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Schwob G, Almendras K, Veas-Mattheos K, Pezoa M, Orlando J. Host specialization and spatial divergence of bacteria associated with Peltigera lichens promote landscape gamma diversity. ENVIRONMENTAL MICROBIOME 2024; 19:57. [PMID: 39103916 DOI: 10.1186/s40793-024-00598-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 07/21/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Lichens are micro-ecosystems relying on diverse microorganisms for nutrient cycling, environmental adaptation, and structural support. We investigated the spatial-scale dependency of factors shaping the ecological processes that govern lichen-associated bacteria. We hypothesize that lichens function as island-like habitats hosting divergent microbiomes and promoting landscape gamma-diversity. Three microenvironments -thalli, substrates, and neighboring soils- were sampled from four geographically overlapping species of Peltigera cyanolichens, spanning three bioclimatic zones in the Chilean Patagonia, to determine how bacterial diversity, assembly processes, ecological drivers, interaction patterns, and niche breadth vary among Peltigera microenvironments on a broad geographical scale. RESULTS The hosts' phylogeny, especially that of the cyanobiont, alongside climate as a secondary factor, impose a strong ecological filtering of bacterial communities within Peltigera thalli. This results in deterministically assembled, low diverse, and phylogenetically convergent yet structurally divergent bacterial communities. Host evolutionary and geographic distances accentuate the divergence in bacterial community composition of Peltigera thalli. Compared to soil and substrate, Peltigera thalli harbor specialized and locally adapted bacterial taxa, conforming sparse and weak ecological networks. CONCLUSIONS The findings suggest that Petigera thalli create fragmented habitats that foster landscape bacterial gamma-diversity. This underscores the importance of preserving lichens for maintaining a potential reservoir of specialized bacteria.
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Affiliation(s)
- Guillaume Schwob
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Katerin Almendras
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Karla Veas-Mattheos
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Matías Pezoa
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile
| | - Julieta Orlando
- Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile.
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, 7800003, Chile.
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Seppey CVW, Cabrol L, Thalasso F, Gandois L, Lavergne C, Martinez-Cruz K, Sepulveda-Jauregui A, Aguilar-Muñoz P, Astorga-España MS, Chamy R, Dellagnezze BM, Etchebehere C, Fochesatto GJ, Gerardo-Nieto O, Mansilla A, Murray A, Sweetlove M, Tananaev N, Teisserenc R, Tveit AT, Van de Putte A, Svenning MM, Barret M. Biogeography of microbial communities in high-latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes. Environ Microbiol 2023; 25:3364-3386. [PMID: 37897125 DOI: 10.1111/1462-2920.16526] [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: 06/24/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023]
Abstract
Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.
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Affiliation(s)
- Christophe V W Seppey
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam-Golm, Germany
| | - Léa Cabrol
- Aix-Marseille University, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Frederic Thalasso
- Centro de Investigacíon y de Estudios Avanzados del Instituto Politecnico Nacional (Cinvestav-IPN), Departamento de Biotecnología y Bioingeniería, México, Mexico
| | - Laure Gandois
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Céline Lavergne
- HUB AMBIENTAL UPLA, Laboratory of Aquatic Environmental Research, Universidad de Playa Ancha, Valparaíso, Chile
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Karla Martinez-Cruz
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
- Environmental Physics Group, Limnological Institute, University of Konstanz, Konstanz, Germany
| | | | - Polette Aguilar-Muñoz
- HUB AMBIENTAL UPLA, Laboratory of Aquatic Environmental Research, Universidad de Playa Ancha, Valparaíso, Chile
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | | | - Rolando Chamy
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Bruna Martins Dellagnezze
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute "Clemente Estable", Montevideo, Uruguay
| | - Claudia Etchebehere
- Microbial Ecology Laboratory, Department of Microbial Biochemistry and Genomic, Biological Research Institute "Clemente Estable", Montevideo, Uruguay
| | - Gilberto J Fochesatto
- Department of Atmospheric Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Oscar Gerardo-Nieto
- Centro de Investigacíon y de Estudios Avanzados del Instituto Politecnico Nacional (Cinvestav-IPN), Departamento de Biotecnología y Bioingeniería, México, Mexico
| | - Andrés Mansilla
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
| | - Alison Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada, USA
| | - Maxime Sweetlove
- Royal Belgian Institute for Natural Sciences, OD-Nature, Brussels, Belgium
| | - Nikita Tananaev
- Melnikov Permafrost Institute, Russian Academy of Sciences, Yakutsk, Russia
- Institute of Natural Sciences, North-Eastern Federal University, Yakutsk, Russia
| | - Roman Teisserenc
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anton Van de Putte
- Royal Belgian Institute for Natural Sciences, OD-Nature, Brussels, Belgium
| | - Mette M Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maialen Barret
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
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3
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Hampel JJ, Moseley RD, Hamdan LJ. Microbiomes respond predictably to built habitats on the seafloor. Mol Ecol 2023; 32:6686-6695. [PMID: 35567341 DOI: 10.1111/mec.16504] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 04/14/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022]
Abstract
The seafloor contains complex ecosystems where habitat heterogeneity influences biodiversity. Natural biological and geological features including vents, seeps and reefs create habitats that select for distinct populations of micro- and macrofauna. While largely studied for macrobiological diversity, built habitats may also select distinct microbiomes. Built habitat density on the seafloor is increasing with ocean sprawl expanding in the continental shelf and slope, potentially having widespread effects on benthic communities. This study addresses one type of built habitat, shipwrecks, on microbiomes in surrounding sediment. Using deep-sea sediment samples (762 total) from the Gulf of Mexico, we report elevated diversity and a predictable core microbiome around nine shipwrecks. We show the sphere of influence of built habitats extends up to 300 m onto the seafloor. Supervised learning made predictions of sample proximity to structures based on frequency of taxa. Strongest predictions occurred in sediments nearest and furthest from sites for archaea and mid-transect for bacteria. The response of archaea to built habitats was consistent across sites, while bacteria showed greater between site variability. The archaeal core shipwreck microbiome was enriched in taxa (e.g., Bathyarchaeia, Lokiarchaeia, Thermoplasmata) not present in the surrounding seafloor. Shipwrecks shaped microbiomes in expected ways, providing insight on how built habitats impact microbiome biodiversity in the Anthropocene.
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Affiliation(s)
- Justyna J Hampel
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Rachel D Moseley
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
| | - Leila J Hamdan
- School of Ocean Science and Engineering, University of Southern Mississippi, Ocean Springs, Mississippi, USA
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Kumar S, Najar IN, Sharma P, Tamang S, Mondal K, Das S, Sherpa MT, Thakur N. Temperature - A critical abiotic paradigm that governs bacterial heterogeneity in natural ecological system. ENVIRONMENTAL RESEARCH 2023; 234:116547. [PMID: 37422118 DOI: 10.1016/j.envres.2023.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/28/2023] [Accepted: 07/01/2023] [Indexed: 07/10/2023]
Abstract
A baseline data has been presented here to prove that among the abiotic factors, temperature is the most critical factor that regulates and governs the bacterial diversity in a natural ecosystem. Present study in Yumesamdong hot springs riverine vicinity (Sikkim), parades a gamut of bacterial communities in it and hosts them from semi-frigid region (- 4-10 °C) to fervid region (50-60 °C) via an intermediate region (25-37 °C) within the same ecosystem. This is an extremely rare intriguing natural ecosystem that has no anthropogenic disturbances nor any artificial regulation of temperature. We scanned the bacterial flora through both the culture-dependent and culture-independent techniques in this naturally complex thermally graded habitat. High-throughput sequencing gave bacterial and archaeal phyla representatives of over 2000 species showcasing their biodiversity. Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi were the predominant phyla. A concave down-curve significance was found in temperature-abundance correlation as the number of microbial taxa decreased when the temperature increased from warm (35 °C) to hot (60 °C). Firmicutes showed significant linear increase from cold to hot environment whereas Proteobacteria followed the opposite trend. No significant correlation was observed for physicochemical parameters against the bacterial diversity. However, only temperature has shown significant positive correlation to the predominant phyla at their respective thermal gradients. The antibiotic resistance patterns correlated with temperature gradient where the prevalence of antibiotic resistance was higher in case of mesophiles than that of psychrophiles and there was no resistance in thermophiles. The antibiotic resistant genes obtained were solely from mesophiles as it conferred high resistance at mesophilic conditions enabling them to adapt and metabolically compete for survival. Our study concludes that the temperature is a major factor that plays a significant contribution in shaping the bacterial community structure in any thermal gradient edifice.
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Affiliation(s)
- Santosh Kumar
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Prayatna Sharma
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Sonia Tamang
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Krishnendu Mondal
- Department of Microbiology, Vidyasagar University, Midnapore, 721102, India
| | - Sayak Das
- Department of Life Science & Bioinformatics, HK School of Life Sciences, Assam University, Silchar, 788011, Assam, India
| | - Mingma Thundu Sherpa
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Nagendra Thakur
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, 737102, Sikkim, India.
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5
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Buschi E, Dell’Anno A, Tangherlini M, Stefanni S, Lo Martire M, Núñez-Pons L, Avila C, Corinaldesi C. Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean. Front Microbiol 2023; 14:1234725. [PMID: 37799611 PMCID: PMC10548270 DOI: 10.3389/fmicb.2023.1234725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/29/2023] [Indexed: 10/07/2023] Open
Abstract
Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment.
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Affiliation(s)
- Emanuela Buschi
- Department of Marine Biotechnology, Stazione Zoologica di Napoli “Anton Dohrn”, Fano Marine Centre, Fano, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Michael Tangherlini
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica di Napoli “Anton Dohrn”, Fano Marine Centre, Fano, Italy
| | - Sergio Stefanni
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica di Napoli “Anton Dohrn”, Naples, Italy
| | - Marco Lo Martire
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology, Stazione Zoologica di Napoli “Anton Dohrn”, Naples, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Catalonia, Spain
- Institut de Recerca de la Biodiversitat, University of Barcelona, Barcelona, Catalonia, Spain
| | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Ancona, Italy
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6
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Han D, Richter-Heitmann T, Kim JH, Friedrich MW, Yin X, Elvert M, Ryu JS, Jang K, Nam SI. Influence of sedimentary deposition on the microbial assembly process in Arctic Holocene marine sediments. Front Microbiol 2023; 14:1231839. [PMID: 37700860 PMCID: PMC10493304 DOI: 10.3389/fmicb.2023.1231839] [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: 05/31/2023] [Accepted: 08/15/2023] [Indexed: 09/14/2023] Open
Abstract
The sea-level rise during the Holocene (11-0 ky BP) and its resulting sedimentation and biogeochemical processes may control microbial life in Arctic sediments. To gain further insight into this interaction, we investigated a sediment core (up to 10.7 m below the seafloor) from the Chuckchi Shelf of the western Arctic Ocean using metabarcoding-based sequencing and qPCR to characterize archaeal and bacterial 16S rRNA gene composition and abundance, respectively. We found that Arctic Holocene sediments harbor local microbial communities, reflecting geochemical and paleoclimate separations. The composition of bacterial communities was more diverse than that of archaeal communities, and specifically distinct at the boundary layer of the sulfate-methane transition zone. Enriched cyanobacterial sequences in the Arctic middle Holocene (8-7 ky BP) methanogenic sediments remarkably suggest past cyanobacterial blooms. Bacterial communities were phylogenetically influenced by interactions between dispersal limitation and environmental selection governing community assembly under past oceanographic changes. The relative influence of stochastic and deterministic processes on the bacterial assemblage was primarily determined by dispersal limitation. We have summarized our findings in a conceptual model that revealed how changes in paleoclimate phases cause shifts in ecological succession and the assembly process. In this ecological model, dispersal limitation is an important driving force for progressive succession for bacterial community assembly processes on a geological timescale in the western Arctic Ocean. This enabled a better understanding of the ecological processes that drive the assembly of communities in Holocene sedimentary habitats affected by sea-level rise, such as in the shallow western Arctic shelves.
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Affiliation(s)
- Dukki Han
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung-si, Gangwon-do, Republic of Korea
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ji-Hoon Kim
- Marine Geology & Energy Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, Republic of Korea
| | - Michael W. Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Organic Geochemistry Group, Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jong-Sik Ryu
- Department of Earth and Environmental Sciences, Pukyong National University, Busan, Republic of Korea
| | - Kwangchul Jang
- Division of Glacial Environment Research, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Seung-Il Nam
- Division of Glacial Environment Research, Korea Polar Research Institute, Incheon, Republic of Korea
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Milojevic T, Cramm MA, Hubert CRJ, Westall F. "Freezing" Thermophiles: From One Temperature Extreme to Another. Microorganisms 2022; 10:2417. [PMID: 36557670 PMCID: PMC9782878 DOI: 10.3390/microorganisms10122417] [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: 09/30/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
New detections of thermophiles in psychrobiotic (i.e., bearing cold-tolerant life forms) marine and terrestrial habitats including Arctic marine sediments, Antarctic accretion ice, permafrost, and elsewhere are continually being reported. These microorganisms present great opportunities for microbial ecologists to examine biogeographical processes for spore-formers and non-spore-formers alike, including dispersal histories connecting warm and cold biospheres. In this review, we examine different examples of thermophiles in cryobiotic locations, and highlight exploration of thermophiles at cold temperatures under laboratory conditions. The survival of thermophiles in psychrobiotic environments provokes novel considerations of physiological and molecular mechanisms underlying natural cryopreservation of microorganisms. Cultures of thermophiles maintained at low temperature may serve as a non-sporulating laboratory model for further exploration of metabolic potential of thermophiles at psychrobiotic temperatures, as well as for elucidating molecular mechanisms behind natural preservation and adaptation to psychrobiotic environments. These investigations are highly relevant for the search for life on other cold and icy planets in the Solar System, such as Mars, Europa and Enceladus.
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Affiliation(s)
- Tetyana Milojevic
- Exobiology Group, CNRS-Centre de Biophysique Moléculaire, University of Orléans, Rue Charles Sadron, CEDEX 2, 45071 Orléans, France
| | - Margaret Anne Cramm
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Casey R. J. Hubert
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Frances Westall
- Exobiology Group, CNRS-Centre de Biophysique Moléculaire, Rue Charles Sadron, CEDEX 2, 45071 Orléans, France
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8
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Walters KE, Capocchi JK, Albright MBN, Hao Z, Brodie EL, Martiny JBH. Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning. THE ISME JOURNAL 2022; 16:2295-2304. [PMID: 35778440 PMCID: PMC9477824 DOI: 10.1038/s41396-022-01269-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 12/21/2022]
Abstract
Recent evidence suggests that, similar to larger organisms, dispersal is a key driver of microbiome assembly; however, our understanding of the rates and taxonomic composition of microbial dispersal in natural environments is limited. Here, we characterized the rate and composition of bacteria dispersing into surface soil via three dispersal routes (from the air above the vegetation, from nearby vegetation and leaf litter near the soil surface, and from the bulk soil and litter below the top layer). We then quantified the impact of those routes on microbial community composition and functioning in the topmost litter layer. The bacterial dispersal rate onto the surface layer was low (7900 cells/cm2/day) relative to the abundance of the resident community. While bacteria dispersed through all three routes at the same rate, only dispersal from above and near the soil surface impacted microbiome composition, suggesting that the composition, not rate, of dispersal influenced community assembly. Dispersal also impacted microbiome functioning. When exposed to dispersal, leaf litter decomposed faster than when dispersal was excluded, although neither decomposition rate nor litter chemistry differed by route. Overall, we conclude that the dispersal routes transport distinct bacterial communities that differentially influence the composition of the surface soil microbiome.
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Affiliation(s)
- Kendra E Walters
- Department of Ecology and Evolutionary Biology, University of California - Irvine, Irvine, CA, USA.
| | - Joia K Capocchi
- Department of Ecology and Evolutionary Biology, University of California - Irvine, Irvine, CA, USA
| | | | - Zhao Hao
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA, 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California - Irvine, Irvine, CA, USA
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9
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Xing Z, Gao H, Wang D, Shang Y, Tuliebieke T, Jiang J, Li C, Wang H, Li Z, Jia L, Wu Y, Wang D, Yang W, Chang Y, Zhang X, Xu L, Jiang C, Huang L, Tian X. A novel biological sources consistency evaluation method reveals high level of biodiversity within wild natural medicine: A case study of Amynthas earthworms as “Guang Dilong”. Acta Pharm Sin B 2022; 13:1755-1770. [PMID: 37139429 PMCID: PMC10150161 DOI: 10.1016/j.apsb.2022.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/28/2022] [Accepted: 10/13/2022] [Indexed: 11/30/2022] Open
Abstract
For wild natural medicine, unanticipated biodiversity as species or varieties with similar morphological characteristics and sympatric distribution may co-exist in a single batch of medical materials, which affects the efficacy and safety of clinical medication. DNA barcoding as an effective species identification tool is limited by its low sample throughput nature. In this study, combining DNA mini-barcode, DNA metabarcoding and species delimitation method, a novel biological sources consistency evaluation strategy was proposed, and high level of interspecific and intraspecific variations were observed and validated among 5376 Amynthas samples from 19 sampling points regarded as "Guang Dilong" and 25 batches of proprietary Chinese medicines. Besides Amynthas aspergillum as the authentic source, 8 other Molecular Operational Taxonomic Units (MOTUs) were elucidated. Significantly, even the subgroups within A. aspergillum revealed here differ significantly on chemical compositions and biological activity. Fortunately, this biodiversity could be controlled when the collection was limited to designated areas, as proved by 2796 "decoction pieces" samples. This batch biological identification method should be introduced as a novel concept regarding natural medicine quality control, and to offer guidelines for in-situ conservation and breeding bases construction of wild natural medicine.
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Affiliation(s)
- Zhimei Xing
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Han Gao
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Dan Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Ye Shang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Tenukeguli Tuliebieke
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Jibao Jiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunxiao Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Hong Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zhenguo Li
- Mudanjiang YouBo Pharmaceutical Co. Ltd., Mudanjiang 157000, China
| | - Lifu Jia
- Guizhou Ruihe Pharmaceutical Co. Ltd., Guizhou 550000, China
| | - Yongsheng Wu
- Mudanjiang YouBo Pharmaceutical Co. Ltd., Mudanjiang 157000, China
| | - Dandan Wang
- Mudanjiang YouBo Pharmaceutical Co. Ltd., Mudanjiang 157000, China
| | - Wenzhi Yang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Yanxu Chang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Xiaoying Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Liuwei Xu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Chao Jiang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100010, China
- Corresponding authors.
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100010, China
- Corresponding authors.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
- Corresponding authors.
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10
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Gittins DA, Desiage PA, Morrison N, Rattray JE, Bhatnagar S, Chakraborty A, Zorz J, Li C, Horanszky O, Cramm MA, Bisiach F, Bennett R, Webb J, MacDonald A, Fowler M, Campbell DC, Hubert CRJ. Geological processes mediate a microbial dispersal loop in the deep biosphere. SCIENCE ADVANCES 2022; 8:eabn3485. [PMID: 36026445 PMCID: PMC9417182 DOI: 10.1126/sciadv.abn3485] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores. Whereas dormancy and survival at theoretical energy minima are hallmarks of microbial physiology in the subsurface, ecological processes such as dispersal and selection in the deep biosphere remain poorly understood. We investigated the biogeography of dispersing bacteria in the deep sea where upward hydrocarbon seepage was confirmed by acoustic imagery and geochemistry. Thermophilic endospores in the permanently cold seabed correlated with underlying seep conduits reveal geofluid-facilitated cell migration pathways originating in deep petroleum-bearing sediments. Endospore genomes highlight adaptations to life in anoxic petroleum systems and bear close resemblance to oil reservoir microbiomes globally. Upon transport out of the subsurface, viable thermophilic endospores reenter the geosphere by sediment burial, enabling germination and environmental selection at depth where new petroleum systems establish. This microbial dispersal loop circulates living biomass in and out of the deep biosphere.
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Affiliation(s)
- Daniel A. Gittins
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
- Corresponding author.
| | | | - Natasha Morrison
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Canada
| | - Jayne E. Rattray
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Srijak Bhatnagar
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | | | - Jackie Zorz
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Carmen Li
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Oliver Horanszky
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Margaret A. Cramm
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Francesco Bisiach
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Robbie Bennett
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, Canada
| | - Jamie Webb
- Applied Petroleum Technology, Calgary, Canada
| | - Adam MacDonald
- Department of Natural Resources and Renewables, Government of Nova Scotia, Halifax, Canada
| | | | - D. Calvin Campbell
- Natural Resources Canada, Geological Survey of Canada-Atlantic, Dartmouth, Canada
| | - Casey R. J. Hubert
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Canada
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11
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Chakraborty A, Rattray JE, Drake SS, Matthews S, Li C, Jørgensen BB, Hubert CRJ. Metabolic responses of thermophilic endospores to sudden heat-induced perturbation in marine sediment samples. Front Microbiol 2022; 13:958417. [PMID: 36033870 PMCID: PMC9411986 DOI: 10.3389/fmicb.2022.958417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Microbially mediated processes in a given habitat tend to be catalyzed by abundant populations that are ecologically adapted to exploit specific environmental characteristics. Typically, metabolic activities of rare populations are limited but may be stimulated in response to acute environmental stressors. Community responses to sudden changes in temperature and pressure can include suppression and activation of different populations, but these dynamics remain poorly understood. The permanently cold ocean floor hosts countless low-abundance microbes including endospores of thermophilic bacteria. Incubating sediments at high temperature resuscitates viable spores, causing the proliferation of bacterial populations. This presents a tractable system for investigating changes in a microbiome's community structure in response to dramatic environmental perturbations. Incubating permanently cold Arctic fjord sediments at 50°C for 216 h with and without volatile fatty acid amendment provoked major changes in community structure. Germination of thermophilic spores from the sediment rare biosphere was tracked using mass spectrometry-based metabolomics, radiotracer-based sulfate reduction rate measurements, and high-throughput 16S rRNA gene sequencing. Comparing community similarity at different intervals of the incubations showed distinct temporal shifts in microbial populations, depending on organic substrate amendment. Metabolite patterns indicated that amino acids and other sediment-derived organics were decomposed by fermentative Clostridia within the first 12–48 h. This fueled early and late phases of exponential increases in sulfate reduction, highlighting the cross-feeding of volatile fatty acids as electron donors for different sulfate-reducing Desulfotomaculia populations. The succession of germinated endospores triggered by sudden exposure to high temperature and controlled by nutrient availability offers a model for understanding the ecological response of dormant microbial communities following major environmental perturbations.
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Affiliation(s)
- Anirban Chakraborty
- Department of Biological Sciences, Idaho State University, Pocatello, ID, United States
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
- *Correspondence: Anirban Chakraborty
| | - Jayne E. Rattray
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Sienna S. Drake
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Stuart Matthews
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Bo Barker Jørgensen
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Casey R. J. Hubert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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12
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Hao YQ, Zhao XF, Ai HX, Gao SM, Teng WK, Zheng J, Shu WS. Microbial biogeography of acid mine drainage sediments at a regional scale across Southern China. FEMS Microbiol Ecol 2022; 98:6520435. [PMID: 35108388 DOI: 10.1093/femsec/fiac002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/03/2022] [Accepted: 01/30/2022] [Indexed: 11/14/2022] Open
Abstract
Investigations of microbial biogeography in extreme environments provide unique opportunities to disentangle the roles of environment and space in microbial community assembly. Here, we reported a comprehensive microbial biogeographic survey of 90 acid mine drainage (AMD) sediment samples from 18 mining sites of various mineral types across southern China. We found that environmental selection was strong in determining the AMD habitat species pool. However, microbial alpha diversity was primarily explained by mining sites rather than environmental factors, and microbial beta diversity correlated more strongly with geographic than environmental distance at both large and small spatial scales. Particularly, the presence/absence of widespread AMD habitat generalists was only correlated with geographic distance and independent of environmental variation. These distance-decay patterns suggested that spatial processes played a more important role in determining microbial compositional variation across space; which could be explained by the reinforced impacts of dispersal limitation in less fluid, spatially structured sediment habitat with diverse pre-existing communities. In summary, our findings suggested that the deterministic assembling and spatial constraints interact to shape microbial biogeography in AMD sediments; and provided implications that spatial processes should be considered when predicting microbial dynamics in response to severe environmental change across large spatial scales.
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Affiliation(s)
- Yi-Qi Hao
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xin-Feng Zhao
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hong-Xia Ai
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wen-Kai Teng
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jin Zheng
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
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13
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Schwob G, Segovia NI, González-Wevar C, Cabrol L, Orlando J, Poulin E. Exploring the Microdiversity Within Marine Bacterial Taxa: Toward an Integrated Biogeography in the Southern Ocean. Front Microbiol 2021; 12:703792. [PMID: 34335536 PMCID: PMC8317501 DOI: 10.3389/fmicb.2021.703792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Most of the microbial biogeographic patterns in the oceans have been depicted at the whole community level, leaving out finer taxonomic resolution (i.e., microdiversity) that is crucial to conduct intra-population phylogeographic study, as commonly done for macroorganisms. Here, we present a new approach to unravel the bacterial phylogeographic patterns combining community-wide survey by 16S rRNA gene metabarcoding and intra-species resolution through the oligotyping method, allowing robust estimations of genetic and phylogeographic indices, and migration parameters. As a proof-of-concept, we focused on the bacterial genus Spirochaeta across three distant biogeographic provinces of the Southern Ocean; maritime Antarctica, sub-Antarctic Islands, and Patagonia. Each targeted Spirochaeta operational taxonomic units were characterized by a substantial intrapopulation microdiversity, and significant genetic differentiation and phylogeographic structure among the three provinces. Gene flow estimations among Spirochaeta populations support the role of the Antarctic Polar Front as a biogeographic barrier to bacterial dispersal between Antarctic and sub-Antarctic provinces. Conversely, the Antarctic Circumpolar Current appears as the main driver of gene flow, connecting sub-Antarctic Islands with Patagonia and maritime Antarctica. Additionally, historical processes (drift and dispersal limitation) govern up to 86% of the spatial turnover among Spirochaeta populations. Overall, our approach bridges the gap between microbial and macrobial ecology by revealing strong congruency with macroorganisms distribution patterns at the populational level, shaped by the same oceanographic structures and ecological processes.
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Affiliation(s)
- Guillaume Schwob
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
| | - Nicolás I. Segovia
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Universidad Católica del Norte, Coquimbo, Chile
| | - Claudio González-Wevar
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Facultad de Ciencias, Centro Fondap IDEAL, Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Valdivia, Chile
| | - Léa Cabrol
- Instituto de Ecología y Biodiversidad, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), Marseille, France
| | - Julieta Orlando
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Elie Poulin
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Instituto de Ecología y Biodiversidad, Santiago, Chile
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14
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Milojevic T, Kish A, Yamagishi A. Editorial: Astrobiology at the Interface: Interactions Between Biospheres, Geospheres, Hydrospheres and Atmospheres Under Planetary Conditions. Front Microbiol 2021; 12:629961. [PMID: 33643257 PMCID: PMC7906982 DOI: 10.3389/fmicb.2021.629961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/26/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Tetyana Milojevic
- Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | | | - Akihiko Yamagishi
- Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
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15
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Bell E, Sherry A, Pilloni G, Suárez‐Suárez A, Cramm MA, Cueto G, Head IM, Hubert CRJ. Sediment cooling triggers germination and sulfate reduction by heat‐resistant thermophilic spore‐forming bacteria. Environ Microbiol 2019; 22:456-465. [DOI: 10.1111/1462-2920.14866] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Emma Bell
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
| | - Angela Sherry
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
| | | | - Ana Suárez‐Suárez
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
| | - Margaret A. Cramm
- Department of Biological SciencesUniversity of Calgary Calgary Alberta Canada
| | - Guillermo Cueto
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
| | - Ian M. Head
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
| | - Casey R. J. Hubert
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
- Department of Biological SciencesUniversity of Calgary Calgary Alberta Canada
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16
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Cramm MA, Chakraborty A, Li C, Ruff SE, Jørgensen BB, Hubert CRJ. Freezing Tolerance of Thermophilic Bacterial Endospores in Marine Sediments. Front Microbiol 2019; 10:945. [PMID: 31130935 PMCID: PMC6509201 DOI: 10.3389/fmicb.2019.00945] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/15/2019] [Indexed: 01/18/2023] Open
Abstract
Dormant endospores of anaerobic, thermophilic bacteria found in cold marine sediments offer a useful model for studying microbial biogeography, dispersal, and survival. The dormant endospore phenotype confers resistance to unfavorable environmental conditions, allowing dispersal to be isolated and studied independently of other factors such as environmental selection. To study the resilience of thermospores to conditions relevant for survival in extreme cold conditions, their viability following different freezing treatments was tested. Marine sediment was frozen at either −80°C or −20°C for 10 days prior to pasteurization and incubation at +50°C for 21 days to assess thermospore viability. Sulfate reduction commenced at +50°C following both freezing pretreatments indicating persistence of thermophilic endospores of sulfate-reducing bacteria. The onset of sulfate reduction at +50°C was delayed in −80°C pretreated microcosms, which exhibited more variability between triplicates, compared to −20°C pretreated microcosms and parallel controls that were not frozen in advance. Microbial communities were evaluated by 16S rRNA gene amplicon sequencing, revealing an increase in the relative sequence abundance of thermophilic endospore-forming Firmicutes in all microcosms. Different freezing pretreatments (−80°C and −20°C) did not appreciably influence the shift in overall bacterial community composition that occurred during the +50°C incubations. Communities that had been frozen prior to +50°C incubation showed an increase in the relative sequence abundance of operational taxonomic units (OTUs) affiliated with the class Bacilli, relative to unfrozen controls. These results show that freezing impacts but does not obliterate thermospore populations and their ability to germinate and grow under appropriate conditions. Indeed the majority of the thermospore OTUs detected in this study (21 of 22) could be observed following one or both freezing treatments. These results are important for assessing thermospore viability in frozen samples and following cold exposure such as the very low temperatures that would be encountered during panspermia.
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Affiliation(s)
- Margaret A Cramm
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Anirban Chakraborty
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Carmen Li
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - S Emil Ruff
- Energy Bioengineering Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Casey R J Hubert
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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