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Bosch J, Lebre PH, Marais E, Maggs‐Kölling G, Cowan DA. Kinetics and pathways of sub-lithic microbial community (hypolithon) development. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13290. [PMID: 38923208 PMCID: PMC11194044 DOI: 10.1111/1758-2229.13290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/03/2024] [Indexed: 06/28/2024]
Abstract
Type I hypolithons are microbial communities dominated by Cyanobacteria. They adhere to the underside of semi-translucent rocks in desert pavements, providing them with a refuge from the harsh abiotic stresses found on the desert soil surface. Despite their crucial role in soil nutrient cycling, our understanding of their growth rates and community development pathways remains limited. This study aimed to quantify the dynamics of hypolithon formation in the pavements of the Namib Desert. We established replicate arrays of sterile rock tiles with varying light transmission in two areas of the Namib Desert, each with different annual precipitation regimes. These were sampled annually over 7 years, and the samples were analysed using eDNA extraction and 16S rRNA gene amplicon sequencing. Our findings revealed that in the zone with higher precipitation, hypolithon formation became evident in semi-translucent rocks 3 years after the arrays were set up. This coincided with a Cyanobacterial 'bloom' in the adherent microbial community in the third year. In contrast, no visible hypolithon formation was observed at the array set up in the hyper-arid zone. This study provides the first quantitative evidence of the kinetics of hypolithon development in hot desert environments, suggesting that development rates are strongly influenced by precipitation regimes.
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Affiliation(s)
- Jason Bosch
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
- Institute of Microbiology of the Czech Academy of SciencesCzech Academy of SciencesPrahaCzech Republic
| | - Pedro H. Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
| | | | | | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and MicrobiologyUniversity of PretoriaPretoriaSouth Africa
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2
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Imminger S, Meier DV, Schintlmeister A, Legin A, Schnecker J, Richter A, Gillor O, Eichorst SA, Woebken D. Survival and rapid resuscitation permit limited productivity in desert microbial communities. Nat Commun 2024; 15:3056. [PMID: 38632260 DOI: 10.1038/s41467-024-46920-6] [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: 06/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.
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Affiliation(s)
- Stefanie Imminger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Dimitri V Meier
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Department of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anton Legin
- Faculty of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel
| | - Stephanie A Eichorst
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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3
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León-Sobrino C, Ramond JB, Coclet C, Kapitango RM, Maggs-Kölling G, Cowan D. Temporal dynamics of microbial transcription in wetted hyperarid desert soils. FEMS Microbiol Ecol 2024; 100:fiae009. [PMID: 38299778 PMCID: PMC10913055 DOI: 10.1093/femsec/fiae009] [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: 06/12/2023] [Revised: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 02/02/2024] Open
Abstract
Rainfall is rare in hyperarid deserts but, when it occurs, it triggers large biological responses essential for the long-term maintenance of the ecosystem. In drylands, microbes play major roles in nutrient cycling, but their responses to short-lived opportunity windows are poorly understood. Due to its ephemeral nature, mRNA is ideally suited to study microbiome dynamics upon abrupt changes in the environment. We analyzed microbial community transcriptomes after simulated rainfall in a Namib Desert soil over 7 days. Using total mRNA from dry and watered plots we infer short-term functional responses in the microbiome. A rapid two-phase cycle of activation and return to basal state was completed in a short period. Motility systems activated immediately, whereas competition-toxicity increased in parallel to predator taxa and the drying of soils. Carbon fixation systems were downregulated, and reactivated upon return to a near-dry state. The chaperone HSP20 was markedly regulated by watering across all major bacteria, suggesting a particularly important role in adaptation to desiccated ecosystems. We show that transcriptomes provide consistent and high resolution information on microbiome processes in a low-biomass environment, revealing shared patterns across taxa. We propose a structured dispersal-predation dynamic as a central driver of desert microbial responses to rainfall.
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Affiliation(s)
- Carlos León-Sobrino
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
- Extreme Ecosystem Microbiomics and Ecogenomics (E²ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Clément Coclet
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
| | | | | | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, 0002 Pretoria, South Africa
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4
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Esposito A, Del Duca S, Vitali F, Bigiotti G, Mocali S, Semenzato G, Papini A, Santini G, Mucci N, Padula A, Greco C, Nasanbat B, Davaakhuu G, Bazarragchaa M, Riga F, Augugliaro C, Cecchi L, Fani R, Zaccaroni M. The Great Gobi A Strictly Protected Area: Characterization of Soil Bacterial Communities from Four Oases. Microorganisms 2024; 12:320. [PMID: 38399724 PMCID: PMC10891509 DOI: 10.3390/microorganisms12020320] [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: 12/31/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Understanding how microbial communities survive in extreme environmental pressure is critical for interpreting ecological patterns and microbial diversity. Great Gobi A Strictly Protected Area represents an intriguing model for studying the bacterial community since it is a protected and intact wild area of the Mongolian desert. In this work, the composition of a bacterial community of the soil from four oases was characterized by extracting total DNA and sequencing through the Illumina NovaSeq platform. In addition, the soil's chemical and physical properties were determined, and their influence on shaping the microbial communities was evaluated. The results showed a high variability of bacterial composition among oases. Moreover, combining specific chemical and physical parameters significantly shapes the bacterial community among oases. Data obtained suggested that the oases were highly variable in physiochemical parameters and bacterial communities despite the similar extreme climate conditions. Moreover, core functional microbiome were constituted by aerobic chemoheterotrophy and chemoheterotrophy, mainly contributed by the most abundant bacteria, such as Actinobacteriota, Pseudomonadota, and Firmicutes. This result supposes a metabolic flexibility for sustaining life in deserts. Furthermore, as the inhabitants of the extreme regions are likely to produce new chemical compounds, isolation of key taxa is thus encouraged.
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Affiliation(s)
- Antonia Esposito
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 50125 Florence, Italy; (A.E.); (S.D.D.); (F.V.); (G.B.); (S.M.)
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
| | - Sara Del Duca
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 50125 Florence, Italy; (A.E.); (S.D.D.); (F.V.); (G.B.); (S.M.)
| | - Francesco Vitali
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 50125 Florence, Italy; (A.E.); (S.D.D.); (F.V.); (G.B.); (S.M.)
| | - Gaia Bigiotti
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 50125 Florence, Italy; (A.E.); (S.D.D.); (F.V.); (G.B.); (S.M.)
| | - Stefano Mocali
- Council for Agricultural Research and Economics, Research Centre for Agriculture and Environment, 50125 Florence, Italy; (A.E.); (S.D.D.); (F.V.); (G.B.); (S.M.)
| | - Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
| | - Alessio Papini
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
| | - Giacomo Santini
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy; (N.M.); (A.P.); (C.G.)
| | - Anna Padula
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy; (N.M.); (A.P.); (C.G.)
| | - Claudia Greco
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy; (N.M.); (A.P.); (C.G.)
| | - Battogtokh Nasanbat
- Institute of Biology, Mongolian Academy of Sciences, Peace Avenue-54B, Bayanzurkh District, Ulaanbaatar 13330, Mongolia; (B.N.); (G.D.)
| | - Gantulga Davaakhuu
- Institute of Biology, Mongolian Academy of Sciences, Peace Avenue-54B, Bayanzurkh District, Ulaanbaatar 13330, Mongolia; (B.N.); (G.D.)
| | - Munkhtsetseg Bazarragchaa
- Department of Molecular Biology and Genetics, School of Bio-Medicine, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia;
| | - Francesco Riga
- Italian Institute for Environmental Protection and Research (ISPRA), Via Brancati 48, 00144 Rome, Italy;
| | | | - Lorenzo Cecchi
- Natural History Museum, Botanical Collections “Filippo Parlatore”—Via Giorgio la Pira 4, 50121 Florence, Italy;
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
| | - Marco Zaccaroni
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; (G.S.); (A.P.); (G.S.)
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5
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Coleine C, Delgado-Baquerizo M, DiRuggiero J, Guirado E, Harfouche AL, Perez-Fernandez C, Singh BK, Selbmann L, Egidi E. Dryland microbiomes reveal community adaptations to desertification and climate change. THE ISME JOURNAL 2024; 18:wrae056. [PMID: 38552152 PMCID: PMC11031246 DOI: 10.1093/ismejo/wrae056] [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: 01/22/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/21/2024]
Abstract
Drylands account for 45% of the Earth's land area, supporting ~40% of the global population. These regions support some of the most extreme environments on Earth, characterized by extreme temperatures, low and variable rainfall, and low soil fertility. In these biomes, microorganisms provide vital ecosystem services and have evolved distinctive adaptation strategies to endure and flourish in the extreme. However, dryland microbiomes and the ecosystem services they provide are under threat due to intensifying desertification and climate change. In this review, we provide a synthesis of our current understanding of microbial life in drylands, emphasizing the remarkable diversity and adaptations of these communities. We then discuss anthropogenic threats, including the influence of climate change on dryland microbiomes and outline current knowledge gaps. Finally, we propose research priorities to address those gaps and safeguard the sustainability of these fragile biomes.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, E-41012, Spain
| | - Jocelyne DiRuggiero
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, United States
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Emilio Guirado
- Multidisciplinary Institute for Environment Studies “Ramón Margalef”, Universidad de Alicante, Alicante E-03071, Spain
| | - Antoine L Harfouche
- Department for Innovation in Biological, Agro-Food and Forest systems, University of Tuscia, Viterbo 01100, Italy
| | | | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith 2750, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith 2750, Australia
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
- Mycological Section, Italian Antarctic National Museum (MNA), Genoa 16128, Italy
| | - Eleonora Egidi
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith 2750, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith 2750, Australia
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6
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Garvin ZK, Abades SR, Trefault N, Alfaro FD, Sipes K, Lloyd KG, Onstott TC. Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert. THE ISME JOURNAL 2024; 18:wrae062. [PMID: 38625060 PMCID: PMC11094475 DOI: 10.1093/ismejo/wrae062] [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: 09/26/2023] [Revised: 01/29/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing their impact on trace gas-oxidizers in the surrounding soils. We assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy/carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.
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Affiliation(s)
- Zachary K Garvin
- Department of Geosciences, Princeton University, Princeton, NJ 08544, United States
| | - Sebastián R Abades
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, 8580745, Santiago, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, 8580745, Santiago, Chile
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, 8580745, Santiago, Chile
| | - Katie Sipes
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
- Department of Environmental Science, Aarhus University, 4000, Roskilde, Denmark
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ 08544, United States
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7
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Ray AE, Tribbia DZ, Cowan DA, Ferrari BC. Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis. Microbiol Mol Biol Rev 2023; 87:e0004823. [PMID: 37914532 PMCID: PMC10732025 DOI: 10.1128/mmbr.00048-23] [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: 11/03/2023] Open
Abstract
SUMMARY Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.
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Affiliation(s)
- Angelique E. Ray
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Dana Z. Tribbia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
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8
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Woern C, Grossmann L. Microbial gas fermentation technology for sustainable food protein production. Biotechnol Adv 2023; 69:108240. [PMID: 37647973 DOI: 10.1016/j.biotechadv.2023.108240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023]
Abstract
The development of novel, sustainable, and robust food production technologies represents one of the major pillars to address the most significant challenges humanity is going to face on earth in the upcoming decades - climate change, population growth, and resource depletion. The implementation of microfoods, i.e., foods formulated with ingredients from microbial cultivation, into the food supply chain has a huge potential to contribute towards energy-efficient and nutritious food manufacturing and represents a means to sustainably feed a growing world population. This review recapitulates and assesses the current state in the establishment and usage of gas fermenting bacteria as an innovative feedstock for protein production. In particular, we focus on the most promising representatives of this taxon: the hydrogen-oxidizing bacteria (hydrogenotrophs) and the methane-oxidizing bacteria (methanotrophs). These unicellular microorganisms can aerobically metabolize gaseous hydrogen and methane, respectively, to provide the required energy for building up cell material. A protein yield over 70% in the dry matter cell mass can be reached with no need for arable land and organic substrates making it a promising alternative to plant- and animal-based protein sources. We illuminate the holistic approach to incorporate protein extracts obtained from the cultivation of gas fermenting bacteria into microfoods. Herein, the fundamental properties of the bacteria, cultivation methods, downstream processing, and potential food applications are discussed. Moreover, this review covers existing and future challenges as well as sustainability aspects associated with the production of microbial protein through gas fermentation.
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Affiliation(s)
- Carlos Woern
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Lutz Grossmann
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA.
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9
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Liu L, Chen Y, Shen J, Pan Y, Lin W. Metabolic versatility of soil microbial communities below the rocks of the hyperarid Dalangtan Playa. Appl Environ Microbiol 2023; 89:e0107223. [PMID: 37902391 PMCID: PMC10686078 DOI: 10.1128/aem.01072-23] [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: 06/24/2023] [Accepted: 09/22/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE The hyperarid Dalangtan Playa in the western Qaidam Basin, northwestern China, is a unique terrestrial analog of Mars. Despite the polyextreme environments of this area, habitats below translucent rocks capable of environmental buffering could serve as refuges for microbial life. In this study, the hybrid assembly of Illumina short reads and Nanopore long reads recovered high-quality and high-continuity genomes, allowing for high-accuracy analysis and a deeper understanding of extremophiles in the sheltered soils of the Dalangtan Playa. Our findings reveal self-supporting and metabolically versatile sheltered soil communities adapted to a hyperarid and hypersaline playa, which provides implications for the search for life signals on Mars.
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Affiliation(s)
- Li Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Chen
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Jianxun Shen
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Yongxin Pan
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Lin
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
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10
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Baril X, Constant P. Carbon amendments in soil microcosms induce uneven response on H2 oxidation activity and microbial community composition. FEMS Microbiol Ecol 2023; 99:fiad159. [PMID: 38040657 PMCID: PMC10716739 DOI: 10.1093/femsec/fiad159] [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: 09/21/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023] Open
Abstract
High-affinity H2-oxidizing bacteria (HA-HOB) thriving in soil are responsible for the most important sink of atmospheric H2. Their activity increases with soil organic carbon content, but the incidence of different carbohydrate fractions on the process has received little attention. Here we tested the hypothesis that carbon amendments impact HA-HOB activity and diversity differentially depending on their recalcitrance and their concentration. Carbon sources (sucrose, starch, cellulose) and application doses (0, 0.1, 1, 3, 5% Ceq soildw-1) were manipulated in soil microcosms. Only 0.1% Ceq soildw-1 cellulose treatment stimulated the HA-HOB activity. Sucrose amendments induced the most significant changes, with an abatement of 50% activity at 1% Ceq soildw-1. This was accompanied with a loss of bacterial and fungal alpha diversity and a reduction of high-affinity group 1 h/5 [NiFe]-hydrogenase gene (hhyL) abundance. A quantitative classification framework was elaborated to assign carbon preference traits to 16S rRNA gene, ITS and hhyL genotypes. The response was uneven at the taxonomic level, making carbon preference a difficult trait to predict. Overall, the results suggest that HA-HOB activity is more susceptible to be stimulated by low doses of recalcitrant carbon, while labile carbon-rich environment is an unfavorable niche for HA-HOB, inducing catabolic repression of hydrogenase.
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Affiliation(s)
- Xavier Baril
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - Philippe Constant
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
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11
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Demergasso C, Neilson JW, Tebes-Cayo C, Véliz R, Ayma D, Laubitz D, Barberán A, Chong-Díaz G, Maier RM. Hyperarid soil microbial community response to simulated rainfall. Front Microbiol 2023; 14:1202266. [PMID: 37779711 PMCID: PMC10537920 DOI: 10.3389/fmicb.2023.1202266] [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: 04/07/2023] [Accepted: 07/31/2023] [Indexed: 10/03/2023] Open
Abstract
The exceptionally long and protracted aridity in the Atacama Desert (AD), Chile, provides an extreme, terrestrial ecosystem that is ideal for studying microbial community dynamics under hyperarid conditions. Our aim was to characterize the temporal response of hyperarid soil AD microbial communities to ex situ simulated rainfall (5% g water/g dry soil for 4 weeks) without nutrient amendment. We conducted replicated microcosm experiments with surface soils from two previously well-characterized AD hyperarid locations near Yungay at 1242 and 1609 masl (YUN1242 and YUN1609) with distinct microbial community compositions and average soil relative humidity levels of 21 and 17%, respectively. The bacterial and archaeal response to soil wetting was evaluated by 16S rRNA gene qPCR, and amplicon sequencing. Initial YUN1242 bacterial and archaeal 16S rRNA gene copy numbers were significantly higher than for YUN1609. Over the next 4 weeks, qPCR results showed significant increases in viable bacterial abundance, whereas archaeal abundance decreased. Both communities were dominated by 10 prokaryotic phyla (Actinobacteriota, Proteobacteria, Chloroflexota, Gemmatimonadota, Firmicutes, Bacteroidota, Planctomycetota, Nitrospirota, Cyanobacteriota, and Crenarchaeota) but there were significant site differences in the relative abundances of Gemmatimonadota and Chloroflexota, and specific actinobacterial orders. The response to simulated rainfall was distinct for the two communities. The actinobacterial taxa in the YUN1242 community showed rapid changes while the same taxa in the YUN1609 community remained relatively stable until day 30. Analysis of inferred function of the YUN1242 microbiome response implied an increase in the relative abundance of known spore-forming taxa with the capacity for mixotrophy at the expense of more oligotrophic taxa, whereas the YUN1609 community retained a stable profile of oligotrophic, facultative chemolithoautotrophic and mixotrophic taxa. These results indicate that bacterial communities in extreme hyperarid soils have the capacity for growth in response to simulated rainfall; however, historic variations in long-term hyperaridity exposure produce communities with distinct putative metabolic capacities.
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Affiliation(s)
- Cecilia Demergasso
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Julia W. Neilson
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Cinthya Tebes-Cayo
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Roberto Véliz
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Diego Ayma
- Department of Mathematics, Faculty of Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Daniel Laubitz
- Steele Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, United States
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Guillermo Chong-Díaz
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Raina M. Maier
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
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Li S, Yang S, Wei X, Jiao S, Luo W, Chen W, Wei G. Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands. THE ISME JOURNAL 2023; 17:1257-1266. [PMID: 37253970 PMCID: PMC10356767 DOI: 10.1038/s41396-023-01437-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/03/2023] [Accepted: 05/19/2023] [Indexed: 06/01/2023]
Abstract
Atmospheric trace gases, such as H2 and CO, are important energy sources for microbial growth and maintenance in various ecosystems, especially in arid deserts with little organic substrate. Nonetheless, the impact of soil organic C availability on microbial trace gas oxidation and the underlying mechanisms are unclear at the community level. This study investigated the energy and life-history strategies of soil microbiomes along an organic C gradient inside and out of Hedysarum scoparium islands dispersed in the Mu Us Desert, China. Metagenomic analysis showed that with increasing organic C availability from bare areas into "fertile islands", the abundance of trace gas oxidizers (TGOs) decreased, but that of trace gas nonoxidizers (TGNOs) increased. The variation in their abundance was more related to labile/soluble organic C levels than to stable/insoluble organic C levels. The consumption rates of H2 and CO confirmed that organic C addition, especially soluble organic C addition, inhibited microbial trace gas oxidation. Moreover, microorganisms with distinct energy-acquiring strategies showed different life-history traits. The TGOs had lower 16 S rRNA operon copy numbers, lower predicted maximum growth rates and higher proportions of labile C degradation genes, implying the prevalence of oligotrophs. In contrast, copiotrophs were prevalent in the TGNOs. These results revealed a mechanism for the microbial community to adapt to the highly heterogeneous distribution of C resources by adjusting the abundances of taxa with distinct energy and life-history strategies, which would further affect trace gas consumption and C turnover in desert ecosystems.
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Affiliation(s)
- Shuyue Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shanshan Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaomeng Wei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Wen Luo
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
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13
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Mashamaite L, Lebre PH, Varliero G, Maphosa S, Ortiz M, Hogg ID, Cowan DA. Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient. Front Microbiol 2023; 14:1203216. [PMID: 37555066 PMCID: PMC10406297 DOI: 10.3389/fmicb.2023.1203216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
INTRODUCTION The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica. METHODS We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons. RESULTS AND DISCUSSION Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.
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Affiliation(s)
- Lefentse Mashamaite
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Pedro H. Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Silindile Maphosa
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Max Ortiz
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Clemson University Genomics & Bioinformatics Facility, Clemson University, Clemson, SC, United States
| | - Ian D. Hogg
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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Cowan DA, Cary SC, DiRuggiero J, Eckardt F, Ferrari B, Hopkins DW, Lebre PH, Maggs-Kölling G, Pointing SB, Ramond JB, Tribbia D, Warren-Rhodes K. 'Follow the Water': Microbial Water Acquisition in Desert Soils. Microorganisms 2023; 11:1670. [PMID: 37512843 PMCID: PMC10386458 DOI: 10.3390/microorganisms11071670] [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: 05/03/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments.
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Affiliation(s)
- Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - S Craig Cary
- School of Biological Sciences, University of Waikato, Hamilton 3216, New Zealand
| | - Jocelyne DiRuggiero
- Departments of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Departments of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Frank Eckardt
- Department of Environmental and Geographical Science, University of Cape Town, Cape Town 7701, South Africa
| | - Belinda Ferrari
- School of Biotechnology and Biological Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - David W Hopkins
- Scotland's Rural College, West Mains Road, Edinburgh EH9 3JG, UK
| | - Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | | | - Stephen B Pointing
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Departamento Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Dana Tribbia
- School of Biotechnology and Biological Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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15
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Marasco R, Ramond JB, Van Goethem MW, Rossi F, Daffonchio D. Diamonds in the rough: Dryland microorganisms are ecological engineers to restore degraded land and mitigate desertification. Microb Biotechnol 2023. [PMID: 36641786 PMCID: PMC10364308 DOI: 10.1111/1751-7915.14216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/16/2023] Open
Abstract
Our planet teeters on the brink of massive ecosystem collapses, and arid regions experience manifold environmental and climatic challenges that increase the magnitude of selective pressures on already stressed ecosystems. Ultimately, this leads to their aridification and desertification, that is, to simplified and barren ecosystems (with proportionally less microbial load and diversity) with altered functions and food webs and modification of microbial community network. Thus, preserving and restoring soil health in such a fragile biome could help buffer climate change's effects. We argue that microorganisms and the protection of their functional properties and networks are key to fight desertification. Specifically, we claim that it is rational, possible and certainly practical to rely on native dryland edaphic microorganisms and microbial communities as well as dryland plants and their associated microbiota to conserve and restore soil health and mitigate soil depletion in newly aridified lands. Furthermore, this will meet the objective of protecting/stabilizing (and even enhancing) soil biodiversity globally. Without urgent conservation and restoration actions that take into account microbial diversity, we will ultimately, and simply, not have anything to protect anymore.
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Affiliation(s)
- Ramona Marasco
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Jean-Baptiste Ramond
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marc W Van Goethem
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Federico Rossi
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Pisa, Italy
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
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16
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Inhibitory Effect of Select Nitrocompounds and Chlorate against Yersinia ruckeri and Yersinia aleksiciae In Vitro. Pathogens 2022; 11:pathogens11111381. [DOI: 10.3390/pathogens11111381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
Yersinia ruckeri is an important fish pathogen causing enteric redmouth disease. Antibiotics have traditionally been used to control this pathogen, but concerns of antibiotic resistance have created a need for alternative interventions. Presently, chlorate and certain nitrocompounds were tested against Y. ruckeri as well as a related species within the genus, Y. aleksiciae, to assess the effects of these inhibitors. The results reveal that 9 mM chlorate had no inhibitory effect against Y. ruckeri, but inhibited growth rates and maximum optical densities of Y. aleksciciae by 20–25% from those of untreated controls (0.46 h−1 and 0.29 maximum optical density, respectively). The results further reveal that 2-nitropropanol and 2-nitroethanol (9 mM) eliminated the growth of both Y. ruckeri and Y. aleksiciae during anaerobic or aerobic culture. Nitroethane, ethyl nitroacetate and ethyl-2-nitropropionate (9 mM) were less inhibitory when tested similarly. Results from a mixed culture of Y. ruckeri with fish tank microbes and of Y. aleksiciae with porcine fecal microbes reveal that the anti-Yersinia activity of the tested nitrocompounds was bactericidal, with 2-nitropropanol and 2-nitroethanol being more potent than the other tested nitrocompounds. The anti-Yersinia activity observed with these tested compounds warrants further study to elucidate the mechanisms of action and strategies for their practical application.
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Chown SL. Macrophysiology for decision‐making. J Zool (1987) 2022. [DOI: 10.1111/jzo.13029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- S. L. Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences Monash University Melbourne Victoria Australia
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18
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Microorganisms as New Sources of Energy. ENERGIES 2022. [DOI: 10.3390/en15176365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The use of fossil energy sources has a negative impact on the economic and socio-political stability of specific regions and countries, causing environmental changes due to the emission of greenhouse gases. Moreover, the stocks of mineral energy are limited, causing the demand for new types and forms of energy. Biomass is a renewable energy source and represents an alternative to fossil energy sources. Microorganisms produce energy from the substrate and biomass, i.e., from substances in the microenvironment, to maintain their metabolism and life. However, specialized microorganisms also produce specific metabolites under almost abiotic circumstances that often do not have the immediate task of sustaining their own lives. This paper presents the action of biogenic and biogenic–thermogenic microorganisms, which produce methane, alcohols, lipids, triglycerides, and hydrogen, thus often creating renewable energy from waste biomass. Furthermore, some microorganisms acquire new or improved properties through genetic interventions for producing significant amounts of energy. In this way, they clean the environment and can consume greenhouse gases. Particularly suitable are blue-green algae or cyanobacteria but also some otherwise pathogenic microorganisms (E. coli, Klebsiella, and others), as well as many other specialized microorganisms that show an incredible ability to adapt. Microorganisms can change the current paradigm, energy–environment, and open up countless opportunities for producing new energy sources, especially hydrogen, which is an ideal energy source for all systems (biological, physical, technological). Developing such energy production technologies can significantly change the already achieved critical level of greenhouse gases that significantly affect the climate.
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19
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Cowan DA, Lebre PH, Amon C, Becker RW, Boga HI, Boulangé A, Chiyaka TL, Coetzee T, de Jager PC, Dikinya O, Eckardt F, Greve M, Harris MA, Hopkins DW, Houngnandan HB, Houngnandan P, Jordaan K, Kaimoyo E, Kambura AK, Kamgan-Nkuekam G, Makhalanyane TP, Maggs-Kölling G, Marais E, Mondlane H, Nghalipo E, Olivier BW, Ortiz M, Pertierra LR, Ramond JB, Seely M, Sithole-Niang I, Valverde A, Varliero G, Vikram S, Wall DH, Zeze A. Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes. MICROBIOME 2022; 10:131. [PMID: 35996183 PMCID: PMC9396824 DOI: 10.1186/s40168-022-01297-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/15/2022] [Indexed: 05/20/2023]
Abstract
BACKGROUND Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents. RESULTS The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation. CONCLUSION This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.
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Affiliation(s)
- D A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - P H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
| | - Cer Amon
- Institut National Polytechnique Houphouet-Boigny, Cote d'Ivoire, Yamoussoukro, South Africa
| | - R W Becker
- Biodiversity Research Centre, Department of Agriculture and Natural Resources Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - H I Boga
- Taita Taveta University, Voi, Kenya
| | - A Boulangé
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
- UMR InterTryp, CIRAD-IRD, 34398, Montpellier, France
| | - T L Chiyaka
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - T Coetzee
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - P C de Jager
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - O Dikinya
- Department of Environmental Science, University of Botswana, Gaborone, Botswana
| | - F Eckardt
- Department of Geography, University of Cape Town, Cape Town, South Africa
| | - M Greve
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - M A Harris
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - D W Hopkins
- Scotland's Rural College, Edinburgh, EH9 3JG, UK
| | - H B Houngnandan
- Université Nationale d'Agriculture, Porto-Novo, Benin (Laboratoire de Microbiologie Des Sols Et d'Ecologie Microbienne), Porto-Novo, Benin
| | - P Houngnandan
- Université Nationale d'Agriculture, Porto-Novo, Benin (Laboratoire de Microbiologie Des Sols Et d'Ecologie Microbienne), Porto-Novo, Benin
| | - K Jordaan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Departamento de Genética Molecular Y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - E Kaimoyo
- University of Zambia, Lusaka, Zambia
| | | | - G Kamgan-Nkuekam
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - T P Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - E Marais
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | - H Mondlane
- Centro de Biotecnologia, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - E Nghalipo
- Biodiversity Research Centre, Department of Agriculture and Natural Resources Sciences, Namibia University of Science and Technology, Windhoek, Namibia
| | - B W Olivier
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - M Ortiz
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - L R Pertierra
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - J-B Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Departamento de Genética Molecular Y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - M Seely
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | - I Sithole-Niang
- Department of Biotechnology and Biochemistry, University of Zimbabwe, Harare, Zimbabwe
| | - A Valverde
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - G Varliero
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - S Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - D H Wall
- Department of Biology, Colorado State University, Fort Collins, USA
| | - A Zeze
- Institut National Polytechnique Houphouet-Boigny, Cote d'Ivoire, Yamoussoukro, South Africa
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Lin L, Huang H, Zhang X, Dong L, Chen Y. Hydrogen-oxidizing bacteria and their applications in resource recovery and pollutant removal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155559. [PMID: 35483467 DOI: 10.1016/j.scitotenv.2022.155559] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/16/2022] [Accepted: 04/23/2022] [Indexed: 06/14/2023]
Abstract
Hydrogen oxidizing bacteria (HOB), a type of chemoautotroph, are a group of bacteria from different genera that share the ability to oxidize H2 and fix CO2 to provide energy and synthesize cellular material. Recently, HOB have received growing attention due to their potential for CO2 capture and waste recovery. This review provides a comprehensive overview of the biological characteristics of HOB and their application in resource recovery and pollutant removal. Firstly, the enzymes, genes and corresponding regulation systems responsible for the key metabolic processes of HOB are discussed in detail. Then, the enrichment and cultivation methods including the coupled water splitting-biosynthetic system cultivation, mixed cultivation and two-stage cultivation strategies for HOB are summarized, which is the critical prerequisite for their application. On the basis, recent advances of HOB application in the recovery of high-value products and the removal of pollutants are presented. Finally, the key points for future investigation are proposed that more attention should be paid to the main limitations in the large-scale industrial application of HOB, including the mass transfer rate of the gases, the safety of the production processes and products, and the commercial value of the products.
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Affiliation(s)
- Lin Lin
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Xin Zhang
- Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Rd, Shanghai 200092, China
| | - Lei Dong
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China; Shanghai Municipal Engineering Design Institute (Group) Co. LTD, 901 Zhongshan North Second Rd, Shanghai 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China.
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21
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Ray AE, Zaugg J, Benaud N, Chelliah DS, Bay S, Wong HL, Leung PM, Ji M, Terauds A, Montgomery K, Greening C, Cowan DA, Kong W, Williams TJ, Hugenholtz P, Ferrari BC. Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. THE ISME JOURNAL 2022; 16:2547-2560. [PMID: 35933499 PMCID: PMC9561532 DOI: 10.1038/s41396-022-01298-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/05/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022]
Abstract
Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H2 oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly (p < 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic diversity within RuBisCO form IE (rbcL1E), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.
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22
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Baril X, Durand AA, Srei N, Lamothe S, Provost C, Martineau C, Dunfield K, Constant P. The biological sink of atmospheric H 2 is more sensitive to spatial variation of microbial diversity than N 2O and CO 2 emissions in a winter cover crop field trial. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153420. [PMID: 35092770 DOI: 10.1016/j.scitotenv.2022.153420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
The integration of winter cover crop (WCC) in culture rotations promotes multiple ecosystem services, but concomitant microbial diversity and functioning responses in soil have received less attention. A field trial was established to test the hypothesis that enhanced crop diversity with the integration of WCC in a conventional maize-soy rotation promotes microbial diversity and the biological sink of H2 in soil, while reducing N2O emissions to the atmosphere. Vicia villosa (hairy vetch), Avena sativa (oat), and Raphanus sativus (Daikon radish) were cultivated alone or in combinations and flux measurements were performed throughout two subsequent growing seasons. Soil acted as a net sink for H2 and as a net source for CO2 and N2O. CO2 flux was the most sensitive to WCC whereas a significant spatial variation was observed for H2 flux with soil uptake rates observed in the most productive area two-fold greater than the baseline level. Sequencing and quantification of taxonomic and functional genes were integrated to explain variation in trace gas fluxes with compositional changes in soil microbial communities. Fungal communities were the most sensitive to WCC, but neither community abundance nor beta diversity were found to be indicative of fluxes. The alpha diversity of taxonomic and functional genes, expressed as the number of effective species, was integrated into composite variables extracted from multivariate analyses. Only the composite variable computed with the inverse Simpson's index displayed a reproducible pattern throughout both growing seasons, with functional genes and bacterial 16S rRNA gene defining the two most contrasting gradients. The composite variable was decoupled from WCC treatment and explained 19-20% spatial variation of H2 fluxes. The coupling of composite alpha diversity metrics derived from multiple genes with soil processes warrants further investigations to implement novel indicators of soil health in response to changing management practices at the local scale.
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Affiliation(s)
- Xavier Baril
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - Audrey-Anne Durand
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - Narin Srei
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - Steve Lamothe
- Centre de recherche agroalimentaire de Mirabel, 9850, rue de Belle-Rivière, Mirabel, Québec J7N 2X8, Canada
| | - Caroline Provost
- Centre de recherche agroalimentaire de Mirabel, 9850, rue de Belle-Rivière, Mirabel, Québec J7N 2X8, Canada
| | - Christine Martineau
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Sainte-Foy, Québec G1V 4C7, Canada
| | - Kari Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Philippe Constant
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada.
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23
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Greening C, Grinter R. Microbial oxidation of atmospheric trace gases. Nat Rev Microbiol 2022; 20:513-528. [PMID: 35414013 DOI: 10.1038/s41579-022-00724-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H2), carbon monoxide (CO) and methane (CH4). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial oxidation of these atmospheric trace gases, as well as the ecological, environmental, medical and astrobiological importance of this process. Most soil bacteria and some archaea can survive by using atmospheric H2 and CO as alternative energy sources, as illustrated through genetic studies on Mycobacterium cells and Streptomyces spores. Certain specialist bacteria can also grow on air alone, as confirmed by the landmark characterization of Methylocapsa gorgona, which grows by simultaneously consuming atmospheric CH4, H2 and CO. Bacteria use high-affinity lineages of metalloenzymes, namely hydrogenases, CO dehydrogenases and methane monooxygenases, to utilize atmospheric trace gases for aerobic respiration and carbon fixation. More broadly, trace gas oxidizers enhance the biodiversity and resilience of soil and marine ecosystems, drive primary productivity in extreme environments such as Antarctic desert soils and perform critical regulatory services by mitigating anthropogenic emissions of greenhouse gases and toxic pollutants.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia. .,Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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24
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Abstract
Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N2O), a potent greenhouse gas.
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25
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Buzzard V, Thorne D, Gil-Loaiza J, Cueva A, Meredith LK. Sensitivity of soil hydrogen uptake to natural and managed moisture dynamics in a semiarid urban ecosystem. PeerJ 2022; 10:e12966. [PMID: 35317075 PMCID: PMC8934528 DOI: 10.7717/peerj.12966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/28/2022] [Indexed: 01/11/2023] Open
Abstract
The North American Monsoon season (June-September) in the Sonoran Desert brings thunderstorms and heavy rainfall. These rains bring cooler temperature and account for roughly half of the annual precipitation making them important for biogeochemical processes. The intensity of the monsoon rains also increase flooding in urban areas and rely on green infrastructure (GI) stormwater management techniques such as water harvesting and urban rain gardens to capture runoff. The combination of increased water availability during the monsoon and water management provide a broad moisture regime for testing responses in microbial metabolism to natural and managed soil moisture pulses in drylands. Soil microbes rely on atmospheric hydrogen (H2) as an important energy source in arid and semiarid landscapes with low soil moisture and carbon availability. Unlike mesic ecosystems, transient water availability in arid and semiarid ecosystems has been identified as a key limiting driver of microbe-mediated H2 uptake. We measured soil H2 uptake in rain gardens exposed to three commonly used water harvesting practices during the monsoon season in Tucson AZ, USA. In situ static chamber measurements were used to calculate H2 uptake in each of the three water harvesting treatments passive (stormwater runoff), active (stored rooftop runoff), and greywater (used laundry water) compared to an unaltered control treatment to assess the effects of water management practices on soil microbial activity. In addition, soils were collected from each treatment and brought to the lab for an incubation experiment manipulating the soil moisture to three levels capturing the range observed from field samples. H2 fluxes from all treatments ranged between -0.72 nmol m-2 s-1 and -3.98 nmol m-2 s-1 over the monsoon season. Soil H2 uptake in the greywater treatment was on average 53% greater than the other treatments during pre-monsoon, suggesting that the increased frequency and availability of water in the greywater treatment resulted in higher H2 uptake during the dry season. H2 uptake was significantly correlated with soil moisture (r = -0.393, p = 0.001, df = 62) and temperature (r = 0.345, p = 0.005, df = 62). Our findings suggest that GI managed residential soils can maintain low levels of H2 uptake during dry periods, unlike unmanaged systems. The more continuous H2 uptake associated with GI may help reduce the impacts of drought on H2 cycling in semiarid urban ecosystems.
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Affiliation(s)
- Vanessa Buzzard
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States
| | - Dana Thorne
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States
| | - Juliana Gil-Loaiza
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States
| | - Alejandro Cueva
- Biosphere2, University of Arizona, Oracle, Arizona, United States
| | - Laura K. Meredith
- School of Natural Resources and the Environment, University of Arizona, Tucson, Arizona, United States,BIO5 Institute, University of Arizona, Tucson, Arizona, United States
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26
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Cowan DA, Ferrari BC, McKay CP. Out of Thin Air? Astrobiology and Atmospheric Chemotrophy. ASTROBIOLOGY 2022; 22:225-232. [PMID: 35025628 PMCID: PMC8861918 DOI: 10.1089/ast.2021.0066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The emerging understanding of microbial trace gas chemotrophy as a metabolic strategy to support energy and carbon acquisition for microbial survival and growth has significant implications in the search for past, and even extant, life beyond Earth. The use of trace gases, including hydrogen and carbon monoxide as substrates for microbial oxidation, potentially offers a viable strategy with which to support life on planetary bodies that possess a suitable atmospheric composition, such as Mars and Titan. Here, we discuss the current state of knowledge of this process and explore its potential in the field of astrobiological exploration.
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Affiliation(s)
- Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Address correspondence to: Don A. Cowan, Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Building NW2, Room 3-12, Hatfield Campus, Lynnwood Road, Pretoria 0002, South Africa
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, Australian Centre for Astrobiology, UNSW Sydney, Randwick, Australia
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27
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Monteiro MR, Marshall AJ, Hawes I, Lee CK, McDonald IR, Cary SC. Geochemically Defined Space-for-Time Transects Successfully Capture Microbial Dynamics Along Lacustrine Chronosequences in a Polar Desert. Front Microbiol 2022; 12:783767. [PMID: 35173689 PMCID: PMC8841834 DOI: 10.3389/fmicb.2021.783767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/15/2021] [Indexed: 11/15/2022] Open
Abstract
The space-for-time substitution approach provides a valuable empirical assessment to infer temporal effects of disturbance from spatial gradients. Applied to predict the response of different ecosystems under current climate change scenarios, it remains poorly tested in microbial ecology studies, partly due to the trophic complexity of the ecosystems typically studied. The McMurdo Dry Valleys (MDV) of Antarctica represent a trophically simple polar desert projected to experience drastic changes in water availability under current climate change scenarios. We used this ideal model system to develop and validate a microbial space-for-time sampling approach, using the variation of geochemical profiles that follow alterations in water availability and reflect past changes in the system. Our framework measured soil electrical conductivity, pH, and water activity in situ to geochemically define 17 space-for-time transects from the shores of four dynamic and two static Dry Valley lakes. We identified microbial taxa that are consistently responsive to changes in wetness in the soils and reliably associated with long-term dry or wet edaphic conditions. Comparisons between transects defined at static (open-basin) and dynamic (closed-basin) lakes highlighted the capacity for geochemically defined space-for-time gradients to identify lasting deterministic impacts of historical changes in water presence on the structure and diversity of extant microbial communities. We highlight the potential for geochemically defined space-for-time transects to resolve legacy impacts of environmental change when used in conjunction with static and dynamic scenarios, and to inform future environmental scenarios through changes in the microbial community structure, composition, and diversity.
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Affiliation(s)
- Maria R. Monteiro
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Alexis J. Marshall
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Ian Hawes
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Charles K. Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Ian R. McDonald
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Stephen Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
- *Correspondence: Stephen Craig Cary,
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28
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Bay SK, Waite DW, Dong X, Gillor O, Chown SL, Hugenholtz P, Greening C. Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient. THE ISME JOURNAL 2021; 15:3339-3356. [PMID: 34035443 PMCID: PMC8528921 DOI: 10.1038/s41396-021-01001-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 02/04/2023]
Abstract
Desert soils harbour diverse communities of aerobic bacteria despite lacking substantial organic carbon inputs from vegetation. A major question is therefore how these communities maintain their biodiversity and biomass in these resource-limiting ecosystems. Here, we investigated desert topsoils and biological soil crusts collected along an aridity gradient traversing four climatic regions (sub-humid, semi-arid, arid, and hyper-arid). Metagenomic analysis indicated these communities vary in their capacity to use sunlight, organic compounds, and inorganic compounds as energy sources. Thermoleophilia, Actinobacteria, and Acidimicrobiia were the most abundant and prevalent bacterial classes across the aridity gradient in both topsoils and biocrusts. Contrary to the classical view that these taxa are obligate organoheterotrophs, genome-resolved analysis suggested they are metabolically flexible, with the capacity to also use atmospheric H2 to support aerobic respiration and often carbon fixation. In contrast, Cyanobacteria were patchily distributed and only abundant in certain biocrusts. Activity measurements profiled how aerobic H2 oxidation, chemosynthetic CO2 fixation, and photosynthesis varied with aridity. Cell-specific rates of atmospheric H2 consumption increased 143-fold along the aridity gradient, correlating with increased abundance of high-affinity hydrogenases. Photosynthetic and chemosynthetic primary production co-occurred throughout the gradient, with photosynthesis dominant in biocrusts and chemosynthesis dominant in arid and hyper-arid soils. Altogether, these findings suggest that the major bacterial lineages inhabiting hot deserts use different strategies for energy and carbon acquisition depending on resource availability. Moreover, they highlight the previously overlooked roles of Actinobacteriota as abundant primary producers and trace gases as critical energy sources supporting productivity and resilience of desert ecosystems.
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Affiliation(s)
- Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
| | - David W Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Xiyang Dong
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Sde Boker, Israel
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.
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29
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Greening C, Islam ZF, Bay SK. Hydrogen is a major lifeline for aerobic bacteria. Trends Microbiol 2021; 30:330-337. [PMID: 34462186 DOI: 10.1016/j.tim.2021.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/31/2022]
Abstract
Molecular hydrogen (H2) is available in trace amounts in most ecosystems through atmospheric, biological, geochemical, and anthropogenic sources. Aerobic bacteria use this energy-dense gas, including at atmospheric concentrations, to support respiration and carbon fixation. While it was thought that aerobic H2 consumers are rare community members, here we summarize evidence suggesting that they are dominant throughout soils and other aerated ecosystems. Bacterial cultures from at least eight major phyla can consume atmospheric H2. At the ecosystem scale, H2 consumers are abundant, diverse, and active across diverse soils and are key primary producers in extreme environments such as hyper-arid deserts. On this basis, we propose that H2 is a universally available energy source for the survival of aerobic bacteria.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia.
| | - Zahra F Islam
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; STEM College, RMIT University, Bundoora, VIC 3083, Australia
| | - Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
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30
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Hughes ER, Winter MG, Alves da Silva L, Muramatsu MK, Jimenez AG, Gillis CC, Spiga L, Chanin RB, Santos RL, Zhu W, Winter SE. Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation. eLife 2021; 10:e58609. [PMID: 34085924 PMCID: PMC8177889 DOI: 10.7554/elife.58609] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/20/2021] [Indexed: 12/24/2022] Open
Abstract
The composition of gut-associated microbial communities changes during intestinal inflammation, including an expansion of Enterobacteriaceae populations. The mechanisms underlying microbiota changes during inflammation are incompletely understood. Here, we analyzed previously published metagenomic datasets with a focus on microbial hydrogen metabolism. The bacterial genomes in the inflamed murine gut and in patients with inflammatory bowel disease contained more genes encoding predicted hydrogen-utilizing hydrogenases compared to communities found under non-inflamed conditions. To validate these findings, we investigated hydrogen metabolism of Escherichia coli, a representative Enterobacteriaceae, in mouse models of colitis. E. coli mutants lacking hydrogenase-1 and hydrogenase-2 displayed decreased fitness during colonization of the inflamed cecum and colon. Utilization of molecular hydrogen was in part dependent on respiration of inflammation-derived electron acceptors. This work highlights the contribution of hydrogenases to alterations of the gut microbiota in the context of non-infectious colitis.
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Affiliation(s)
| | - Maria G Winter
- Department of Microbiology, UT SouthwesternDallasUnited States
| | - Laice Alves da Silva
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Angel G Jimenez
- Department of Microbiology, UT SouthwesternDallasUnited States
| | | | - Luisella Spiga
- Department of Microbiology, UT SouthwesternDallasUnited States
| | | | - Renato L Santos
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Wenhan Zhu
- Department of Microbiology, UT SouthwesternDallasUnited States
| | - Sebastian E Winter
- Department of Microbiology, UT SouthwesternDallasUnited States
- Department of Immunology, UT SouthwesternDallasUnited States
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