Austria
| | - Bernhard Resch
- Division of Neonatology; Department of Paediatrics and Adolescent Medicine, Medical University of Graz, Graz, Styria, 8036, Austria.
- Research Unit for Neonatal Infectious Diseases and Epidemiology, Medical University of Graz, Graz, Styria, 8036, Austria.
| | - Lindsay J Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Chair of Intestinal Microbiome, School of Life Sciences, ZIEL-Institute for Food & Health; Technical University of Munich, Freising, Bavaria, 85354, Germany
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine; Medical University of Graz, Graz, Styria, 8010, Austria.
- BioTechMed, Graz, Styria, 8010, Austria.
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43
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Strains Colonizing Different Intestinal Sites within an Individual Are Derived from a Single Founder Population. mBio 2023; 14:e0345622. [PMID: 36719226 PMCID: PMC9972980 DOI: 10.1128/mbio.03456-22] [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] [Indexed: 02/01/2023] Open
Abstract
Metagenomics has improved our understanding of commensal bacteria that colonize human intestines yet relies almost exclusively on fecal samples. Thus, spatial information about the niche range of these gut microbes and the level of specialized adaptation that they undergo has been inaccessible to fecal metagenomic studies. Here, we leveraged metagenomic data obtained through colonoscopy aspirates from three intestinal sites of healthy adults, and reconstructed metagenome-assembled genomes of several common gut bacteria to address intestinal site-specific evolution. We show that the genomes of bacterial strains at specific intestinal sites are clearly distinct yet are interrelated and are derived from a single founder strain colonizing multiple sites. We also reveal that within those intestinal sites, purifying selection is the dominant evolutionary force acting on Escherichia coli genomes within human hosts. Importantly, no site-specific adaptations at the level of accessory genes were detected, implying that these commensals are well-adapted to several host microniches and can therefore colonize multiple intestinal sites with high efficiency. Nevertheless, bacterial in situ growth rates differ markedly across different sections of the intestine. Metagenomics of aspirate samples can reveal unique strain- and intestinal tissue-specific genomic information. Such information may be critical for understanding bacterial contribution to gastrointestinal diseases, which involve only a part of the intestine, as is often the case in inflammatory bowel disease. IMPORTANCE By reconstructing bacterial genomes from samples taken from specific sites within the human intestines, via aspiration, we show that strains at specific intestinal sites are genetically distinct yet interrelated and are derived from a single founder population. Organ-specific metagenomic information represents a powerful tool to generate insights into gastrointestinal diseases, which involve only a part of the intestine, such as inflammatory bowel disease.
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44
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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: 7] [Impact Index Per Article: 7.0] [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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45
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Larkin AA, Hagstrom GI, Brock ML, Garcia NS, Martiny AC. Basin-scale biogeography of Prochlorococcus and SAR11 ecotype replication. THE ISME JOURNAL 2023; 17:185-194. [PMID: 36273241 PMCID: PMC9589681 DOI: 10.1038/s41396-022-01332-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022]
Abstract
Establishing links between microbial diversity and environmental processes requires resolving the high degree of functional variation among closely related lineages or ecotypes. Here, we implement and validate an improved metagenomic approach that estimates the spatial biogeography and environmental regulation of ecotype-specific replication patterns (RObs) across ocean regions. A total of 719 metagenomes were analyzed from meridional Bio-GO-SHIP sections in the Atlantic and Indian Ocean. Accounting for sequencing bias and anchoring replication estimates in genome structure were critical for identifying physiologically relevant biological signals. For example, ecotypes within the dominant marine cyanobacteria Prochlorococcus exhibited distinct diel cycles in RObs that peaked between 19:00-22:00. Additionally, both Prochlorococcus ecotypes and ecotypes within the highly abundant heterotroph Pelagibacter (SAR11) demonstrated systematic biogeographies in RObs that differed from spatial patterns in relative abundance. Finally, RObs was significantly regulated by nutrient stress and temperature, and explained by differences in the genomic potential for nutrient transport, energy production, cell wall structure, and replication. Our results suggest that our new approach to estimating replication is reflective of gross population growth. Moreover, this work reveals that the interaction between adaptation and environmental change drives systematic variability in replication patterns across ocean basins that is ecotype-specific, adding an activity-based dimension to our understanding of microbial niche space.
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Affiliation(s)
- Alyse A Larkin
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - George I Hagstrom
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Melissa L Brock
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Nathan S Garcia
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Adam C Martiny
- Department of Earth System Science, University of California, Irvine, CA, USA.
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
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46
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Hammer TJ, Easton-Calabria A, Moran NA. Microbiome assembly and maintenance across the lifespan of bumble bee workers. Mol Ecol 2023; 32:724-740. [PMID: 36333950 PMCID: PMC9871002 DOI: 10.1111/mec.16769] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/13/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
Abstract
How a host's microbiome changes over its lifespan can influence development and ageing. As these temporal patterns have only been described in detail for a handful of hosts, an important next step is to compare microbiome succession more broadly and investigate why it varies. Here we characterize the temporal dynamics and stability of the bumble bee worker gut microbiome. Bumble bees have simple and host-specific gut microbiomes, and their microbial dynamics may influence health and pollination services. We used 16S rRNA gene sequencing, quantitative PCR and metagenomics to characterize gut microbiomes over the lifespan of Bombus impatiens workers. We also sequenced gut transcriptomes to examine host factors that may control the microbiome. At the community level, microbiome assembly is highly predictable and similar to patterns of primary succession observed in the human gut. However, at the strain level, partitioning of bacterial variants among colonies suggests stochastic colonization events similar to those observed in flies and nematodes. We also find strong differences in temporal dynamics among symbiont species, suggesting ecological differences among microbiome members in colonization and persistence. Finally, we show that both the gut microbiome and host transcriptome-including expression of key immunity genes-stabilize, as opposed to senesce, with age. We suggest that in highly social groups such as bumble bees, maintenance of both microbiomes and immunity contribute to inclusive fitness, and thus remain under selection even in old age. Our findings provide a foundation for exploring the mechanisms and functional outcomes of bee microbiome succession.
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Affiliation(s)
- Tobin J. Hammer
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697,Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703,Corresponding author:
| | | | - Nancy A. Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78703
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47
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Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins. PLoS Biol 2023; 21:e3001980. [PMID: 36701369 PMCID: PMC9879509 DOI: 10.1371/journal.pbio.3001980] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 12/23/2022] [Indexed: 01/27/2023] Open
Abstract
Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate the characteristics of TRs in all ten complete Borg genomes. We find that TR regions are rapidly evolving, recently formed, arise independently, and are virtually absent in host Methanoperedens genomes. Flanking partial repeats and A-enriched character constrain the TR formation mechanism. TRs can be in intergenic regions, where they might serve as regulatory RNAs, or in open reading frames (ORFs). TRs in ORFs are under very strong selective pressure, leading to perfect amino acid TRs (aaTRs) that are commonly intrinsically disordered regions. Proteins with aaTRs are often extracellular or membrane proteins, and functionally similar or homologous proteins often have aaTRs composed of the same amino acids. We propose that Borg aaTR-proteins functionally diversify Methanoperedens and all TRs are crucial for specific Borg-host associations and possibly cospeciation.
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48
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Beauchemin ET, Hunter C, Maurice CF. Actively replicating gut bacteria identified by 5-ethynyl-2'-deoxyuridine (EdU) click chemistry and cell sorting. Gut Microbes 2023; 15:2180317. [PMID: 36823031 PMCID: PMC9980609 DOI: 10.1080/19490976.2023.2180317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The composition of the intestinal bacterial community is well described, but recent research suggests that the metabolism of these bacteria plays a larger role in health than which species are present. One fundamental aspect of gut bacterial metabolism that remains understudied is bacterial replication. Indeed, there exist few techniques which can identify actively replicating gut bacteria. In this study, we aimed to address this gap by adapting 5-ethynyl-2'-deoxyuridine (EdU) click chemistry (EdU-click), a metabolic labeling method, coupled with fluorescence-activated cell sorting and sequencing (FACS-Seq) to characterize replicating gut bacteria. We first used EdU-click with human gut bacterial isolates and show that many of them are amenable to this technique. We then optimized EdU-click and FACS-Seq for murine fecal bacteria and reveal that Prevotella UCG-001 and Ileibacterium are enriched in the replicating fraction. Finally, we labeled the actively replicating murine gut bacteria during exposure to cell wall-specific antibiotics in vitro. We show that regardless of the antibiotic used, the actively replicating bacteria largely consist of Ileibacterium, suggesting the resistance of this taxon to perturbations. Overall, we demonstrate how combining EdU-click and FACSeq can identify the actively replicating gut bacteria and their link with the composition of the whole community in both homeostatic and perturbed conditions. This technique will be instrumental in elucidating in situ bacterial replication dynamics in a variety of other ecological states, including colonization and species invasion, as well as for investigating the relationship between the replication and abundance of bacteria in complex communities.
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Affiliation(s)
- Eve T. Beauchemin
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Claire Hunter
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Corinne F. Maurice
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada,McGill Centre for Microbiome Research, McGill University, Montreal, Quebec, Canada,CONTACT Corinne F. Maurice Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
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Hechard T, Wang H. Determination of Growth Rate and Virulence Plasmid Copy Number During Yersinia pseudotuberculosis Infection Using Droplet Digital PCR. Methods Mol Biol 2023; 2674:101-115. [PMID: 37258963 DOI: 10.1007/978-1-0716-3243-7_7] [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: 06/02/2023]
Abstract
Pathogenic bacteria have evolved the ability to evade their host defenses and cause diseases. Virulence factors encompass a wide range of adaptations that allow pathogens to survive and proliferate in the hostile host environment during successful infection. In human pathogenic Yersinia species, the potent type III secretion system (T3SS) and other essential virulence factors are encoded on a virulence plasmid. Here, we investigated the bacterial growth rate and plasmid copy number following a Yersinia infection using droplet digital PCR (ddPCR). ddPCR is an exceptionally sensitive, highly precise, and cost-efficient method. It enables precise quantification even from very small amounts of target DNA. This method also enables analysis of complex samples with large amounts of interfering DNA, such as infected tissues or microbiome studies.
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Affiliation(s)
- Tifaine Hechard
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Helen Wang
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
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50
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Transcriptional Potential Determines the Adaptability of Escherichia coli Strains with Different Fitness Backgrounds. Microbiol Spectr 2022; 10:e0252822. [PMID: 36445144 PMCID: PMC9769844 DOI: 10.1128/spectrum.02528-22] [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] [Indexed: 12/03/2022] Open
Abstract
Adaptation through the fitness landscape may be influenced by the gene pool or expression network. However, genetic factors that determine the contribution of beneficial mutations during adaptive evolution are poorly understood. In this study, we experimentally evolved wild-type Escherichia coli K-12 MG1655 and its isogenic derivative that has two additional replication origins and shows higher background fitness. During the short time of experimental evolution, the fitness gains of the two E. coli strains with different fitness backgrounds converged. Populational genome sequencing revealed various mutations with different allele frequencies in evolved populations. Several mutations occurred in genes affecting transcriptional regulation (e.g., RNA polymerase subunit, RNase, ppGpp synthetase, and transcription termination/antitermination factor genes). When we introduced mutations into the ancestral E. coli strains, beneficial effects tended to be lower in the ancestor with higher initial fitness. Replication rate analysis showed that the various replication indices do not correlate with the growth rate. Transcriptome profiling showed that gene expression and gene ontology are markedly enriched in populations with lower background fitness after experimental evolution. Further, the degree of transcriptional change was proportional to the fitness gain. Thus, the evolutionary trajectories of bacteria with different fitness backgrounds can be complex and counterintuitive. Notably, transcriptional change is a major contributor to adaptability. IMPORTANCE Predicting the adaptive potential of bacterial populations can be difficult due to their complexity and dynamic environmental conditions. Also, epistatic interaction between mutations affects the adaptive trajectory. Nevertheless, next-generation sequencing sheds light on understanding evolutionary dynamics through high-throughput genome and transcriptome information. Experimental evolution of two E. coli strains with different background fitness showed that the trajectories of fitness gain, which slowed down during the later stages of evolution, became convergent. This suggests that the adaptability of bacteria can be counterintuitive and that predicting the evolutionary path of bacteria can be difficult even in a constant environment. In addition, transcriptional change is associated with fitness gain during the evolutionary process. Thus, the adaptability of cells depends on their intrinsic genetic capacity for a given evolutionary period. This should be considered when genetically engineered bacteria are optimized through adaptive evolution.
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