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Pellegrinetti TA, de Cássia Mesquita da Cunha I, Chaves MGD, Freitas ASD, Passos GS, Silva AVRD, Cotta SR, Tsai SM, Mendes LW. Genomic insights of Fictibacillus terranigra sp. nov., a versatile metabolic bacterium from Amazonian Dark Earths. Braz J Microbiol 2024; 55:1817-1828. [PMID: 38358421 PMCID: PMC11153436 DOI: 10.1007/s42770-024-01268-3] [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: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
The Amazon rainforest, a hotspot for biodiversity, is a crucial research area for scientists seeking novel microorganisms with ecological and biotechnological significance. A key region within the Amazon rainforest is the Amazonian Dark Earths (ADE), noted for supporting diverse plant and microbial communities, and its potential as a blueprint for sustainable agriculture. This study delineates the isolation, morphological traits, carbon source utilization, and genomic features of Fictibacillus terranigra CENA-BCM004, a candidate novel species of the Fictibacillus genus isolated from ADE. The genome of Fictibacillus terranigra was sequenced, resulting in 16 assembled contigs, a total length of 4,967,627 bp, and a GC content of 43.65%. Genome annotation uncovered 3315 predicted genes, encompassing a wide range of genes linked to various metabolic pathways. Phylogenetic analysis indicated that CENA-BCM004 is a putative new species, closely affiliated with other unidentified Fictibacillus species and Bacillus sp. WQ 8-8. Moreover, this strain showcased a multifaceted metabolic profile, revealing its potential for diverse biotechnological applications. It exhibited capabilities to antagonize pathogens, metabolize multiple sugars, mineralize organic matter compounds, and solubilize several minerals. These insights substantially augment our comprehension of microbial diversity in ADE and underscore the potential of Fictibacillus terranigra as a precious resource for biotechnological endeavors. The genomic data generated from this study will serve as a foundational resource for subsequent research and exploration of the biotechnological capabilities of this newly identified species.
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Affiliation(s)
- Thierry Alexandre Pellegrinetti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Izadora de Cássia Mesquita da Cunha
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
- Luiz de Queiroz College of Agriculture (ESALQ), University of Sao Paulo, Piracicaba, Brazil
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Anderson Santos de Freitas
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Gabriel Schimmelpfeng Passos
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Ana Vitória Reina da Silva
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Simone Raposo Cotta
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil.
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Gtari M, Beauchemin NJ, Sarker I, Sen A, Ghodhbane-Gtari F, Tisa LS. An overview of Parafrankia (Nod+/Fix+) and Pseudofrankia (Nod+/Fix-) interactions through genome mining and experimental modeling in co-culture and co-inoculation of Elaeagnus angustifolia. Appl Environ Microbiol 2024; 90:e0028824. [PMID: 38651928 PMCID: PMC11107149 DOI: 10.1128/aem.00288-24] [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: 02/18/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
In many frankia, the ability to nodulate host plants (Nod+) and fix nitrogen (Fix+) is a common strategy. However, some frankia within the Pseudofrankia genus lack one or two of these traits. This phenomenon has been consistently observed across various actinorhizal nodule isolates, displaying Nod- and/or Fix- phenotypes. Yet, the mechanisms supporting the colonization and persistence of these inefficient frankia within nodules, both with and without symbiotic strains (Nod+/Fix+), remain unclear. It is also uncertain whether these associations burden or benefit host plants. This study delves into the ecological interactions between Parafrankia EUN1f and Pseudofrankia inefficax EuI1c, isolated from Elaeagnus umbellata nodules. EUN1f (Nod+/Fix+) and EuI1c (Nod+/Fix-) display contrasting symbiotic traits. While the prediction suggests a competitive scenario, the absence of direct interaction evidence implies that the competitive advantage of EUN1f and EuI1c is likely contingent on contextual factors such as substrate availability and the specific nature of stressors in their respective habitats. In co-culture, EUN1f outperforms EuI1c, especially under specific conditions, driven by its nitrogenase activity. Iron-depleted conditions favor EUN1f, emphasizing iron's role in microbial competition. Both strains benefit from host root exudates in pure culture, but EUN1f dominates in co-culture, enhancing its competitive traits. Nodulation experiments show that host plant preferences align with inoculum strain abundance under nitrogen-depleted conditions, while consistently favoring EUN1f in nitrogen-supplied media. This study unveils competitive dynamics and niche exclusion between EUN1f and EuI1c, suggesting that host plant may penalize less effective strains and even all strains. These findings highlight the complex interplay between strain competition and host selective pressure, warranting further research into the underlying mechanisms shaping plant-microbe-microbe interactions in diverse ecosystems. IMPORTANCE While Pseudofrankia strains typically lack the common traits of ability to nodulate the host plant (Nod-) and/or fix nitrogen (Fix-), they are still recovered from actinorhizal nodules. The enigmatic question of how and why these unconventional strains establish themselves within nodule tissue, thriving either alongside symbiotic strains (Nod+/Fix+) or independently, while considering potential metabolic costs to the host plant, remains a perplexing puzzle. This study endeavors to unravel the competitive dynamics between Pseudofrankia inefficax strain EuI1c (Nod+/Fix-) and Parafrankia strain EU1Nf (Nod+/Fix+) through a comprehensive exploration of genomic data and empirical modeling, conducted both in controlled laboratory settings and within the host plant environment.
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Affiliation(s)
- Maher Gtari
- Department of Biological and Chemical Engineering USCR Molecular Bacteriology and Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Carthage, Tunisia
| | - Nicholas J. Beauchemin
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Indrani Sarker
- Bioinformatics Facility, University of North Bengal, Raja Rammohanpur, Siliguri, West Bengal, India
| | - Arnab Sen
- Bioinformatics Facility, University of North Bengal, Raja Rammohanpur, Siliguri, West Bengal, India
| | - Faten Ghodhbane-Gtari
- Department of Biological and Chemical Engineering USCR Molecular Bacteriology and Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Carthage, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, University of La Manouba, Sidi Thabet, Tunisia
| | - Louis S. Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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3
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Isokpehi RD, Kim Y, Krejci SE, Trivedi VD. Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential. Microorganisms 2024; 12:791. [PMID: 38674735 PMCID: PMC11052009 DOI: 10.3390/microorganisms12040791] [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: 03/25/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.
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Affiliation(s)
| | - Yungkul Kim
- Oyster Microbiome Project, College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (S.E.K.); (V.D.T.)
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Abs E, Chase AB, Manzoni S, Ciais P, Allison SD. Microbial evolution-An under-appreciated driver of soil carbon cycling. GLOBAL CHANGE BIOLOGY 2024; 30:e17268. [PMID: 38562029 DOI: 10.1111/gcb.17268] [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: 12/20/2023] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Although substantial advances in predicting the ecological impacts of global change have been made, predictions of the evolutionary impacts have lagged behind. In soil ecosystems, microbes act as the primary energetic drivers of carbon cycling; however, microbes are also capable of evolving on timescales comparable to rates of global change. Given the importance of soil ecosystems in global carbon cycling, we assess the potential impact of microbial evolution on carbon-climate feedbacks in this system. We begin by reviewing the current state of knowledge concerning microbial evolution in response to global change and its specific effect on soil carbon dynamics. Through this integration, we synthesize a roadmap detailing how to integrate microbial evolution into ecosystem biogeochemical models. Specifically, we highlight the importance of microscale mechanistic soil carbon models, including choosing an appropriate evolutionary model (e.g., adaptive dynamics, quantitative genetics), validating model predictions with 'omics' and experimental data, scaling microbial adaptations to ecosystem level processes, and validating with ecosystem-scale measurements. The proposed steps will require significant investment of scientific resources and might require 10-20 years to be fully implemented. However, through the application of multi-scale integrated approaches, we will advance the integration of microbial evolution into predictive understanding of ecosystems, providing clarity on its role and impact within the broader context of environmental change.
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Affiliation(s)
- Elsa Abs
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
- Laboratoire Des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alexander B Chase
- Department of Earth Sciences, Southern Methodist University, Dallas, Texas, USA
| | - Stefano Manzoni
- Department of Physical Geography and Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Philippe Ciais
- Laboratoire Des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, California, USA
- Department of Earth System Science, University of California, Irvine, Irvine, California, USA
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5
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Marschmann GL, Tang J, Zhalnina K, Karaoz U, Cho H, Le B, Pett-Ridge J, Brodie EL. Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model. Nat Microbiol 2024; 9:421-433. [PMID: 38316928 PMCID: PMC10847045 DOI: 10.1038/s41564-023-01582-w] [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: 04/20/2023] [Accepted: 12/08/2023] [Indexed: 02/07/2024]
Abstract
Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.
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Affiliation(s)
- Gianna L Marschmann
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jinyun Tang
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kateryna Zhalnina
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Heejung Cho
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Beatrice Le
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
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6
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Bao Y, Ruan Y, Wu J, Wang WX, Leung KMY, Lee PKH. Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:780-794. [PMID: 38118133 DOI: 10.1021/acs.est.3c08076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Assessing the impacts of cumulative anthropogenic disturbances on estuarine ecosystem health is challenging. Using spatially distributed sediments from the Pearl River Estuary (PRE) in southern China, which are significantly influenced by anthropogenic activities, we demonstrated that metagenomics-based surveillance of benthic microbial communities is a robust approach to assess anthropogenic impacts on estuarine benthic ecosystems. Correlational and threshold analyses between microbial compositions and environmental conditions indicated that anthropogenic disturbances in the PRE sediments drove the taxonomic and functional variations in the benthic microbial communities. An ecological community threshold of anthropogenic disturbances was identified, which delineated the PRE sediments into two groups (H and L) with distinct taxa and functional traits. Group H, located nearshore and subjected to a higher level of anthropogenic disturbances, was enriched with pollutant degraders, putative human pathogens, fecal pollution indicators, and functional traits related to stress tolerance. In contrast, Group L, located offshore and subjected to a lower level of anthropogenic disturbances, was enriched with halotolerant and oligotrophic taxa and functional traits related to growth and resource acquisition. The machine learning random forest model identified a number of taxonomic and functional indicators that could differentiate PRE sediments between Groups H and L. The identified ecological community threshold and microbial indicators highlight the utility of metagenomics-based microbial surveillance in assessing the adverse impacts of anthropogenic disturbances in estuarine sediments, which can assist environmental management to better protect ecosystem health.
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Affiliation(s)
- Yingyu Bao
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| | - Yuefei Ruan
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Jiaxue Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Kenneth M Y Leung
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Patrick K H Lee
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
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Espada‐Hinojosa S, Karthäuser C, Srivastava A, Schuster L, Winter T, de Oliveira AL, Schulz F, Horn M, Sievert S, Bright M. Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free-living relative. Mol Ecol Resour 2024; 24:e13889. [PMID: 38010882 PMCID: PMC10952691 DOI: 10.1111/1755-0998.13889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/31/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
Thiotrophic symbioses between sulphur-oxidizing bacteria and various unicellular and metazoan eukaryotes are widespread in reducing marine environments. The giant colonial ciliate Zoothamnium niveum, however, is the only host of thioautotrophic symbionts that has been cultivated along with its symbiont, the vertically transmitted ectosymbiont Candidatus Thiobius zoothamnicola (short Thiobius). Because theoretical predictions posit a smaller genome in vertically transmitted endosymbionts compared to free-living relatives, we investigated whether this is true also for an ectosymbiont. We used metagenomics to recover the high-quality draft genome of this bacterial symbiont. For comparison we have also sequenced a closely related free-living cultured but not formally described strain Milos ODIII6 (short ODIII6). We then performed comparative genomics to assess the functional capabilities at gene, metabolic pathway and trait level. 16S rRNA gene trees and average amino acid identity confirmed the close phylogenetic relationship of both bacteria. Indeed, Thiobius has about a third smaller genome than its free-living relative ODIII6, with reduced metabolic capabilities and fewer functional traits. The functional capabilities of Thiobius were a subset of those of the more versatile ODIII6, which possessed additional genes for oxygen, sulphur and hydrogen utilization and for the acquisition of phosphorus illustrating features that may be adaptive for the unstable environmental conditions at hydrothermal vents. In contrast, Thiobius possesses genes potentially enabling it to utilize lactate and acetate heterotrophically, compounds that may be provided as byproducts by the host. The present study illustrates the effect of strict host-dependence of a bacterial ectosymbiont on genome evolution and host adaptation.
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Affiliation(s)
| | - Clarissa Karthäuser
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Abhishek Srivastava
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - Lukas Schuster
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Present address:
Deakin UniversityBurwoodAustralia
| | - Teresa Winter
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - André Luiz de Oliveira
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Present address:
Max Planck Institute for Marine MicrobiologyBremenGermany
| | - Frederik Schulz
- Center for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
- Present address:
DOE Joint Genome InstituteBerkeleyCaliforniaUSA
| | - Matthias Horn
- Center for Microbiology and Environmental Systems ScienceUniversity of ViennaViennaAustria
| | - Stefan Sievert
- Biology DepartmentWoods Hole Oceanographic InstitutionWoods HoleMassachusettsUSA
| | - Monika Bright
- Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
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Graham EB, Knelman JE. Implications of Soil Microbial Community Assembly for Ecosystem Restoration: Patterns, Process, and Potential. MICROBIAL ECOLOGY 2023; 85:809-819. [PMID: 36735065 DOI: 10.1007/s00248-022-02155-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/02/2022] [Indexed: 05/04/2023]
Abstract
While it is now widely accepted that microorganisms provide essential functions in restoration ecology, the nature of relationships between microbial community assembly and ecosystem recovery remains unclear. There has been a longstanding challenge to decipher whether microorganisms facilitate or simply follow ecosystem recovery, and evidence for each is mixed at best. We propose that understanding microbial community assembly processes is critical to understanding the role of microorganisms during ecosystem restoration and thus optimizing management strategies. We examine how the connection between environment, community structure, and function is fundamentally underpinned by the processes governing community assembly of these microbial communities. We review important factors to consider in evaluating microbial community structure in the context of ecosystem recovery as revealed in studies of microbial succession: (1) variation in community assembly processes, (2) linkages to ecosystem function, and (3) measurable microbial community attributes. We seek to empower restoration ecology with microbial assembly and successional understandings that can generate actionable insights and vital contexts for ecosystem restoration efforts.
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Affiliation(s)
- Emily B Graham
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
- School of Biological Sciences, Washington State University, Richland, WA, USA.
| | - Joseph E Knelman
- Institute for Arctic and Alpine Research, University of Colorado, Boulder, CO, USA
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Metagenome-assembled genome extraction and analysis from microbiomes using KBase. Nat Protoc 2023; 18:208-238. [PMID: 36376589 DOI: 10.1038/s41596-022-00747-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/28/2022] [Indexed: 11/16/2022]
Abstract
Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. To realize the hope of capturing Earth's microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform ( http://www.kbase.us/ ). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).
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