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Gundogdu A, Nalbantoglu OU, Karis G, Sarikaya I, Erdogan MN, Hora M, Aslan H. Comparing microbial communities in mucilage and seawater samples: Metagenomic insights into mucilage formation in the Marmara Sea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:58363-58374. [PMID: 39307865 DOI: 10.1007/s11356-024-34968-2] [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: 05/15/2024] [Accepted: 09/09/2024] [Indexed: 10/11/2024]
Abstract
Marine environments are subject to various naturally occurring phenomena, including marine snow and mucilage. In 2021, the rapid emergence of mucilage in the Marmara Sea raised concerns about its environmental impact. This study investigates the microbial communities in mucilage and seawater samples from the Marmara Sea using metagenomic-scale comparative analyses. The results indicate significant differences in microbial composition and diversity, with mucilage samples showing higher levels of polysaccharide biosynthesis-related enzymes. Over 50% of reads in mucilage samples remained unclassified (dark matter), highlighting unknown microbial taxa. Clean seawater was characterized by a higher presence of Euryarchaeota, Proteobacteria, and Rhodothermaeota, while Chlamydiae and Fusobacteria were dominant in mucilage. The study underscores the necessity for comprehensive metagenomic analyses to understand microbial roles in mucilage formation and persistence. Early detection of microbial shifts could serve as a warning system for mucilage outbreaks, aiding in the development of management strategies.
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Affiliation(s)
- Aycan Gundogdu
- Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Erciyes University, Kayseri, Turkey.
- Genome and Stem Cell Center (GenKok), Erciyes University, Melikgazi, Kayseri, 38280, Turkey.
| | - Ozkan Ufuk Nalbantoglu
- Genome and Stem Cell Center (GenKok), Erciyes University, Melikgazi, Kayseri, 38280, Turkey
- Department of Computer Engineering, Faculty of Engineering, Erciyes University, Kayseri, Turkey
| | - Gizem Karis
- Department of Molecular Biology and Genetics, Gevher Nesibe Genome and Stem Cell Institute, Erciyes University, Kayseri, Turkey
| | - Ilknur Sarikaya
- Department of Bioinformatics Systems Biology, Institute of Health Sciences, Erciyes University, Kayseri, Turkey
| | - Meryem Nisa Erdogan
- Department of Molecular Biology and Genetics, Gevher Nesibe Genome and Stem Cell Institute, Erciyes University, Kayseri, Turkey
| | - Mehmet Hora
- Department of Bioinformatics Systems Biology, Institute of Health Sciences, Erciyes University, Kayseri, Turkey
- Enbiosis Biotechnology, Istanbul, Turkey
| | - Herdem Aslan
- Department of Biology, Faculty of Science, Canakkale Onsekiz Mart University, Canakkale, Turkey
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2
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Sipes K, Buongiorno J, Steen AD, Abramov AA, Abuah C, Peters SL, Gianonne RJ, Hettich RL, Boike J, Garcia SL, Vishnivetskaya TA, Lloyd KG. Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny Ålesund, Svalbard (79°N). Syst Appl Microbiol 2024; 47:126544. [PMID: 39303414 DOI: 10.1016/j.syapm.2024.126544] [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: 02/14/2024] [Revised: 08/19/2024] [Accepted: 08/22/2024] [Indexed: 09/22/2024]
Abstract
Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018-2019) at the Bayelva monitoring station, Ny Ålesund, Svalbard. We show VWC increases with depth, whereas in situ temperature is more stable vertically, ranging from -5°C to 5 °C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2-4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were Acidobacteriota, Actinomycetota, and Chloroflexota. Actinomycetota and Chloroflexota increase with depth, while Acidobacteriota classes Thermoanaerobaculia Gp7-AA8, Blastocatellia UBA7656, and Vicinamibacteria Vicinamibacterales are found above 6 cm, below 6 cm, and below 20 cm, respectively. All MAGs have diverse carbon-degrading genes, and Actinomycetota and Chloroflexota have autotrophic genes. Genes encoding β -glucosidase, N-acetyl-β-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. Acidobacteriota dominate the top 6 cm with their classes segregating by depth, whereas Actinomycetota and Chloroflexota dominate below ∼6 cm. This suggests that Acidobacteriota classes adapt to lower VWC at the surface, while Actinomycetota and Chloroflexota persist below 6 cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the Acidobacteriota, Onstottus arcticum, Onstottus frigus, and Gilichinskyi gelida and in the Actinobacteriota, Mayfieldus profundus.
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Affiliation(s)
- Katie Sipes
- Department of Microbiology, University of Tennessee, Knoxville, United States.
| | - Joy Buongiorno
- Department of Microbiology, University of Tennessee, Knoxville, United States
| | - Andrew D Steen
- Department of Microbiology, University of Tennessee, Knoxville, United States; Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, United States
| | - Andrey A Abramov
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Russia
| | | | - Samantha L Peters
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Richard J Gianonne
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Julia Boike
- Alfred Wegener Institute for Polar and Marine Research, Potsdam, Germany; Department of Geography, Humboldt University, Berlin, Germany
| | - Sarahi L Garcia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden; Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | | | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, United States
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3
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Marshall IPG. Electromicrobiological concentration cells are an overlooked potential energy conservation mechanism for subsurface microorganisms. Front Microbiol 2024; 15:1407868. [PMID: 39234547 PMCID: PMC11371792 DOI: 10.3389/fmicb.2024.1407868] [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: 03/27/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024] Open
Abstract
Thermodynamics has predicted many different kinds of microbial metabolism by determining which pairs of electron acceptors and donors will react to produce an exergonic reaction (a negative net change in Gibbs free energy). In energy-limited environments, such as the deep subsurface, such an approach can reveal the potential for unexpected or counter-intuitive energy sources for microbial metabolism. Up until recently, these thermodynamic calculations have been carried out with the assumption that chemical species appearing on the reactant and product side of a reaction formula have a constant concentration, and thus do not count towards net concentration changes and the overall direction of the reaction. This assumption is reasonable considering microorganisms are too small (~1 μm) for any significant differences in concentration to overcome diffusion. However, recent discoveries have demonstrated that the reductive and oxidative halves of reactions can be separated by much larger distances, from millimetres to centimetres via conductive filamentous bacteria, mineral conductivity, and biofilm conductivity. This means that the concentrations of reactants and products can indeed be different, and that concentration differences can contribute to the net negative change in Gibbs free energy. It even means that the same redox reaction, simultaneously running in forward and reverse, can drive energy conservation, in an ElectroMicrobiological Concentration Cell (EMCC). This paper presents a model to investigate this phenomenon and predict under which circumstances such concentration-driven metabolism might take place. The specific cases of oxygen concentration cells, sulfide concentration cells, and hydrogen concentration cells are examined in more detail.
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Affiliation(s)
- Ian P G Marshall
- Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
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4
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Chen M, Li W, Teng H, Hu W, Dong Z, Zhang D, Liu T, Zheng Q. Impact of Combined Pollution of Ciprofloxacin and Copper on the Diversity of Archaeal Communities and Antibiotic-Resistance Genes. Antibiotics (Basel) 2024; 13:734. [PMID: 39200034 PMCID: PMC11350791 DOI: 10.3390/antibiotics13080734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 09/01/2024] Open
Abstract
This study aimed to explore the response of archaeal communities and antibiotic-resistance genes (ARGs) to ciprofloxacin (CIP, 0.05-40 mg/L) and copper (Cu, 3 mg/L) combined pollution during stress- and post-effect periods in an activated sludge system. With the increase in the CIP concentration, the diversity of archaea decreased, but the richness increased under the stress of 10 mg/L CIP. Under stress and post effects, the change in unknown archaeal community structure was more significant than that of the known archaea. The relative abundance of unknown archaea was significantly reduced with the increase in CIP concentration. Meanwhile, there were certain archaea that belonged to abundant and rare taxa with different resistance and recovery characteristics. Among them, Methanosaeta (49.15-83.66%), Methanoculleus (0.11-0.45%), and Nitrososphaera (0.03-0.36%) were the typical resistant archaea to combined pollution. And the resistance of the abundant taxa to combined pollution was significantly higher than that of the rare taxa. Symbiotic and competitive relationships were observed between the known and the unknown archaea. The interactions of abundant known taxa were mainly symbiotic relationships. While the rare unknown taxa were mainly competitive relationships in the post-effect period. Rare archaea showed an important ecological niche under the stress-effect. Some archaea displayed positive correlation with ARGs and played important roles as potential hosts of ARGs during stress- and post-periods. Methanospirillum, Methanosphaerula, Nitrososphaera and some rare unknown archaea also significantly co-occurred with a large number of ARGs. Overall, this study points out the importance of interactions among known and unknown archaeal communities and ARGs in a wastewater treatment system under the stress of antibiotics and heavy metal combined pollution.
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Affiliation(s)
- Meijuan Chen
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; (M.C.); (Z.D.); (D.Z.)
- East Line Smart Water of China South-to-North Water Diversion Corporation Limited, Beijing 100071, China; (H.T.); (W.H.); (T.L.); (Q.Z.)
| | - Weiying Li
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; (M.C.); (Z.D.); (D.Z.)
| | - Haibo Teng
- East Line Smart Water of China South-to-North Water Diversion Corporation Limited, Beijing 100071, China; (H.T.); (W.H.); (T.L.); (Q.Z.)
| | - Wenxin Hu
- East Line Smart Water of China South-to-North Water Diversion Corporation Limited, Beijing 100071, China; (H.T.); (W.H.); (T.L.); (Q.Z.)
| | - Zhiqiang Dong
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; (M.C.); (Z.D.); (D.Z.)
| | - Dawei Zhang
- College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; (M.C.); (Z.D.); (D.Z.)
| | - Tianyi Liu
- East Line Smart Water of China South-to-North Water Diversion Corporation Limited, Beijing 100071, China; (H.T.); (W.H.); (T.L.); (Q.Z.)
| | - Quan Zheng
- East Line Smart Water of China South-to-North Water Diversion Corporation Limited, Beijing 100071, China; (H.T.); (W.H.); (T.L.); (Q.Z.)
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5
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Sampara P, Lawson CE, Scarborough MJ, Ziels RM. Advancing environmental biotechnology with microbial community modeling rooted in functional 'omics. Curr Opin Biotechnol 2024; 88:103165. [PMID: 39033648 DOI: 10.1016/j.copbio.2024.103165] [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: 02/28/2024] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 07/23/2024]
Abstract
Emerging biotechnologies that solve pressing environmental and climate emergencies will require harnessing the vast functional diversity of the underlying microbiomes driving such engineered processes. Modeling is a critical aspect of process engineering that informs system design as well as aids diagnostic optimization of performance. 'Conventional' bioprocess models assume homogenous biomass within functional guilds and thus fail to predict emergent properties of diverse microbial physiologies, such as product specificity and community interactions. Yet, recent advances in functional 'omics-based approaches can provide a 'lens' through which we can probe and measure in situ ecophysiologies of environmental microbiomes. Here, we overview microbial community modeling approaches that incorporate functional 'omics data, which we posit can advance our ability to design and control new environmental biotechnologies going forward.
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Affiliation(s)
- Pranav Sampara
- Department of Civil Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher E Lawson
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Matthew J Scarborough
- Department of Civil and Environmental Engineering, University of Vermont, Burlington, VT, United States
| | - Ryan M Ziels
- Department of Civil Engineering, The University of British Columbia, Vancouver, British Columbia, Canada.
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6
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Single-cell exploration of the microbiota driving soil phosphorus mobilization. NATURE FOOD 2024; 5:654-655. [PMID: 39117953 DOI: 10.1038/s43016-024-01025-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
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7
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Vijayan J, Ezhuthanikkunnel AP, Punnorkodu SAK, Poikayil SS, Mohan M, Ammanamveetil MHA. Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:52132-52146. [PMID: 39143383 DOI: 10.1007/s11356-024-34665-0] [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: 03/20/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024]
Abstract
Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2 cm) and bottom depth (250 cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.
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Affiliation(s)
- Jasna Vijayan
- Department of Marine Biology, Microbiology and Biochemistry; School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682016, Kerala, India.
| | - Akhil Prakash Ezhuthanikkunnel
- Department of Marine Biology, Microbiology and Biochemistry; School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682016, Kerala, India
| | - Sabira Abdul Kareem Punnorkodu
- Department of Marine Biology, Microbiology and Biochemistry; School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682016, Kerala, India
| | - Sunil Sukumaran Poikayil
- Department of Marine Geology and Geophysics; School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682016, Kerala, India
| | - Mahesh Mohan
- School of Environmental Sciences, Mahatma Gandhi University, Priyadarshini Hills P.O, Kottayam, 686560, Kerala, India
| | - Mohamed Hatha Abdulla Ammanamveetil
- Department of Marine Biology, Microbiology and Biochemistry; School of Marine Sciences, Cochin University of Science and Technology, Cochin, 682016, Kerala, India
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8
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Katayama T, Nobu MK, Imachi H, Hosogi N, Meng XY, Morinaga K, Yoshioka H, Takahashi HA, Kamagata Y, Tamaki H. A Marine Group A isolate relies on other growing bacteria for cell wall formation. Nat Microbiol 2024; 9:1954-1963. [PMID: 38831032 DOI: 10.1038/s41564-024-01717-7] [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: 12/06/2023] [Accepted: 04/29/2024] [Indexed: 06/05/2024]
Abstract
Most of Earth's prokaryotes live under energy limitation, yet the full breadth of strategies that enable survival under such conditions remain poorly understood. Here we report the isolation of a bacterial strain, IA91, belonging to the candidate phylum Marine Group A (SAR406 or 'Candidatus Marinimicrobia') that is unable to synthesize the central cell wall compound peptidoglycan itself. Using cultivation experiments and microscopy, we show that IA91 growth and cell shape depend on other bacteria, deriving peptidoglycan, energy and carbon from exogenous muropeptide cell wall fragments released from growing bacteria. Reliance on exogenous muropeptides is traceable to the phylum's ancestor, with evidence of vertical inheritance across several classes. This dependency may be widespread across bacteria (16 phyla) based on the absence of key peptidoglycan synthesis genes. These results suggest that uptake of exogenous cell wall components could be a relevant and potentially common survival strategy in energy-limited habitats like the deep biosphere.
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Affiliation(s)
- Taiki Katayama
- Research Institute for Geo-Resources and Environment, Geological Survey of Japan (GSJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan.
| | - Masaru K Nobu
- Bioproduction Research Institute, AIST, Tsukuba, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hiroyuki Imachi
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Naoki Hosogi
- EM Application Department, EM Business Unit, JEOL, Ltd., Akishima, Japan
| | | | - Kana Morinaga
- Bioproduction Research Institute, AIST, Tsukuba, Japan
| | - Hideyoshi Yoshioka
- Research Institute for Geo-Resources and Environment, Geological Survey of Japan (GSJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hiroshi A Takahashi
- Research Institute of Earthquake and Volcano Geology, GSJ, AIST, Tsukuba, Japan
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9
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Bényei ÉB, Nazeer RR, Askenasy I, Mancini L, Ho PM, Sivarajan GAC, Swain JEV, Welch M. The past, present and future of polymicrobial infection research: Modelling, eavesdropping, terraforming and other stories. Adv Microb Physiol 2024; 85:259-323. [PMID: 39059822 DOI: 10.1016/bs.ampbs.2024.04.002] [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] [Indexed: 07/28/2024]
Abstract
Over the last two centuries, great advances have been made in microbiology as a discipline. Much of this progress has come about as a consequence of studying the growth and physiology of individual microbial species in well-defined laboratory media; so-called "axenic growth". However, in the real world, microbes rarely live in such "splendid isolation" (to paraphrase Foster) and more often-than-not, share the niche with a plethora of co-habitants. The resulting interactions between species (and even between kingdoms) are only very poorly understood, both on a theoretical and experimental level. Nevertheless, the last few years have seen significant progress, and in this review, we assess the importance of polymicrobial infections, and show how improved experimental traction is advancing our understanding of these. A particular focus is on developments that are allowing us to capture the key features of polymicrobial infection scenarios, especially as those associated with the human airways (both healthy and diseased).
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Affiliation(s)
| | | | - Isabel Askenasy
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Leonardo Mancini
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Pok-Man Ho
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | | | - Jemima E V Swain
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom.
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10
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Gago JF, Viver T, Urdiain M, Ferreira E, Robledo P, Rossello-Mora R. Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode. Syst Appl Microbiol 2024; 47:126506. [PMID: 38640749 DOI: 10.1016/j.syapm.2024.126506] [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: 12/05/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/21/2024]
Abstract
Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.
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Affiliation(s)
- Juan F Gago
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain.
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain; Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Elaine Ferreira
- The Deep Blue Sea Enterprise S.L., Barcelona, Spain; Lipotrue S.L., Barcelona, Spain
| | - Pedro Robledo
- Unit of Geological and Mining Institute of Spain in Balearic Islands (IGME-CSIC), Palma de Mallorca, Spain
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain.
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11
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Cifuente JO, Colleoni C, Kalscheuer R, Guerin ME. Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes. Chem Rev 2024; 124:4863-4934. [PMID: 38606812 PMCID: PMC11046441 DOI: 10.1021/acs.chemrev.3c00811] [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] [Indexed: 04/13/2024]
Abstract
Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.
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Affiliation(s)
- Javier O. Cifuente
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, E-48940 Leioa, Spain
| | - Christophe Colleoni
- University
of Lille, CNRS, UMR8576-UGSF -Unité de Glycobiologie Structurale
et Fonctionnelle, F-59000 Lille, France
| | - Rainer Kalscheuer
- Institute
of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Dusseldorf, Germany
| | - Marcelo E. Guerin
- Structural
Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish
National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
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12
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Zhang Z, Zhang L, Zhang L, Chu H, Zhou J, Ju F. Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes. mSystems 2024; 9:e0126323. [PMID: 38470142 PMCID: PMC11019929 DOI: 10.1128/msystems.01263-23] [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: 11/28/2023] [Accepted: 01/26/2024] [Indexed: 03/13/2024] Open
Abstract
Bacterial secondary metabolites serve as an important source of molecules for drug discovery. They also play an important function in mediating the interactions of microbial producers with their living environment and surrounding organisms. However, little is known about the genetic novelty, distribution, and community-level impacts of soil bacterial biosynthetic potential on a large geographic scale. Here, we constructed the first catalog of 11,149 biosynthetic gene clusters (BGCs) from agricultural soils across China and unearthed hidden biosynthetic potential for new natural product discovery from the not-yet-cultivated soil bacteria. Notably, we revealed soil pH as the strongest environmental driver of BGC biogeography and predicted that soil acidification and global climate change could damage the biosynthetic potential of the soil microbiome. The co-occurrence network of bacterial genomes revealed two BGC-rich species, i.e., Nocardia niigatensis from Actinobacteriota and PSRF01 from Acidobacteriota, as the module hub and connector, respectively, indicating their keystone positions in the soil microbial communities. We also uncovered a dominant role of BGC-inferred biotic interactions over environmental drivers in structuring the soil microbiome. Overall, this study achieved novel insights into the BGC landscape in agricultural soils of China, substantially expanding our understanding of the diversity and novelty of bacterial secondary metabolism and the potential role of secondary metabolites in microbiota assembly.IMPORTANCEBacterial secondary metabolites not only serve as the foundation for numerous therapeutics (e.g., antibiotics and anticancer drugs), but they also play critical ecological roles in mediating microbial interactions (e.g., competition and communication). However, our knowledge of bacterial secondary metabolism is limited to only a small fraction of cultured strains, thus restricting our comprehensive understanding of their diversity, novelty, and potential ecological roles in soil ecosystems. Here, we used culture-independent metagenomics to explore biosynthetic potentials in agricultural soils of China. Our analyses revealed a high degree of genetic diversity and novelty within biosynthetic gene clusters in agricultural soil environments, offering valuable insights for biochemists seeking to synthesize novel bioactive products. Furthermore, we uncovered the pivotal role of BGC-rich species in microbial communities and the significant relationship between BGC richness and microbial phylogenetic turnover. This information emphasizes the importance of biosynthetic potential in the assembly of microbial communities.
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Affiliation(s)
- Zhiguo Zhang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lu Zhang
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Lihan Zhang
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- Department of Chemistry, Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Hangzhou, Zhejiang, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources Research of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, Zhejiang, China
- Center of Synthetic Biology and Integrated Bioengineering, Westlake University, Hangzhou, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
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13
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Zhang Z, Zhang Q, Yang H, Cui L, Qian H. Mining strategies for isolating plastic-degrading microorganisms. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123572. [PMID: 38369095 DOI: 10.1016/j.envpol.2024.123572] [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: 12/27/2023] [Revised: 01/29/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Plastic waste is a growing global pollutant. Plastic degradation by microorganisms has captured attention as an earth-friendly tactic. Although the mechanisms of plastic degradation by bacteria, fungi, and algae have been explored over the past decade, a large knowledge gap still exists regarding the identification, sorting, and cultivation of efficient plastic degraders, primarily because of their uncultivability. Advances in sequencing techniques and bioinformatics have enabled the identification of microbial degraders and related enzymes and genes involved in plastic biodegradation. In this review, we provide an outline of the situation of plastic degradation and summarize the methods for effective microbial identification using multidisciplinary techniques such as multiomics, meta-analysis, and spectroscopy. This review introduces new strategies for controlling plastic pollution in an environmentally friendly manner. Using this information, highly efficient and colonizing plastic degraders can be mined via targeted sorting and cultivation. In addition, based on the recognized rules and plastic degraders, we can perform an in-depth analysis of the associated degradation mechanism, metabolic features, and interactions.
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Affiliation(s)
- Ziyao Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Huihui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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14
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Zhou J, Stringlis IA, Wen J, Liu Y, Xu S, Wang R. Interplay between Amaryllidaceae alkaloids, the bacteriome and phytopathogens in Lycoris radiata. THE NEW PHYTOLOGIST 2024; 241:2258-2274. [PMID: 38105545 DOI: 10.1111/nph.19479] [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: 04/26/2023] [Accepted: 11/28/2023] [Indexed: 12/19/2023]
Abstract
Alkaloids are a large group of plant secondary metabolites with various structures and activities. It is important to understand their functions in the interplay between plants and the beneficial and pathogenic microbiota. Amaryllidaceae alkaloids (AAs) are unique secondary metabolites in Amaryllidaceae plants. Here, we studied the interplay between AAs and the bacteriome in Lycoris radiata, a traditional Chinese medicinal plant containing high amounts of AAs. The relationship between AAs and bacterial composition in different tissues of L. radiata was studied. In vitro experiments revealed that AAs have varying levels of antimicrobial activity against endophytic bacteria and pathogenic fungi, indicating the importance of AA synthesis in maintaining a balance between plants and beneficial/pathogenic microbiota. Using bacterial synthetic communities with different compositions, we observed a positive feedback loop between bacteria insensitive to AAs and their ability to increase accumulation of AAs in L. radiata, especially in leaves. This may allow insensitive bacteria to outcompete sensitive ones for plant resources. Moreover, the accumulation of AAs enhanced by insensitive bacteria could benefit plants when challenged with fungal pathogens. This study highlights the functions of alkaloids in plant-microbe interactions, opening new avenues for designing plant microbiomes that could contribute to sustainable agriculture.
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Affiliation(s)
- Jiayu Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, 210014, Nanjing, China
| | - Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, the Netherlands
- Laboratory of Plant Pathology, Agricultural University of Athens, 75 Iera Odos St., 11855, Athens, Greece
| | - Jian Wen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, 210014, Nanjing, China
| | - Yifang Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, 210014, Nanjing, China
| | - Sheng Xu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, 210014, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, 210014, Nanjing, China
| | - Ren Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, 210014, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, 210014, Nanjing, China
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15
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van Bergeijk DA, Augustijn HE, Elsayed SS, Willemse J, Carrión VJ, Du C, Urem M, Grigoreva LV, Cheprasov MY, Grigoriev S, Jansen H, Wintermans B, Budding AE, Spaink HP, Medema MH, van Wezel GP. Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000-year-old mammoth. Environ Microbiol 2024; 26:e16589. [PMID: 38356049 DOI: 10.1111/1462-2920.16589] [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: 07/25/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024]
Abstract
Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.
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Affiliation(s)
- Doris A van Bergeijk
- Department of Microbiology, Immunology and Transplantation (Laboratory of Molecular Bacteriology), KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Hannah E Augustijn
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | | | - Joost Willemse
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Victor J Carrión
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Department of Microbiology, University of Málaga, Málaga, Spain
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Chao Du
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Mia Urem
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | | | | | | | - Bas Wintermans
- Department of Medical Microbiology, Adrz Hospital, Goes, The Netherlands
| | | | - Herman P Spaink
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
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16
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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024:1-40. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [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: 03/13/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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17
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Jiménez DJ, Rosado AS. SeqCode in the golden age of prokaryotic systematics. THE ISME JOURNAL 2024; 18:wrae109. [PMID: 38896025 PMCID: PMC11384910 DOI: 10.1093/ismejo/wrae109] [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: 03/03/2024] [Revised: 05/08/2024] [Accepted: 06/18/2024] [Indexed: 06/21/2024]
Abstract
The SeqCode is a new code of prokaryotic nomenclature that was developed to validate taxon names using genome sequences as the type material. The present article provides an independent view about the SeqCode, highlighting its history, current status, basic features, pros and cons, and use to date. We also discuss important topics to consider for validation of novel prokaryotic taxon names using genomes as the type material. Owing to significant advances in metagenomics and cultivation methods, hundreds of novel prokaryotic species are expected to be discovered in the coming years. This manuscript aims to stimulate and enrich the debate around the use of the SeqCode in the upcoming golden age of prokaryotic taxon discovery and systematics.
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Affiliation(s)
- Diego Javier Jiménez
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Alexandre Soares Rosado
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
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18
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Lee SM, Thapa Magar R, Jung MK, Kong HG, Song JY, Kwon JH, Choi M, Lee HJ, Lee SY, Khan R, Kim JF, Lee SW. Rhizobacterial syntrophy between a helper and a beneficiary promotes tomato plant health. THE ISME JOURNAL 2024; 18:wrae120. [PMID: 38952008 PMCID: PMC11253211 DOI: 10.1093/ismejo/wrae120] [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: 05/14/2024] [Revised: 06/17/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Microbial interactions impact the functioning of microbial communities. However, microbial interactions within host-associated communities remain poorly understood. Here, we report that the beneficiary rhizobacterium Niallia sp. RD1 requires the helper Pseudomonas putida H3 for bacterial growth and beneficial interactions with the plant host. In the absence of the helper H3 strain, the Niallia sp. RD1 strain exhibited weak respiration and elongated cell morphology without forming bacterial colonies. A transposon mutant of H3 in a gene encoding succinate-semialdehyde dehydrogenase displayed much attenuated support of RD1 colony formation. Through the subsequent addition of succinate to the media, we found that succinate serves as a public good that supports RD1 growth. Comparative genome analysis highlighted that RD1 lacked the gene for sufficient succinate, suggesting its evolution as a beneficiary of succinate biosynthesis. The syntrophic interaction between RD1 and H3 efficiently protected tomato plants from bacterial wilt and promoted tomato growth. The addition of succinate to the medium restored complex II-dependent respiration in RD1 and facilitated the cultivation of various bacterial isolates from the rhizosphere. Taken together, we delineate energy auxotrophic beneficiaries ubiquitous in the microbial community, and these beneficiaries could benefit host plants with the aid of helpers in the rhizosphere.
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Affiliation(s)
- Sang-Moo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Roniya Thapa Magar
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Min Kyeong Jung
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyun Gi Kong
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Plant Medicine, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ju Yeon Song
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Joo Hwan Kwon
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Minseo Choi
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Hyoung Ju Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Seung Yeup Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
| | - Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
- Department of Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Jihyun F Kim
- Department of Systems Biology and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Microbiome Initiative, Yonsei University, Seoul 03722, Republic of Korea
| | - Seon-Woo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Republic of Korea
- Department of Applied Bioscience, Dong-A University, Busan 49315, Republic of Korea
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19
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Sanchez FB, Sato Guima SE, Setubal JC. How to Obtain and Compare Metagenome-Assembled Genomes. Methods Mol Biol 2024; 2802:135-163. [PMID: 38819559 DOI: 10.1007/978-1-0716-3838-5_6] [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] [Indexed: 06/01/2024]
Abstract
Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from prokaryotic species that have not been isolated or cultivated in the lab. They, therefore, provide us with information on these species that are impossible to obtain otherwise, at least until new cultivation methods are devised. Thanks to improvements and cost reductions of DNA sequencing technologies and growing interest in microbial ecology, the rise in number of MAGs in genome repositories has been exponential. This chapter covers the basics of MAG retrieval and processing and provides a practical step-by-step guide using a real dataset and state-of-the-art tools for MAG analysis and comparison.
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Affiliation(s)
- Fabio Beltrame Sanchez
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Suzana Eiko Sato Guima
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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20
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Lo HY, Wink K, Nitz H, Kästner M, Belder D, Müller JA, Kaster AK. scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling. mSystems 2023; 8:e0099823. [PMID: 37982643 PMCID: PMC10734494 DOI: 10.1128/msystems.00998-23] [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: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE A central question in microbial ecology is which member of a community performs a particular metabolism. Several sophisticated isotope labeling techniques are available for analyzing the metabolic function of populations and individual cells in a community. However, these methods are generally either insufficiently sensitive or throughput-limited and thus have limited applicability for the study of complex environmental samples. Here, we present a novel approach that combines highly sensitive radioisotope tracking, microfluidics, high-throughput sorting, and single-cell genomics to simultaneously detect and identify individual microbial cells based solely on their in situ metabolic activity, without prior information on community structure.
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Affiliation(s)
- Hao-Yu Lo
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Konstantin Wink
- Institute for Analytical Chemistry, Leipzig University, Leipzig, Germany
| | - Henrike Nitz
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Matthias Kästner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Detlev Belder
- Institute for Analytical Chemistry, Leipzig University, Leipzig, Germany
| | - Jochen A. Müller
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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21
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Reyes-Umana V, Ewens SD, Meier DAO, Coates JD. Integration of molecular and computational approaches paints a holistic portrait of obscure metabolisms. mBio 2023; 14:e0043123. [PMID: 37855625 PMCID: PMC10746228 DOI: 10.1128/mbio.00431-23] [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] [Indexed: 10/20/2023] Open
Abstract
Microorganisms are essential drivers of earth's geochemical cycles. However, the significance of elemental redox cycling mediated by microorganisms is often underestimated beyond the most well-studied nutrient cycles. Phosphite, (per)chlorate, and iodate are each considered esoteric substrates metabolized by microorganisms. However, recent investigations have indicated that these metabolisms are widespread and ubiquitous, affirming a need to continue studying the underlying microbiology to understand their biogeochemical effects and their interface with each other and our biosphere. This review focuses on combining canonical techniques of culturing microorganisms with modern omic approaches to further our understanding of obscure metabolic pathways and elucidate their importance in global biogeochemical cycles. Using these approaches, marker genes of interest have already been identified for phosphite, (per)chlorate, and iodate using traditional microbial physiology and genetics. Subsequently, their presence was queried to reveal the distribution of metabolic pathways in the environment using publicly available databases. In conjunction with each other, computational and experimental techniques provide a more comprehensive understanding of the location of these microorganisms, their underlying biochemistry and genetics, and how they tie into our planet's geochemical cycles.
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Affiliation(s)
- Victor Reyes-Umana
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Sophia D. Ewens
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - David A. O. Meier
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - John D. Coates
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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22
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Zhang Z, Yang Y, Zhao J, Li Y, Stephenson SL, Qiu J, Liu P. Environmental factors influencing the diversity and distribution of dictyostelid cellular slime molds in forest and farmland soils of western China. Microbiol Spectr 2023; 11:e0173223. [PMID: 37962389 PMCID: PMC10715086 DOI: 10.1128/spectrum.01732-23] [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: 04/25/2023] [Accepted: 10/04/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE Soil protists are an essential yet seriously understudied component of the soil microbiome. In this study, 11 new records of dictyostelids belonging to 2 orders, 3 families, and 4 genera were identified from 99 soil samples collected from different elevations and habitats in central Gansu and the southeastern and southcentral portions of Guizhou Province, China. We found that dictyostelid communities were significantly different between Gansu and Guizhou Provinces, apparently in response to different environmental factors. Moreover, dictyostelids were found to have the highest species diversity in mixed forests. Soil pH, temperature, and elevation were determined to be the primary factors that affect the distribution and occurrence of dictyostelids in Guizhou and Gansu Provinces. This work supplements the survey data available for dictyostelids elsewhere in China. These new findings have significant implications for our understanding of the diversity of soil microorganisms.
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Affiliation(s)
- Zhaojuan Zhang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yingkun Yang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Jing Zhao
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Steven L. Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Junzhi Qiu
- Key Lab of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Pu Liu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, China
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23
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Rafiq M, Hassan N, Rehman M, Hayat M, Nadeem G, Hassan F, Iqbal N, Ali H, Zada S, Kang Y, Sajjad W, Jamal M. Challenges and Approaches of Culturing the Unculturable Archaea. BIOLOGY 2023; 12:1499. [PMID: 38132325 PMCID: PMC10740628 DOI: 10.3390/biology12121499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Since Carl Woese's discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.
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Affiliation(s)
- Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
- FF Institute (Huzhou) Co., Ltd., Huzhou 313000, China
| | - Noor Hassan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Maliha Rehman
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
| | - Muhammad Hayat
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Jinan 266101, China
| | - Gullasht Nadeem
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
| | - Farwa Hassan
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Naveed Iqbal
- Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of IT, Engineering and Management Sciences, Quetta 87100, Pakistan
- The Department of Paediatrics and Child Health, Aga Khan University, Karachi 74800, Pakistan
| | - Hazrat Ali
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering-College, Pakistan Institute of Engineering and Applied Sciences, Islamabad 44000, Pakistan
| | - Sahib Zada
- Guangzhou Institute of Energy Conservation, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yingqian Kang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education of Guizhou, Guiyang 550025, China
- Key Laboratory of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang 550025, China
| | - Wasim Sajjad
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Garden Campus, Mardan 23200, Pakistan
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Diaz GR, Gaire TN, Ferm P, Case L, Caixeta LS, Goldsmith TJ, Armstrong J, Noyes NR. Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves. Anim Microbiome 2023; 5:61. [PMID: 38041127 PMCID: PMC10691087 DOI: 10.1186/s42523-023-00284-2] [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: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described. RESULTS Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance. CONCLUSIONS Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.
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Affiliation(s)
- Gerardo R Diaz
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tara N Gaire
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peter Ferm
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lacey Case
- North Central Research and Outreach Center, Department of Animal Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Luciano S Caixeta
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Timothy J Goldsmith
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Joe Armstrong
- Agricultural and Natural Resource Systems, University of Minnesota Extension, University of Minnesota, St. Paul, MN, 55108, USA
| | - Noelle R Noyes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA.
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25
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Bährle R, Böhnke S, Englhard J, Bachmann J, Perner M. Current status of carbon monoxide dehydrogenases (CODH) and their potential for electrochemical applications. BIORESOUR BIOPROCESS 2023; 10:84. [PMID: 38647803 PMCID: PMC10992861 DOI: 10.1186/s40643-023-00705-9] [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: 07/07/2023] [Accepted: 11/16/2023] [Indexed: 04/25/2024] Open
Abstract
Anthropogenic carbon dioxide (CO2) levels are rising to alarming concentrations in earth's atmosphere, causing adverse effects and global climate changes. In the last century, innovative research on CO2 reduction using chemical, photochemical, electrochemical and enzymatic approaches has been addressed. In particular, natural CO2 conversion serves as a model for many processes and extensive studies on microbes and enzymes regarding redox reactions involving CO2 have already been conducted. In this review we focus on the enzymatic conversion of CO2 to carbon monoxide (CO) as the chemical conversion downstream of CO production render CO particularly attractive as a key intermediate. We briefly discuss the different currently known natural autotrophic CO2 fixation pathways, focusing on the reversible reaction of CO2, two electrons and protons to CO and water, catalyzed by carbon monoxide dehydrogenases (CODHs). We then move on to classify the different type of CODHs, involved catalyzed chemical reactions and coupled metabolisms. Finally, we discuss applications of CODH enzymes in photochemical and electrochemical cells to harness CO2 from the environment transforming it into commodity chemicals.
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Affiliation(s)
- Rebecca Bährle
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Stefanie Böhnke
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Jonas Englhard
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Julien Bachmann
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Mirjam Perner
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany.
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26
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Wang M, Zheng N, Li X, Zhao K, Xie BB. Enrichment Pretreatment Expands the Microbial Diversity Cultivated from Marine Sediments. Microorganisms 2023; 11:2771. [PMID: 38004782 PMCID: PMC10673404 DOI: 10.3390/microorganisms11112771] [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: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The majority of the microbial diversity in nature has not been recovered through cultivation. Enrichment is a classical technique widely used in the selective cultivation of specific taxa. Whether enrichment is suitable for cultivation studies that aim to recover large numbers of species remains little explored. To address this issue, we evaluated the potential of enrichment pretreatment in the cultivation of bacteria from marine sediments. Upon obtaining and classifying a total of 943 pure cultures from chitin and cellulose enrichment pretreatment systems and a control system, our results showed that species obtained using enrichment pretreatment differed greatly from those without enrichment. Multiple enrichment media and different enrichment times increased the number of cultivated species in a sample. Amplicon sequencing showed that the increased relative abundance during pretreatment contributed greatly to bacterial cultivation. The testing of degradation abilities against chitin and cellulose and the whole-genome sequencing of representative strains suggested that microorganism-microorganism interactions play roles in the expanded diversity of cultivated bacteria. This study provides new insights into the abilities of enrichment in exploring cultivable diversity and mining microbial resources.
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Affiliation(s)
| | | | | | | | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (M.W.); (N.Z.); (X.L.); (K.Z.)
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27
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Rivas-Marin E, Moyano-Palazuelo D, Henriques V, Merino E, Devos DP. Essential gene complement of Planctopirus limnophila from the bacterial phylum Planctomycetes. Nat Commun 2023; 14:7224. [PMID: 37940686 PMCID: PMC10632474 DOI: 10.1038/s41467-023-43096-3] [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: 04/15/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023] Open
Abstract
Planctopirus limnophila belongs to the bacterial phylum Planctomycetes, a relatively understudied lineage with remarkable cell biology features. Here, we report a genome-wide analysis of essential gene content in P. limnophila. We show that certain genes involved in peptidoglycan synthesis or cell division, which are essential in most other studied bacteria, are not essential for growth under laboratory conditions in this species. We identify essential genes likely involved in lipopolysaccharide biosynthesis, consistent with the view of Planctomycetes as diderm bacteria, and highlight other essential genes of unknown functions. Furthermore, we explore potential stages of evolution of the essential gene repertoire in Planctomycetes and the related phyla Verrucomicrobia and Chlamydiae. Our results provide insights into the divergent molecular and cellular biology of Planctomycetes.
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Affiliation(s)
- Elena Rivas-Marin
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain.
| | - David Moyano-Palazuelo
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain
| | - Valentina Henriques
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain
| | - Enrique Merino
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Sevilla, Spain.
- Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, University of Lille, Lille, France.
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28
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Van Etten J, Stephens TG, Bhattacharya D. A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data. Syst Biol 2023; 72:1101-1118. [PMID: 37314057 DOI: 10.1093/sysbio/syad037] [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: 11/07/2022] [Revised: 03/20/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023] Open
Abstract
In the age of genome sequencing, whole-genome data is readily and frequently generated, leading to a wealth of new information that can be used to advance various fields of research. New approaches, such as alignment-free phylogenetic methods that utilize k-mer-based distance scoring, are becoming increasingly popular given their ability to rapidly generate phylogenetic information from whole-genome data. However, these methods have not yet been tested using environmental data, which often tends to be highly fragmented and incomplete. Here, we compare the results of one alignment-free approach (which utilizes the D2 statistic) to traditional multi-gene maximum likelihood trees in 3 algal groups that have high-quality genome data available. In addition, we simulate lower-quality, fragmented genome data using these algae to test method robustness to genome quality and completeness. Finally, we apply the alignment-free approach to environmental metagenome assembled genome data of unclassified Saccharibacteria and Trebouxiophyte algae, and single-cell amplified data from uncultured marine stramenopiles to demonstrate its utility with real datasets. We find that in all instances, the alignment-free method produces phylogenies that are comparable, and often more informative, than those created using the traditional multi-gene approach. The k-mer-based method performs well even when there are significant missing data that include marker genes traditionally used for tree reconstruction. Our results demonstrate the value of alignment-free approaches for classifying novel, often cryptic or rare, species, that may not be culturable or are difficult to access using single-cell methods, but fill important gaps in the tree of life.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ 08901, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA
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Laux M, Piroupo CM, Setubal JC, Giani A. The Raphidiopsis (= Cylindrospermopsis) raciborskii pangenome updated: Two new metagenome-assembled genomes from the South American clade. HARMFUL ALGAE 2023; 129:102518. [PMID: 37951618 DOI: 10.1016/j.hal.2023.102518] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 11/14/2023]
Abstract
Two Raphidiopsis (=Cylindrospermopsis) raciborskii metagenome-assembled genomes (MAGs) were recovered from two freshwater metagenomic datasets sampled in 2011 and 2012 in Pampulha Lake, a hypereutrophic, artificial, shallow reservoir, located in the city of Belo Horizonte (MG), Brazil. Since the late 1970s, the lake has undergone increasing eutrophication pressure, due to wastewater input, leading to the occurrence of frequent cyanobacterial blooms. The major difference observed between PAMP2011 and PAMP2012 MAGs was the lack of the saxitoxin gene cluster in PAMP2012, which also presented a smaller genome, while PAMP2011 presented the complete sxt cluster and all essential proteins and clusters. The pangenome analysis was performed with all Raphidiopsis/Cylindrospermopsis genomes available at NCBI to date, with the addition of PAMP2011 and PAMP2012 MAGs (All33 subset), but also without the South American strains (noSA subset), and only among the South American strains (SA10 and SA8 subsets). We observed a substantial increase in the core genome size for the 'noSA' subset, in comparison to 'All33' subset, and since the core genome reflects the closeness among the pangenome members, the results strongly suggest that the conservation level of the essential gene repertoire seems to be affected by the geographic origin of the strains being analyzed, supporting the existence of a distinct SA clade. The Raphidiopsis pangenome comprised a total of 7943 orthologous protein clusters, and the two new MAGs increased the pangenome size by 11%. The pangenome based phylogenetic relationships among the 33 analyzed genomes showed that the SA genomes clustered together with 99% bootstrap support, reinforcing the metabolic particularity of the Raphidiopsis South American clade, related to its saxitoxin producing unique ability, while also indicating a different evolutionary history due to its geographic isolation.
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Affiliation(s)
- Marcele Laux
- Department of Botany, Phycology Laboratory, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
| | - Carlos Morais Piroupo
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Alessandra Giani
- Department of Botany, Phycology Laboratory, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil.
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Bäuerle F, Döbel GO, Camus L, Heilbronner S, Dräger A. Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum. FRONTIERS IN BIOINFORMATICS 2023; 3:1214074. [PMID: 37936955 PMCID: PMC10626998 DOI: 10.3389/fbinf.2023.1214074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/02/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction: Genome-scale metabolic models (GEMs) are organism-specific knowledge bases which can be used to unravel pathogenicity or improve production of specific metabolites in biotechnology applications. However, the validity of predictions for bacterial proliferation in in vitro settings is hardly investigated. Methods: The present work combines in silico and in vitro approaches to create and curate strain-specific genome-scale metabolic models of Corynebacterium striatum. Results: We introduce five newly created strain-specific genome-scale metabolic models (GEMs) of high quality, satisfying all contemporary standards and requirements. All these models have been benchmarked using the community standard test suite Metabolic Model Testing (MEMOTE) and were validated by laboratory experiments. For the curation of those models, the software infrastructure refineGEMs was developed to work on these models in parallel and to comply with the quality standards for GEMs. The model predictions were confirmed by experimental data and a new comparison metric based on the doubling time was developed to quantify bacterial growth. Discussion: Future modeling projects can rely on the proposed software, which is independent of specific environmental conditions. The validation approach based on the growth rate calculation is now accessible and closely aligned with biological questions. The curated models are freely available via BioModels and a GitHub repository and can be used. The open-source software refineGEMs is available from https://github.com/draeger-lab/refinegems.
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Affiliation(s)
- Famke Bäuerle
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karl University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Gwendolyn O. Döbel
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Laura Camus
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, Eberhard Karl University of Tübingen, Tübingen, Germany
- Faculty of Biology, Microbiology, Ludwig Maximilian University of Munich, Munich, Germany
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, Eberhard Karl University of Tübingen, Tübingen, Germany
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31
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Jaarsma AH, Sipes K, Zervas A, Jiménez FC, Ellegaard-Jensen L, Thøgersen MS, Stougaard P, Benning LG, Tranter M, Anesio AM. Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches. FEMS Microbiol Ecol 2023; 99:fiad119. [PMID: 37791411 PMCID: PMC10580271 DOI: 10.1093/femsec/fiad119] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/22/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023] Open
Abstract
The microbiome of Greenland Ice Sheet supraglacial habitats is still underinvestigated, and as a result there is a lack of representative genomes from these environments. In this study, we investigated the supraglacial microbiome through a combination of culturing-dependent and -independent approaches. We explored ice, cryoconite, biofilm, and snow biodiversity to answer: (1) how microbial diversity differs between supraglacial habitats, (2) if obtained bacterial genomes reflect dominant community members, and (3) how culturing versus high throughput sequencing changes our observations of microbial diversity in supraglacial habitats. Genomes acquired through metagenomic sequencing (133 high-quality MAGs) and whole genome sequencing (73 bacterial isolates) were compared to the metagenome assemblies to investigate abundance within the total environmental DNA. Isolates obtained in this study were not dominant taxa in the habitat they were sampled from, in contrast to the obtained MAGs. We demonstrate here the advantages of using metagenome SSU rRNA genes to reflect whole-community diversity. Additionally, we demonstrate a proof-of-concept of the application of in situ culturing in a supraglacial setting.
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Affiliation(s)
- Ate H Jaarsma
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Katie Sipes
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | | | - Lea Ellegaard-Jensen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Mariane S Thøgersen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Peter Stougaard
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Liane G Benning
- German Research Centre for Geosciences, Helmholtz Centre Potsdam, Telegrafenberg, 14473 Potsdam, Germany
- Department of Earth Sciences, Freie Universität Berlin, Malteserstr. 74-100, 12249 Berlin, Germany
| | - Martyn Tranter
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Alexandre M Anesio
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
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32
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Adam-Beyer N, Laufer-Meiser K, Fuchs S, Schippers A, Indenbirken D, Garbe-Schönberg D, Petersen S, Perner M. Microbial ecosystem assessment and hydrogen oxidation potential of newly discovered vent systems from the Central and South-East Indian Ridge. Front Microbiol 2023; 14:1173613. [PMID: 37886064 PMCID: PMC10598711 DOI: 10.3389/fmicb.2023.1173613] [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: 02/24/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
In order to expand the knowledge of microbial ecosystems from deep-sea hydrothermal vent systems located on the Central and South-East Indian Ridge, we sampled hydrothermal fluids, massive sulfides, ambient water and sediments of six distinct vent fields. Most of these vent sites were only recently discovered in the course of the German exploration program for massive sulfide deposits and no previous studies of the respective microbial communities exist. Apart from typically vent-associated chemosynthetic members of the orders Campylobacterales, Mariprofundales, and Thiomicrospirales, high numbers of uncultured and unspecified Bacteria were identified via 16S rRNA gene analyses in hydrothermal fluid and massive sulfide samples. The sampled sediments however, were characterized by an overall lack of chemosynthetic Bacteria and the presence of high proportions of low abundant bacterial groups. The archaeal communities were generally less diverse and mostly dominated by members of Nitrosopumilales and Woesearchaeales, partly exhibiting high proportions of unassigned Archaea. Correlations with environmental parameters were primarily observed for sediment communities and for microbial species (associated with the nitrogen cycle) in samples from a recently identified vent field, which was geochemically distinct from all other sampled sites. Enrichment cultures of diffuse fluids demonstrated a great potential for hydrogen oxidation coupled to the reduction of various electron-acceptors with high abundances of Hydrogenovibrio and Sulfurimonas species. Overall, given the large number of currently uncultured and unspecified microorganisms identified in the vent communities, their respective metabolic traits, ecosystem functions and mediated biogeochemical processes have still to be resolved for estimating consequences of potential environmental disturbances by future mining activities.
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Affiliation(s)
- Nicole Adam-Beyer
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Katja Laufer-Meiser
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sebastian Fuchs
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | | | | | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Mirjam Perner
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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Barnett SE, Buckley DH. Metagenomic stable isotope probing reveals bacteriophage participation in soil carbon cycling. Environ Microbiol 2023; 25:1785-1795. [PMID: 37139849 DOI: 10.1111/1462-2920.16395] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 04/25/2023] [Indexed: 05/05/2023]
Abstract
Soil viruses are important components of the carbon (C) cycle, yet we still know little about viral ecology in soils. We added diverse 13 C-labelled carbon sources to soil and we used metagenomic-SIP to detect 13 C assimilation by viruses and their putative bacterial hosts. These data allowed us to link a 13 C-labelled bacteriophage to its 13 C-labelled Streptomyces putative host, and we used qPCR to track the dynamics of the putative host and phage in response to C inputs. Following C addition, putative host numbers increased rapidly for 3 days, and then more gradually, reaching maximal abundance on Day 6. Viral abundance and virus:host ratio increased dramatically over 6 days, and remained high thereafter (8.42 ± 2.94). From Days 6 to 30, virus:host ratio remained high, while putative host numbers declined more than 50%. Putative host populations were 13 C-labelled on Days 3-30, while 13 C-labelling of phage was detected on Days 14 and 30. This dynamic suggests rapid growth and 13 C-labelling of the host fueled by new C inputs, followed by extensive host mortality driven by phage lysis. These findings indicate that the viral shunt promotes microbial turnover in soil following new C inputs, thereby altering microbial community dynamics, and facilitating soil organic matter production.
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Affiliation(s)
- Samuel E Barnett
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Daniel H Buckley
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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Malard LA, Guisan A. Into the microbial niche. Trends Ecol Evol 2023; 38:936-945. [PMID: 37236880 DOI: 10.1016/j.tree.2023.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.
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Affiliation(s)
- Lucie A Malard
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Institute of Earth Surface Dynamics, University of Lausanne, 1015 Lausanne, Switzerland
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Rey-Velasco X, Deulofeu-Capo O, Sanz-Sáez I, Cardelús C, Ferrera I, Gasol JM, Sánchez O. Expanding success in the isolation of abundant marine bacteria after reduction in grazing and viral pressure and increase in nutrient availability. Microbiol Spectr 2023; 11:e0089023. [PMID: 37747249 PMCID: PMC10580928 DOI: 10.1128/spectrum.00890-23] [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: 02/28/2023] [Accepted: 08/03/2023] [Indexed: 09/26/2023] Open
Abstract
Isolation of microorganisms is a useful approach to gathering knowledge about their genomic properties, physiology, and ecology, in addition to allowing the characterization of novel taxa. We performed an extensive isolation effort on samples from seawater manipulation experiments that were carried out during the four astronomical seasons in a coastal site of the northwest Mediterranean to evaluate the impact of grazing, viral mortality, resource competition reduction, and light presence/absence on bacterioplankton growth. Isolates were retrieved using two growth media, and their full 16S rRNA gene was sequenced to assess their identity and calculate their culturability across seasons and experimental conditions. A total of 1,643 isolates were obtained, mainly affiliated to the classes Gammaproteobacteria (44%), Alphaproteobacteria (26%), and Bacteroidia (17%). Isolates pertaining to class Gammaproteobacteria were the most abundant in all experiments, while Bacteroidia were preferentially enriched in the treatments with reduced grazing. Sixty-one isolates had a similarity below 97% to cultured taxa and are thus putatively novel. Comparison of isolate sequences with 16S rRNA gene amplicon sequences from the same samples showed that the percentage of reads corresponding to isolates was 21.4% within the whole data set, with dramatic increases in the summer virus-reduced (71%) and diluted (47%) treatments. In fact, we were able to isolate the top 10 abundant taxa in several experiments and from the whole data set. We also show that top-down and bottom-up controls differentially affect taxa in terms of culturability. Our results indicate that culturing marine bacteria using agar plates can be successful in certain ecological situations. IMPORTANCE Bottom-up and top-down controls greatly influence marine microbial community composition and dynamics, which in turn have effects on their culturability. We isolated a high amount of heterotrophic bacterial strains from experiments where seawater environmental conditions had been manipulated and found that decreasing grazing and viral pressure as well as rising nutrient availability are key factors increasing the success in culturing marine bacteria. Our data hint at factors influencing culturability and underpin bacterial cultures as a powerful way to discover new taxa.
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Affiliation(s)
| | - Ona Deulofeu-Capo
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Isabel Sanz-Sáez
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
- Instituto de Diagnóstico Ambiental y Estudios del Agua (IDAEA-CSIC), Barcelona, Catalonia, Spain
| | - Clara Cardelús
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Isabel Ferrera
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
- Centro Oceanográfico de Málaga, Instituto Español de Oceanografía, (IEO-CSIC), Fuengirola, Málaga, Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalonia, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Sanz-Sáez I, Sánchez P, Salazar G, Sunagawa S, de Vargas C, Bowler C, Sullivan MB, Wincker P, Karsenti E, Pedrós-Alió C, Agustí S, Gojobori T, Duarte CM, Gasol JM, Sánchez O, Acinas SG. Top abundant deep ocean heterotrophic bacteria can be retrieved by cultivation. ISME COMMUNICATIONS 2023; 3:92. [PMID: 37660234 PMCID: PMC10475052 DOI: 10.1038/s43705-023-00290-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 09/04/2023]
Abstract
Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation. These global datasets represent 60 322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the genera Sulfitobacter, Halomonas and Erythrobacter. These isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living fraction (0.2-0.8 µm) and up to 45% in the largest particles (20-200 µm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.
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Affiliation(s)
- Isabel Sanz-Sáez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
| | - Pablo Sánchez
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, CH-8093, Zurich, Switzerland
| | - Colomban de Vargas
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering; The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Eric Karsenti
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 75016, Paris, France
- Directors' Research European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Carlos Pedrós-Alió
- Department of Systems Biology, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Susana Agustí
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Carlos M Duarte
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, ICM-CSIC, 08003, Barcelona, Spain.
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Palmer M, Covington JK, Zhou EM, Thomas SC, Habib N, Seymour CO, Lai D, Johnston J, Hashimi A, Jiao JY, Muok AR, Liu L, Xian WD, Zhi XY, Li MM, Silva LP, Bowen BP, Louie K, Briegel A, Pett-Ridge J, Weber PK, Tocheva EI, Woyke T, Northen TR, Mayali X, Li WJ, Hedlund BP. Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past. THE ISME JOURNAL 2023; 17:952-966. [PMID: 37041326 PMCID: PMC10284905 DOI: 10.1038/s41396-023-01405-0] [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: 10/17/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/13/2023]
Abstract
Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.
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Affiliation(s)
- Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA.
| | - Jonathan K Covington
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - En-Min Zhou
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Scott C Thomas
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Neeli Habib
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
- Department of Microbiology, Shaheed Benazir Bhutto Women University, Peshawar, Khyber Pakhtunkhwa (KPK), Pakistan
| | - Cale O Seymour
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Dengxun Lai
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Juliet Johnston
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Ameena Hashimi
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Jian-Yu Jiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Alise R Muok
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China of Ministry of Education, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, 650091, Kunming, People's Republic of China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - Leslie P Silva
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Benjamin P Bowen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katherine Louie
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ariane Briegel
- Institute of Biology, Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Tanja Woyke
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Trent R Northen
- The Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 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), Sun Yat-Sen University, 510275, Guangzhou, People's Republic of China
| | - 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.
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Wu X, Gushgari-Doyle S, Lui LM, Hendrickson AJ, Liu Y, Jagadamma S, Nielsen TN, Justice NB, Simmons T, Hess NJ, Joyner DC, Hazen TC, Arkin AP, Chakraborty R. Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone. Appl Environ Microbiol 2023; 89:e0050023. [PMID: 37272792 PMCID: PMC10304653 DOI: 10.1128/aem.00500-23] [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: 03/29/2023] [Accepted: 04/16/2023] [Indexed: 06/06/2023] Open
Abstract
Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ. IMPORTANCE In this study, we explored the links between geochemical parameters, microbial community structure and metabolic potential across the depth of sediment, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone. Our results revealed that microbes in the terrestrial subsurface can be highly localized, with communities rarely being interconnected along the depth. Overall, our research demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolic potential in different depths of subsurface terrestrial sediment. Such studies correlating microbial community analyses and geochemistry analyses, including high resolution mass spectrometry analyses of natural organic carbon, will further the fundamental understanding of microbial ecology and biogeochemistry in subsurface terrestrial ecosystems and will benefit the future development of predictive models on nutrient turnover in these environments.
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Affiliation(s)
- Xiaoqin Wu
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sara Gushgari-Doyle
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Lauren M. Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Andrew J. Hendrickson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yina Liu
- Department of Oceanography, Texas A&M University, College Station, Texas, USA
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Torben N. Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicholas B. Justice
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tuesday Simmons
- University of California, Berkeley, Berkeley, California, USA
| | - Nancy J. Hess
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Terry C. Hazen
- University of Tennessee, Knoxville, Tennessee, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- University of California, Berkeley, Berkeley, California, USA
| | - Romy Chakraborty
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Carlton JD, Langwig MV, Gong X, Aguilar-Pine EJ, Vázquez-Rosas-Landa M, Seitz KW, Baker BJ, De Anda V. Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles. ISME COMMUNICATIONS 2023; 3:64. [PMID: 37355707 PMCID: PMC10290634 DOI: 10.1038/s43705-023-00269-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/22/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Marine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. Recent studies using metagenomic techniques have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here, we obtained 77 metagenome-assembled genomes (MAGs) from the bacterial phylum Armatimonadota in the Guaymas Basin, Gulf of California, and the Bohai Sea, China. These MAGs comprise two previously undescribed classes within Armatimonadota, which we propose naming Hebobacteria and Zipacnadia. They are globally distributed in hypoxic and anoxic environments and are dominant members of deep-sea sediments (up to 1.95% of metagenomic raw reads). The classes described here also have unique metabolic capabilities, possessing pathways to reduce carbon dioxide to acetate via the Wood-Ljungdahl pathway (WLP) and generating energy through the oxidative branch of glycolysis using carbon dioxide as an electron sink, maintaining the redox balance using the WLP. Hebobacteria may also be autotrophic, not previously identified in Armatimonadota. Furthermore, these Armatimonadota may play a role in sulfur and nitrogen cycling, using the intermediate compounds hydroxylamine and sulfite. Description of these MAGs enhances our understanding of diversity and metabolic potential within anoxic habitats worldwide.
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Affiliation(s)
- John D Carlton
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
| | - Marguerite V Langwig
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Xianzhe Gong
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Emily J Aguilar-Pine
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Mirna Vázquez-Rosas-Landa
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- Unidad Académica de Ecologia y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnologia, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Kiley W Seitz
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
- EMBL Heidelberg, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
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40
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Tyne RL, Barry PH, Lawson M, Lloyd KG, Giovannelli D, Summers ZM, Ballentine CJ. Identifying and Understanding Microbial Methanogenesis in CO 2 Storage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37327355 DOI: 10.1021/acs.est.2c08652] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Carbon capture and storage (CCS) is an important component in many national net-zero strategies. Ensuring that CO2 can be safely and economically stored in geological systems is critical. To date, CCS research has focused on the physiochemical behavior of CO2, yet there has been little consideration of the subsurface microbial impact on CO2 storage. However, recent discoveries have shown that microbial processes (e.g., methanogenesis) can be significant. Importantly, methanogenesis may modify the fluid composition and the fluid dynamics within the storage reservoir. Such changes may subsequently reduce the volume of CO2 that can be stored and change the mobility and future trapping systematics of the evolved supercritical fluid. Here, we review the current knowledge of how microbial methanogenesis could impact CO2 storage, including the potential scale of methanogenesis and the range of geologic settings under which this process operates. We find that methanogenesis is possible in all storage target types; however, the kinetics and energetics of methanogenesis will likely be limited by H2 generation. We expect that the bioavailability of H2 (and thus potential of microbial methanogenesis) will be greatest in depleted hydrocarbon fields and least within saline aquifers. We propose that additional integrated monitoring requirements are needed for CO2 storage to trace any biogeochemical processes including baseline, temporal, and spatial studies. Finally, we suggest areas where further research should be targeted in order to fully understand microbial methanogenesis in CO2 storage sites and its potential impact.
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Affiliation(s)
- R L Tyne
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - P H Barry
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | | | - K G Lloyd
- University of Tennessee, Knoxville, Tennessee 37996, United States
| | - D Giovannelli
- University of Naples Federico II, Naples 80138 Italy
| | - Z M Summers
- LanzaTech, Skokie, Illinois 60077, United States
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41
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Pu J, Yang J, Lu S, Jin D, Luo X, Xiong Y, Bai X, Zhu W, Huang Y, Wu S, Niu L, Liu L, Xu J. Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika. Microbiol Spectr 2023; 11:e0349522. [PMID: 37067438 PMCID: PMC10269723 DOI: 10.1128/spectrum.03495-22] [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: 08/31/2022] [Accepted: 02/13/2023] [Indexed: 04/18/2023] Open
Abstract
Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a "core microbiota." They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema, the families Muribaculaceae, Lachnospiraceae, and Oscillospiraceae, and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.
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Affiliation(s)
- Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuelian Luo
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiangning Bai
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Lina Niu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Public Health, Nankai University, Tianjing, China
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He Q, Wang S, Feng K, Michaletz ST, Hou W, Zhang W, Li F, Zhang Y, Wang D, Peng X, Yang X, Deng Y. High speciation rate of niche specialists in hot springs. THE ISME JOURNAL 2023:10.1038/s41396-023-01447-4. [PMID: 37286739 DOI: 10.1038/s41396-023-01447-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/09/2023]
Abstract
Ecological and evolutionary processes simultaneously regulate microbial diversity, but the evolutionary processes and their driving forces remain largely unexplored. Here we investigated the ecological and evolutionary characteristics of microbiota in hot springs spanning a broad temperature range (54.8-80 °C) by sequencing the 16S rRNA genes. Our results demonstrated that niche specialists and niche generalists are embedded in a complex interaction of ecological and evolutionary dynamics. On the thermal tolerance niche axis, thermal (T) sensitive (at a specific temperature) versus T-resistant (at least in five temperatures) species were characterized by different niche breadth, community abundance and dispersal potential, consequently differing in potential evolutionary trajectory. The niche-specialized T-sensitive species experienced strong temperature barriers, leading to completely species shift and high fitness but low abundant communities at each temperature ("home niche"), and such trade-offs thus reinforced peak performance, as evidenced by high speciation across temperatures and increasing diversification potential with temperature. In contrast, T-resistant species are advantageous of niche expansion but with poor local performance, as shown by wide niche breadth with high extinction, indicating these niche generalists are "jack-of-all-trades, master-of-none". Despite of such differences, the T-sensitive and T-resistant species are evolutionarily interacted. Specifically, the continuous transition from T-sensitive to T-resistant species insured the exclusion probability of T-resistant species at a relatively constant level across temperatures. The co-evolution and co-adaptation of T-sensitive and T-resistant species were in line with the red queen theory. Collectively, our findings demonstrate that high speciation of niche specialists could alleviate the environmental-filtering-induced negative effect on diversity.
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Affiliation(s)
- Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Shang Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
| | - Sean T Michaletz
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Weiguo Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Wenhui Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Fangru Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Yidi Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing, 100083, China
| | - Danrui Wang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xi Peng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Xingsheng Yang
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, 100085, China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100190, China.
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Chen B, Zhang Z, Wang T, Hu H, Qin G, Lu T, Hong W, Hu J, Penuelas J, Qian H. Global distribution of marine microplastics and potential for biodegradation. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131198. [PMID: 36921415 DOI: 10.1016/j.jhazmat.2023.131198] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
Microplastics are a growing marine environmental concern globally due to their high abundance and persistent degradation. We created a global map for predicting marine microplastic pollution using a machine-learning model based on 9445 samples and found that microplastics converged in zones of accumulation in subtropical gyres and near polar seas. The predicted global potential for the biodegradation of microplastics in 1112 metagenome-assembled genomes from 485 marine metagenomes indicated high potential in areas of high microplastic pollution, such as the northern Atlantic Ocean and the Mediterranean Sea. However, the limited number of samples hindered our prediction, a priority issue that needs to be addressed in the future. We further identified hosts with microplastic degradation genes (MDGs) and found that Proteobacteria accounted for a high proportion of MDG hosts, mainly Alphaproteobacteria and Gammaproteobacteria, with host-specific patterns. Our study is essential for raising awareness, identifying areas with microplastic pollution, providing a prediction method of machine learning to prioritize surveillance, and identifying the global potential of marine microbiomes to degrade microplastics, providing a reference for selecting bacteria that have the potential to degrade microplastics for further applied research.
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Affiliation(s)
- Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tingzhang Wang
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, PR China
| | - Hang Hu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Wenjie Hong
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310012, PR China
| | - Jun Hu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Barcelona 08193, Catalonia, Spain; CREAF, Campus Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona 08193, Catalonia, Spain
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China.
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Schultz J, Modolon F, Peixoto RS, Rosado AS. Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles. Front Microbiol 2023; 14:1167718. [PMID: 37333658 PMCID: PMC10272570 DOI: 10.3389/fmicb.2023.1167718] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.
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Affiliation(s)
- Júnia Schultz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Flúvio Modolon
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Silva Peixoto
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Park H, Shabarova T, Salcher MM, Kosová L, Rychtecký P, Mukherjee I, Šimek K, Porcal P, Seďa J, Znachor P, Kasalický V. In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model. MICROBIOME 2023; 11:112. [PMID: 37210505 DOI: 10.1186/s40168-023-01522-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 03/17/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND Planktonic microbial communities have critical impacts on the pelagic food web and water quality status in freshwater ecosystems, yet no general model of bacterial community assembly linked to higher trophic levels and hydrodynamics has been assessed. In this study, we utilized a 2-year survey of planktonic communities from bacteria to zooplankton in three freshwater reservoirs to investigate their spatiotemporal dynamics. RESULTS We observed site-specific occurrence and microdiversification of bacteria in lacustrine and riverine environments, as well as in deep hypolimnia. Moreover, we determined recurrent bacterial seasonal patterns driven by both biotic and abiotic conditions, which could be integrated into the well-known Plankton Ecology Group (PEG) model describing primarily the seasonalities of larger plankton groups. Importantly, bacteria with different ecological potentials showed finely coordinated successions affiliated with four seasonal phases, including the spring bloom dominated by fast-growing opportunists, the clear-water phase associated with oligotrophic ultramicrobacteria, the summer phase characterized by phytoplankton bloom-associated bacteria, and the fall/winter phase driven by decay-specialists. CONCLUSIONS Our findings elucidate the major principles driving the spatiotemporal microbial community distribution in freshwater ecosystems. We suggest an extension to the original PEG model by integrating new findings on recurrent bacterial seasonal trends. Video Abstract.
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Grants
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- CZ.02.1.01/0.0/0.0/16_025/0007417 Ministerstvo Školství, Mládeže a Tělovýchovy
- 20-12496X Grantová Agentura České Republiky
- 19-00113S Grantová Agentura České Republiky
- 19-23469S Grantová Agentura České Republiky
- 19-00113S Grantová Agentura České Republiky
- 22-33245S Grantová Agentura České Republiky
- 20-12496X Grantová Agentura České Republiky
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Affiliation(s)
- Hongjae Park
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Tanja Shabarova
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Lenka Kosová
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Pavel Rychtecký
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Indranil Mukherjee
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Karel Šimek
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Petr Porcal
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Jaromír Seďa
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Petr Znachor
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vojtěch Kasalický
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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Münch JM, Sobol MS, Brors B, Kaster AK. Single-cell transcriptomics and data analyses for prokaryotes-Past, present and future concepts. ADVANCES IN APPLIED MICROBIOLOGY 2023; 123:1-39. [PMID: 37400172 DOI: 10.1016/bs.aambs.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Transcriptomics, or more specifically mRNA sequencing, is a powerful tool to study gene expression at the single-cell level (scRNA-seq) which enables new insights into a plethora of biological processes. While methods for single-cell RNA-seq in eukaryotes are well established, application to prokaryotes is still challenging. Reasons for that are rigid and diverse cell wall structures hampering lysis, the lack of polyadenylated transcripts impeding mRNA enrichment, and minute amounts of RNA requiring amplification steps before sequencing. Despite those obstacles, several promising scRNA-seq approaches for bacteria have been published recently, albeit difficulties in the experimental workflow and data processing and analysis remain. In particular, bias is often introduced by amplification which makes it difficult to distinguish between technical noise and biological variation. Future optimization of experimental procedures and data analysis algorithms are needed for the improvement of scRNA-seq but also to aid in the emergence of prokaryotic single-cell multi-omics. to help address 21st century challenges in the biotechnology and health sector.
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Affiliation(s)
- Julia M Münch
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany; Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Heidelberg, Germany; HIDSS4Health - Helmholtz Information and Data Science School for Health, Karlsruhe/Heidelberg, Germany
| | - Morgan S Sobol
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany; HIDSS4Health - Helmholtz Information and Data Science School for Health, Karlsruhe/Heidelberg, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany; HIDSS4Health - Helmholtz Information and Data Science School for Health, Karlsruhe/Heidelberg, Germany.
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Yu T, Wu W, Liang W, Wang Y, Hou J, Chen Y, Elvert M, Hinrichs KU, Wang F. Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments. MICROBIOME 2023; 11:81. [PMID: 37081504 PMCID: PMC10116835 DOI: 10.1186/s40168-023-01531-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies suggested that many of these uncultured microbes contribute to the degradation of organic matter, accompanied by acetogenesis, but the supporting experimental evidence is limited. RESULTS Estuarine sediments were incubated with different types of organic matters under anaerobic conditions, and the increase of uncultured bacterial populations was monitored. We found that (1) lignin stimulated the increase of uncultured bacteria within the class Dehalococcoidia. Their ability to metabolize lignin was further supported by the presence of genes associated with a nearly complete degradation pathway of phenolic monomers in the Dehalococcoidia metagenome-assembled genomes (MAGs). (2) The addition of cellulose stimulated the increase of bacteria in the phylum Ca. Fermentibacterota and family Fibrobacterales, a high copy number of genes encoding extracellular endoglucanase or/and 1,4-beta-cellobiosidase for cellulose decomposition and multiple sugar transporters were present in their MAGs. (3) Uncultured lineages in the order Bacteroidales and the family Leptospiraceae were enriched by the addition of casein and oleic acid, respectively, a high copy number of genes encoding extracellular peptidases, and the complete β-oxidation pathway were found in those MAGs of Bacteroidales and Leptospiraceae, respectively. (4) The growth of unclassified bacteria of the order Clostridiales was found after the addition of both casein and cellulose. Their MAGs contained multiple copies of genes for extracellular peptidases and endoglucanase. Additionally, 13C-labeled acetate was produced in the incubations when 13C-labeled dissolved inorganic carbon was provided. CONCLUSIONS Our results provide new insights into the roles of microorganisms during organic carbon degradation in anaerobic estuarine sediments and suggest that these macro and single molecular organic carbons support the persistence and increase of uncultivated bacteria. Acetogenesis is an additional important microbial process alongside organic carbon degradation. Video Abstract.
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Affiliation(s)
- Tiantian Yu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weichao Wu
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Wenyue Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yunru Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
- Faculty of Geosciences, University of Bremen, 28359, Bremen, Germany
| | - Fengping Wang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, China.
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Lee JYY, Miao Y, Chau RLT, Hernandez M, Lee PKH. Artificial intelligence-based prediction of indoor bioaerosol concentrations from indoor air quality sensor data. ENVIRONMENT INTERNATIONAL 2023; 174:107900. [PMID: 37012194 DOI: 10.1016/j.envint.2023.107900] [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: 01/16/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Exposure to bioaerosols in indoor environments, especially public venues that have a high occupancy and poor ventilation, is a serious public health concern. However, it remains challenging to monitor and determine real-time or predict near-future concentrations of airborne biological matter. In this study, we developed artificial intelligence (AI) models using physical and chemical data from indoor air quality sensors and physical data from ultraviolet light-induced fluorescence observations of bioaerosols. This enabled us to effectively estimate the bioaerosol (bacteria-, fungi- and pollen-like particle) and 2.5-µm and 10-µm particulate matter (PM2.5 and PM10) on a real-time and near-future (≤60 min) basis. Seven AI models were developed and evaluated using measured data from an occupied commercial office and a shopping mall. A long short-term memory model required a relatively short training time and gave the highest prediction accuracy of ∼ 60 %-80 % for bioaerosols and ∼ 90 % for PM on the testing and time series datasets from the two venues. This work demonstrates how AI-based methods can leverage bioaerosol monitoring into predictive scenarios that building operators can use for improving indoor environmental quality in near real-time.
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Affiliation(s)
- Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yanhao Miao
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ricky L T Chau
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Mark Hernandez
- Civil, Environmental and Architectural Engineering Department, Environmental Engineering Program, University of Colorado, Boulder, CO, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region, China; State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong Special Administrative Region, China.
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49
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van der Gulik PTS, Hoff WD, Speijer D. Renewing Linnaean taxonomy: a proposal to restructure the highest levels of the Natural System. Biol Rev Camb Philos Soc 2023; 98:584-602. [PMID: 36366773 DOI: 10.1111/brv.12920] [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: 04/11/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
During the last century enormous progress has been made in the understanding of biological diversity, involving a dramatic shift from macroscopic to microscopic organisms. The question now arises as to whether the Natural System introduced by Carl Linnaeus, which has served as the central system for organizing biological diversity, can accommodate the great expansion of diversity that has been discovered. Important discoveries regarding biological diversity have not been fully integrated into a formal, coherent taxonomic system. In addition, because of taxonomic challenges and conflicts, various proposals have been made to abandon key aspects of the Linnaean system. We review the current status of taxonomy of the living world, focussing on groups at the taxonomic level of phylum and above. We summarize the main arguments against and in favour of abandoning aspects of the Linnaean system. Based on these considerations, we conclude that retaining the Linnaean Natural System provides important advantages. We propose a relatively small number of amendments for extending this system, particularly to include the named rank of world (Latin alternative mundis) formally to include non-cellular entities (viruses), and the named rank of empire (Latin alternative imperium) to accommodate the depth of diversity in (unicellular) eukaryotes that has been uncovered. We argue that in the case of both the eukaryotic domain and the viruses the cladistic approach intrinsically fails. However, the resulting semi-cladistic system provides a productive way forward that can help resolve taxonomic challenges. The amendments proposed allow us to: (i) retain named taxonomic levels and the three-domain system, (ii) improve understanding of the main eukaryotic lineages, and (iii) incorporate viruses into the Natural System. Of note, the proposal described herein is intended to serve as the starting point for a broad scientific discussion regarding the modernization of the Linnaean system.
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Affiliation(s)
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics and Department of Chemistry, Oklahoma State University, Stillwater, OK, 74078, USA
| | - David Speijer
- Department of Medical Biochemistry, AmsterdamUMC, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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50
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Tessler M, Cunningham SW, Ingala MR, Warring SD, Brugler MR. An Environmental DNA Primer for Microbial and Restoration Ecology. MICROBIAL ECOLOGY 2023; 85:796-808. [PMID: 36735064 DOI: 10.1007/s00248-022-02168-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 12/28/2022] [Indexed: 05/04/2023]
Abstract
Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.
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Affiliation(s)
- Michael Tessler
- Department of Biology, St. Francis College, Brooklyn, NY, USA.
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA.
| | - Seth W Cunningham
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Melissa R Ingala
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, 07940, USA
| | | | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
- Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, SC, 29902, USA
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