1
|
Structure and Function Analysis of Cultivated Meconopsis integrifolia Soil Microbial Community Based on High-Throughput Sequencing and Culturability. BIOLOGY 2023; 12:biology12020160. [PMID: 36829439 PMCID: PMC9952792 DOI: 10.3390/biology12020160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
(1) Background: The structure, function, and community interactions of soil microbial communities of cultivated Meconopsis integrifolia were characterized by studying this alpine flower and traditional endangered Tibetan medicine. (2) Methods: Soil bacteria and fungi were studied based on high-throughput sequencing technology. Bacteria were isolated using culturomics and functionally identified as IAA-producing, organic phosphorus-dissolving, inorganic phosphorus-dissolving, and iron-producing carriers. (3) Results: The dominant bacterial phyla were found to be Proteobacteria and Acidobacteria, and unclassified_Rhizobiales was the most abundant genus. Ascomycota and Mortierellomycota were the dominant fungal phyla. The bacteria were mainly carbon and nitrogen metabolizers, and the fungi were predominantly Saprotroph-Symbiotroph. The identified network was completely dominated by positive correlations, but the fungi were more complex than the bacteria, and the bacterial keystones were unclassified_Caulobacteraceae and Pedobacter. Most of the keystones of fungi belonged to the phyla Ascomycetes and Basidiomycota. The highest number of different species of culturable bacteria belonged to the genus Streptomyces, with three strains producing IAA, 12 strains solubilizing organic phosphorus, one strain solubilizing inorganic phosphorus, and nine strains producing iron carriers. (4) Conclusions: At the cost of reduced ecological stability, microbial communities increase cooperation toward promoting overall metabolic efficiency and enabling their survival in the extreme environment of the Tibetan Plateau. These pioneering results have value for the protection of endangered Meconopsis integrifolia under global warming and the sustainable utilization of its medicinal value.
Collapse
|
2
|
Díaz M, Monfort-Lanzas P, Quiroz-Moreno C, Rivadeneira E, Castillejo P, Arnau V, Díaz W, Agathos SN, Sangari FJ, Jarrín-V P, Molina CA. The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador. Front Microbiol 2023; 14:1154815. [PMID: 37213502 PMCID: PMC10196084 DOI: 10.3389/fmicb.2023.1154815] [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: 01/31/2023] [Accepted: 04/17/2023] [Indexed: 05/23/2023] Open
Abstract
A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40 years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change.
Collapse
Affiliation(s)
- Magdalena Díaz
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
- Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, Quito, Ecuador
- Facultad de Ingeniería Química, Universidad Central del Ecuador, Quito, Ecuador
- Institute of Integrative Systems Biology (ISysBio), University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- *Correspondence: Magdalena Díaz,
| | - Pablo Monfort-Lanzas
- Institute of Integrative Systems Biology (ISysBio), University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Cristian Quiroz-Moreno
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, United States
| | - Erika Rivadeneira
- Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, Quito, Ecuador
| | - Pablo Castillejo
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad Internacional SEK, Quito, Ecuador
| | - Vicente Arnau
- Institute of Integrative Systems Biology (ISysBio), University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Wladimiro Díaz
- Institute of Integrative Systems Biology (ISysBio), University of Valencia and Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Spiros N. Agathos
- Earth and Life Institute (ELI), Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Félix J. Sangari
- Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC – Universidad de Cantabria, Santander, Spain
| | - Pablo Jarrín-V
- Dirección de Innovación, Instituto Nacional de Biodiversidad INABIO, Quito, Ecuador
| | - C. Alfonso Molina
- Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, Quito, Ecuador
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito, Ecuador
- C. Alfonso Molina,
| |
Collapse
|
3
|
Weber B, Belnap J, Büdel B, Antoninka AJ, Barger NN, Chaudhary VB, Darrouzet-Nardi A, Eldridge DJ, Faist AM, Ferrenberg S, Havrilla CA, Huber-Sannwald E, Malam Issa O, Maestre FT, Reed SC, Rodriguez-Caballero E, Tucker C, Young KE, Zhang Y, Zhao Y, Zhou X, Bowker MA. What is a biocrust? A refined, contemporary definition for a broadening research community. Biol Rev Camb Philos Soc 2022; 97:1768-1785. [PMID: 35584903 PMCID: PMC9545944 DOI: 10.1111/brv.12862] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 12/22/2022]
Abstract
Studies of biological soil crusts (biocrusts) have proliferated over the last few decades. The biocrust literature has broadened, with more studies assessing and describing the function of a variety of biocrust communities in a broad range of biomes and habitats and across a large spectrum of disciplines, and also by the incorporation of biocrusts into global perspectives and biogeochemical models. As the number of biocrust researchers increases, along with the scope of soil communities defined as ‘biocrust’, it is worth asking whether we all share a clear, universal, and fully articulated definition of what constitutes a biocrust. In this review, we synthesize the literature with the views of new and experienced biocrust researchers, to provide a refined and fully elaborated definition of biocrusts. In doing so, we illustrate the ecological relevance and ecosystem services provided by them. We demonstrate that biocrusts are defined by four distinct elements: physical structure, functional characteristics, habitat, and taxonomic composition. We describe outgroups, which have some, but not all, of the characteristics necessary to be fully consistent with our definition and thus would not be considered biocrusts. We also summarize the wide variety of different types of communities that fall under our definition of biocrusts, in the process of highlighting their global distribution. Finally, we suggest the universal use of the Belnap, Büdel & Lange definition, with minor modifications: Biological soil crusts (biocrusts) result from an intimate association between soil particles and differing proportions of photoautotrophic (e.g. cyanobacteria, algae, lichens, bryophytes) and heterotrophic (e.g. bacteria, fungi, archaea) organisms, which live within, or immediately on top of, the uppermost millimetres of soil. Soil particles are aggregated through the presence and activity of these often extremotolerant biota that desiccate regularly, and the resultant living crust covers the surface of the ground as a coherent layer. With this detailed definition of biocrusts, illustrating their ecological functions and widespread distribution, we hope to stimulate interest in biocrust research and inform various stakeholders (e.g. land managers, land users) on their overall importance to ecosystem and Earth system functioning.
Collapse
Affiliation(s)
- Bettina Weber
- Division of Plant Sciences, Institute for Biology, University of Graz, Holteigasse 6, 8010, Graz, Austria.,Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128, Mainz, Germany
| | - Jayne Belnap
- Southwest Biological Science Center, U.S. Geological Survey, 2290 S. Resource Blvd, Moab, UT, 84532, USA
| | - Burkhard Büdel
- Biology Institute, University of Kaiserslautern, PO Box 3049, 67653, Kaiserslautern, Germany
| | - Anita J Antoninka
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll Drive, Box 15018, Flagstaff, AZ, 86011, USA
| | - Nichole N Barger
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Campus Box 334, Boulder, CO, 80309, USA
| | - V Bala Chaudhary
- Department of Environmental Studies, Dartmouth College, 6182 Steele Hall, 39 College Street, Hanover, NH, 03755, USA
| | - Anthony Darrouzet-Nardi
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Ave, El Paso, TX, 79968, USA
| | - David J Eldridge
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Akasha M Faist
- Department of Animal and Range Sciences, New Mexico State University, PO Box 30003, MSC 3-I, Las Cruces, NM, 88003, USA
| | - Scott Ferrenberg
- Department of Biology, New Mexico State University, PO Box 30001, MSC 3AF, Las Cruces, NM, 88003, USA
| | - Caroline A Havrilla
- Department of Forest and Rangeland Stewardship, Colorado State University, 1472 Campus Delivery, Colorado State University, Fort Collins, CO, 80521, USA
| | - Elisabeth Huber-Sannwald
- Division of Environmental Sciences, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, Col. 4ta Sección, CP 78216, San Luis Potosi, SLP, Mexico
| | - Oumarou Malam Issa
- Institute of Ecology and Environmental Sciences of Paris (IEES-Paris), SU/IRD/CNRS/INRAE/UPEC, 32, Avenue Henry Varagnat, F-93143, Bondy Cedex, France
| | - Fernando T Maestre
- Instituto Multidisciplinar para el Estudio del Medio "Ramón Margalef", Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente del Raspeig, Spain.,Departamento de Ecología, Universidad de Alicante, Carretera de San Vicente del Raspeig s/n, 03690, San Vicente del Raspeig, Spain
| | - Sasha C Reed
- Southwest Biological Science Center, U.S. Geological Survey, 2290 S. Resource Blvd, Moab, UT, 84532, USA
| | - Emilio Rodriguez-Caballero
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128, Mainz, Germany.,Department of Agronomy and Centro de Investigación de Colecciones Científicas (CECOUAL), Universidad de Almería, carretera Sacramento s/n, 04120, La cañada de San Urbano, Almeria, Spain
| | - Colin Tucker
- USDA Forest Service, Northern Research Station, 410 MacInnes Drive, Houghton, MI, 49931-1134, USA
| | - Kristina E Young
- Extension Agriculture and Natural Resources, Utah State University, 1850 S. Aggie Blvd, Moab, UT, 84532, USA
| | - Yuanming Zhang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Bejing Road, Urumqi City, 830011, Xinjiang, China
| | - Yunge Zhao
- Institute of Soil and Water Conservation, Northwest A & F University, 26 Xinong Road, Yangling, Shaanxi, 712100, China
| | - Xiaobing Zhou
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 818 South Bejing Road, Urumqi City, 830011, Xinjiang, China
| | - Matthew A Bowker
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll Drive, Box 15018, Flagstaff, AZ, 86011, USA
| |
Collapse
|
4
|
Tolypocladium reniformisporum sp. nov. and Tolypocladium cylindrosporum (Ophiocordycipitaceae, Hypocreales) co-occurring on Ophiocordyceps sinensis. Mycol Prog 2022. [DOI: 10.1007/s11557-021-01675-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
5
|
Keuter S, Koch H, Sass K, Wegen S, Lee N, Lücker S, Spieck E. Some like it cold: The cellular organization and physiological limits of cold-tolerant nitrite-oxidizing Nitrotoga. Environ Microbiol 2022; 24:2059-2077. [PMID: 35229435 DOI: 10.1111/1462-2920.15958] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 11/30/2022]
Abstract
Chemolithoautotrophic production of nitrate is accomplished by the polyphyletic functional group of nitrite-oxidizing bacteria (NOB). A widely distributed and important NOB clade in nitrogen removal processes at low temperatures is Nitrotoga, which however remains understudied due to the scarcity of cultivated representatives. Here, we present physiological, ultrastructural and genomic features of Nitrotoga strains from various habitats, including the first marine species enriched from an aquaculture system. Immunocytochemical analyses localized the nitrite-oxidizing enzyme machinery in the wide irregularly shaped periplasm, apparently without contact to the cytoplasmic membrane, confirming previous genomic data suggesting a soluble nature. Interestingly, in two strains we also observed multicellular complexes with a shared periplasmic space, which seem to form through incomplete cell division and might enhance fitness or survival. Physiological tests revealed differing tolerance limits towards dissolved inorganic nitrogen concentrations and confirmed the generally psychrotolerant nature of the genus was. Moreover, comparative analysis of 15 Nitrotoga genomes showed, e.g., a unique gene repertoire of the marine strain that could be advantageous in its natural habitat and confirmed the lack of genes for assimilatory nitrite reduction in a strain found to require ammonium for growth. Overall, these novel insights largely broaden our knowledge of Nitrotoga and elucidate the metabolic variability, physiological limits and thus potential ecological roles of this group of nitrite oxidizers. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Sabine Keuter
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Hanna Koch
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
| | - Katharina Sass
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Simone Wegen
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Natuschka Lee
- Department of Ecology and Environmental Science and Research Infrastructure Fluorescence in situ Hybridization (FISH), Chemical Biological Centre, Umeå University, Umeå, Sweden.,Department of Microbiology, Technical University of Munich, Freising, Germany
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
| | - Eva Spieck
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| |
Collapse
|
6
|
OUP accepted manuscript. FEMS Microbiol Ecol 2022; 98:6551890. [DOI: 10.1093/femsec/fiac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/22/2021] [Accepted: 03/17/2022] [Indexed: 11/14/2022] Open
|
7
|
Hussain S, Liu H, Liu S, Yin Y, Yuan Z, Zhao Y, Cao H. Distribution and Assembly Processes of Soil Fungal Communities along an Altitudinal Gradient in Tibetan Plateau. J Fungi (Basel) 2021; 7:jof7121082. [PMID: 34947064 PMCID: PMC8706254 DOI: 10.3390/jof7121082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/25/2022] Open
Abstract
In soil ecosystems, fungi exhibit diverse biodiversity and play an essential role in soil biogeochemical cycling. Fungal diversity and assembly processes across soil strata along altitudinal gradients are still unclear. In this study, we investigated the structure and abundance of soil fungal communities among soil strata and elevational gradients on the Tibetan Plateau using Illumina MiSeq sequencing of internal transcribed spacer1 (ITS1). The contribution of neutral and niche ecological processes were quantified using a neutral community model and a null model-based methodology. Our results showed that fungal gene abundance increased along altitudinal gradients, while decreasing across soil strata. Along with altitudinal gradients, fungal α-diversity (richness) decreased from surface to deeper soil layers, while β-diversity showed weak correlations with elevations. The neutral community model showed an excellent fit for neutral processes and the lowest migration rate (R2 = 0.75). The null model showed that stochastic processes dominate in all samples (95.55%), dispersal limitations were dominated at the surface layer and decreased significantly with soil strata, while undominated processes (ecological drift) show a contrary trend. The log-normal model and the null model (βNTI) correlation analysis also neglect the role of niche-based processes. We conclude that stochastic dispersal limitations, together with ecological drifts, drive fungal communities.
Collapse
Affiliation(s)
- Sarfraz Hussain
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Senlin Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Yifan Yin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Zhongyuan Yuan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Yuguo Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
- Correspondence:
| |
Collapse
|
8
|
Spieck E, Wegen S, Keuter S. Relevance of Candidatus Nitrotoga for nitrite oxidation in technical nitrogen removal systems. Appl Microbiol Biotechnol 2021; 105:7123-7139. [PMID: 34508283 PMCID: PMC8494671 DOI: 10.1007/s00253-021-11487-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 01/10/2023]
Abstract
Abstract Many biotechnological applications deal with nitrification, one of the main steps of the global nitrogen cycle. The biological oxidation of ammonia to nitrite and further to nitrate is critical to avoid environmental damage and its functioning has to be retained even under adverse conditions. Bacteria performing the second reaction, oxidation of nitrite to nitrate, are fastidious microorganisms that are highly sensitive against disturbances. One important finding with relevance for nitrogen removal systems was the discovery of the mainly cold-adapted Cand. Nitrotoga, whose activity seems to be essential for the recovery of nitrite oxidation in wastewater treatment plants at low temperatures, e.g., during cold seasons. Several new strains of this genus have been recently described and ecophysiologically characterized including genome analyses. With increasing diversity, also mesophilic Cand. Nitrotoga representatives have been detected in activated sludge. This review summarizes the natural distribution and driving forces defining niche separation in artificial nitrification systems. Further critical aspects for the competition with Nitrospira and Nitrobacter are discussed. Knowledge about the physiological capacities and limits of Cand. Nitrotoga can help to define physico-chemical parameters for example in reactor systems that need to be run at low temperatures. Key points • Characterization of the psychrotolerant nitrite oxidizer Cand. Nitrotoga • Comparison of the physiological features of Cand. Nitrotoga with those of other NOB • Identification of beneficial environmental/operational parameters for proliferation Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11487-5.
Collapse
Affiliation(s)
- Eva Spieck
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany.
| | - Simone Wegen
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| | - Sabine Keuter
- Department of Microbiology and Biotechnology, Universität Hamburg, Hamburg, Germany
| |
Collapse
|
9
|
Hu W, Schmidt SK, Sommers P, Darcy JL, Porazinska DL. Multiple‐trophic patterns of primary succession following retreat of a high‐elevation glacier. Ecosphere 2021. [DOI: 10.1002/ecs2.3400] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Weiming Hu
- Department of Entomology and Nematology University of Florida Gainesville Florida32611USA
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology University of Colorado, Boulder Boulder Colorado80309USA
| | - Pacifica Sommers
- Department of Ecology and Evolutionary Biology University of Colorado, Boulder Boulder Colorado80309USA
| | - John L. Darcy
- Anschutz Medical Campus University of Colorado, Denver Denver Colorado80204USA
| | - Dorota L. Porazinska
- Department of Entomology and Nematology University of Florida Gainesville Florida32611USA
- Department of Ecology and Evolutionary Biology University of Colorado, Boulder Boulder Colorado80309USA
| |
Collapse
|
10
|
Reider KE, Larson DJ, Barnes BM, Donnelly MA. Thermal adaptations to extreme freeze–thaw cycles in the high tropical Andes. Biotropica 2020. [DOI: 10.1111/btp.12875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Kelsey E. Reider
- Department of Biological Sciences Florida International University Miami FL USA
| | - Don J. Larson
- Institute of Arctic Biology University of Alaska Fairbanks Fairbanks AK USA
| | - Brian M. Barnes
- Institute of Arctic Biology University of Alaska Fairbanks Fairbanks AK USA
| | - Maureen A. Donnelly
- College of Arts, Sciences, and Education Florida International University Miami FL USA
| |
Collapse
|
11
|
Lee JS, Yu JD, Han K, Kim SY. Strength Characteristics of Sand-Silt Mixtures Subjected to Cyclic Freezing-Thawing-Repetitive Loading. SENSORS 2020; 20:s20185381. [PMID: 32962214 PMCID: PMC7570540 DOI: 10.3390/s20185381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/18/2020] [Accepted: 09/18/2020] [Indexed: 12/03/2022]
Abstract
Daily freezing-thawing-repetitive loading is a critical factor affecting soil stability. This study assesses the strength of sand–silt mixtures with various silt fractions (SFs) subjected to cyclic freezing-thawing-repetitive loading. Specimens with SF of 0–100% were prepared with a fixed relative density of 60%. The number of repetitive loadings (N) was 1, 100, and 1000 for each specimen with different SFs. After three cycles of freezing-thawing-repetitive loading, the specimens were frozen at −5 °C for the uniaxial compression test. Test results show that the change in relative density (∆Dr) increases with the increase in SF up to 30% and decreases as SF increases beyond 30% owing to the change in the void ratio. The volumetric unfrozen water content (θu) increases with the increase in both SF and N owing to the effect of the physicochemical characteristics of soils on small voids. Unconfined compressive strength of sand-dominant mixtures (SF ≤ 30%) is reinforced by ∆Dr. By contrast, for silt-dominant mixtures (SF > 30%), the unconfined compressive strength decreases with the increase in θu and N due to lubricant role and sands dispersion. Thus, the effects of SF and N should be considered for sand–silt mixtures that have a probability to undergo cyclic freezing-thawing-repetitive loading.
Collapse
Affiliation(s)
- Jong-Sub Lee
- School of Civil, Environmental and Architectural Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Korea; (J.-S.L.); (J.-D.Y.)
| | - Jung-Doung Yu
- School of Civil, Environmental and Architectural Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Korea; (J.-S.L.); (J.-D.Y.)
| | - Kyungsoo Han
- Lyles School of Civil Engineering, Purdue University, 550, Stadium Mall Drive, West Lafayette, IN 47907, USA;
| | - Sang Yeob Kim
- School of Civil, Environmental and Architectural Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Korea; (J.-S.L.); (J.-D.Y.)
- Correspondence: ; Tel.: +82-2-3290-3838; Fax: +82-2-3290-5999
| |
Collapse
|
12
|
Vimercati L, Bueno de Mesquita CP, Schmidt SK. Limited Response of Indigenous Microbes to Water and Nutrient Pulses in High-Elevation Atacama Soils: Implications for the Cold-Dry Limits of Life on Earth. Microorganisms 2020; 8:E1061. [PMID: 32708721 PMCID: PMC7409055 DOI: 10.3390/microorganisms8071061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 01/05/2023] Open
Abstract
Soils on the world's highest volcanoes in the Atacama region represent some of the harshest ecosystems yet discovered on Earth. Life in these environments must cope with high UV flux, extreme diurnal freeze-thaw cycles, low atmospheric pressure and extremely low nutrient and water availability. Only a limited spectrum of bacterial and fungal lineages seems to have overcome the harshness of this environment and may have evolved the ability to function in situ. However, these communities may lay dormant for most of the time and spring to life only when enough water and nutrients become available during occasional snowfalls and aeolian depositions. We applied water and nutrients to high-elevation soils (5100 meters above sea level) from Volcán Llullaillaco, both in lab microcosms and in the field, to investigate how microbial communities respond when resource limitations are alleviated. The dominant taxon in these soils, the extremophilic yeast Naganishia sp., increased in relative sequence abundance and colony-forming unit counts after water + nutrient additions in microcosms, and marginally in the field after only 6 days. Among bacteria, only a Noviherbaspirillum sp. (Oxalobacteraceae) significantly increased in relative abundance both in the lab and field in response to water addition but not in response to water and nutrients together, indicating that it might be an oligotroph uniquely suited to this extreme environment. The community structure of both bacteria and eukaryotes changed significantly with water and water + nutrient additions in the microcosms and taxonomic richness declined with amendments to water and nutrients. These results indicate that only a fraction of the detected community is able to become active when water and nutrients limitations are alleviated in lab microcosms, and that water alone can dramatically change community structure. Our study sheds light on which extremophilic organisms are likely to respond when favorable conditions occur in extreme earthly environments and perhaps in extraterrestrial environments as well.
Collapse
Affiliation(s)
- Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309-0334, USA; (L.V.); (C.P.B.d.M.)
| | - Clifton P. Bueno de Mesquita
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309-0334, USA; (L.V.); (C.P.B.d.M.)
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309-0450, USA
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309-0334, USA; (L.V.); (C.P.B.d.M.)
| |
Collapse
|
13
|
Ishii K, Fujitani H, Sekiguchi Y, Tsuneda S. Physiological and genomic characterization of a new 'Candidatus Nitrotoga' isolate. Environ Microbiol 2020; 22:2365-2382. [PMID: 32285573 DOI: 10.1111/1462-2920.15015] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 11/28/2022]
Abstract
Oxidation of nitrite to nitrate is an important process in the global nitrogen cycle. Recent molecular biology-based studies have revealed that the widespread nitrite-oxidizing bacteria (NOB) belonging to the genus 'Candidatus Nitrotoga' may be highly important for the environment. However, the insufficient availability of pure Nitrotoga cultures has limited our understanding of their physiological and genomic characteristics. Here, we isolated the 'Ca. Nitrotoga' sp. strain AM1P, from a previously enriched Nitrotoga culture, using an improved isolation strategy. Although 'Ca. Nitrotoga' have been recognized as cold-adapted NOB, the strain AM1P had a slightly higher optimum growth temperature at 23°C. Strain AM1P showed a pH optimum of 8.3 and was not inhibited even at high nitrite concentrations (20 mM). We obtained the complete genome of the strain and compared the genome profile to five previously sequenced 'Ca. Nitrotoga' strains. Comparative genomics suggested that lactate dehydrogenase may be only encoded in the strain AM1P and closely related genomes. While the growth yield of AM1P did not change, we observed faster growth in the presence of lactate in comparison to purely chemolithoautotrophic growth. The characterization of the new strain AM1P sheds light on the physiological adaptation of this environmentally important, but understudied genus 'Ca. Nitrotoga'.
Collapse
Affiliation(s)
- Kento Ishii
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| | - Hirotsugu Fujitani
- Research Organization for Nano and Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan.,Research Organization for Nano and Life Innovation, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, Japan
| |
Collapse
|
14
|
The disappearing periglacial ecosystem atop Mt. Kilimanjaro supports both cosmopolitan and endemic microbial communities. Sci Rep 2019; 9:10676. [PMID: 31337772 PMCID: PMC6650471 DOI: 10.1038/s41598-019-46521-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 06/18/2019] [Indexed: 11/08/2022] Open
Abstract
Microbial communities have not been studied using molecular approaches at high elevations on the African continent. Here we describe the diversity of microbial communities from ice and periglacial soils from near the summit of Mt. Kilimanjaro by using both Illumina and Sanger sequencing of 16S and 18S rRNA genes. Ice and periglacial soils contain unexpectedly diverse and rich assemblages of Bacteria and Eukarya indicating that there may be high rates of dispersal to the top of this tropical mountain and/or that the habitat is more conducive to microbial life than was previously thought. Most bacterial OTUs are cosmopolitan and an analysis of isolation by geographic distance patterns of the genus Polaromonas emphasized the importance of global Aeolian transport in the assembly of bacterial communities on Kilimanjaro. The eukaryotic communities were less diverse than the bacterial communities and showed more evidence of dispersal limitations and apparent endemism. Cercozoa dominated the 18S communities, including a high abundance of testate amoebae and a high diversity of endemic OTUs within the Vampyrellida. These results argue for more intense study of this unique high-elevation "island of the cryosphere" before the glaciers of Kilimanjaro disappear forever.
Collapse
|
15
|
Low Temperature and Neutral pH Define " Candidatus Nitrotoga sp." as a Competitive Nitrite Oxidizer in Coculture with Nitrospira defluvii. Appl Environ Microbiol 2019; 85:AEM.02569-18. [PMID: 30824434 DOI: 10.1128/aem.02569-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/07/2019] [Indexed: 11/20/2022] Open
Abstract
Nitrification is an essential process for N removal in activated sludge to avoid toxicity of ammonium and nitrite. Besides Nitrospira, "Candidatus Nitrotoga" has been identified as a key nitrite-oxidizing bacterium (NOB) performing the second step of nitrification, nitrite oxidation to nitrate, in wastewater treatment plants (WWTPs). However, the driving forces for the dominance of Nitrotoga in certain plants have often remained unclear and could not be explained solely by temperature effects. In this study, we characterized the physiology of the ammonium-dependent Nitrotoga sp. BS with regard to temperature and pH variations and evaluated its competitiveness against Nitrospira defluvii Both NOB originated from the same WWTP and shared a comparable pH optimum of 7.3. Based on these results, coculturing experiments with these NOB were performed in batch reactors operated at either 17°C or 22°C to compare their abundances under optimal (pH 7.4) or suboptimal (pH 6.4) conditions using 1 mM nitrite. As revealed by quantitative PCR (qPCR), fluorescence in situ hybridization (FISH), and 16S amplicon sequencing, Nitrotoga sp. BS was clearly favored by its optimal growth parameters and dominated over Ns. defluvii at pH 7.4 and 17°C, whereas a pH of 6.4 was more selective for Ns. defluvii Our synthetic communities revealed that niche differentiation of NOB is influenced by a complex interaction of environmental parameters and has to be evaluated for single species.IMPORTANCE "Ca. Nitrotoga" is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between Nitrotoga and Nitrospira in bioreactors and identified conditions where the K strategist Ns. defluvii was almost replaced by Nitrotoga sp. BS. We show that the pH value is an important factor that regulates the composition of the nitrite-oxidizing enrichment with a dominance of Nitrotoga sp. BS versus Ns. defluvii at a neutral pH of 7.4 in combination with a temperature of 17°C. The physiological diversity of novel Nitrotoga cultures improves our knowledge about niche differentiation of NOB with regard to functional nitrification under suboptimal conditions.
Collapse
|
16
|
Schmidt SK, Vimercati L. Growth of cyanobacterial soil crusts during diurnal freeze-thaw cycles. J Microbiol 2019; 57:243-251. [PMID: 30721458 DOI: 10.1007/s12275-019-8359-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/16/2018] [Accepted: 10/29/2018] [Indexed: 11/27/2022]
Abstract
Various Nostoc spp. and related cyanobacteria are able to survive extreme temperatures and are among the most successful colonists of high-elevation sites being exposed due to glacial retreat. It is unclear, however, if cyanobacteria can grow during the extreme freeze-thaw cycles that occur on a year-round basis at high-elevation, peri-glacial sites or if they only grow during the rare periods when freeze-thaw cycles do not occur. We conducted several experiments to determine if cyanobacteria that form biological soil crusts (BSCs) at high-elevation sites (> 5,000 m.a.s.l.) in the Andes can grow during diurnal freeze-thaw cycles on a par with those that occur in the field. Here we show that a soil crust that had been frozen at -20°C for five years was able to increase from 40% to 100% soil coverage during a 45-day incubation during which the soil temperature cycled between -12°C and 26°C every day. In a second, experiment an undeveloped soil with no visible BSCs showed a statistically significant shift in the bacterial community from one containing few cyanobacterial sequences (8% of sequences) to one dominated (27%) by Nostoc, Microcoleus, and Leptolyngbya phylotypes during a 77-day incubation with daily freeze-thaw cycles. In addition, counts of spherical Nostoc-like colonies increased significantly on the soil surface during the experiment, especially in microcosms receiving phosphorus. Taken together these results show that freeze-thaw cycles alone do not limit the growth of BSCs in high-elevation soils, and provide new insight into how life is able to thrive in one of the most extreme terrestrial environments on Earth.
Collapse
Affiliation(s)
- Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| |
Collapse
|
17
|
Boddicker AM, Mosier AC. Genomic profiling of four cultivated Candidatus Nitrotoga spp. predicts broad metabolic potential and environmental distribution. THE ISME JOURNAL 2018; 12:2864-2882. [PMID: 30050164 PMCID: PMC6246548 DOI: 10.1038/s41396-018-0240-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 12/21/2022]
Abstract
Nitrite-oxidizing bacteria (NOB) play a critical role in the mitigation of nitrogen pollution by metabolizing nitrite to nitrate, which is removed via assimilation, denitrification, or anammox. Recent studies showed that NOB are phylogenetically and metabolically diverse, yet most of our knowledge of NOB comes from only a few cultured representatives. Using cultivation and genomic sequencing, we identified four putative Candidatus Nitrotoga NOB species from freshwater sediments and water column samples in Colorado, USA. Genome analyses indicated highly conserved 16S rRNA gene sequences, but broad metabolic potential including genes for nitrogen, sulfur, hydrogen, and organic carbon metabolism. Genomic predictions suggested that Ca. Nitrotoga can metabolize in low oxygen or anoxic conditions, which may support an expanded environmental niche for Ca. Nitrotoga similar to other NOB. An array of antibiotic and metal resistance genes likely allows Ca. Nitrotoga to withstand environmental pressures in impacted systems. Phylogenetic analyses highlighted a deeply divergent nitrite oxidoreductase alpha subunit (NxrA), suggesting a novel evolutionary trajectory for Ca. Nitrotoga separate from any other NOB and further revealing the complex evolutionary history of nitrite oxidation in the bacterial domain. Ca. Nitrotoga-like 16S rRNA gene sequences were prevalent in globally distributed environments over a range of reported temperatures. This work considerably expands our knowledge of the Ca. Nitrotoga genus and suggests that their contribution to nitrogen cycling should be considered alongside other NOB in wide variety of habitats.
Collapse
Affiliation(s)
- Andrew M Boddicker
- Department of Integrative Biology, University of Colorado Denver, Campus Box 171, Denver, CO, USA
| | - Annika C Mosier
- Department of Integrative Biology, University of Colorado Denver, Campus Box 171, Denver, CO, USA.
| |
Collapse
|
18
|
Effect of Freeze-Thaw on a Midtemperate Soil Bacterial Community and the Correlation Network of Its Members. BIOMED RESEARCH INTERNATIONAL 2018; 2018:8412429. [PMID: 30050943 PMCID: PMC6040300 DOI: 10.1155/2018/8412429] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/17/2018] [Indexed: 11/17/2022]
Abstract
Freeze-thaw (FT) events can influence soil functions. However, the overall impact of FTs on soil bacterial communities, especially in temperate regions, remains unclear. In this study, soil samples were collected from a midtemperate region in the northeast of China, and three incubation tests were then designed with varied FT amplitudes (i.e., at a freezing temperature of −15, −9, and −3°C, respectively), frequencies of FT cycles (i.e., under one, six, and 15 FT cycles, respectively) and soil water content (SWC) values (i.e., at 10 and 30% SWC, respectively). High-throughput sequencing of 16S rRNA gene amplicons was performed and the functional profile was further predicted based on these data, in addition to examinations of bulk microbial properties. Data analyses suggested that, first of all, the FT amplitude significantly influenced the bulk microbial properties and bacterial community (composition and function); certain taxa showed a nonlinear response to the three amplitudes. Next, compared to a single FTC, multiple FT cycles had only minor effects on the bacterial functional capabilities, although the bulk microbial properties changed significantly after multiple FT cycles. In addition, the bacterial response to FTs was influenced by the SWC, characterized by the significantly different bacterial community structures (composition and function) and the opposite trends of enzyme activities. Finally, RDA plots and a correlation network assembled data from all soil samples across the three tests and suggested that bacterial response trajectories changed because some species were influenced mainly by other species (i.e., biotic environment) during FT processes.
Collapse
|
19
|
Schmidt SK, Gendron EMS, Vincent K, Solon AJ, Sommers P, Schubert ZR, Vimercati L, Porazinska DL, Darcy JL, Sowell P. Life at extreme elevations on Atacama volcanoes: the closest thing to Mars on Earth? Antonie van Leeuwenhoek 2018; 111:1389-1401. [PMID: 29557533 DOI: 10.1007/s10482-018-1066-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/14/2018] [Indexed: 12/21/2022]
Abstract
Here we describe recent breakthroughs in our understanding of microbial life in dry volcanic tephra ("soil") that covers much of the surface area of the highest elevation volcanoes on Earth. Dry tephra above 6000 m.a.s.l. is perhaps the best Earth analog for the surface of Mars because these "soils" are acidic, extremely oligotrophic, exposed to a thin atmosphere, high UV fluxes, and extreme temperature fluctuations across the freezing point. The simple microbial communities found in these extreme sites have among the lowest alpha diversity of any known earthly ecosystem and contain bacteria and eukaryotes that are uniquely adapted to these extreme conditions. The most abundant eukaryotic organism across the highest elevation sites is a Naganishia species that is metabolically versatile, can withstand high levels of UV radiation and can grow at sub-zero temperatures, and during extreme diurnal freeze-thaw cycles (e.g. - 10 to + 30 °C). The most abundant bacterial phylotype at the highest dry sites sampled (6330 m.a.s.l. on Volcán Llullaillaco) belongs to the enigmatic B12-WMSP1 clade which is related to the Ktedonobacter/Thermosporothrix clade that includes versatile organisms with the largest known bacterial genomes. Close relatives of B12-WMSP1 are also found in fumarolic soils on Volcán Socompa and in oligotrophic, fumarolic caves on Mt. Erebus in Antarctica. In contrast to the extremely low diversity of dry tephra, fumaroles found at over 6000 m.a.s.l. on Volcán Socompa support very diverse microbial communities with alpha diversity levels rivalling those of low elevation temperate soils. Overall, the high-elevation biome of the Atacama region provides perhaps the best "natural experiment" in which to study microbial life in both its most extreme setting (dry tephra) and in one of its least extreme settings (fumarolic soils).
Collapse
Affiliation(s)
- S K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
| | - E M S Gendron
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
- Molecular, Cellular, and Developmental Biology Department, University of Colorado, Boulder, CO, USA
| | - K Vincent
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - A J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - P Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Z R Schubert
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
- Molecular, Cellular, and Developmental Biology Department, University of Colorado, Boulder, CO, USA
| | - L Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - D L Porazinska
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - J L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - P Sowell
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| |
Collapse
|
20
|
Stock W, Pinseel E, De Decker S, Sefbom J, Blommaert L, Chepurnova O, Sabbe K, Vyverman W. Expanding the toolbox for cryopreservation of marine and freshwater diatoms. Sci Rep 2018. [PMID: 29523856 PMCID: PMC5844899 DOI: 10.1038/s41598-018-22460-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Diatoms constitute the most diverse group of microalgae and have long been recognised for their large biotechnological potential. In the wake of growing research interest in new model species and development of commercial applications, there is a pressing need for long-term preservation of diatom strains. While cryopreservation using dimethylsulfoxide (DMSO) as a cryoprotective agent is the preferred method for long-term strain preservation, many diatom species cannot be successfully cryopreserved using DMSO. Therefore, in this study, we studied cryopreservation success in six different diatom species, representing the major morphological and ecological diatom groups, using a range of DMSO concentrations and Plant Vitrification Solution 2 (PVS2) as an alternative cryoprotectant to DMSO. In addition, we tested whether suppressing bacterial growth by antibiotics accelerates the post-thaw recovery process. Our results show that the effects of cryoprotectant choice, its concentration and the addition of antibiotics are highly species specific. In addition, we showed that PVS2 and antibiotics are useful agents to optimize cryopreservation of algae that cannot survive the traditional cryopreservation protocol using DMSO. We conclude that a species-specific approach will remain necessary to develop protocols for diatom cryopreservation and to increase their representation in public culture collections.
Collapse
Affiliation(s)
- Willem Stock
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281-S8, B-9000, Ghent, Belgium
| | - Eveline Pinseel
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281-S8, B-9000, Ghent, Belgium.,Department of Bryophyta and Thallophyta, Botanic Garden Meise, Nieuwelaan 38, B-1860, Meise, Belgium.,Ecosystem Management Research Group (ECOBE), University of Antwerp, Universiteitsplein 1, B-2610, Wilrijk, Belgium
| | - Sam De Decker
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281-S8, B-9000, Ghent, Belgium
| | - Josefin Sefbom
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281-S8, B-9000, Ghent, Belgium.,Department of Marine Sciences, University of Gothenburg, Box 461, 405 30, Göteborg, Sweden
| | - Lander Blommaert
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281-S8, B-9000, Ghent, Belgium.,Institut de Biologie Physico-Chimique (IBPC), UMR 7141, Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie, 13 Rue Pierre et Marie Curie, F-75005, Paris, France
| | - Olga Chepurnova
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281-S8, B-9000, Ghent, Belgium
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281-S8, B-9000, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281-S8, B-9000, Ghent, Belgium.
| |
Collapse
|
21
|
Schmidt SK, Vimercati L, Darcy JL, Arán P, Gendron EM, Solon AJ, Porazinska D, Dorador C. A Naganishia in high places: functioning populations or dormant cells from the atmosphere? Mycology 2017; 8:153-163. [PMID: 30123637 PMCID: PMC6059072 DOI: 10.1080/21501203.2017.1344154] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/15/2017] [Indexed: 12/16/2022] Open
Abstract
Here, we review the current state of knowledge concerning high-elevation members of the extremophilic Cryptococcus albidus clade (now classified as the genus Naganishia). These fungi dominate eukaryotic microbial communities across the highest elevation, soil-like material (tephra) on volcanoes such as Llullaillaco, Socompa, and Saírecabur in the Atacama region of Chile, Argentina, and Bolivia. Recent studies indicate that Naganishia species are among the most resistant organisms to UV radiation, and a strain of N. friedmannii from Volcán Llullaillaco is the first organism that is known to grow during the extreme, diurnal freeze-thaw cycles that occur on a continuous basis at elevations above 6000 m.a.s.l. in the Atacama region. These and other extremophilic traits discussed in this review may serve a dual purpose of allowing Naganishia species to survive long-distance transport through the atmosphere and to survive the extreme conditions found at high elevations. Current evidence indicates that there are frequent dispersal events between high-elevation volcanoes of Atacama region and the Dry Valleys of Antarctica via "Rossby Wave" merging of the polar and sub-tropical jet streams. This dispersal hypothesis needs further verification, as does the hypothesis that Naganishia species are flexible "opportunitrophs" that can grow during rare periods of water (from melting snow) and nutrient availability (from Aeolian inputs) in one of the most extreme terrestrial habitats on Earth.
Collapse
Affiliation(s)
- Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - John L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Pablo Arán
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Eli M.S Gendron
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
- Molecular, Cellular, and Developmental Biology Department, University of Colorado, Boulder, CO, USA
| | - Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Dorota Porazinska
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| |
Collapse
|
22
|
Enrichment and Physiological Characterization of a Cold-Adapted Nitrite-Oxidizing Nitrotoga sp. from an Eelgrass Sediment. Appl Environ Microbiol 2017; 83:AEM.00549-17. [PMID: 28500038 DOI: 10.1128/aem.00549-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/02/2017] [Indexed: 12/26/2022] Open
Abstract
Nitrite-oxidizing bacteria (NOB) are responsible for the second step of nitrification in natural and engineered ecosystems. The recently discovered genus Nitrotoga belongs to the Betaproteobacteria and potentially has high environmental importance. Although environmental clones affiliated with Nitrotoga are widely distributed, the limited number of cultivated Nitrotoga spp. results in a poor understanding of their ecophysiological features. In this study, we successfully enriched the nonmarine cold-adapted Nitrotoga sp. strain AM1 from coastal sand in an eelgrass zone and investigated its physiological characteristics. Multistep-enrichment approaches led to an increase in the abundance of AM1 to approximately 80% of the total bacterial population. AM1 was the only detectable NOB in the bacterial community. The 16S rRNA gene sequence of AM1 was 99.6% identical to that of "Candidatus Nitrotoga arctica," which was enriched from permafrost-affected soil. The highest nitrogen oxidation rate of AM1 was observed at 16°C. The half-saturation constant (Km ) and the generation time were determined to be 25 μM NO2- and 54 h, respectively. The nitrite oxidation rate of AM1 was stimulated at concentrations of <30 mM NH4Cl but completely inhibited at 50 mM NH4Cl. AM1 can grow well under specific environmental conditions, such as low temperature and in the presence of a relatively high concentration of free ammonia. These results help improve our comprehension of the functional importance of NitrotogaIMPORTANCE Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process of the nitrogen cycle. Recent studies have suggested that the organisms of the novel NOB genus Nitrotoga were widely distributed and played a functional role in natural and engineered ecosystems. However, only a few Nitrotoga enrichments have been obtained, and little is known about their ecology and physiology. In this study, we successfully enriched a Nitrotoga sp. from sand in a shallow coastal marine ecosystem and undertook a physiological characterization. The laboratory experiments showed that the Nitrotoga enrichment culture could adapt not only to low temperature but also to relatively high concentrations of free ammonia. The determination of as-yet-unknown unique characteristics of Nitrotoga contributes to the improvement of our insights into the microbiology of nitrification.
Collapse
|
23
|
Freeze-thaw revival of rotifers and algae in a desiccated, high-elevation (5500 meters) microbial mat, high Andes, Perú. Extremophiles 2017; 21:573-580. [PMID: 28321614 DOI: 10.1007/s00792-017-0926-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/06/2017] [Indexed: 12/24/2022]
Abstract
This is the first study of the highest elevation cyanobacteria-dominated microbial mat yet described. The desiccated mat was sampled in 2010 from an ephemeral rock pool at 5500 m above sea level in the Cordillera Vilcanota of southern Perú. After being frozen for 6 years at -20 °C in the lab, pieces of the mat were sequenced to fully characterize both the 16 and 18S microbial communities and experiments were conducted to determine if organisms in the mat could revive and become active under the extreme freeze-thaw conditions that these mats experience in the field. Sequencing revealed an unexpectedly diverse, multi-trophic microbial community with 16S OTU richness comparable to similar, seasonally desiccated mats from the Dry Valleys of Antarctica and low elevation sites in the Atacama Desert region. The bacterial community of the mat was dominated by phototrophs in the Cyanobacteria (Nostoc) and the Rhodospirillales, whereas the eukaryotic community was dominated by predators such as bdelloid rotifers (Philodinidae). Microcosm experiments showed that bdelloid rotifers in the mat were able to come out of dormancy and actively forage even under realistic field conditions (diurnal temperature fluctuations of -12 °C at night to + 27 °C during the day), and after being frozen for 6 years. Our results broaden our understanding of the diversity of life in periodically desiccated, high-elevation habitats and demonstrate that extreme freeze-thaw cycles per se are not a major factor limiting the development of at least some members of these unique microbial mat systems.
Collapse
|
24
|
Growth of high-elevation Cryptococcus sp. during extreme freeze-thaw cycles. Extremophiles 2016; 20:579-88. [PMID: 27315166 DOI: 10.1007/s00792-016-0844-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
Soils above 6000 m.a.s.l. are among the most extreme environments on Earth, especially on high, dry volcanoes where soil temperatures cycle between -10 and 30 °C on a typical summer day. Previous studies have shown that such sites are dominated by yeast in the cryophilic Cryptococcus group, but it is unclear if they can actually grow (or are just surviving) under extreme freeze-thaw conditions. We carried out a series of experiments to determine if Cryptococcus could grow during freeze-thaw cycles similar to those measured under field conditions. We found that Cryptococcus phylotypes increased in relative abundance in soils subjected to 48 days of freeze-thaw cycles, becoming the dominant organisms in the soil. In addition, pure cultures of Cryptococcus isolated from these same soils were able to grow in liquid cultures subjected to daily freeze-thaw cycles, despite the fact that the culture medium froze solid every night. Furthermore, we showed that this organism is metabolically versatile and phylogenetically almost identical to strains from Antarctic Dry Valley soils. Taken together these results indicate that this organism has unique metabolic and temperature adaptations that make it able to thrive in one of the harshest and climatically volatile places on Earth.
Collapse
|
25
|
Biogeochemical Stoichiometry Reveals P and N Limitation Across the Post-glacial Landscape of Denali National Park, Alaska. Ecosystems 2016. [DOI: 10.1007/s10021-016-9992-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
26
|
Archer SDJ, McDonald IR, Herbold CW, Lee CK, Niederberger TS, Cary C. Temporal, regional and geochemical drivers of microbial community variation in the melt ponds of the Ross Sea region, Antarctica. Polar Biol 2016. [DOI: 10.1007/s00300-015-1780-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
27
|
Hüpeden J, Wegen S, Off S, Lücker S, Bedarf Y, Daims H, Kühn C, Spieck E. Relative Abundance of Nitrotoga spp. in a Biofilter of a Cold-Freshwater Aquaculture Plant Appears To Be Stimulated by Slightly Acidic pH. Appl Environ Microbiol 2016; 82:1838-45. [PMID: 26746710 PMCID: PMC4784051 DOI: 10.1128/aem.03163-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/31/2015] [Indexed: 12/22/2022] Open
Abstract
The functioning of recirculation aquaculture systems (RAS) is essential to maintain water quality for fish health, and one crucial process here is nitrification. The investigated RAS was connected to a rainbow trout production system and operated at an average temperature of 13°C and pH 6.8. Community analyses of the nitrifying biofilm revealed a coexistence of Nitrospira and Nitrotoga, and it is hypothesized that a slightly acidic pH in combination with lower temperatures favors the growth of the latter. Modification of the standard cultivation approach toward lower pH values of 5.7 to 6.0 resulted in the successful enrichment (99% purity) of Nitrotoga sp. strain HW29, which had a 16S rRNA sequence similarity of 99.0% to Nitrotoga arctica. Reference cultures of Nitrospira defluvii and the novel Nitrotoga sp. HW29 were used to confirm differentiation of these nitrite oxidizers in distinct ecological niches. Nitrotoga sp. HW29 revealed pH and temperature optima of 6.8 and 22°C, respectively, whereas Nitrospira defluvii displayed the highest nitrite oxidation rate at pH 7.3 and 32°C. We report here the occurrence of Nitrotoga as one of the main nitrite-oxidizing bacteria in freshwater aquaculture systems and indicate that a slightly acidic pH, in addition to temperatures below 20°C, can be applied as a selective isolation criterion for this microorganism.
Collapse
Affiliation(s)
- Jennifer Hüpeden
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Simone Wegen
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Sandra Off
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Sebastian Lücker
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, The Netherlands Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Yvonne Bedarf
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Holger Daims
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Carsten Kühn
- State Research Centre of Agriculture and Fisheries Mecklenburg-Vorpommern, Institute of Fisheries, Rostock, Germany
| | - Eva Spieck
- Biocenter Klein Flottbek, Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| |
Collapse
|
28
|
Suyal DC, Yadav A, Shouche Y, Goel R. Diversified diazotrophs associated with the rhizosphere of Western Indian Himalayan native red kidney beans (Phaseolus vulgaris L.). 3 Biotech 2015; 5:433-441. [PMID: 28324543 PMCID: PMC4522724 DOI: 10.1007/s13205-014-0238-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/30/2014] [Indexed: 12/17/2022] Open
Abstract
Red kidney beans (RKBs) are one of the major components in the human diet of Western Indian Himalaya (WIH). Their cultivation in these habitats is strongly influenced by various biotic and abiotic stresses and therefore, there must be a selection of RKB associated microorganisms that are adapted to these harsh conditions. Seven cold adaptive diazotrophs from the same rhizosphere were isolated in our previous study to reveal the low-temperature associated proteins and mechanisms. However, the diversity and phylogenetic affiliations of these rhizosphere diazotrophs are still unknown. In this study, RKB rhizospheric soil from two different agro-ecosystems of WIH namely S1 (Chhiplakot, 30.70°N/80.30°E) and S2 (Munsyari, 30.60°N/80.20°E) were explored for the assessment of nitrogenase reductase gene (nifH) diversity by plating respective clone libraries SN1 and SN2. The RKB rhizosphere diazotroph assemblage was very diverse and apparently consists mainly of the genera Rhizobium, followed by unknown diazotrophic microorganisms. Deduced amino acid sequence analysis revealed the presence of diverse nifH sequences, affiliated with a wide range of taxa, encompassing members of the Proteobacteria, Actinobacteria and Firmicutes. Members of cyanobacteria, methanotrophs and archaea were also detected. To the best of our knowledge, this is the first major metagenomic effort that revealed the presence of diverse nitrogen-fixing microbial assemblages in indigenous RKB rhizospheric soil which can further be explored for improved crop yield/productivity.
Collapse
Affiliation(s)
- Deep Chandra Suyal
- Department of Microbiology, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India
| | - Amit Yadav
- Microbial Culture Collection, National Centre for Cell Science, Pune University Campus, Ganeshkhind, 411 007, Pune, India
| | - Yogesh Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pune University Campus, Ganeshkhind, 411 007, Pune, India
| | - Reeta Goel
- Department of Microbiology, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India.
| |
Collapse
|
29
|
Suyal DC, Yadav A, Shouche Y, Goel R. Bacterial diversity and community structure of Western Indian Himalayan red kidney bean (Phaseolus vulgaris) rhizosphere as revealed by 16S rRNA gene sequences. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0048] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
30
|
Lynch RC, Darcy JL, Kane NC, Nemergut DR, Schmidt SK. Metagenomic evidence for metabolism of trace atmospheric gases by high-elevation desert Actinobacteria. Front Microbiol 2014; 5:698. [PMID: 25566214 PMCID: PMC4269115 DOI: 10.3389/fmicb.2014.00698] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 11/25/2014] [Indexed: 11/26/2022] Open
Abstract
Previous surveys of very dry Atacama Desert mineral soils have consistently revealed sparse communities of non-photosynthetic microbes. The functional nature of these microorganisms remains debatable given the harshness of the environment and low levels of biomass and diversity. The aim of this study was to gain an understanding of the phylogenetic community structure and metabolic potential of a low-diversity mineral soil metagenome that was collected from a high-elevation Atacama Desert volcano debris field. We pooled DNA extractions from over 15 g of volcanic material, and using whole genome shotgun sequencing, observed only 75-78 total 16S rRNA gene OTUs3%. The phylogenetic structure of this community is significantly under dispersed, with actinobacterial lineages making up 97.9-98.6% of the 16S rRNA genes, suggesting a high degree of environmental selection. Due to this low diversity and uneven community composition, we assembled and analyzed the metabolic pathways of the most abundant genome, a Pseudonocardia sp. (56-72% of total 16S genes). Our assembly and binning efforts yielded almost 4.9 Mb of Pseudonocardia sp. contigs, which accounts for an estimated 99.3% of its non-repetitive genomic content. This genome contains a limited array of carbohydrate catabolic pathways, but encodes for CO2 fixation via the Calvin cycle. The genome also encodes complete pathways for the catabolism of various trace gases (H2, CO and several organic C1 compounds) and the assimilation of ammonia and nitrate. We compared genomic content among related Pseudonocardia spp. and estimated rates of non-synonymous and synonymous nucleic acid substitutions between protein coding homologs. Collectively, these comparative analyses suggest that the community structure and various functional genes have undergone strong selection in the nutrient poor desert mineral soils and high-elevation atmospheric conditions.
Collapse
Affiliation(s)
- Ryan C. Lynch
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - John L. Darcy
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Diana R. Nemergut
- Environmental Studies Program, University of ColoradoBoulder, CO, USA
- Institute of Arctic and Alpine Research, University of ColoradoBoulder, CO, USA
- Department of Biology, Duke UniversityDurham, NC, USA
| | - Steve K. Schmidt
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| |
Collapse
|
31
|
|
32
|
Comparison of oxidation kinetics of nitrite-oxidizing bacteria: nitrite availability as a key factor in niche differentiation. Appl Environ Microbiol 2014; 81:745-53. [PMID: 25398863 DOI: 10.1128/aem.02734-14] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrification has an immense impact on nitrogen cycling in natural ecosystems and in wastewater treatment plants. Mathematical models function as tools to capture the complexity of these biological systems, but kinetic parameters especially of nitrite-oxidizing bacteria (NOB) are lacking because of a limited number of pure cultures until recently. In this study, we compared the nitrite oxidation kinetics of six pure cultures and one enrichment culture representing three genera of NOB (Nitrobacter, Nitrospira, Nitrotoga). With half-saturation constants (Km) between 9 and 27 μM nitrite, Nitrospira bacteria are adapted to live under significant substrate limitation. Nitrobacter showed a wide range of lower substrate affinities, with Km values between 49 and 544 μM nitrite. However, the advantage of Nitrobacter emerged under excess nitrite supply, sustaining high maximum specific activities (Vmax) of 64 to 164 μmol nitrite/mg protein/h, contrary to the lower activities of Nitrospira of 18 to 48 μmol nitrite/mg protein/h. The Vmax (26 μmol nitrite/mg protein/h) and Km (58 μM nitrite) of "Candidatus Nitrotoga arctica" measured at a low temperature of 17°C suggest that Nitrotoga can advantageously compete with other NOB, especially in cold habitats. The kinetic parameters determined represent improved basis values for nitrifying models and will support predictions of community structure and nitrification rates in natural and engineered ecosystems.
Collapse
|
33
|
Knelman JE, Schmidt SK, Lynch RC, Darcy JL, Castle SC, Cleveland CC, Nemergut DR. Nutrient addition dramatically accelerates microbial community succession. PLoS One 2014; 9:e102609. [PMID: 25050551 PMCID: PMC4106831 DOI: 10.1371/journal.pone.0102609] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/12/2014] [Indexed: 12/02/2022] Open
Abstract
The ecological mechanisms driving community succession are widely debated, particularly for microorganisms. While successional soil microbial communities are known to undergo predictable changes in structure concomitant with shifts in a variety of edaphic properties, the causal mechanisms underlying these patterns are poorly understood. Thus, to specifically isolate how nutrients – important drivers of plant succession – affect soil microbial succession, we established a full factorial nitrogen (N) and phosphorus (P) fertilization plot experiment in recently deglaciated (∼3 years since exposure), unvegetated soils of the Puca Glacier forefield in Southeastern Peru. We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization. Fertilized soils were then compared to samples from three reference successional transects representing advancing stages of soil development ranging from 5 years to 85 years since exposure. We found that a single application of +NP fertilizer caused the soil bacterial community structure of the three-year old soils to most resemble the 85-year old soils after one year. Despite differences in a variety of soil edaphic properties between fertilizer plots and late successional soils, bacterial community composition of +NP plots converged with late successional communities. Thus, our work suggests a mechanism for microbial succession whereby changes in resource availability drive shifts in community composition, supporting a role for nutrient colimitation in primary succession. These results suggest that nutrients alone, independent of other edaphic factors that change with succession, act as an important control over soil microbial community development, greatly accelerating the rate of succession.
Collapse
Affiliation(s)
- Joseph E. Knelman
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, United States of America
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Ryan C. Lynch
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - John L. Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Sarah C. Castle
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, Montana, United States of America
| | - Cory C. Cleveland
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, Montana, United States of America
| | - Diana R. Nemergut
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, United States of America
- Environmental Studies Program, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
| |
Collapse
|
34
|
Ganzert L, Bajerski F, Wagner D. Bacterial community composition and diversity of five different permafrost-affected soils of Northeast Greenland. FEMS Microbiol Ecol 2014; 89:426-41. [DOI: 10.1111/1574-6941.12352] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/05/2014] [Accepted: 05/07/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lars Ganzert
- Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; Potsdam Germany
| | - Felizitas Bajerski
- Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; Potsdam Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences; Section 4.5 Geomicrobiology; Potsdam Germany
| |
Collapse
|
35
|
Schmidt SK, Nemergut DR, Darcy JL, Lynch R. Do bacterial and fungal communities assemble differently during primary succession? Mol Ecol 2014; 23:254-8. [DOI: 10.1111/mec.12589] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 11/12/2013] [Indexed: 11/26/2022]
Affiliation(s)
- S. K. Schmidt
- Department of Ecology and Evolutionary Biology; University of Colorado; Boulder CO 80309 USA
| | - D. R. Nemergut
- Institute of Arctic and Alpine Research; University of Colorado; Boulder CO 80309 USA
- Environmental Studies Program; University of Colorado; Boulder CO 80309 USA
| | - J. L. Darcy
- Department of Ecology and Evolutionary Biology; University of Colorado; Boulder CO 80309 USA
| | - R. Lynch
- Department of Ecology and Evolutionary Biology; University of Colorado; Boulder CO 80309 USA
| |
Collapse
|
36
|
Naff CS, Darcy JL, Schmidt SK. Phylogeny and biogeography of an uncultured clade of snow chytrids. Environ Microbiol 2013; 15:2672-80. [PMID: 23551529 DOI: 10.1111/1462-2920.12116] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/27/2013] [Accepted: 03/04/2013] [Indexed: 11/27/2022]
Abstract
Numerous studies have shown that snow can contain a diverse array of algae known as 'snow algae'. Some reports also indicate that parasites of algae (e.g. chytrids) are also found in snow, but efforts to phylogenetically identify 'snow chytrids' have not been successful. We used culture-independent molecular approaches to phylogenetically identify chytrids that are common in long-lived snowpacks of Colorado and Europe. The most remarkable finding of the present study was the discovery of a new clade of chytrids that has representatives in snowpacks of Colorado and Switzerland and cold sites in Nepal and France, but no representatives from warmer ecosystems. This new clade ('Snow Clade 1' or SC1) is as deeply divergent as its sister clade, the Lobulomycetales, and phylotypes of SC1 show significant (P < 0.003) genetic-isolation by geographic distance patterns, perhaps indicating a long evolutionary history in the cryosphere. In addition to SC1, other snow chytrids were phylogenetically shown to be in the order Rhizophydiales, a group with known algal parasites and saprotrophs. We suggest that these newly discovered snow chytrids are important components of snow ecosystems where they contribute to snow food-web dynamics and the release of nutrients due to their parasitic and saprotrophic activities.
Collapse
Affiliation(s)
- C S Naff
- Department of Ecology and Evolutionary Biology, University of Colorado, N122 Ramaley Hall, Campus Box 334, Boulder, CO, 80309-0334, USA
| | | | | |
Collapse
|
37
|
Farías ME, Rascovan N, Toneatti DM, Albarracín VH, Flores MR, Poiré DG, Collavino MM, Aguilar OM, Vazquez MP, Polerecky L. The discovery of stromatolites developing at 3570 m above sea level in a high-altitude volcanic lake Socompa, Argentinean Andes. PLoS One 2013; 8:e53497. [PMID: 23308236 PMCID: PMC3538587 DOI: 10.1371/journal.pone.0053497] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 11/29/2012] [Indexed: 11/24/2022] Open
Abstract
We describe stromatolites forming at an altitude of 3570 m at the shore of a volcanic lake Socompa, Argentinean Andes. The water at the site of stromatolites formation is alkaline, hypersaline, rich in inorganic nutrients, very rich in arsenic, and warm (20-24°C) due to a hydrothermal input. The stromatolites do not lithify, but form broad, rounded and low-domed bioherms dominated by diatom frustules and aragonite micro-crystals agglutinated by extracellular substances. In comparison to other modern stromatolites, they harbour an atypical microbial community characterized by highly abundant representatives of Deinococcus-Thermus, Rhodobacteraceae, Desulfobacterales and Spirochaetes. Additionally, a high proportion of the sequences that could not be classified at phylum level showed less than 80% identity to the best hit in the NCBI database, suggesting the presence of novel distant lineages. The primary production in the stromatolites is generally high and likely dominated by Microcoleus sp. Through negative phototaxis, the location of these cyanobacteria in the stromatolites is controlled by UV light, which greatly influences their photosynthetic activity. Diatoms, dominated by Amphora sp., are abundant in the anoxic, sulfidic and essentially dark parts of the stromatolites. Although their origin in the stromatolites is unclear, they are possibly an important source of anaerobically degraded organic matter that induces in situ aragonite precipitation. To the best of our knowledge, this is so far the highest altitude with documented actively forming stromatolites. Their generally rich, diverse and to a large extent novel microbial community likely harbours valuable genetic and proteomic reserves, and thus deserves active protection. Furthermore, since the stromatolites flourish in an environment characterized by a multitude of extremes, including high exposure to UV radiation, they can be an excellent model system for studying microbial adaptations under conditions that, at least in part, resemble those during the early phase of life evolution on Earth.
Collapse
Affiliation(s)
- María E. Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Nicolás Rascovan
- Instituto de Agrobiotecnologia Rosario (INDEAR), Rosario, Santa Fe, Argentina
| | - Diego M. Toneatti
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Virginia H. Albarracín
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina
- Max-Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - María R. Flores
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Daniel G. Poiré
- Centro de Investigaciones Geológicas, Universidad Nacional de La Plata-CONICET, La Plata, Argentina
| | - Mónica M. Collavino
- Instituto de Biotecnología y Biología Molecular (IBBM), Universidad Nacional de La Plata-CONICET, La Plata, Argentina
| | - O. Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), Universidad Nacional de La Plata-CONICET, La Plata, Argentina
| | - Martin P. Vazquez
- Instituto de Agrobiotecnologia Rosario (INDEAR), Rosario, Santa Fe, Argentina
| | - Lubos Polerecky
- Max-Planck Institute for Marine Microbiology, Bremen, Germany
| |
Collapse
|
38
|
|
39
|
Lynch RC, King AJ, Farías ME, Sowell P, Vitry C, Schmidt SK. The potential for microbial life in the highest-elevation (>6000 m.a.s.l.) mineral soils of the Atacama region. ACTA ACUST UNITED AC 2012. [DOI: 10.1029/2012jg001961] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
40
|
Microbial degradation of 2,4-dichlorophenoxyacetic acid on the Greenland ice sheet. Appl Environ Microbiol 2012; 78:5070-6. [PMID: 22582066 DOI: 10.1128/aem.00400-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Greenland ice sheet (GrIS) receives organic carbon (OC) of anthropogenic origin, including pesticides, from the atmosphere and/or local sources, and the fate of these compounds in the ice is currently unknown. The ability of supraglacial heterotrophic microbes to mineralize different types of OC is likely a significant factor determining the fate of anthropogenic OC on the ice sheet. Here we determine the potential of the microbial community from the surface of the GrIS to mineralize the widely used herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). Surface ice cores were collected and incubated for up to 529 days in microcosms simulating in situ conditions. Mineralization of side chain- and ring-labeled [(14)C]2,4-D was measured in the samples, and quantitative PCR targeting the tfdA genes in total DNA extracted from the ice after the experiment was performed. We show that the supraglacial microbial community on the GrIS contains microbes that are capable of degrading 2,4-D and that they are likely present in very low numbers. They can mineralize 2,4-D at a rate of up to 1 nmol per m(2) per day, equivalent to ∼26 ng C m(-2) day(-1). Thus, the GrIS should not be considered a mere reservoir of all atmospheric contaminants, as it is likely that some deposited compounds will be removed from the system via biodegradation processes before their potential release due to the accelerated melting of the ice sheet.
Collapse
|
41
|
Lapanje A, Wimmersberger C, Furrer G, Brunner I, Frey B. Pattern of elemental release during the granite dissolution can be changed by aerobic heterotrophic bacterial strains isolated from Damma Glacier (central Alps) deglaciated granite sand. MICROBIAL ECOLOGY 2012; 63:865-882. [PMID: 22105516 DOI: 10.1007/s00248-011-9976-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 10/21/2011] [Indexed: 05/31/2023]
Abstract
Colonisation and weathering of freshly deglaciated granite are key processes in initial soil formation and development. We have obtained 438 isolates from granite sand covering glacial toe, 284 isolates at 22°C and 154 at 4°C incubation temperatures, respectively, to obtain cultures for the investigation of their weathering capabilities under laboratory conditions. The isolation of bacteria from granite sand was performed on rich-, intermediate- and low-nutrient-content solid media. Isolates were identified by 16S rRNA gene sequencing. According to the genera-associated weathering capabilities described in the literature and according to their abundance in our culture collection, we selected eight strains to analyse their effects on the weathering dynamics of granite sand during the batch culture experiment. Analysis of culturable bacteria showed higher species richness among isolates from 22°C than from 4°C incubations. In the R2A and 1/100 Ravan media, we observed the highest species richness of isolates obtained at 22°C and 4°C incubation temperatures, respectively. The obtained 16S rRNA sequences revealed the presence of alpha-, beta- and gamma-proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The most numerous group of isolates was distantly related to Collimonas representatives, and according to the sequences of the 16S rRNA genes, they can form a new genus. Isolates from this group had the capability of causing increased dissolution rates for Fe, W, Ni and Rb. In general, at each sampling during the 30-day experiment, every strain showed a unique weathering profile resulting from differential rates of the dissolution and the precipitation of different minerals in the batch culture. Consequently, the presence of different strains, their growth stage and changes in proportions of strains in the bacterial community can affect further soil development and the successive colonisation by plants.
Collapse
MESH Headings
- Bacteria, Aerobic/genetics
- Bacteria, Aerobic/growth & development
- Bacteria, Aerobic/isolation & purification
- Bacteria, Aerobic/metabolism
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Ribosomal/genetics
- Genes, rRNA
- Heterotrophic Processes
- Ice Cover/microbiology
- Minerals/chemistry
- Minerals/metabolism
- Molecular Sequence Data
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Silicon Dioxide/chemistry
- Soil Microbiology
Collapse
Affiliation(s)
- Aleš Lapanje
- Snow and Landscape Research, Swiss Federal Institute for Forest, Zürcherstrasse 111, Birmensdorf, Switzerland.
| | | | | | | | | |
Collapse
|
42
|
Wang A, Wu FZ, Yang WQ, Wu ZC, Wang XX, Tan B. Abundance and composition dynamics of soil ammonia-oxidizing archaea in an alpine fir forest on the eastern Tibetan Plateau of China. Can J Microbiol 2012; 58:572-80. [PMID: 22494458 DOI: 10.1139/w2012-032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Real-time qPCR and clone library sequencing targeting amoA genes were used to investigate the seasonal dynamics of an ammonia-oxidizing archaea (AOA) community in an alpine fir forest in western China. AOA were detected at all sampling dates, and there were significant variations in archaeal amoA gene copy numbers (7.63 × 10(5) to 8.35 × 10(8) per gram of dry soil) throughout the nongrowing season. Compared with ammonia-oxidizing bacteria (AOB), the AOA displayed a higher abundance on the majority of sampling dates during the freeze-thaw period. All of the AOA sequences fell within soil and sediment lineages and were affiliated with 7 clusters. Compared with the other clusters, cluster 1 was more sensitive to low temperature and was the dominant group in August. In contrast, cluster 3 dominated the AOA community in winter and probably represents a group of cold-adapted archaea. Redundancy analysis (RDA) revealed that the seasonality of the AOA community was mainly attributed to changes in soil temperature and nutrient availability (e.g., dissolved organic nitrogen and carbon). Our results indicate that AOA exist in frozen soils in the alpine coniferous forest ecosystem of the eastern Tibetan Plateau. Moreover, soil temperature may directly and (or) indirectly affect AOA abundance and composition and may further influence the soil N cycle during the winter.
Collapse
Affiliation(s)
- Ao Wang
- Key Laboratory of Ecological Forestry Engineering, Institute of Ecology & Forestry, Sichuan Agricultural University, No. 211, Huimin Road, Wenjiang District 611130, PR China
| | | | | | | | | | | |
Collapse
|
43
|
Comparison of bacterial diversity in proglacial soil from Kafni Glacier, Himalayan Mountain ranges, India, with the bacterial diversity of other glaciers in the world. Extremophiles 2011; 15:673-90. [PMID: 21918795 DOI: 10.1007/s00792-011-0398-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 08/26/2011] [Indexed: 10/17/2022]
Abstract
Two 16S rRNA gene clone libraries (KF and KS) were constructed using two soil samples (K7s and K8s) collected near Kafni Glacier, Himalayas. The two libraries yielded a total of 648 clones. Phyla Actinobacteria, Bacteroidetes, Chloroflexi Firmicutes, Proteobacteria, Spirochaetae, Tenericutes and Verrucomicrobia were common to the two libraries. Phyla Acidobacteria, Chlamydiae and Nitrospirae were present only in KF library, whereas Lentisphaerae and TM7 were detected only in KS. In the two libraries, clones belonging to phyla Bacteroidetes and Proteobacteria were the most predominant. Principal component analysis (PCA) revealed that KF and KS were different and arsenic content influenced the differences in the percentage of OTUs. PCA indicated that high water content in the K8s sample results in high total bacterial count. PCA also indicated that bacterial diversity of KF and KS was similar to soils from the Pindari Glacier, Himalayas; Samoylov Island, Siberia; Schrimacher Oasis, Antarctica and Siberian tundra. The eleven bacterial strains isolated from the above two soil samples were phylogenetically related to six different genera. All the isolates were psychro-, halo- and alkalitolerant. Amylase, lipase and urease activities were detected in the majority of the strains. Long chain, saturated, unsaturated and branched fatty acids were predominant in the psychrotolerant bacteria.
Collapse
|
44
|
Darcy JL, Lynch RC, King AJ, Robeson MS, Schmidt SK. Global distribution of Polaromonas phylotypes--evidence for a highly successful dispersal capacity. PLoS One 2011; 6:e23742. [PMID: 21897856 PMCID: PMC3163589 DOI: 10.1371/journal.pone.0023742] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 07/25/2011] [Indexed: 11/18/2022] Open
Abstract
Bacteria from the genus Polaromonas are dominant phylotypes in clone libraries and culture collections from polar and high-elevation environments. Although Polaromonas has been found on six continents, we do not know if the same phylotypes exist in all locations or if they exhibit genetic isolation by distance patterns. To examine their biogeographic distribution, we analyzed all available, long-read 16S rRNA gene sequences of Polaromonas phylotypes from glacial and periglacial environments across the globe. Using genetic isolation by geographic distance analyses, including Mantel tests and Mantel correlograms, we found that Polaromonas phylotypes are globally distributed showing weak isolation by distance patterns at global scales. More focused analyses using discrete, equally sampled distances classes, revealed that only two distance classes (out of 12 total) showed significant spatial structuring. Overall, our analyses show that most Polaromonas phylotypes are truly globally distributed, but that some, as yet unknown, environmental variable may be selecting for unique phylotypes at a minority of our global sites. Analyses of aerobiological and genomic data suggest that Polaromonas phylotypes are globally distributed as dormant cells through high-elevation air currents; Polaromonas phylotypes are common in air and snow samples from high altitudes, and a glacial-ice metagenome and the two sequenced Polaromonas genomes contain the gene hipA, suggesting that Polaromonas can form dormant cells.
Collapse
Affiliation(s)
- John L. Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Ryan C. Lynch
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Andrew J. King
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Michael S. Robeson
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
| |
Collapse
|
45
|
Schmidt SK, Lynch RC, King AJ, Karki D, Robeson MS, Nagy L, Williams MW, Mitter MS, Freeman KR. Phylogeography of microbial phototrophs in the dry valleys of the high Himalayas and Antarctica. Proc Biol Sci 2010; 278:702-8. [PMID: 20826485 DOI: 10.1098/rspb.2010.1254] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
High-elevation valleys in dry areas of the Himalayas are among the most extreme, yet least explored environments on Earth. These barren, rocky valleys are subjected to year-round temperature fluctuations across the freezing point and very low availability of water and nutrients, causing previous workers to hypothesize that no photoautotrophic life (primary producers) exists in these locations. However, there has been no work using modern biogeochemical or culture-independent molecular methods to test the hypothesis that photoautotrophs are absent from high Himalayan soil systems. Here, we show that although microbial biomass levels are as low as those of the Dry Valleys of Antarctica, there are abundant microbial photoautotrophs, displaying unexpected phylogenetic diversity, in barren soils from just below the permanent ice line of the central Himalayas. Furthermore, we discovered that one of the dominant algal clades from the high Himalayas also contains the dominant algae in culture-independent surveys of both soil and ice samples from the Dry Valleys of Antarctica, revealing an unexpected link between these environmentally similar but geographically very distant systems. Phylogenetic and biogeographic analyses demonstrated that although this algal clade is globally distributed to other high-altitude and high-latitude soils, it shows significant genetic isolation by geographical distance patterns, indicating local adaptation and perhaps speciation in each region. Our results are the first to demonstrate the remarkable similarities of microbial life of arid soils of Antarctica and the high Himalayas. Our findings are a starting point for future comparative studies of the dry valleys of the Himalayas and Antarctica that will yield new insights into the cold and dry limits to life on Earth.
Collapse
Affiliation(s)
- S K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Can zoosporic true fungi grow or survive in extreme or stressful environments? Extremophiles 2010; 14:417-25. [PMID: 20640865 DOI: 10.1007/s00792-010-0323-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 07/05/2010] [Indexed: 10/19/2022]
Abstract
Zoosporic true fungi are thought to be ubiquitous in many ecosystems, especially in cool, moist soils and freshwater habitats which are rich in organic matter. However, some of the habitats where these fungi are found may periodically experience extreme conditions, such as soils in extremely dry, hot and cold climates, acidic and alkaline soils, polluted rivers, anaerobic soil and water, saline soil and water, periglacial soils, oligotrophic soils, tree canopies and hydrothermal vents. It is clear that many ecotypes of zoosporic true fungi have indeed adapted to extreme or stressful environmental conditions. This conclusion is supported by studies in both the field and in the laboratory. Therefore, in our opinion, at least some true zoosporic fungi can be considered to be extremophiles.
Collapse
|
47
|
Evidence that chytrids dominate fungal communities in high-elevation soils. Proc Natl Acad Sci U S A 2009; 106:18315-20. [PMID: 19826082 DOI: 10.1073/pnas.0907303106] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Periglacial soils are one of the least studied ecosystems on Earth, yet they are widespread and are increasing in area due to retreat of glaciers worldwide. Soils in these environments are cold and during the brief summer are exposed to high levels of UV radiation and dramatic fluctuations in moisture and temperature. Recent research suggests that these environments harbor immense microbial diversity. Here we use sequencing of environmental DNA, culturing of isolates, and analysis of environmental variables to show that members of the Chytridiomycota (chytrids) dominate fungal biodiversity and perhaps decomposition processes in plant-free, high-elevation soils from the highest mountain ranges on Earth. The zoosporic reproduction of chytrids requires free water, yet we found that chytrids constituted over 70% of the ribosomal gene sequences of clone libraries from barren soils of the Himalayas and Rockies; by contrast, they are rare in other soil environments. Very few chytrids have been cultured, although we were successful at culturing chytrids from high-elevation sites throughout the world. In a more focused study of our sites in Colorado, we show that carbon sources that support chytrid growth (eolian deposited pollen and microbial phototrophs) are abundant and that soils are saturated with water for several months under the snow, thus creating ideal conditions for the development of a chytrid-dominated ecosystem. Our work broadens the known biodiversity of the Chytridomycota, and describes previously unsuspected links between aquatic and terrestrial ecosystems in alpine regions.
Collapse
|