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Mashamaite L, Lebre PH, Varliero G, Maphosa S, Ortiz M, Hogg ID, Cowan DA. Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient. Front Microbiol 2023; 14:1203216. [PMID: 37555066 PMCID: PMC10406297 DOI: 10.3389/fmicb.2023.1203216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
INTRODUCTION The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica. METHODS We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons. RESULTS AND DISCUSSION Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.
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Affiliation(s)
- Lefentse Mashamaite
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Pedro H. Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Silindile Maphosa
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Max Ortiz
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Clemson University Genomics & Bioinformatics Facility, Clemson University, Clemson, SC, United States
| | - Ian D. Hogg
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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Trexler RV, Van Goethem MW, Goudeau D, Nath N, Malmstrom RR, Northen TR, Couradeau E. BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event. Front Microbiol 2023; 14:1176751. [PMID: 37434715 PMCID: PMC10330726 DOI: 10.3389/fmicb.2023.1176751] [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: 02/28/2023] [Accepted: 06/05/2023] [Indexed: 07/13/2023] Open
Abstract
Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.
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Affiliation(s)
- Ryan V. Trexler
- Intercollege Graduate Degree Program in Ecology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Marc W. Van Goethem
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Danielle Goudeau
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Nandita Nath
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Rex R. Malmstrom
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Trent R. Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
| | - Estelle Couradeau
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, United States
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3
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Yan C, Huang J, Lin X, Wang Y, Cao C, Qian X. Performance of constructed wetlands with different water level for treating graphene oxide wastewater: Characteristics of plants and microorganisms. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 334:117432. [PMID: 36764192 DOI: 10.1016/j.jenvman.2023.117432] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Constructed wetlands (CWs) have been expected advantages in emerging pollutant removal, but with less known on their characteristic when treating wastewater containing graphene oxide (GO). In present study, we investigated characteristics of Iris pseudacorus, microorganisms, and pollutant removal in CWs with 60 cm and 37 cm water level (termed HCW and LCW). Plants in LCW had higher chlorophyll content and lower activities of antioxidant enzyme (superoxide dismutase, catalase, peroxidase) as well as malondialdehyde content. Substrate enzyme activities were affected by time and CW type. LCW increased only dehydrogenase activities, while HCW increased catalase, urease, neutral phosphatase, and arylsulfatase activities. Sequencing analysis revealed that microbial community showed higher richness and diversity in LCW, but this dissimilarity could be eased by time-effect. Proteobacteria (25.62-60.36%) and Actinobacteria (13.86-56.20%) were stable dominant phyla in CWs. Ratio of Proteobacteria/Acidobacteria indicated that trophic status of plant rhizosphere zone was lower in LCW. Nitrospirae were enriched to 0.16-0.68% and 0.75-1.42% in HCW and LCW. The enrichment of phyla Proteobacteria and Firmicutes in HCW was attributed to class Gammaproteobacteria and genus Enterococcus. GO transformation showed some reductions in CWs, which could be affected by water depth and substrate depth. Overall, HCW achieved nitrogen and phosphorus removal for 48.78-62.99% and 95.01%, which decreased by 8.41% and 7.31% in LCW. COD removal was less affected reaching 93%. This study could provide some new evidence for CWs to treat wastewater containing GO.
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Affiliation(s)
- Chunni Yan
- Dept. of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 211189, China
| | - Juan Huang
- Dept. of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 211189, China.
| | - Xiaoyang Lin
- Dept. of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 211189, China
| | - Yaoyao Wang
- Dept. of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 211189, China
| | - Chong Cao
- Department of Municipal Engineering, College of Civil Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Xiuwen Qian
- Dept. of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, 211189, China
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Vimercati L, Bueno de Mesquita CP, Johnson BW, Mineart D, DeForce E, Vimercati Molano Y, Ducklow H, Schmidt SK. Dynamic trophic shifts in bacterial and eukaryotic communities during the first 30 years of microbial succession following retreat of an Antarctic glacier. FEMS Microbiol Ecol 2022; 98:6762214. [PMID: 36251461 DOI: 10.1093/femsec/fiac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 01/21/2023] Open
Abstract
We examined microbial succession along a glacier forefront in the Antarctic Peninsula representing ∼30 years of deglaciation to contrast bacterial and eukaryotic successional dynamics and abiotic drivers of community assembly using sequencing and soil properties. Microbial communities changed most rapidly early along the chronosequence, and co-occurrence network analysis showed the most complex topology at the earliest stage. Initial microbial communities were dominated by microorganisms derived from the glacial environment, whereas later stages hosted a mixed community of taxa associated with soils. Eukaryotes became increasingly dominated by Cercozoa, particularly Vampyrellidae, indicating a previously unappreciated role for cercozoan predators during early stages of primary succession. Chlorophytes and Charophytes (rather than cyanobacteria) were the dominant primary producers and there was a spatio-temporal sequence in which major groups became abundant succeeding from simple ice Chlorophytes to Ochrophytes and Bryophytes. Time since deglaciation and pH were the main abiotic drivers structuring both bacterial and eukaryotic communities. Determinism was the dominant assembly mechanism for Bacteria, while the balance between stochastic/deterministic processes in eukaryotes varied along the distance from the glacier front. This study provides new insights into the unexpected dynamic changes and interactions across multiple trophic groups during primary succession in a rapidly changing polar ecosystem.
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Affiliation(s)
- Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
| | - Clifton P Bueno de Mesquita
- DOE Joint Genome Institute Lawrence Berkeley National Laboratory 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Ben W Johnson
- Department of Geological and Atmospheric Sciences 253 Science Hall 2237 Osborn Drive Ames, Iowa 50011-3212, United States
| | - Dana Mineart
- Department of Geological and Atmospheric Sciences 253 Science Hall 2237 Osborn Drive Ames, Iowa 50011-3212, United States
| | - Emelia DeForce
- Integrative Oceanography Division Scripps Institution of Oceanography 9500 Gilman Drive La Jolla, CA 92093 5, United States
| | - Ylenia Vimercati Molano
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
| | - Hugh Ducklow
- Lamont-Doherty Earth Observatory P.O. Box 1000 61 Route 9W Palisades, NY 10964-1000, United States
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, UCB 334, 1900 Pleasant St, Boulder, CO 80309, United States
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Ji L, Zhang L, Wang Z, Zhu X, Ning K. High biodiversity and distinct assembly patterns of microbial communities in groundwater compared with surface water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155345. [PMID: 35460778 DOI: 10.1016/j.scitotenv.2022.155345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
The differences in bacterial community assembly mechanism between surface water and groundwater, as well as the driving factors of environmental factors, are still unknown. Here we aimed to answer these questions by analyzing microbial community samples from surface water and groundwater. We observed a strong connection between microbial communities in surface water and groundwater and several human pathogens are shared between surface water and groundwater; however, the richness and diversity of groundwater microbial communities were greater than those of surface water, regardless of the season. Additionally, bacterial community compositions of surface water and groundwater differed significantly between seasons. Most importantly, the groundwater community exhibited a highly deterministic assembly process (56% contributed by deterministic process, with neutral community model R2 = 0.277) compared with surface water (51% contributed by deterministic process, with R2 = 0.526). This study provides a deep understanding of the effects of environmental factors on surface water and groundwater microbial communities, to better protect water resources.
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Affiliation(s)
- Lei Ji
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Lu Zhang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi Wang
- Key Laboratory for Environment and Disaster Monitoring and Evaluation of Hubei, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China.
| | - Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
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6
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Doytchinov VV, Dimov SG. Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach. LIFE (BASEL, SWITZERLAND) 2022; 12:life12060916. [PMID: 35743947 PMCID: PMC9228076 DOI: 10.3390/life12060916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.
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Mezzasoma A, Coleine C, Sannino C, Selbmann L. Endolithic Bacterial Diversity in Lichen-Dominated Communities Is Shaped by Sun Exposure in McMurdo Dry Valleys, Antarctica. MICROBIAL ECOLOGY 2022; 83:328-339. [PMID: 34081148 PMCID: PMC8891110 DOI: 10.1007/s00248-021-01769-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
The diversity and composition of endolithic bacterial diversity of several locations in McMurdo Dry Valleys (Continental Antarctica) were explored using amplicon sequencing, targeting the V3 and V4 of the 16S region. Despite the increasing interest in edaphic factors that drive bacterial community composition in Antarctic rocky communities, few researchers focused attention on the direct effects of sun exposure on bacterial diversity; we herein reported significant differences in the northern and southern communities. The analysis of β-diversity showed significant differences among sampled localities. For instance, the most abundant genera found in the north-exposed rocks were Rhodococcus and Blastococcus in Knobhead Mt.; Ktedonobacter and Cyanobacteria Family I Group I in Finger Mt.; Rhodococcus and Endobacter in University Valley; and Segetibacter and Tetrasphaera in Siegfried Peak samples. In south-exposed rocks, instead, the most abundant genera were Escherichia/Shigella and Streptococcus in Knobhead Mt.; Ktedonobacter and Rhodococcus in Finger Mt.; Ktedonobacter and Roseomonas in University Valley; and Blastocatella, Cyanobacteria Family I Group I and Segetibacter in Siegfried Peak. Significant biomarkers, detected by the Linear discriminant analysis Effect Size, were also found among north- and south-exposed communities. Besides, the large number of positive significant co-occurrences may suggest a crucial role of positive associations over competitions under the harsher conditions where these rock-inhabiting microorganisms spread. Although the effect of geographic distances in these extreme environments play a significant role in shaping biodiversity, the study of an edaphic factor, such as solar exposure, adds an important contribution to the mosaic of microbial biodiversity of Antarctic bacterial cryptoendolithic communities.
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Affiliation(s)
- Ambra Mezzasoma
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
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Monteiro MR, Marshall AJ, Hawes I, Lee CK, McDonald IR, Cary SC. Geochemically Defined Space-for-Time Transects Successfully Capture Microbial Dynamics Along Lacustrine Chronosequences in a Polar Desert. Front Microbiol 2022; 12:783767. [PMID: 35173689 PMCID: PMC8841834 DOI: 10.3389/fmicb.2021.783767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/15/2021] [Indexed: 11/15/2022] Open
Abstract
The space-for-time substitution approach provides a valuable empirical assessment to infer temporal effects of disturbance from spatial gradients. Applied to predict the response of different ecosystems under current climate change scenarios, it remains poorly tested in microbial ecology studies, partly due to the trophic complexity of the ecosystems typically studied. The McMurdo Dry Valleys (MDV) of Antarctica represent a trophically simple polar desert projected to experience drastic changes in water availability under current climate change scenarios. We used this ideal model system to develop and validate a microbial space-for-time sampling approach, using the variation of geochemical profiles that follow alterations in water availability and reflect past changes in the system. Our framework measured soil electrical conductivity, pH, and water activity in situ to geochemically define 17 space-for-time transects from the shores of four dynamic and two static Dry Valley lakes. We identified microbial taxa that are consistently responsive to changes in wetness in the soils and reliably associated with long-term dry or wet edaphic conditions. Comparisons between transects defined at static (open-basin) and dynamic (closed-basin) lakes highlighted the capacity for geochemically defined space-for-time gradients to identify lasting deterministic impacts of historical changes in water presence on the structure and diversity of extant microbial communities. We highlight the potential for geochemically defined space-for-time transects to resolve legacy impacts of environmental change when used in conjunction with static and dynamic scenarios, and to inform future environmental scenarios through changes in the microbial community structure, composition, and diversity.
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Affiliation(s)
- Maria R. Monteiro
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Alexis J. Marshall
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Ian Hawes
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Charles K. Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Ian R. McDonald
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
| | - Stephen Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- Te Aka Matuatua—School of Science, University of Waikato, Hamilton, New Zealand
- *Correspondence: Stephen Craig Cary,
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González-Pleiter M, Velázquez D, Casero MC, Tytgat B, Verleyen E, Leganés F, Rosal R, Quesada A, Fernández-Piñas F. Microbial colonizers of microplastics in an Arctic freshwater lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 795:148640. [PMID: 34246139 DOI: 10.1016/j.scitotenv.2021.148640] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/03/2021] [Accepted: 06/20/2021] [Indexed: 05/12/2023]
Abstract
Microplastics (MPs) have been found everywhere as they are easily transported between environmental compartments. Through their transport, MPs are quickly colonized by microorganisms; this microbial community is known as the plastisphere. Here, we characterized the plastisphere of three MPs, one biodegradable (PHB) and two non-biodegradables (HDPE and LDPE), deployed in an Arctic freshwater lake for eleven days. The plastisphere was found to be complex, confirming that about a third of microbial colonizers were viable. Plastisphere was compared to microbial communities on the surrounding water and microbial mats on rocks at the bottom of the lake. Microbial mats followed by MPs showed the highest diversity regarding both prokaryotes and eukaryotes as compared to water samples; however, for fungi, MPs showed the highest diversity of the tested substrates. Significant differences on microbial assemblages on the three tested substrates were found; regarding microbial assemblages on MPs, bacterial genera found in polar environments such as Mycoplana, Erythromicrobium and Rhodoferax with species able to metabolize recalcitrant chemicals were abundant. Eukaryotic communities on MPs were characterized by the presence of ciliates of the genera Stentor, Vorticella and Uroleptus and the algae Cryptomonas, Chlamydomonas, Tetraselmis and Epipyxis. These ciliates normally feed on algae so that the complexity of these assemblages may serve to unravel trophic relationships between co-existing taxa. Regarding fungal communities on MPs, the most abundant genera were Betamyces, Cryptococcus, Arrhenia and Paranamyces. MPs, particularly HDPE, were enriched in the sulI and ermB antibiotic resistance genes (ARGs) which may raise concerns about human health-related issues as ARGs may be transferred horizontally between bacteria. This study highlights the importance of proper waste management and clean-up protocols to protect the environmental health of pristine environments such as polar regions in a context of global dissemination of MPs which may co-transport microorganisms, some of them including ARGs.
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Affiliation(s)
- Miguel González-Pleiter
- Departamento de Biología, Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
| | - David Velázquez
- Departamento de Biología, Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
| | - María Cristina Casero
- Departamento de Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales, CSIC, E-28006 Madrid, Spain
| | - Bjorn Tytgat
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Krijgslaan 281-S8, 9000 Gent, Belgium
| | - Elie Verleyen
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Krijgslaan 281-S8, 9000 Gent, Belgium
| | - Francisco Leganés
- Departamento de Biología, Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
| | - Roberto Rosal
- Department of Chemical Engineering, University of Alcalá, E-28871 Alcalá de Henares, Madrid, Spain
| | - Antonio Quesada
- Departamento de Biología, Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
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Phagotrophic protists (protozoa) in Antarctic terrestrial ecosystems: diversity, distribution, ecology, and best research practices. Polar Biol 2021. [DOI: 10.1007/s00300-021-02896-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractPhagotrophic protists (formerly protozoa) are a highly diverse, polyphyletic grouping of generally unicellular, heterotrophic eukaryotes that are key regulators of the soil microbiome. The biodiversity and ecology of soil phagotrophic protists are still largely uncharacterized, especially in the Antarctic, which possesses some of the harshest terrestrial environments known and potentially many physiologically unique and scientifically interesting species. Antarctic soil systems are also highly limited in terms of moisture, temperature, and carbon, and the resulting reduced biological complexity can facilitate fine-tuned investigation of the drivers and functioning of microbial communities. To facilitate and encourage future research into protist biodiversity and ecology, especially in context of the broader functioning of Antarctic terrestrial communities, I review the biodiversity, distribution, and ecology of Antarctic soil phagotrophic protists. Biodiversity appears to be highly structured by region and taxonomic group, with the Antarctic Peninsula having the highest taxonomic diversity and ciliates (Ciliophora) being the most diverse taxonomic group. However, richness estimates are likely skewed by disproportionate sampling (over half of the studies are from the peninsula), habitat type bias (predominately moss-associated soils), investigator bias (toward ciliates and the testate amoeba morphogroup), and methodological approach (toward cultivation and morphological identification). To remedy these biases, a standardized methodology using both morphological and molecular identification and increased emphasis on microflagellate and naked amoeba morphogroups is needed. Additionally, future research should transition away from biodiversity survey studies to dedicated ecological studies that emphasize the function, ecophysiology, endemicity, dispersal, and impact of abiotic drivers beyond moisture and temperature.
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11
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Fernández-Martínez MÁ, García-Villadangos M, Moreno-Paz M, Gangloff V, Carrizo D, Blanco Y, González S, Sánchez-García L, Prieto-Ballesteros O, Altshuler I, Whyte LG, Parro V, Fairén AG. Geomicrobiological Heterogeneity of Lithic Habitats in the Extreme Environment of Antarctic Nunataks: A Potential Early Mars Analog. Front Microbiol 2021; 12:670982. [PMID: 34276605 PMCID: PMC8284421 DOI: 10.3389/fmicb.2021.670982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
Nunataks are permanent ice-free rocky peaks that project above ice caps in polar regions, thus being exposed to extreme climatic conditions throughout the year. They undergo extremely low temperatures and scarcity of liquid water in winter, while receiving high incident and reflected (albedo) UVA-B radiation in summer. Here, we investigate the geomicrobiology of the permanently exposed lithic substrates of nunataks from Livingston Island (South Shetlands, Antarctic Peninsula), with focus on prokaryotic community structure and their main metabolic traits. Contrarily to first hypothesis, an extensive sampling based on different gradients and multianalytical approaches demonstrated significant differences for most geomicrobiological parameters between the bedrock, soil, and loose rock substrates, which overlapped any other regional variation. Brevibacillus genus dominated on bedrock and soil substrates, while loose rocks contained a diverse microbial community, including Actinobacteria, Alphaproteobacteria and abundant Cyanobacteria inhabiting the milder and diverse microhabitats within. Archaea, a domain never described before in similar Antarctic environments, were also consistently found in the three substrates, but being more abundant and potentially more active in soils. Stable isotopic ratios of total carbon (δ 13C) and nitrogen (δ 15N), soluble anions concentrations, and the detection of proteins involved in key metabolisms via the Life Detector Chip (LDChip), suggest that microbial primary production has a pivotal role in nutrient cycling at these exposed areas with limited deposition of nutrients. Detection of stress-resistance proteins, such as molecular chaperons, suggests microbial molecular adaptation mechanisms to cope with these harsh conditions. Since early Mars may have encompassed analogous environmental conditions as the ones found in these Antarctic nunataks, our study also contributes to the understanding of the metabolic features and biomarker profiles of a potential Martian microbiota, as well as the use of LDChip in future life detection missions.
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Affiliation(s)
- Miguel Ángel Fernández-Martínez
- Centro de Astrobiología, CSIC-INTA, Madrid, Spain.,Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | | | | | | | | | | | - Sergi González
- Antarctic Group, Agencia Estatal de Meteorología, Barcelona, Spain
| | | | | | - Ianina Altshuler
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Victor Parro
- Centro de Astrobiología, CSIC-INTA, Madrid, Spain
| | - Alberto G Fairén
- Centro de Astrobiología, CSIC-INTA, Madrid, Spain.,Department of Astronomy, Cornell University, Ithaca, NY, United States
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12
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Solon AJ, Mastrangelo C, Vimercati L, Sommers P, Darcy JL, Gendron EMS, Porazinska DL, Schmidt SK. Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, Antarctica. Front Microbiol 2021; 12:654135. [PMID: 34177836 PMCID: PMC8222675 DOI: 10.3389/fmicb.2021.654135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
Cold, dry, and nutrient-poor, the McMurdo Dry Valleys of Antarctica are among the most extreme terrestrial environments on Earth. Numerous studies have described microbial communities of low elevation soils and streams below glaciers, while less is known about microbial communities in higher elevation soils above glaciers. We characterized microbial life in four landscape features (habitats) of a mountain in Taylor Valley. These habitats varied significantly in soil moisture and include moist soils of a (1) lateral glacial moraine, (2) gully that terminates at the moraine, and very dry soils on (3) a southeastern slope and (4) dry sites near the gully. Using rRNA gene PCR amplicon sequencing of Bacteria and Archaea (16S SSU) and eukaryotes (18S SSU), we found that all habitat types harbored significantly different bacterial and eukaryotic communities and that these differences were most apparent when comparing habitats that had macroscopically visible soil crusts (gully and moraine) to habitats with no visible crusts (near gully and slope). These differences were driven by a relative predominance of Actinobacteria and a Colpodella sp. in non-crust habitats, and by phototrophic bacteria and eukaryotes (e.g., a moss) and predators (e.g., tardigrades) in habitats with biological soil crusts (gully and moraine). The gully and moraine also had significantly higher 16S and 18S ESV richness than the other two habitat types. We further found that many of the phototrophic bacteria and eukaryotes of the gully and moraine share high sequence identity with phototrophs from moist and wet areas elsewhere in the Dry Valleys and other cold desert ecosystems. These include a Moss (Bryum sp.), several algae (e.g., a Chlorococcum sp.) and cyanobacteria (e.g., Nostoc and Phormidium spp.). Overall, the results reported here broaden the diversity of habitat types that have been studied in the Dry Valleys of Antarctica and suggest future avenues of research to more definitively understand the biogeography and factors controlling microbial diversity in this unique ecosystem.
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Affiliation(s)
- Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Claire Mastrangelo
- School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado-Anschutz Medical Campus, Denver, CO, United States
| | - Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - S K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
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13
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George SF, Fierer N, Levy JS, Adams B. Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity. Front Microbiol 2021; 12:616730. [PMID: 33584618 PMCID: PMC7873294 DOI: 10.3389/fmicb.2021.616730] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 11/19/2022] Open
Abstract
Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.
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Affiliation(s)
- Scott F George
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States
| | - Joseph S Levy
- Department of Geology, Colgate University, Hamilton, NY, United States
| | - Byron Adams
- Department of Biology, Brigham Young University, Provo, UT, United States.,Monte L. Bean Museum, Brigham Young University, Provo, UT, United States
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14
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Bottos EM, Laughlin DC, Herbold CW, Lee CK, McDonald IR, Cary SC. Abiotic factors influence patterns of bacterial diversity and community composition in the Dry Valleys of Antarctica. FEMS Microbiol Ecol 2020; 96:5815075. [PMID: 32239205 DOI: 10.1093/femsec/fiaa042] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 03/23/2020] [Indexed: 11/13/2022] Open
Abstract
The Dry Valleys of Antarctica are a unique ecosystem of simple trophic structure, where the abiotic factors that influence soil bacterial communities can be resolved in the absence of extensive biotic interactions. This study evaluated the degree to which aspects of topographic, physicochemical and spatial variation explain patterns of bacterial richness and community composition in 471 soil samples collected across a 220 square kilometer landscape in Southern Victoria Land. Richness was most strongly influenced by physicochemical soil properties, particularly soil conductivity, though significant trends with several topographic and spatial variables were also observed. Structural equation modeling (SEM) supported a final model in which variation in community composition was best explained by physicochemical variables, particularly soil water content, and where the effects of topographic variation were largely mediated through their influence on physicochemical variables. Community dissimilarity increased with distance between samples, and though most of this variation was explained by topographic and physicochemical variation, a small but significant relationship remained after controlling for this environmental variation. As the largest survey of terrestrial bacterial communities of Antarctica completed to date, this work provides fundamental knowledge of the Dry Valleys ecosystem, and has implications globally for understanding environmental factors that influence bacterial distributions.
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Affiliation(s)
- Eric M Bottos
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Daniel C Laughlin
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Craig W Herbold
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Charles K Lee
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Ian R McDonald
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - S Craig Cary
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
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15
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Coyne KJ, Parker AE, Lee CK, Sohm JA, Kalmbach A, Gunderson T, León-Zayas R, Capone DG, Carpenter EJ, Cary SC. The distribution and relative ecological roles of autotrophic and heterotrophic diazotrophs in the McMurdo Dry Valleys, Antarctica. FEMS Microbiol Ecol 2020; 96:5714082. [PMID: 31967635 PMCID: PMC7043275 DOI: 10.1093/femsec/fiaa010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
The McMurdo Dry Valleys (MDV) in Antarctica harbor a diverse assemblage of mat-forming diazotrophic cyanobacteria that play a key role in nitrogen cycling. Prior research showed that heterotrophic diazotrophs also make a substantial contribution to nitrogen fixation in MDV. The goals of this study were to survey autotrophic and heterotrophic diazotrophs across the MDV to investigate factors that regulate the distribution and relative ecological roles of each group. Results indicated that diazotrophs were present only in samples with mats, suggesting a metabolic coupling between autotrophic and heterotrophic diazotrophs. Analysis of 16S rRNA and nifH gene sequences also showed that diazotrophs were significantly correlated to the broader bacterial community, while co-occurrence network analysis revealed potential interspecific interactions. Consistent with previous studies, heterotrophic diazotrophs in MDV were diverse, but largely limited to lakes and their outlet streams, or other environments protected from desiccation. Despite the limited distribution, heterotrophic diazotrophs may make a substantial contribution to the nitrogen budget of MDV due to larger surface area and longer residence times of lakes. This work contributes to our understanding of key drivers of bacterial community structure in polar deserts and informs future efforts to investigate the contribution of nitrogen fixation to MDV ecosystems.
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Affiliation(s)
- Kathryn J Coyne
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA
| | - Alexander E Parker
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton 3240, New Zealand
| | - Jill A Sohm
- Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Andrew Kalmbach
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - Troy Gunderson
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Rosa León-Zayas
- Willamette University, Biology Department, Salem, OR 97301, USA
| | - Douglas G Capone
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 9008-037, USA
| | - Edward J Carpenter
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA 94920, USA
| | - S Craig Cary
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE 19958, USA.,International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton 3240, New Zealand
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16
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Sohm JA, Niederberger TD, Parker AE, Tirindelli J, Gunderson T, Cary SC, Capone DG, Carpenter EJ. Microbial Mats of the McMurdo Dry Valleys, Antarctica: Oases of Biological Activity in a Very Cold Desert. Front Microbiol 2020; 11:537960. [PMID: 33193125 PMCID: PMC7654227 DOI: 10.3389/fmicb.2020.537960] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/28/2020] [Indexed: 11/29/2022] Open
Abstract
Cyanobacterial mats in the Antarctic Dry Valleys are photosynthetic microbial ecosystems living at the extreme of conditions on Earth with respect to temperature, light, water and nutrient availability. They are metabolically active for about 8 weeks during the austral summer when temperatures briefly rise above freezing and glacial and lake melt waters are available. There is much to learn about the biogeochemical impact of mats in these environments and the microbial communities associated with them. Our data demonstrate that these mats attain surprisingly high rates of carbon (CO2) and dinitrogen (N2) fixation when liquid water is available, in some cases comparable to rates in warmer temperate or tropical environments. C and N2 fixation in Dry Valley mats in turn substantially elevate dissolved organic C and inorganic N pools and thereby promote enhanced microbial secondary production. Moreover, the microbial community fingerprint of these mats is unique compared with the more ubiquitous dry soils that do not contain mats. Components of the heterotrophic microbiota may also contribute substantially to N inputs through N2 fixation.
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Affiliation(s)
- Jill A Sohm
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, United States.,Environmental Studies Program, University of Southern California, Los Angeles, CA, United States
| | - Thomas D Niederberger
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
| | - Alexander E Parker
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA, United States.,Department of Sciences and Mathematics, California State University Maritime Academy, Vallejo, CA, United States
| | - Joëlle Tirindelli
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA, United States
| | - Troy Gunderson
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, United States
| | - Stephen Craig Cary
- College of Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Douglas G Capone
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, United States
| | - Edward J Carpenter
- Estuary and Ocean Science Center, San Francisco State University, Tiburon, CA, United States
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17
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Rodriguez R, Durán P. Natural Holobiome Engineering by Using Native Extreme Microbiome to Counteract the Climate Change Effects. Front Bioeng Biotechnol 2020; 8:568. [PMID: 32582678 PMCID: PMC7287022 DOI: 10.3389/fbioe.2020.00568] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/11/2020] [Indexed: 12/14/2022] Open
Abstract
In the current scenario of climate change, the future of agriculture is uncertain. Climate change and climate-related disasters have a direct impact on biotic and abiotic factors that govern agroecosystems compromising the global food security. In the last decade, the advances in high throughput sequencing techniques have significantly improved our understanding about the composition, function and dynamics of plant microbiome. However, despite the microbiome have been proposed as a new platform for the next green revolution, our knowledge about the mechanisms that govern microbe-microbe and microbe-plant interactions are incipient. Currently, the adaptation of plants to environmental changes not only suggests that the plants can adapt or migrate, but also can interact with their surrounding microbial communities to alleviate different stresses by natural microbiome selection of specialized strains, phenomenon recently called "Cry for Help". From this way, plants have been co-evolved with their microbiota adapting to local environmental conditions to ensuring the survival of the entire holobiome to improve plant fitness. Thus, the strong selective pressure of native extreme microbiomes could represent a remarkable microbial niche of plant stress-amelioration to counteract the negative effect of climate change in food crops. Currently, the microbiome engineering has recently emerged as an alternative to modify and promote positive interactions between microorganisms and plants to improve plant fitness. In the present review, we discuss the possible use of extreme microbiome to alleviate different stresses in crop plants under the current scenario of climate change.
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Affiliation(s)
- Rodrigo Rodriguez
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
| | - Paola Durán
- Biocontrol Research Laboratory, Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
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18
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Barnard S, Van Goethem MW, de Scally SZ, Cowan DA, van Rensburg PJ, Claassens S, Makhalanyane TP. Increased temperatures alter viable microbial biomass, ammonia oxidizing bacteria and extracellular enzymatic activities in Antarctic soils. FEMS Microbiol Ecol 2020; 96:5818763. [DOI: 10.1093/femsec/fiaa065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/03/2020] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT
The effects of temperature on microorganisms in high latitude regions, and their possible feedbacks in response to change, are unclear. Here, we assess microbial functionality and composition in response to a substantial temperature change. Total soil biomass, amoA gene sequencing, extracellular activity assays and soil physicochemistry were measured to assess a warming scenario. Soil warming to 15°C for 30 days triggered a significant decrease in microbial biomass compared to baseline soils (0°C; P < 0.05) after incubations had induced an initial increase. These changes coincided with increases in extracellular enzymatic activity for peptide hydrolysis and phenolic oxidation at higher temperatures, but not for the degradation of carbon substrates. Shifts in ammonia-oxidising bacteria (AOB) community composition related most significantly to changes in soil carbon content (P < 0.05), which gradually increased in microcosms exposed to a persistently elevated temperature relative to baseline incubations, while temperature did not influence AOBs. The concentration of soil ammonium (NH4+) decreased significantly at higher temperatures subsequent to an initial increase, possibly due to higher conversion rates of NH4+ to nitrate by nitrifying bacteria. We show that higher soil temperatures may reduce viable microbial biomass in cold environments but stimulate their activity over a short period.
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Affiliation(s)
- Sebastian Barnard
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Marc W Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Storme Z de Scally
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
| | - Peet Jansen van Rensburg
- Focus Area Human Metabolomics, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Sarina Claassens
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Natural Sciences 2 Building, University of Pretoria, Pretoria, 0028, South Africa
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19
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Understanding the Response of Nitrifying Communities to Disturbance in the McMurdo Dry Valleys, Antarctica. Microorganisms 2020; 8:microorganisms8030404. [PMID: 32183078 PMCID: PMC7143839 DOI: 10.3390/microorganisms8030404] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 01/07/2023] Open
Abstract
Polar ecosystems are generally limited in nitrogen (N) nutrients, and the patchy availability of N is partly determined by biological pathways, such as nitrification, which are carried out by distinctive prokaryotic functional groups. The activity and diversity of microorganisms are generally strongly influenced by environmental conditions. However, we know little of the attributes that control the distribution and activity of specific microbial functional groups, such as nitrifiers, in extreme cold environments and how they may respond to change. To ascertain relationships between soil geochemistry and the ecology of nitrifying microbial communities, we carried out a laboratory-based manipulative experiment to test the selective effect of key geochemical variables on the activity and abundance of ammonia-oxidizing communities in soils from the McMurdo Dry Valleys of Antarctica. We hypothesized that nitrifying communities, adapted to different environmental conditions within the Dry Valleys, will have distinct responses when submitted to similar geochemical disturbances. In order to test this hypothesis, soils from two geographically distant and geochemically divergent locations, Miers and Beacon Valleys, were incubated over 2 months under increased conductivity, ammonia concentration, copper concentration, and organic matter content. Amplicon sequencing of the 16S rRNA gene and transcripts allowed comparison of the response of ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) to each treatment over time. This approach was combined with measurements of 15NH4+ oxidation rates using 15N isotopic additions. Our results showed a higher potential for nitrification in Miers Valley, where environmental conditions are milder relative to Beacon Valley. AOA exhibited better adaptability to geochemical changes compared to AOB, particularly to the increase in copper and conductivity. AOA were also the only nitrifying group found in Beacon Valley soils. This laboratorial manipulative experiment provided new knowledge on how nitrifying groups respond to changes on key geochemical variables of Antarctic desert soils, and we believe these results offer new insights on the dynamics of N cycling in these ecosystems.
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20
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Staebe K, Meiklejohn KI, Singh SM, Matcher GF. Biogeography of soil bacterial populations in the Jutulsessen and Ahlmannryggen of Western Dronning Maud Land, Antarctica. Polar Biol 2019. [DOI: 10.1007/s00300-019-02532-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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21
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Chan-Yam K, Goordial J, Greer C, Davila A, McKay CP, Whyte LG. Microbial Activity and Habitability of an Antarctic Dry Valley Water Track. ASTROBIOLOGY 2019; 19:757-770. [PMID: 30958705 DOI: 10.1089/ast.2018.1884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Water tracks in the Antarctic Dry Valleys are dark linear features of increased soil moisture that flow downslope over the spring and summer, providing a source of moisture in a cold-arid desert. They are typically sourced from melting snow, ground ice, and deliquescence (Levy et al., 2011 ). This research presents the first in-depth study of the activity potential and diversity of microbial communities of Antarctic water tracks. We investigated whether these water track soils are more habitable to microbial communities by ascertaining the differences in diversity, total and culturable cell counts, and microbial respiratory activity in water track soils compared with the adjacent dry soils in Pearse Valley. Total cell counts ranged from 1.47 × 103 to 4.17 × 105 cells/g dry weight soil. Water track soils had higher total and culturable biomass, in addition to higher microbial activity at 5° and -5°C, compared with adjacent dry soils. Microbial respiration was positively correlated with soil moisture content, but total cell counts and plate counts were not. Surprisingly, microbial community composition did not differ between wet and dry soil communities, and was not related to soil moisture content. The microbial community composition instead appeared to differ spatially based on location and depth. Overall, the data suggest that cold water tracks are more habitable than the surrounding cold-arid soils. Our results suggest that recurring slope lineae, which are dark linear features that grow downslope on Mars over the spring and summer, where liquid water might be a recurring phenomenon, could be sites of astrobiological potential.
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Affiliation(s)
- Kelly Chan-Yam
- 1 Department of Natural Resource Sciences, McGill University, Montreal, Canada
| | - Jacqueline Goordial
- 1 Department of Natural Resource Sciences, McGill University, Montreal, Canada
- 2 Bigelow Laboratory for Ocean Sciences, East Boothbay Harbor, Maine
| | - Charles Greer
- 3 National Research Council of Canada, Montreal, Canada
| | | | | | - Lyle G Whyte
- 1 Department of Natural Resource Sciences, McGill University, Montreal, Canada
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22
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Niederberger TD, Bottos EM, Sohm JA, Gunderson T, Parker A, Coyne KJ, Capone DG, Carpenter EJ, Cary SC. Rapid Microbial Dynamics in Response to an Induced Wetting Event in Antarctic Dry Valley Soils. Front Microbiol 2019; 10:621. [PMID: 31019494 PMCID: PMC6458288 DOI: 10.3389/fmicb.2019.00621] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/12/2019] [Indexed: 11/13/2022] Open
Abstract
The cold deserts of the McMurdo Dry Valleys (MDV), Antarctica, host a high level of microbial diversity. Microbial composition and biomass in arid vs. ephemerally wetted regions are distinctly different, with wetted communities representing hot spots of microbial activity that are important zones for biogeochemical cycling. While climatic change is likely to cause wetting in areas not historically subject to wetting events, the responses of microorganisms inhabiting arid soils to water addition is unknown. The purpose of this study was to observe how an associated, yet non-wetted microbial community responds to an extended addition of water. Water from a stream was diverted to an adjacent area of arid soil with changes in microbial composition and activities monitored via molecular and biochemical methods over 7 weeks. The frequency of genetic signatures related to both prokaryotic and eukaryotic organisms adapted to MDV aquatic conditions increased during the limited 7 week period, indicating that the soil community was transitioning into a typical "high-productivity" MDV community. This work is consistent with current predictions that MDV microbial communities in arid regions are highly sensitive to climate change, and further supports the notion that changes in community structure and associated biogeochemical cycling may occur much more rapidly than predicted.
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Affiliation(s)
- Thomas D Niederberger
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
| | - Eric M Bottos
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton, New Zealand.,Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Jill A Sohm
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Troy Gunderson
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Alex Parker
- Romberg Tiburon Center, San Francisco State University, Tiburon, CA, United States
| | - Kathryn J Coyne
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
| | - Douglas G Capone
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Edward J Carpenter
- Romberg Tiburon Center, San Francisco State University, Tiburon, CA, United States
| | - Stephen Craig Cary
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States.,International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton, New Zealand
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23
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Zhao H, Li X, Zhang Z, Zhao Y, Chen P, Zhu Y. Drivers and assemblies of soil eukaryotic microbes among different soil habitat types in a semi-arid mountain in China. PeerJ 2018; 6:e6042. [PMID: 30568857 PMCID: PMC6286657 DOI: 10.7717/peerj.6042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/30/2018] [Indexed: 11/30/2022] Open
Abstract
The effects of environmental and species structure on soil eukaryotic microbes inhabiting semi-arid mountains remain unclear. Furthermore, whether community assembly differs in a variety of soil habitat types, for example, artificial forest, artificial bush, farmland, and natural grassland, is not well understood. Here, we explored species diversity and composition of soil eukaryotic microbes south of the Taihang Mountains (mid-western region of China) using Illumina sequencing of the 18S rRNA gene (V4) region on the MiSeq platform. The results suggest that the forest soil habitat type improved the diversity and abundance of soil eukaryotic microbes that will benefit the restoration of degraded soil. The SAR (Stramenopiles, Alveolates, Rhizaria) supergroup and Metazoa were the dominant soil eukaryotic microbial groups at the phylum level. About 26% of all operational taxonomic units were common among the different soil habitat types. The O-elements, water content, soil organic matter, and elevation significantly influenced the abundance of soil eukaryote communities (P < 0.05). Our findings provide some reference for the effectiveness of local ecological restoration and the establishment of a soil eukaryotic microbe resource databases in a semi-arid area.
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Affiliation(s)
- He Zhao
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Xuanzhen Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Zhiming Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yong Zhao
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Peng Chen
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yiwei Zhu
- College of Forestry, Henan Agricultural University, Zhengzhou, China
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24
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Lee KC, Caruso T, Archer SD, Gillman LN, Lau MC, Cary SC, Lee CK, Pointing SB. Stochastic and Deterministic Effects of a Moisture Gradient on Soil Microbial Communities in the McMurdo Dry Valleys of Antarctica. Front Microbiol 2018; 9:2619. [PMID: 30450087 PMCID: PMC6225844 DOI: 10.3389/fmicb.2018.02619] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/12/2018] [Indexed: 11/13/2022] Open
Abstract
Antarctic soil supports surface microbial communities that are dependent on ephemeral moisture. Understanding the response to availability of this resource is essential to predicting how the system will respond to climate change. The McMurdo Dry Valleys are the largest ice-free soil region in Antarctica. They are a hyper-arid polar desert with extremely limited moisture availability. Microbial colonization dominates this ecosystem but surprisingly little is known about how communities respond to changing moisture regimes. We utilized the natural model system provided by transiently wetted soil at lake margins in the Dry Valleys to interrogate microbial responses along a well-defined contiguous moisture gradient and disentangle responses between and within phyla. We identified a striking non-linear response among bacteria where at low moisture levels small changes resulted in a large impact on diversity. At higher moister levels community responses were less pronounced, resulting in diversity asymptotes. We postulate that whilst the main drivers of observed community diversity were deterministic, a switch in the major influence occurred from abiotic factors at low moisture levels to biotic interactions at higher moisture. Response between and within phyla was markedly different, highlighting the importance of taxonomic resolution in community analysis. Furthermore, we resolved apparent stochasticity at high taxonomic ranks as the result of deterministic interactions taking place at finer taxonomic and spatial scales. Overall the findings provide new insight on the response to moisture and this will be useful in advancing understanding of potential ecosystem responses in the threatened McMurdo Dry Valleys system.
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Affiliation(s)
- Kevin C. Lee
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Tancredi Caruso
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Stephen D.J. Archer
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Len N. Gillman
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Maggie C.Y. Lau
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - S. Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Charles K. Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Stephen B. Pointing
- Yale-NUS College, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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25
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Feeser KL, Van Horn DJ, Buelow HN, Colman DR, McHugh TA, Okie JG, Schwartz E, Takacs-Vesbach CD. Local and Regional Scale Heterogeneity Drive Bacterial Community Diversity and Composition in a Polar Desert. Front Microbiol 2018; 9:1928. [PMID: 30186257 PMCID: PMC6110917 DOI: 10.3389/fmicb.2018.01928] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/30/2018] [Indexed: 02/01/2023] Open
Abstract
The distribution of organisms in an environment is neither uniform nor random but is instead spatially patterned. The factors that control this patterning are complex and the underlying mechanisms are poorly understood. Soil microbes are critical to ecosystem function but exhibit highly complex distributions and community dynamics due in large part to the scale-dependent effects of environmental heterogeneity. To better understand the impact of environmental heterogeneity on the distribution of soil microbes, we sequenced the 16S rRNA gene from bacterial communities in the microbe-dominated polar desert ecosystem of the McMurdo Dry Valleys (MDV), Antarctica. Significant differences in key edaphic variables and alpha diversity were observed among the three lake basins of the Taylor Valley (Kruskal-Wallis; pH: χ2 = 68.89, P < 0.001, conductivity: χ2 = 35.03, P < 0.001, observed species: χ2 = 7.98, P = 0.019 and inverse Simpson: χ2 = 18.52, P < 0.001) and each basin supported distinctive microbial communities (ANOSIM R = 0.466, P = 0.001, random forest ratio of 14.1). However, relationships between community structure and edaphic characteristics were highly variable and contextual, ranging in magnitude and direction across regional, basin, and local scales. Correlations among edaphic factors (pH and soil conductivity) and the relative abundance of specific phyla were most pronounced along local environmental gradients in the Lake Fryxell basin where Acidobacteria, Bacteroidetes, and Proteobacteria declined while Deinococcus-Thermus and Gemmatimonadetes increased with soil conductivity (all P < 0.1). Species richness was most strongly related to the soil conductivity gradient present within this study system. We suggest that the relative importance of pH versus soil conductivity in structuring microbial communities is related to the length of edaphic gradients and the spatial scale of sampling. These results highlight the importance of conducting studies over large ranges of key environmental gradients and across multiple spatial scales to assess the influence of environmental heterogeneity on the composition and diversity of microbial communities.
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Affiliation(s)
- Kelli L. Feeser
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - David J. Van Horn
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Heather N. Buelow
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Daniel R. Colman
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Theresa A. McHugh
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO, United States
| | - Jordan G. Okie
- School of Life Sciences, School of Earth and Space Exploration, Arizona State University, Tempe, AZ, United States
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States
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26
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Andriuzzi WS, Stanish LF, Simmons BL, Jaros C, Adams BJ, Wall DH, McKnight DM. Spatial and temporal patterns of microbial mats and associated invertebrates along an Antarctic stream. Polar Biol 2018. [DOI: 10.1007/s00300-018-2331-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Ni N, Shi R, Liu Z, Bian Y, Wang F, Song Y, Jiang X. Effects of biochars on the bioaccessibility of phenanthrene/pyrene/zinc/lead and microbial community structure in a soil under aerobic and anaerobic conditions. J Environ Sci (China) 2018; 63:296-306. [PMID: 29406113 DOI: 10.1016/j.jes.2017.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/22/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
The immobilization of co-contaminants of organic and inorganic pollutants by biochar is an efficient remediation strategy. However, the effect of biochar amendments on the bioaccessibility of the co-contaminants in dry versus flooded soils has rarely been compared. In batch experiments, bamboo-derived biochar (BB) had a higher sorption capacity for phenanthrene (Phe)/pyrene (Pyr)/zinc (Zn) than corn straw-derived biochar (CB), while CB had a higher sorption capacity for lead (Pb) than BB. After 150days of incubation, the amendments of 2% CB, 0.5% BB and 2% BB effectively suppressed the dissipation and reduced the bioaccessibility of Phe/Pyr by 15.65%/18.02%, 17.07%/18.31% and 25.43%/27.11%, respectively, in the aerobic soils. This effectiveness was more significant than that in the anaerobic soils. The accessible Zn/Pb concentrations were also significantly lower in the aerobic soils than in the anaerobic soils, regardless of treatments. The Gram-negative bacterial biomass and the Shannon-Weaver index in the aerobic soil amended with 2% CB were the highest. The soil microbial community structure was jointly affected by changes in the bioaccessibility of the co-contaminants and the soil physiochemical properties caused by biochar amendments under the two conditions. Therefore, dry land farming may be more reliable than paddy soil cultivation at reducing the bioaccessibility of Phe/Pyr/Zn/Pb and enhancing the soil microbial diversity in the short term.
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Affiliation(s)
- Ni Ni
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Renyong Shi
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zongtang Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Yancheng Teachers University, Yancheng, Jiangsu 224051, China
| | - Yongrong Bian
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Fang Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yang Song
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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28
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Higuera-Llantén S, Vásquez-Ponce F, Núñez-Gallegos M, Pavlov MS, Marshall S, Olivares-Pacheco J. Phenotypic and genotypic characterization of a novel multi-antibiotic-resistant, alginate hyperproducing strain of Pseudomonas mandelii isolated in Antarctica. Polar Biol 2017. [DOI: 10.1007/s00300-017-2206-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Koo H, Hakim JA, Morrow CD, Eipers PG, Davila A, Andersen DT, Bej AK. Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica. J Microbiol Methods 2017; 140:15-22. [PMID: 28655556 PMCID: PMC6108183 DOI: 10.1016/j.mimet.2017.06.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 01/01/2023]
Abstract
In this study, using NextGen sequencing of the collective 16S rRNA genes obtained from two sets of samples collected from Lake Obersee, Antarctica, we compared and contrasted two bioinformatics tools, PICRUSt and Tax4Fun. We then developed an R script to assess the taxonomic and predictive functional profiles of the microbial communities within the samples. Taxa such as Pseudoxanthomonas, Planctomycetaceae, Cyanobacteria Subsection III, Nitrosomonadaceae, Leptothrix, and Rhodobacter were exclusively identified by Tax4Fun that uses SILVA database; whereas PICRUSt that uses Greengenes database uniquely identified Pirellulaceae, Gemmatimonadetes A1-B1, Pseudanabaena, Salinibacterium and Sinobacteraceae. Predictive functional profiling of the microbial communities using Tax4Fun and PICRUSt separately revealed common metabolic capabilities, while also showing specific functional IDs not shared between the two approaches. Combining these functional predictions using a customized R script revealed a more inclusive metabolic profile, such as hydrolases, oxidoreductases, transferases; enzymes involved in carbohydrate and amino acid metabolisms; and membrane transport proteins known for nutrient uptake from the surrounding environment. Our results present the first molecular-phylogenetic characterization and predictive functional profiles of the microbial mat communities in Lake Obersee, while demonstrating the efficacy of combining both the taxonomic assignment information and functional IDs using the R script created in this study for a more streamlined evaluation of predictive functional profiles of microbial communities.
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Affiliation(s)
- Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Casey D Morrow
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Peter G Eipers
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alfonso Davila
- NASA Ames Research Center, MS 245-3, Moffett Field, CA, USA
| | | | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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30
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La Ferla R, Azzaro M, Michaud L, Caruso G, Lo Giudice A, Paranhos R, Cabral AS, Conte A, Cosenza A, Maimone G, Papale M, Rappazzo AC, Guglielmin M. Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica). MICROBIAL ECOLOGY 2017; 74:402-415. [PMID: 28289836 DOI: 10.1007/s00248-017-0955-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
Victoria Land permafrost harbours a potentially large pool of cold-affected microorganisms whose metabolic potential still remains underestimated. Three cores (BC-1, BC-2 and BC-3) drilled at different depths in Boulder Clay (Northern Victoria Land) and one sample (DY) collected from a core in the Dry Valleys (Upper Victoria Valley) were analysed to assess the prokaryotic abundance, viability, physiological profiles and potential metabolic rates. The cores drilled at Boulder Clay were a template of different ecological conditions (different temperature regime, ice content, exchanges with atmosphere and with liquid water) in the same small basin while the Dry Valleys site was very similar to BC-2 conditions but with a complete different geological history and ground ice type. Image analysis was adopted to determine cell abundance, size and shape as well as to quantify the potential viable and respiring cells by live/dead and 5-cyano-2,3-ditolyl-tetrazolium chloride staining, respectively. Subpopulation recognition by apparent nucleic acid contents was obtained by flow cytometry. Moreover, the physiological profiles at community level by Biolog-Ecoplate™ as well as the ectoenzymatic potential rates on proteinaceous (leucine-aminopeptidase) and glucidic (ß-glucosidase) organic matter and on organic phosphates (alkaline-phosphatase) by fluorogenic substrates were tested. The adopted methodological approach gave useful information regarding viability and metabolic performances of microbial community in permafrost. The occurrence of a multifaceted prokaryotic community in the Victoria Land permafrost and a large number of potentially viable and respiring cells (in the order of 104-105) were recognised. Subpopulations with a different apparent DNA content within the different samples were observed. The physiological profiles stressed various potential metabolic pathways among the samples and intense utilisation rates of polymeric carbon compounds and carbohydrates, mainly in deep samples. The measured enzymatic activity rates suggested the potential capability of the microbial community to decompose proteins and polysaccharides. The microbial community seems to be appropriate to contribute to biogeochemical cycling in this extreme environment.
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Affiliation(s)
- Rosabruna La Ferla
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy.
| | - Maurizio Azzaro
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Luigi Michaud
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Gabriella Caruso
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Angelina Lo Giudice
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Rodolfo Paranhos
- Institute of Biology, Federal University of Rio de Janeiro, Prédio do CCS, Cidade Universitária do Fundao, Rio de Janeiro, Brazil
| | - Anderson S Cabral
- Institute of Biology, Federal University of Rio de Janeiro, Prédio do CCS, Cidade Universitária do Fundao, Rio de Janeiro, Brazil
| | - Antonella Conte
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Alessandro Cosenza
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Giovanna Maimone
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Maria Papale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Alessandro Ciro Rappazzo
- National Council of Research (IAMC-CNR), Institute for Coastal Marine Environment, Spianata San Raineri 86, 98122, Messina, Italy
| | - Mauro Guglielmin
- Department of Theoretical and Applied Sciences, University of Insubria, Via J.H. Dunant 3, Varese, Italy
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31
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Geyer KM, Takacs-Vesbach CD, Gooseff MN, Barrett JE. Primary productivity as a control over soil microbial diversity along environmental gradients in a polar desert ecosystem. PeerJ 2017; 5:e3377. [PMID: 28761776 PMCID: PMC5530992 DOI: 10.7717/peerj.3377] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/04/2017] [Indexed: 11/20/2022] Open
Abstract
Primary production is the fundamental source of energy to foodwebs and ecosystems, and is thus an important constraint on soil communities. This coupling is particularly evident in polar terrestrial ecosystems where biological diversity and activity is tightly constrained by edaphic gradients of productivity (e.g., soil moisture, organic carbon availability) and geochemical severity (e.g., pH, electrical conductivity). In the McMurdo Dry Valleys of Antarctica, environmental gradients determine numerous properties of soil communities and yet relatively few estimates of gross or net primary productivity (GPP, NPP) exist for this region. Here we describe a survey utilizing pulse amplitude modulation (PAM) fluorometry to estimate rates of GPP across a broad environmental gradient along with belowground microbial diversity and decomposition. PAM estimates of GPP ranged from an average of 0.27 μmol O2/m2/s in the most arid soils to an average of 6.97 μmol O2/m2/s in the most productive soils, the latter equivalent to 217 g C/m2/y in annual NPP assuming a 60 day growing season. A diversity index of four carbon-acquiring enzyme activities also increased with soil productivity, suggesting that the diversity of organic substrates in mesic environments may be an additional driver of microbial diversity. Overall, soil productivity was a stronger predictor of microbial diversity and enzymatic activity than any estimate of geochemical severity. These results highlight the fundamental role of environmental gradients to control community diversity and the dynamics of ecosystem-scale carbon pools in arid systems.
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Affiliation(s)
- Kevin M. Geyer
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | | | - Michael N. Gooseff
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA
- Department of Civil, Environmental and Architectural Engineering, University of Colorado, Boulder, CO, USA
| | - John E. Barrett
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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32
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Adriaenssens EM, Kramer R, Van Goethem MW, Makhalanyane TP, Hogg I, Cowan DA. Environmental drivers of viral community composition in Antarctic soils identified by viromics. MICROBIOME 2017; 5:83. [PMID: 28724405 PMCID: PMC5518109 DOI: 10.1186/s40168-017-0301-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 07/06/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of microorganisms from primary producers to grazers, yet their ecology and particularly the role of viruses is poorly understood. In this study, we examined the virus community structures of 14 soil samples from the Mackay Glacier region. METHODS Viral communities were extracted from soil and the dsDNA was extracted, amplified using single-primer amplification, and sequenced using the Ion Torrent Proton platform. Metadata on soil physico-chemistry was collected from all sites. Both read and contig datasets were analyzed with reference-independent and reference-dependent methods to assess viral community structures and the influence of environmental parameters on their distribution. RESULTS We observed a high heterogeneity in virus signatures, independent of geographical proximity. Tailed bacteriophages were dominant in all samples, but the incidences of the affiliated families Siphoviridae and Myoviridae were inversely correlated, suggesting direct competition for hosts. Viruses of the families Phycodnaviridae and Mimiviridae were present at significant levels in high-diversity soil samples and were found to co-occur, implying little competition between them. Combinations of soil factors, including pH, calcium content, and site altitude, were found to be the main drivers of viral community structure. CONCLUSIONS The pattern of viral community structure with higher levels of diversity at lower altitude and pH, and co-occurring viral families, suggests that these cold desert soil viruses interact with each other, the host, and the environment in an intricate manner, playing a potentially crucial role in maintaining host diversity and functioning of the microbial ecosystem in the extreme environments of Antarctic soil.
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Affiliation(s)
- Evelien M. Adriaenssens
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Rolf Kramer
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Marc W. Van Goethem
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Thulani P. Makhalanyane
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Ian Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Polar Knowledge Canada, 170 Laurier Avenue West, Ottawa, Ontario K1P 5V5 Canada
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
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33
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Pudasaini S, Wilson J, Ji M, van Dorst J, Snape I, Palmer AS, Burns BP, Ferrari BC. Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods. Front Microbiol 2017; 8:591. [PMID: 28439263 PMCID: PMC5383709 DOI: 10.3389/fmicb.2017.00591] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 03/22/2017] [Indexed: 01/07/2023] Open
Abstract
Browning Peninsula is an ice-free polar desert situated in the Windmill Islands, Eastern Antarctica. The entire site is described as a barren landscape, comprised of frost boils with soils dominated by microbial life. In this study, we explored the microbial diversity and edaphic drivers of community structure across this site using traditional cultivation methods, a novel approach the soil substrate membrane system (SSMS), and culture-independent 454-tag pyrosequencing. The measured soil environmental and microphysical factors of chlorine, phosphate, aspect and elevation were found to be significant drivers of the bacterial community, while none of the soil parameters analyzed were significantly correlated to the fungal community. Overall, Browning Peninsula soil harbored a distinctive microbial community in comparison to other Antarctic soils comprised of a unique bacterial diversity and extremely limited fungal diversity. Tag pyrosequencing data revealed the bacterial community to be dominated by Actinobacteria (36%), followed by Chloroflexi (18%), Cyanobacteria (14%), and Proteobacteria (10%). For fungi, Ascomycota (97%) dominated the soil microbiome, followed by Basidiomycota. As expected the diversity recovered from culture-based techniques was lower than that detected using tag sequencing. However, in the SSMS enrichments, that mimic the natural conditions for cultivating oligophilic “k-selected” bacteria, a larger proportion of rare bacterial taxa (15%), such as Blastococcus, Devosia, Herbaspirillum, Propionibacterium and Methylocella and fungal (11%) taxa, such as Nigrospora, Exophiala, Hortaea, and Penidiella were recovered at the genus level. At phylum level, a comparison of OTU's showed that the SSMS shared 21% of Acidobacteria, 11% of Actinobacteria and 10% of Proteobacteria OTU's with soil. For fungi, the shared OTUs was 4% (Basidiomycota) and <0.5% (Ascomycota). This was the first known attempt to culture microfungi using the SSMS which resulted in an increase in diversity from 14 to 57 microfungi OTUs compared to standard cultivation. Furthermore, the SSMS offers the opportunity to retrieve a greater diversity of bacterial and fungal taxa for future exploitation.
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Affiliation(s)
- Sarita Pudasaini
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - John Wilson
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Mukan Ji
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Josie van Dorst
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Ian Snape
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and CommunitiesKingston, TAS, Australia
| | - Anne S Palmer
- Australian Antarctic Division, Department of Sustainability, Environment, Water, Population and CommunitiesKingston, TAS, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South WalesKensington, NSW, Australia
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Tytgat B, Verleyen E, Sweetlove M, D'hondt S, Clercx P, Van Ranst E, Peeters K, Roberts S, Namsaraev Z, Wilmotte A, Vyverman W, Willems A. Bacterial community composition in relation to bedrock type and macrobiota in soils from the Sør Rondane Mountains, East Antarctica. FEMS Microbiol Ecol 2016; 92:fiw126. [PMID: 27402710 DOI: 10.1093/femsec/fiw126] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 01/06/2023] Open
Abstract
Antarctic soils are known to be oligotrophic and of having low buffering capacities. It is expected that this is particularly the case for inland high-altitude regions. We hypothesized that the bedrock type and the presence of macrobiota in these soils enforce a high selective pressure on their bacterial communities. To test this, we analyzed the bacterial community structure in 52 soil samples from the western Sør Rondane Mountains (Dronning Maud Land, East Antarctica), using the Illumina MiSeq platform in combination with ARISA fingerprinting. The samples were taken along broad environmental gradients in an area covering nearly 1000 km(2) Ordination and variation partitioning analyses revealed that the total organic carbon content was the most significant variable in structuring the bacterial communities, followed by pH, electric conductivity, bedrock type and the moisture content, while spatial distance was of relatively minor importance. Acidobacteria (Chloracidobacteria) and Actinobacteria (Actinomycetales) dominated gneiss derived mineral soil samples, while Proteobacteria (Sphingomonadaceae), Cyanobacteria, Armatimonadetes and candidate division FBP-dominated soil samples with a high total organic carbon content that were mainly situated on granite derived bedrock.
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Affiliation(s)
- Bjorn Tytgat
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Maxime Sweetlove
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Sofie D'hondt
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Pia Clercx
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Eric Van Ranst
- Laboratory of Soil Science, Department of Geology and Soil Science, Ghent University, 9000 Ghent, Belgium
| | - Karolien Peeters
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Stephen Roberts
- British Antarctic Survey, Natural Environment Research, Cambridge, CB3 0ET, UK
| | - Zorigto Namsaraev
- Department of Biotechnology and Bioenergy, NRC 'Kurchatov Institute', Moscow, 123182, Russia Winogradsky Institute of Microbiology RAS, Moscow, 117312, Russia
| | - Annick Wilmotte
- Centre for Protein Engineering, Department of Life Sciences, Liège University, 4000 Liège, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
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Morgan MJ, Halstrom S, Wylie JT, Walsh T, Kaksonen AH, Sutton D, Braun K, Puzon GJ. Characterization of a Drinking Water Distribution Pipeline Terminally Colonized by Naegleria fowleri. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:2890-2898. [PMID: 26853055 DOI: 10.1021/acs.est.5b05657] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Free-living amoebae, such as Naegleria fowleri, Acanthamoeba spp., and Vermamoeba spp., have been identified as organisms of concern due to their role as hosts for pathogenic bacteria and as agents of human disease. In particular, N. fowleri is known to cause the disease primary amoebic meningoencephalitis (PAM) and can be found in drinking water systems in many countries. Understanding the temporal dynamics in relation to environmental and biological factors is vital for developing management tools for mitigating the risks of PAM. Characterizing drinking water systems in Western Australia with a combination of physical, chemical and biological measurements over the course of a year showed a close association of N. fowleri with free chlorine and distance from treatment over the course of a year. This information can be used to help design optimal management strategies for the control of N. fowleri in drinking-water-distribution systems.
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Affiliation(s)
- Matthew J Morgan
- CSIRO Land and Water , Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Samuel Halstrom
- CSIRO Land and Water , Centre for Environment and Life Sciences, Private Bag No. 5, Wembley, Western Australia 6913, Australia
- School of Pathology and Laboratory Medicine and Oceans Institute, University of Western Australia , 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Jason T Wylie
- CSIRO Land and Water , Centre for Environment and Life Sciences, Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Tom Walsh
- CSIRO Land and Water , Black Mountain Laboratories, P.O. Box 1700, Canberra, ACT, 2601, Australia
| | - Anna H Kaksonen
- CSIRO Land and Water , Centre for Environment and Life Sciences, Private Bag No. 5, Wembley, Western Australia 6913, Australia
- School of Pathology and Laboratory Medicine and Oceans Institute, University of Western Australia , 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - David Sutton
- School of Pathology and Laboratory Medicine and Oceans Institute, University of Western Australia , 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Kalan Braun
- Water Corporation of Western Australia , 629 Newcastle Street, Leederville, Western Australia 6007, Australia
| | - Geoffrey J Puzon
- CSIRO Land and Water , Centre for Environment and Life Sciences, Private Bag No. 5, Wembley, Western Australia 6913, Australia
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Obbels D, Verleyen E, Mano MJ, Namsaraev Z, Sweetlove M, Tytgat B, Fernandez-Carazo R, De Wever A, D'hondt S, Ertz D, Elster J, Sabbe K, Willems A, Wilmotte A, Vyverman W. Bacterial and eukaryotic biodiversity patterns in terrestrial and aquatic habitats in the Sør Rondane Mountains, Dronning Maud Land, East Antarctica. FEMS Microbiol Ecol 2016; 92:fiw041. [PMID: 26936447 DOI: 10.1093/femsec/fiw041] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2016] [Indexed: 11/12/2022] Open
Abstract
The bacterial and microeukaryotic biodiversity were studied using pyrosequencing analysis on a 454 GS FLX+ platform of partial SSU rRNA genes in terrestrial and aquatic habitats of the Sør Rondane Mountains, including soils, on mosses, endolithic communities, cryoconite holes and supraglacial and subglacial meltwater lenses. This inventory was complemented with Denaturing Gradient Gel Electrophoresis targeting Chlorophyta and Cyanobacteria. OTUs belonging to the Rotifera, Chlorophyta, Tardigrada, Ciliophora, Cercozoa, Fungi, Bryophyta, Bacillariophyta, Collembola and Nematoda were present with a relative abundance of at least 0.1% in the eukaryotic communities. Cyanobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, FBP and Actinobacteria were the most abundant bacterial phyla. Multivariate analyses of the pyrosequencing data revealed a general lack of differentiation of both eukaryotes and prokaryotes according to habitat type. However, the bacterial community structure in the aquatic habitats was dominated by the filamentous cyanobacteria Leptolyngbya and appeared to be significantly different compared with those in dry soils, on mosses, and in endolithic habitats. A striking feature in all datasets was the detection of a relatively large amount of sequences new to science, which underscores the need for additional biodiversity assessments in Antarctic inland locations.
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Affiliation(s)
- Dagmar Obbels
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Marie-José Mano
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium
| | - Zorigto Namsaraev
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium Winogradsky Institute of Microbiology RAS, Pr-t 60-letya Oktyabrya, 7/2, Moscow 117312, Russia NRC Kurchatov Institute, Akademika Kurchatova pl. 1, Moscow, 12 31 82, Russia
| | - Maxime Sweetlove
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Bjorn Tytgat
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Rafael Fernandez-Carazo
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium
| | - Aaike De Wever
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium Operational Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium
| | - Sofie D'hondt
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Damien Ertz
- Botanic Garden Meise, Department Bryophytes-Thallophytes, Nieuwelaan 38, B-1860 Meise, Belgium Federation Wallonia-Brussels, General Administration of the Non-Compulsory Education and Scientific Research, Rue A. Lavallée 1, 1080 Brussels, Belgium
| | - Josef Elster
- Centre for Polar Ecology, Faculty of Sciences, University of South Bohemia, Institute of Botany, Academy of Sciences of the Czech Republic, Dukelská 135, 379 82, Třeboň, Czech republic
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
| | - Anne Willems
- Laboratory for Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Annick Wilmotte
- Centre for Protein Engineering, Institute of Chemistry, Université de Liège, Sart-TilmanB6, B-4000 Liège, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Krijgslaan 281, S8, B-9000 Ghent, Belgium
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Bradley JA, Anesio AM, Arndt S. Bridging the divide: a model-data approach to Polar and Alpine microbiology. FEMS Microbiol Ecol 2016; 92:fiw015. [PMID: 26832206 PMCID: PMC4765003 DOI: 10.1093/femsec/fiw015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2016] [Indexed: 11/13/2022] Open
Abstract
Advances in microbial ecology in the cryosphere continue to be driven by empirical approaches including field sampling and laboratory-based analyses. Although mathematical models are commonly used to investigate the physical dynamics of Polar and Alpine regions, they are rarely applied in microbial studies. Yet integrating modelling approaches with ongoing observational and laboratory-based work is ideally suited to Polar and Alpine microbial ecosystems given their harsh environmental and biogeochemical characteristics, simple trophic structures, distinct seasonality, often difficult accessibility, geographical expansiveness and susceptibility to accelerated climate changes. In this opinion paper, we explain how mathematical modelling ideally complements field and laboratory-based analyses. We thus argue that mathematical modelling is a powerful tool for the investigation of these extreme environments and that fully integrated, interdisciplinary model-data approaches could help the Polar and Alpine microbiology community address some of the great research challenges of the 21st century (e.g. assessing global significance and response to climate change). However, a better integration of field and laboratory work with model design and calibration/validation, as well as a stronger focus on quantitative information is required to advance models that can be used to make predictions and upscale processes and fluxes beyond what can be captured by observations alone.
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Affiliation(s)
- James A Bradley
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, BS8 1SS, UK BRIDGE, School of Geographical Sciences, University of Bristol, BS8 1SS, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, BS8 1SS, UK
| | - Sandra Arndt
- BRIDGE, School of Geographical Sciences, University of Bristol, BS8 1SS, UK
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Bacterial diversity of Drass, cold desert in Western Himalaya, and its comparison with Antarctic and Arctic. Arch Microbiol 2015; 197:851-60. [PMID: 26055487 DOI: 10.1007/s00203-015-1121-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/12/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
Abstract
Drass is the coldest inhabited place in India and the second coldest, inhabited place in the world, after Siberia. Using the 16SrDNA amplicon pyrosequencing, bacterial diversity patterns were cataloged across the Drass cold desert. In order to identify the ecotype abundance across cold desert environment, bacterial diversity patterns of Drass were further compared with the bacterial diversity of two other cold deserts, i.e., Antarctic and Arctic. Acidobacteria, Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria and Gemmatimonadetes were among the highly abundant taxonomic groups present across all the three cold deserts and were designated as the core phyla. However, Firmicutes, Nitrospirae, Armatimonadetes (former candidate division OP10), Planctomycetes, TM7, Chloroflexi, Deinococcus-Thermus, Tenericutes and candidate phyla WS3 were identified as rare phyla in Drass, Antarctic and Arctic samples. Differential abundance patterns were also computed across all the three samples, i.e., Acidobacteria (32.1 %) were dominant in Drass and Firmicutes (52.9 ± 17.6 %) and Proteobacteria (42 ± 1.3 %) were dominant in Antarctic and Arctic reference samples, respectively. Alpha diversity values Shannon's (H) and Simpson's (1-D) diversity indices were highest for Antarctic samples, whereas richness estimators (ACE and Chao1) were maximum for Drass soil suggesting greater species richness in bacterial communities in Drass than the Antarctic and Arctic samples.
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