1
|
Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583560. [PMID: 38559265 PMCID: PMC10979853 DOI: 10.1101/2024.03.08.583560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible platform that bridges the gap between genomics and biotechnological solutions.
Collapse
Affiliation(s)
- Josh L. Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Allan Phillips
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Gene S. Tan
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Karen G. Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN 37917, USA
| | - Chris L. Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| |
Collapse
|
2
|
Scheel M, Zervas A, Rijkers R, Tveit AT, Ekelund F, Campuzano Jiménez F, Christensen TR, Jacobsen CS. Abrupt permafrost thaw triggers activity of copiotrophs and microbiome predators. FEMS Microbiol Ecol 2023; 99:fiad123. [PMID: 37796894 PMCID: PMC10599396 DOI: 10.1093/femsec/fiad123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/31/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023] Open
Abstract
Permafrost soils store a substantial part of the global soil carbon and nitrogen. However, global warming causes abrupt erosion and gradual thaw, which make these stocks vulnerable to microbial decomposition into greenhouse gases. Here, we investigated the microbial response to abrupt in situ permafrost thaw. We sequenced the total RNA of a 1 m deep soil core consisting of up to 26 500-year-old permafrost material from an active abrupt erosion site. We analysed the microbial community in the active layer soil, the recently thawed, and the intact permafrost, and found maximum RNA:DNA ratios in recently thawed permafrost indicating a high microbial activity. In thawed permafrost, potentially copiotrophic Burkholderiales and Sphingobacteriales, but also microbiome predators dominated the community. Overall, both thaw-dependent and long-term soil properties significantly correlated with changes in community composition, as did microbiome predator abundance. Bacterial predators were dominated in shallower depths by Myxococcota, while protozoa, especially Cercozoa and Ciliophora, almost tripled in relative abundance in thawed layers. Our findings highlight the ecological importance of a diverse interkingdom and active microbial community highly abundant in abruptly thawing permafrost, as well as predation as potential biological control mechanism.
Collapse
Affiliation(s)
- Maria Scheel
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
- Department of Ecoscience, Aarhus University, Roskilde 4000, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
| | - Ruud Rijkers
- Department of Ecological Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Department of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø 9019, Norway
| | - Flemming Ekelund
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
- Department of Biology, Copenhagen University, DK-2200 Copenhagen, Denmark
| | | | - Torben R Christensen
- Department of Ecoscience, Aarhus University, Roskilde 4000, Denmark
- Water, Energy and Environmental Engineering Research Unit, University of Oulu, FI-90014 Oulu, Finland
| | - Carsten S Jacobsen
- Department of Environmental Science, Aarhus University, Roskilde 4000, Denmark
| |
Collapse
|
3
|
Cui Y, Peng S, Delgado-Baquerizo M, Rillig MC, Terrer C, Zhu B, Jing X, Chen J, Li J, Feng J, He Y, Fang L, Moorhead DL, Sinsabaugh RL, Peñuelas J. Microbial communities in terrestrial surface soils are not widely limited by carbon. GLOBAL CHANGE BIOLOGY 2023; 29:4412-4429. [PMID: 37277945 DOI: 10.1111/gcb.16765] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/07/2023]
Abstract
Microbial communities in soils are generally considered to be limited by carbon (C), which could be a crucial control for basic soil functions and responses of microbial heterotrophic metabolism to climate change. However, global soil microbial C limitation (MCL) has rarely been estimated and is poorly understood. Here, we predicted MCL, defined as limited availability of substrate C relative to nitrogen and/or phosphorus to meet microbial metabolic requirements, based on the thresholds of extracellular enzyme activity across 847 sites (2476 observations) representing global natural ecosystems. Results showed that only about 22% of global sites in terrestrial surface soils show relative C limitation in microbial community. This finding challenges the conventional hypothesis of ubiquitous C limitation for soil microbial metabolism. The limited geographic extent of C limitation in our study was mainly attributed to plant litter, rather than soil organic matter that has been processed by microbes, serving as the dominant C source for microbial acquisition. We also identified a significant latitudinal pattern of predicted MCL with larger C limitation at mid- to high latitudes, whereas this limitation was generally absent in the tropics. Moreover, MCL significantly constrained the rates of soil heterotrophic respiration, suggesting a potentially larger relative increase in respiration at mid- to high latitudes than low latitudes, if climate change increases primary productivity that alleviates MCL at higher latitudes. Our study provides the first global estimates of MCL, advancing our understanding of terrestrial C cycling and microbial metabolic feedback under global climate change.
Collapse
Affiliation(s)
- Yongxing Cui
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Shushi Peng
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | | | - César Terrer
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Boston, Massachusetts, USA
| | - Biao Zhu
- Institute of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Xin Jing
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Ji Chen
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Jinquan Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiao Feng
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yue He
- Sino-French Institute for Earth System Science, College of Urban and Environmental Sciences, Peking University, Beijing, China
| | - Linchuan Fang
- School of Resource and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - Daryl L Moorhead
- Department of Environmental Sciences, University of Toledo, Toledo, Ohio, USA
| | - Robert L Sinsabaugh
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Josep Peñuelas
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Bellaterra, Catalonia, Spain
- CREAF, Cerdanyola del Vallès, Catalonia, Spain
| |
Collapse
|
4
|
Kichko A, Sergaliev N, Ivanova E, Chernov T, Kimeklis A, Orlova O, Kalmenov M, Akhmedenov K, Pinaev A, Provorov N, Shashkov N, Andronov E. The microbiome of buried soils demonstrates significant shifts in taxonomic structure and a general trend towards mineral horizons. Heliyon 2023; 9:e17208. [PMID: 37360114 PMCID: PMC10285259 DOI: 10.1016/j.heliyon.2023.e17208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 06/09/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023] Open
Abstract
Burial mounds represent a challenge for microbiologists. Could ancient buried soils preserve microbiomes as they do archaeological artifacts? To investigate this question, we studied the soil microbiome under a burial mound dating from 2500 years ago in Western Kazakhstan. Two soil profile cuts were established: one under the burial mound and another adjacent to the mound surface steppe soil. Both soils represented the same dark chestnut soil type and had the same horizontal stratification (A, B, C horizons) with slight alterations. DNA samples isolated from all horizons were studied with molecular techniques including qPCR and high throughput sequencing of amplicon libraries of the 16S rRNA gene fragment. The taxonomic structure of the microbiome of the buried horizons demonstrated a deep divergence from ones of the surface, comparable to the variation between different soil types (representatives of the soil types were included in the survey). The cause of this divergence could be attributed to diagenetic processes characterized by the reduction of organic matter content and changes in its structure. Corresponding trends in the microbiome structure are obvious from the beta-diversity pattern: the A and B horizons of the buried soils form one cluster with the C horizons of both buried and surface soil. This trend could generally be designated as 'mineralization'. Statistically significant changes between the buried and surface soils microbiomes were detected in the number of phylogenetic clusters, the biology of which is in the line of diagenesis. The trend of 'mineralization' was also supported by PICRUSt2 functional prediction, demonstrating a higher occurrence of the processes of degradation in the buried microbiome. Our results show a profound shift in the buried microbiome relatively the "surface" microbiome, indicating the deep difference between the original and buried microbiomes.
Collapse
Affiliation(s)
- A.A. Kichko
- All-Russian Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - N.K. Sergaliev
- West Kazakhstan Innovation and Technology University, Uralsk, Kazakhstan
| | - E.A. Ivanova
- All-Russian Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Dokuchaev Soil Science Institute, Moscow, Russia
| | - T.I. Chernov
- Dokuchaev Soil Science Institute, Moscow, Russia
| | - A.K. Kimeklis
- All-Russian Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia
| | - O.V. Orlova
- All-Russian Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - M.D. Kalmenov
- West Kazakhstan Innovation and Technology University, Uralsk, Kazakhstan
| | | | - A.G. Pinaev
- All-Russian Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - N.A. Provorov
- All-Russian Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - N.A. Shashkov
- All-Russian Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Federal State Budget-Financed Educational Institution of Higher Education The Bonch-Bruevich Saint Petersburg State University of Telecommunications, Saint-Petersburg, Russia
| | - E.E. Andronov
- All-Russian Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Dokuchaev Soil Science Institute, Moscow, Russia
| |
Collapse
|
5
|
Li B, Liu X, Zhu D, Su H, Guo K, Sun G, Li X, Sun L. Crop diversity promotes the recovery of fungal communities in saline-alkali areas of the Western Songnen Plain. Front Microbiol 2023; 14:1091117. [PMID: 36819047 PMCID: PMC9930164 DOI: 10.3389/fmicb.2023.1091117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
Introduction Phytoremediation is an effective strategy for saline land restoration. In the Western Songnen Plain, northeast China, soil fungal community recovery for saline phytoremediation has not been well documented among different cropping patterns. In this study, we tested how rotation, mixture, and monoculture cropping patterns impact fungal communities in saline-alkali soils to assess the variability between cropping patterns. Methods The fungal communities of the soils of the different cropping types were determined using Illumina Miseq sequencing. Results Mixture and rotation promoted an increase in operational taxonomic unit (OTU) richness, and OTU richness in the mixture system decreased with increasing soil depth. A principal coordinate analysis (PCoA) showed that cropping patterns and soil depths influenced the structure of fungal communities, which may be due to the impact of soil chemistry. This was reflected by soil total nitrogen (TN) and electrical conductivity (EC) being the key factors driving OTU richness, while soil available potassium (AK) and total phosphorus (TP) were significantly correlated with the relative abundance of fungal dominant genus. The relative abundance of Leptosphaerulina, Alternaria, Myrothecium, Gibberella, and Tetracladium varied significantly between cropping patterns, and Leptosphaerulina was significantly associated with soil chemistry. Soil depth caused significant differences in the relative abundance of Fusarium in rotation and mixture soils, with Fusarium more commonly active at 0-15 cm deep soil. Null-model analysis revealed that the fungal community assembly of the mixture soils in 0-15 cm deep soil was dominated by deterministic processes, unlike the other two cropping patterns. Furthermore, fungal symbiotic networks were more complex in rotation and mixture than in monoculture soils, reflected in more nodes, more module hubs, and connectors. The fungal networks in rotation and mixture soils were more stable than in monoculture soils, and mixture networks were obviously more connected than rotations. FUNGuild showed that the relative proportion of saprotroph in rotation and mixture was significantly higher than that in monocultures. The highest proportion of pathotroph and symbiotroph was exhibited in rotation and mixture soils, respectively. Discussion Overall, mixture is superior to crop rotation and monocultures in restoring fungal communities of the saline-alkali soils of the Western Songnen Plain, northeast China.
Collapse
Affiliation(s)
- Bin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Xiaoqian Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Dan Zhu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Heng Su
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Kaiwen Guo
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Guangyu Sun
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Xin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China,School of Forestry, Northeast Forestry University, Harbin, China,*Correspondence: Xin Li, ✉
| | - Lei Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, China,Lei Sun, ✉
| |
Collapse
|
6
|
Romanowicz KJ, Kling GW. Summer thaw duration is a strong predictor of the soil microbiome and its response to permafrost thaw in arctic tundra. Environ Microbiol 2022; 24:6220-6237. [PMID: 36135820 PMCID: PMC10092252 DOI: 10.1111/1462-2920.16218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/19/2022] [Indexed: 01/12/2023]
Abstract
Climate warming has increased permafrost thaw in arctic tundra and extended the duration of annual thaw (number of thaw days in summer) along soil profiles. Predicting the microbial response to permafrost thaw depends largely on knowing how increased thaw duration affects the composition of the soil microbiome. Here, we determined soil microbiome composition from the annually thawed surface active layer down through permafrost from two tundra types at each of three sites on the North Slope of Alaska, USA. Variations in soil microbial taxa were found between sites up to ~90 km apart, between tundra types, and between soil depths. Microbiome differences at a site were greatest across transitions from thawed to permafrost depths. Results from correlation analysis based on multi-decadal thaw surveys show that differences in thaw duration by depth were significantly, positively correlated with the abundance of dominant taxa in the active layer and negatively correlated with dominant taxa in the permafrost. Microbiome composition within the transition zone was statistically similar to that in the permafrost, indicating that recent decades of intermittent thaw have not yet induced a shift from permafrost to active-layer microbes. We suggest that thaw duration rather than thaw frequency has a greater impact on the composition of microbial taxa within arctic soils.
Collapse
Affiliation(s)
- Karl J Romanowicz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - George W Kling
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
7
|
Zaitseva S, Badmaev N, Kozyreva L, Dambaev V, Barkhutova D. Microbial Community in the Permafrost Thaw Gradient in the South of the Vitim Plateau (Buryatia, Russia). Microorganisms 2022; 10:2202. [PMID: 36363794 PMCID: PMC9695985 DOI: 10.3390/microorganisms10112202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/03/2022] [Accepted: 11/03/2022] [Indexed: 12/23/2023] Open
Abstract
Soil microbial communities play key roles in biogeochemical cycles and greenhouse gas formation during the decomposition of the released organic matter in the thawing permafrost. The aim of our research was to assess the taxonomic prokaryotic diversity in soil-ecological niches of the Darkhituy-Khaimisan transect during the initial period of soil thawing. We investigated changes in the microbial communities present in the active layer of four sites representing distinct habitats (larch forest, birch forest, meadow steppe and thermokarst lake). We explore the relationship between the biogeochemical differences among habitats and the active layer microbial community via a spatial (across habitats, and with depth through the active layer) community survey using high-throughput Illumina sequencing. Microbial communities showed significant differences between active and frozen layers and across ecosystem types, including a high relative abundance of Alphaproteobacteria, Firmicutes, Crenarchaeota, Bacteroidota and Gemmatimonadota in the active layer and a high relative abundance of Actinobacteriota and Desulfobacterota in the frozen layer. Soil pH, temperature and moisture were the most significant parameters underlying the variations in the microbial community composition. CCA suggested that the differing environmental conditions between the four soil habitats had strong influences on microbial distribution and diversity and further explained the variability of soil microbial community structures.
Collapse
Affiliation(s)
- Svetlana Zaitseva
- Institute of General and Experimental Biology SD RAS, 670047 Ulan-Ude, Russia
| | | | | | | | | |
Collapse
|
8
|
Overgaard CK, Tao K, Zhang S, Christensen BT, Blahovska Z, Radutoiu S, Kelly S, Dueholm MKD. Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling. Front Microbiol 2022; 13:942396. [DOI: 10.3389/fmicb.2022.942396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
Intensive agriculture systems have paved the way for a growing human population. However, the abundant use of mineral fertilizers and pesticides may negatively impact nutrient cycles and biodiversity. One potential alternative is to harness beneficial relationships between plants and plant-associated rhizobacteria to increase nutrient-use efficiency and provide pathogen resistance. Plant-associated microbiota profiling can be achieved using high-throughput 16S rRNA gene amplicon sequencing. However, interrogation of these data is limited by confident taxonomic classifications at high taxonomic resolution (genus- or species level) with the commonly applied universal reference databases. High-throughput full-length 16S rRNA gene sequencing combined with automated taxonomy assignment (AutoTax) can be used to create amplicon sequence variant resolved ecosystems-specific reference databases that are superior to the traditional universal reference databases. This approach was used here to create a custom reference database for bacteria and archaea based on 987,353 full-length 16S rRNA genes from Askov and Cologne soils. We evaluated the performance of the database using short-read amplicon data and found that it resulted in the increased genus- and species-level classification compared to commonly use universal reference databases. The custom database was utilized to evaluate the ecosystem-specific primer bias and taxonomic resolution of amplicon primers targeting the V5–V7 region of the 16S rRNA gene commonly used within the plant microbiome field. Finally, we demonstrate the benefits of custom ecosystem-specific databases through the analysis of V5–V7 amplicon data to identify new plant-associated microbes for two legumes and two cereal species.
Collapse
|
9
|
West JR, Whitman T. Disturbance by soil mixing decreases microbial richness and supports homogenizing community assembly processes. FEMS Microbiol Ecol 2022; 98:6649207. [PMID: 35869965 PMCID: PMC9397575 DOI: 10.1093/femsec/fiac089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
The spatial heterogeneity of soil’s microhabitats warrants the study of ecological patterns and community assembly processes in the context of physical disturbance that disrupts the inherent spatial isolation of soil microhabitats and microbial communities. By mixing soil at various frequencies in a 16-week lab incubation, we explored the effects of physical disturbance on soil bacterial richness, community composition, and community assembly processes. We hypothesized that well-mixed soil would harbor a less rich microbial community, with community assembly marked by homogenizing dispersal and homogeneous selection. Using 16S rRNA gene sequencing, we inferred community assembly processes, estimated richness and differential abundance, and calculated compositional dissimilarity. Findings supported our hypotheses, with > 20% decrease in soil bacterial richness in well-mixed soil. Soil mixing caused communities to diverge from unmixed controls (Bray–Curtis dissimilarity; 0.75 vs. 0.25), while reducing within-group heterogeneity. Our results imply that the vast diversity observed in soil may be supported by spatial heterogeneity and isolation of microbial communities, and also provide insight into the effects of physical disturbance and community coalescence events. By isolating and better understanding the effects of spatial heterogeneity and disconnectivity on soil microbial communities, we can better extrapolate how anthropogenic disturbances may affect broad soil functions.
Collapse
Affiliation(s)
- Jaimie R West
- University of Wisconsin – Madison, Department of Soil Science , 1525 Observatory Drive, Madison, WI 53706 , USA
| | - Thea Whitman
- University of Wisconsin – Madison, Department of Soil Science , 1525 Observatory Drive, Madison, WI 53706 , USA
| |
Collapse
|
10
|
Li X, Cui Y, Ma D, Song D, Liu L. Vertical distribution of bacterial community diversity in the Greater Khingan Mountain permafrost region. Ecol Evol 2022; 12:e9106. [PMID: 35845356 PMCID: PMC9272067 DOI: 10.1002/ece3.9106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/10/2022] [Accepted: 06/23/2022] [Indexed: 11/08/2022] Open
Abstract
Soil microorganisms are crucial contributors to the function of permafrost ecosystems, as well as the regulation of biogeochemical cycles. However, little is known about the distribution patterns and drivers of high‐latitude permafrost microbial communities subject to climate change and human activities. In this study, the vertical distribution patterns of soil bacterial communities in the Greater Khingan Mountain permafrost region were systematically analyzed via Illumina Miseq high‐throughput sequencing. Bacterial diversity in the active layer was significantly higher than in the permafrost layer. Principal coordinate analysis (PCoA) indicated that the bacterial community structure in the active layer and the permafrost layer was completely separated. Permutational multivariate analysis of variance (PERMANOVA) detected statistically significant differentiation across the different depths. The relative abundance of the dominant phyla Chloroflexi (17.92%–52.79%) and Actinobacteria (6.34%–34.52%) was significantly higher in the permafrost layer than in the active layer, whereas that of Acidobacteria (4.98%–38.82%) exhibited the opposite trend, and the abundance of Proteobacteria (2.49%–22.51%) generally decreased with depth. More importantly, the abundance of bacteria linked to human infectious diseases was significantly higher in the permafrost layer according to Tax4Fun prediction analysis. Redundancy analysis (RDA) showed that ammonium nitrogen (NH4+‐N), total organic carbon (TOC), and total phosphorus (TP) were major factors affecting the bacterial community composition. Collectively, our findings provide insights into the soil bacterial vertical distribution patterns and major environmental drivers in high‐latitude permafrost regions, which is key to grasping the response of cold region ecosystem processes to global climate changes.
Collapse
Affiliation(s)
- Xin Li
- College of Geographical Sciences Harbin Normal University Harbin China
| | - Yuanquan Cui
- Personnel department Harbin Normal University Harbin China
| | - Dalong Ma
- College of Geographical Sciences Harbin Normal University Harbin China
| | - Dandan Song
- College of Geographical Sciences Harbin Normal University Harbin China
| | - Lin Liu
- College of Geographical Sciences Harbin Normal University Harbin China
| |
Collapse
|
11
|
Scheel M, Zervas A, Jacobsen CS, Christensen TR. Microbial Community Changes in 26,500-Year-Old Thawing Permafrost. Front Microbiol 2022; 13:787146. [PMID: 35401488 PMCID: PMC8988141 DOI: 10.3389/fmicb.2022.787146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/09/2022] [Indexed: 12/02/2022] Open
Abstract
Northern permafrost soils store more than half of the global soil carbon. Frozen for at least two consecutive years, but often for millennia, permafrost temperatures have increased drastically in the last decades. The resulting thermal erosion leads not only to gradual thaw, resulting in an increase of seasonally thawing soil thickness, but also to abrupt thaw events, such as sudden collapses of the soil surface. These could affect 20% of the permafrost zone and half of its organic carbon, increasing accessibility for deeper rooting vegetation and microbial decomposition into greenhouse gases. Knowledge gaps include the impact of permafrost thaw on the soil microfauna as well as key taxa to change the microbial mineralization of ancient permafrost carbon stocks during erosion. Here, we present the first sequencing study of an abrupt permafrost erosion microbiome in Northeast Greenland, where a thermal erosion gully collapsed in the summer of 2018, leading to the thawing of 26,500-year-old permafrost material. We investigated which soil parameters (pH, soil carbon content, age and moisture, organic and mineral horizons, and permafrost layers) most significantly drove changes of taxonomic diversity and the abundance of soil microorganisms in two consecutive years of intense erosion. Sequencing of the prokaryotic 16S rRNA and fungal ITS2 gene regions at finely scaled depth increments revealed decreasing alpha diversity with depth, soil age, and pH. The most significant drivers of variation were found in the soil age, horizons, and permafrost layer for prokaryotic and fungal beta diversity. Permafrost was mainly dominated by Proteobacteria and Firmicutes, with Polaromonas identified as the most abundant taxon. Thawed permafrost samples indicated increased abundance of several copiotrophic phyla, such as Bacteroidia, suggesting alterations of carbon utilization pathways within eroding permafrost.
Collapse
Affiliation(s)
- Maria Scheel
- Department of Ecoscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | | | - Torben R. Christensen
- Department of Ecoscience, Arctic Research Centre, Aarhus University, Roskilde, Denmark
- Oulanka Research Station, Oulu University, Oulu, Finland
| |
Collapse
|
12
|
Kim H, Kim M, Kim S, Lee YM, Shin SC. Characterization of antimicrobial resistance genes and virulence factor genes in an Arctic permafrost region revealed by metagenomics. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 294:118634. [PMID: 34875269 DOI: 10.1016/j.envpol.2021.118634] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 06/13/2023]
Abstract
Antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) constitute a serious threat to public health, and climate change has been predicted to affect the increase in bacterial pathogens harboring ARGs and VFGs. However, studies on bacterial pathogens and their ARGs and VFGs in permafrost region have received limited attention. In this study, a metagenomic approach was applied to a comprehensive survey to detect potential ARGs, VFGs, and pathogenic antibiotic resistant bacteria (PARB) carrying both ARGs and VFGs in the active layer and permafrost. Overall, 70 unique ARGs against 18 antimicrobial drug classes and 599 VFGs classified as 38 virulence factors were detected in the Arctic permafrost region. Eight genes with mobile genetic elements (MGEs) carrying ARGs were identified; most MGEs were classified as phages. In the metagenome-assembled genomes, the presence of 15 PARB was confirmed. The soil profile showed that the transcripts per million (TPM) values of ARGs and VFGs in the sub-soil horizon were significantly lower than those in the top soil horizon. Based on the TPM value of each gene, major ARGs, VFGs, and these genes in PARB from the Arctic permafrost region were identified and their distribution was confirmed. The major host bacteria for ARGs and VFGs and PARB were identified. A comparison of the percentage identity distribution of ARGs and VFGs to reference databases indicated that ARGs and VFGs in the Arctic soils differ from previously identified genes. Our results may help understand the characteristics and distribution of ARGs, VFGs, and these genes in PARB in the Arctic permafrost region. This findings suggest that the Arctic permafrost region may serve as potential reservoirs for ARGs, VFGs, and PARB. These genes could pose a new threat to human health if they are released by permafrost thawing owing to global warming and propagate to other regions.
Collapse
Affiliation(s)
- Heesoo Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Mincheol Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Sanghee Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
| |
Collapse
|
13
|
Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network. Microorganisms 2021; 9:microorganisms9091943. [PMID: 34576837 PMCID: PMC8466989 DOI: 10.3390/microorganisms9091943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 01/16/2023] Open
Abstract
Permafrost-affected soil stores a significant amount of organic carbon. Identifying the biological constraints of soil organic matter transformation, e.g., the interaction of major soil microbial soil organic matter decomposers, is crucial for predicting carbon vulnerability in permafrost-affected soil. Fungi are important players in the decomposition of soil organic matter and often interact in various mutualistic relationships during this process. We investigated four different soil horizon types (including specific horizons of cryoturbated soil organic matter (cryoOM)) across different types of permafrost-affected soil in the Western Canadian Arctic, determined the composition of fungal communities by sequencing (Illumina MPS) the fungal internal transcribed spacer region, assigned fungal lifestyles, and by determining the co-occurrence of fungal network properties, identified the topological role of keystone fungal taxa. Compositional analysis revealed a significantly higher relative proportion of the litter saprotroph Lachnum and root-associated saprotroph Phialocephala in the topsoil and the ectomycorrhizal close-contact exploring Russula in cryoOM, whereas Sites 1 and 2 had a significantly higher mean proportion of plant pathogens and lichenized trophic modes. Co-occurrence network analysis revealed the lowest modularity and average path length, and highest clustering coefficient in cryoOM, which suggested a lower network resistance to environmental perturbation. Zi-Pi plot analysis suggested that some keystone taxa changed their role from generalist to specialist, depending on the specific horizon concerned, Cladophialophora in topsoil, saprotrophic Mortierella in cryoOM, and Penicillium in subsoil were classified as generalists for the respective horizons but specialists elsewhere. The litter saprotrophic taxon Cadophora finlandica played a role as a generalist in Site 1 and specialist in the rest of the sites. Overall, these results suggested that fungal communities within cryoOM were more susceptible to environmental change and some taxa may shift their role, which may lead to changes in carbon storage in permafrost-affected soil.
Collapse
|
14
|
Bacterial Number and Genetic Diversity in a Permafrost Peatland (Western Siberia): Testing a Link with Organic Matter Quality and Elementary Composition of a Peat Soil Profile. DIVERSITY 2021. [DOI: 10.3390/d13070328] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Permafrost peatlands, containing a sizable amount of soil organic carbon (OC), play a pivotal role in soil (peat) OC transformation into soluble and volatile forms and greatly contribute to overall natural CO2 and CH4 emissions to the atmosphere under ongoing permafrost thaw and soil OC degradation. Peat microorganisms are largely responsible for the processing of this OC, yet coupled studies of chemical and bacterial parameters in permafrost peatlands are rather limited and geographically biased. Towards testing the possible impact of peat and peat pore water chemical composition on microbial population and diversity, here we present results of a preliminary study of the western Siberia permafrost peatland discontinuous permafrost zone. The quantitative evaluation of microorganisms and determination of microbial diversity along a 100 cm thick peat soil column, which included thawed and frozen peat and bottom mineral horizon, was performed by RT-PCR and 16S rRNA gene-based metagenomic analysis, respectively. Bacteria (mainly Proteobacteria, Acidobacteria, Actinobacteria) strongly dominated the microbial diversity (99% sequences), with a negligible proportion of archaea (0.3–0.5%). There was a systematic evolution of main taxa according to depth, with a maximum of 65% (Acidobacteria) encountered in the active layer, or permafrost boundary (50–60 cm). We also measured C, N, nutrients and ~50 major and trace elements in peat (19 samples) as well as its pore water and dispersed ice (10 samples), sampled over the same core, and we analyzed organic matter quality in six organic and one mineral horizon of this core. Using multiparametric statistics (PCA), we tested the links between the total microbial number and 16S rRNA diversity and chemical composition of both the solid and fluid phase harboring the microorganisms. Under climate warming and permafrost thaw, one can expect a downward movement of the layer of maximal genetic diversity following the active layer thickening. Given a one to two orders of magnitude higher microbial number in the upper (thawed) layers compared to bottom (frozen) layers, an additional 50 cm of peat thawing in western Siberia may sizably increase the total microbial population and biodiversity of active cells.
Collapse
|
15
|
Reduced microbial stability in the active layer is associated with carbon loss under alpine permafrost degradation. Proc Natl Acad Sci U S A 2021; 118:2025321118. [PMID: 34131077 DOI: 10.1073/pnas.2025321118] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Permafrost degradation may induce soil carbon (C) loss, critical for global C cycling, and be mediated by microbes. Despite larger C stored within the active layer of permafrost regions, which are more affected by warming, and the critical roles of Qinghai-Tibet Plateau in C cycling, most previous studies focused on the permafrost layer and in high-latitude areas. We demonstrate in situ that permafrost degradation alters the diversity and potentially decreases the stability of active layer microbial communities. These changes are associated with soil C loss and potentially a positive C feedback. This study provides insights into microbial-mediated mechanisms responsible for C loss within the active layer in degraded permafrost, aiding in the modeling of C emission under future scenarios.
Collapse
|
16
|
Swei A, Kwan JY. Response to Holmes - practical considerations for vector microbiome studies. Mol Ecol 2021; 30:2214-2219. [PMID: 33904214 DOI: 10.1111/mec.15922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/12/2021] [Indexed: 01/04/2023]
Affiliation(s)
- Andrea Swei
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Jessica Y Kwan
- School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| |
Collapse
|
17
|
Varsadiya M, Urich T, Hugelius G, Bárta J. Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic. FEMS Microbiol Ecol 2021; 97:6102547. [PMID: 33452882 DOI: 10.1093/femsec/fiab008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/13/2021] [Indexed: 01/12/2023] Open
Abstract
Substantial amounts of topsoil organic matter (OM) in Arctic Cryosols have been translocated by the process of cryoturbation into deeper soil horizons (cryoOM), reducing its decomposition. Recent Arctic warming deepens the Cryosols´ active layer, making more topsoil and cryoOM carbon accessible for microbial transformation. To quantify bacteria, archaea and selected microbial groups (methanogens - mcrA gene and diazotrophs - nifH gene) and to investigate bacterial and archaeal diversity, we collected 83 soil samples from four different soil horizons of three distinct tundra types located in Qikiqtaruk (Hershel Island, Western Canada). In general, the abundance of bacteria and diazotrophs decreased from topsoil to permafrost, but not for cryoOM. No such difference was observed for archaea and methanogens. CryoOM was enriched with oligotrophic (slow-growing microorganism) taxa capable of recalcitrant OM degradation. We found distinct microbial patterns in each tundra type: topsoil from wet-polygonal tundra had the lowest abundance of bacteria and diazotrophs, but the highest abundance of methanogens. Wet-polygonal tundra, therefore, represented a hotspot for methanogenesis. Oligotrophic and copiotrophic (fast-growing microorganism) genera of methanogens and diazotrophs were distinctly distributed in topsoil and cryoOM, resulting in different rates of nitrogen flux into these horizons affecting OM vulnerability and potential CO2 and CH4 release.
Collapse
Affiliation(s)
- Milan Varsadiya
- Department of Ecosystems Biology, University of South Bohemia in České Budějovice, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8 17487 Greifswald, Germany
| | - Gustaf Hugelius
- Department of Physical Geography, Stockholm University, 106 91, Stockholm, Sweden
| | - Jiří Bárta
- Department of Ecosystems Biology, University of South Bohemia in České Budějovice, Branišovská 31, 370 05 České Budějovice, Czech Republic
| |
Collapse
|
18
|
Meisner A, Snoek BL, Nesme J, Dent E, Jacquiod S, Classen AT, Priemé A. Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles. THE ISME JOURNAL 2021; 15:1207-1221. [PMID: 33408369 PMCID: PMC8115648 DOI: 10.1038/s41396-020-00844-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.
Collapse
Affiliation(s)
- Annelein Meisner
- grid.4514.40000 0001 0930 2361Microbial Ecology, Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden ,grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.418375.c0000 0001 1013 0288Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Present Address: Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, The Netherlands
| | - Basten L. Snoek
- grid.5477.10000000120346234Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Joseph Nesme
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Elizabeth Dent
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Samuel Jacquiod
- grid.5613.10000 0001 2298 9313Agroécologie, AgroSup Dijon, INRAE Centre Dijon, Université de Bourgogne Franche-Comté, Dijon, France
| | - Aimée T. Classen
- grid.214458.e0000000086837370Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, MI 48109 USA ,grid.59062.380000 0004 1936 7689The Gund Institute for Environment, University of Vermont, Burlington, VT USA ,grid.5254.60000 0001 0674 042XThe Center for Macroecology, Evolution and Climate, The University of Copenhagen, Copenhagen Ø, Denmark
| | - Anders Priemé
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, 1350 Copenhagen, Denmark
| |
Collapse
|
19
|
Choma M, Tahovská K, Kaštovská E, Bárta J, Růžek M, Oulehle F. Bacteria but not fungi respond to soil acidification rapidly and consistently in both a spruce and beech forest. FEMS Microbiol Ecol 2021; 96:5894924. [PMID: 32815987 DOI: 10.1093/femsec/fiaa174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/18/2020] [Indexed: 11/13/2022] Open
Abstract
Anthropogenically enhanced atmospheric sulphur (S) and nitrogen (N) deposition has acidified and eutrophied forest ecosystems worldwide. However, both S and N mechanisms have an impact on microbial communities and the consequences for microbially driven soil functioning differ. We conducted a two-forest stand (Norway spruce and European beech) field experiment involving acidification (sulphuric acid addition) and N (ammonium nitrate) loading and their combination. For 4 years, we monitored separate responses of soil microbial communities to the treatments and investigated the relationship to changes in the activity of extracellular enzymes. We observed that acidification selected for acidotolerant and oligotrophic taxa of Acidobacteria and Actinobacteria decreased bacterial community richness and diversity in both stands in parallel, disregarding their original dissimilarities in soil chemistry and composition of microbial communities. The shifts in bacterial community influenced the stoichiometry and magnitude of enzymatic activity. The bacterial response to experimental N addition was much weaker, likely due to historically enhanced N availability. Fungi were not influenced by any treatment during 4-year manipulation. We suggest that in the onset of acidification when fungi remain irresponsive, bacterial reaction might govern the changes in soil enzymatic activity.
Collapse
Affiliation(s)
- Michal Choma
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Karolina Tahovská
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Eva Kaštovská
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Jiří Bárta
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Michal Růžek
- Czech Geological Survey, Department of Environmental Geochemistry and Biogeochemistry, Geologická 6, Prague 5, 152 00, Czech Republic.,Department of Physical Geography, Faculty of Science, Charles University, Albertov 6, 128 43 Prague, Czech Republic
| | - Filip Oulehle
- Czech Geological Survey, Department of Environmental Geochemistry and Biogeochemistry, Geologická 6, Prague 5, 152 00, Czech Republic
| |
Collapse
|
20
|
Choe YH, Kim M, Lee YK. Distinct Microbial Communities in Adjacent Rock and Soil Substrates on a High Arctic Polar Desert. Front Microbiol 2021; 11:607396. [PMID: 33488547 PMCID: PMC7819959 DOI: 10.3389/fmicb.2020.607396] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/08/2020] [Indexed: 01/04/2023] Open
Abstract
Understanding microbial niche variability in polar regions can provide insights into the adaptive diversification of microbial lineages in extreme environments. Compositions of microbial communities in Arctic soils are well documented but a comprehensive multidomain diversity assessment of rocks remains insufficiently studied. In this study, we obtained two types of rocks (sandstone and limestone) and soils around the rocks in a high Arctic polar desert (Svalbard), and examined the compositions of archaeal, bacterial, fungal, and protistan communities in the rocks and soils. The microbial community structure differed significantly between rocks and soils across all microbial groups at higher taxonomic levels, indicating that Acidobacteria, Gemmatimonadetes, Latescibacteria, Rokubacteria, Leotiomycetes, Pezizomycetes, Mortierellomycetes, Sarcomonadea, and Spirotrichea were more abundant in soils, whereas Cyanobacteria, Deinococcus-Thermus, FBP, Lecanoromycetes, Eurotiomycetes, Trebouxiophyceae, and Ulvophyceae were more abundant in rocks. Interestingly, fungal communities differed markedly between two different rock types, which is likely to be ascribed to the predominance of distinct lichen-forming fungal taxa (Verrucariales in limestone, and Lecanorales in sandstone). This suggests that the physical or chemical properties of rocks could be a major determinant in the successful establishment of lichens in lithic environments. Furthermore, the biotic interactions among microorganisms based on co-occurrence network analysis revealed that Polyblastia and Verrucaria in limestone, and Atla, Porpidia, and Candelariella in sandstone play an important role as keystone taxa in the lithic communities. Our study shows that even in niches with the same climate regime and proximity to each other, heterogeneity of edaphic and lithic niches can affect microbial community assembly, which could be helpful in comprehensively understanding the effects of niche on microbial assembly in Arctic terrestrial ecosystems.
Collapse
Affiliation(s)
- Yong-Hoe Choe
- Korea Polar Research Institute, Incheon, South Korea
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon, South Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon, South Korea
| |
Collapse
|
21
|
Soil fungal community composition differs significantly among the Antarctic, Arctic, and Tibetan Plateau. Extremophiles 2020; 24:821-829. [PMID: 32974723 DOI: 10.1007/s00792-020-01197-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/31/2020] [Indexed: 10/23/2022]
Abstract
Fungi are widely distributed in all terrestrial ecosystems, and they are essential to the recycling of nutrients in all terrestrial habitats on earth. We wanted to determine the relationship between soil fungal communities and geochemical factors (geographical location and soil physicochemical properties) in three widely separated geographical regions (the Antarctic, Arctic, and Tibet Plateau). Using high-throughput Illumina amplicon sequencing, we characterized the fungal communities in 53 soil samples collected from the three regions. The fungal richness and diversity indices were not significantly different among the three regions. However, fungal community composition and many fungal taxa (Thelebolales, Verrucariales, Sordariales, Chaetothyriales, Hypocreales, Pleosporales, Capnodiales, and Dothideales) significantly differed among three regions. Furthermore, geographical location (latitude and altitude) and six soil physicochemical properties (SiO42--Si, pH, NO3--N, organic nitrogen, NO2--N, and organic carbon) were significant geochemical factors those were correlated with the soil fungal community composition. These results suggest that many geochemical factors influence the distribution of the fungal species within the Antarctic, Arctic, and Tibet Plateau.
Collapse
|
22
|
in 't Zandt MH, Frank J, Yilmaz P, Cremers G, Jetten MSM, Welte CU. Long-term enriched methanogenic communities from thermokarst lake sediments show species-specific responses to warming. FEMS MICROBES 2020; 1:xtaa008. [PMID: 37333957 PMCID: PMC10117432 DOI: 10.1093/femsmc/xtaa008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/14/2020] [Indexed: 04/05/2024] Open
Abstract
Thermokarst lakes are large potential greenhouse gas (GHG) sources in a changing Arctic. In a warming world, an increase in both organic matter availability and temperature is expected to boost methanogenesis and potentially alter the microbial community that controls GHG fluxes. These community shifts are, however, challenging to detect by resolution-limited 16S rRNA gene-based approaches. Here, we applied full metagenome sequencing on long-term thermokarst lake sediment enrichments on acetate and trimethylamine at 4°C and 10°C to unravel species-specific responses to the most likely Arctic climate change scenario. Substrate amendment was used to mimic the increased organic carbon availability upon permafrost thaw. By performing de novo assembly, we reconstructed five high-quality and five medium-quality metagenome-assembled genomes (MAGs) that represented 59% of the aligned metagenome reads. Seven bacterial MAGs belonged to anaerobic fermentative bacteria. Within the Archaea, the enrichment of methanogenic Methanosaetaceae/Methanotrichaceae under acetate amendment and Methanosarcinaceae under trimethylamine (TMA) amendment was not unexpected. Surprisingly, we observed temperature-specific methanogenic (sub)species responses with TMA amendment. These highlighted distinct and potentially functional climate-induced shifts could not be revealed with 16S rRNA gene-based analyses. Unraveling these temperature- and nutrient-controlled species-level responses is essential to better comprehend the mechanisms that underlie GHG production from Arctic lakes in a warming world.
Collapse
Affiliation(s)
- Michiel H in 't Zandt
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
- Netherlands Earth System Science Centre, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, the Netherlands
| | - Jeroen Frank
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Polen Yilmaz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
- Netherlands Earth System Science Centre, Utrecht University, Heidelberglaan 2, 3584 CS Utrecht, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands
| |
Collapse
|
23
|
Rogala MM, Gawor J, Gromadka R, Kowalczyk M, Grzesiak J. Biodiversity and Habitats of Polar Region Polyhydroxyalkanoic Acid-Producing Bacteria: Bioprospection by Popular Screening Methods. Genes (Basel) 2020; 11:genes11080873. [PMID: 32752049 PMCID: PMC7464897 DOI: 10.3390/genes11080873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 01/31/2023] Open
Abstract
Polyhydroxyalkanoates (PHAs), the intracellular polymers produced by various microorganisms as carbon and energy storage, are of great technological potential as biodegradable versions of common plastics. PHA-producing microbes are therefore in great demand and a plethora of different environments, especially extreme habitats, have been probed for the presence of PHA-accumulators. However, the polar region has been neglected in this regard, probably due to the low accessibility of the sampling material and unusual cultivation regime. Here, we present the results of a screening procedure involving 200 bacterial strains isolated from 25 habitats of both polar regions. Agar-based tests, microscopy, and genetic methods were conducted to elucidate the biodiversity and potential of polar-region PHA-accumulators. Microscopic observation of Nile Red stained cells proved to be the most reliable screening method as it allowed to confirm the characteristic bright orange glow of the Nile Red–PHA complex as well as the typical morphology of the PHA inclusions. Psychrophilic PHA-producers belonged mostly to the Comamonadaceae family (Betaproteobacteria) although actinobacterial PHA synthesizers of the families, Microbacteriaceae and Micrococcaceae also featured prominently. Glacial and postglacial habitats as well as developed polar region soils, were evaluated as promising for PHA-producer bioprospection. This study highlights the importance of psychrophiles as biodiverse and potent polyhydroxyalkanoate sources for scientific and application-aimed research.
Collapse
Affiliation(s)
- Małgorzata Marta Rogala
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawińskiego 5A, 02-106 Warszawa, Poland;
| | - Jan Gawor
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland; (J.G.); (R.G.)
| | - Robert Gromadka
- Laboratory of DNA Sequencing and Oligonucleotide Synthesis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland; (J.G.); (R.G.)
| | - Magdalena Kowalczyk
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawińskiego 5A, 02-106 Warszawa, Poland;
| | - Jakub Grzesiak
- Department of Antarctic Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences Pawińskiego 5A, 02-106 Warszawa, Poland;
- Correspondence:
| |
Collapse
|
24
|
Soil fungal taxonomic diversity along an elevation gradient on the semi-arid Xinglong Mountain, Northwest China. Arch Microbiol 2020; 202:2291-2302. [PMID: 32556390 DOI: 10.1007/s00203-020-01948-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/02/2020] [Accepted: 06/07/2020] [Indexed: 10/24/2022]
Abstract
Elevation gradients, often regarded as "natural experiments or laboratories", can be used to study changes in the distribution of microbial diversity related to changes in environmental conditions that typically occur over small geographical scales. We exploited this feature by characterizing fungal composition and diversity along an elevation gradient on Xinglong Mountain, northwest China. For this, we used MiSeq sequencing to obtain fungal sequences and clustered them into operational taxonomic units (OTUs). In total, we obtained 1,203,302 reads, 133,700 on average in each sample of soil collected at three selected elevations (2807, 3046, and 3536 m). The reads were assigned to 2192 OTUs. Inconsistent variations were observed in fungal alpha-diversity in samples from the three elevations. However, Principal Coordinate Analysis based on Bray-Curtis and UniFrac (weighted and unweighted) distance metrics revealed that fungal communities in soil samples from 3046 and 3536 m elevations were most similar. Principal Component Analysis based on relative abundances of shared OTUs confirmed that OTUs in samples from 3536 m elevation were more closely related to OTUs from 3046 m than samples from 2807 m elevation. Ascomycota, Basidiomycota, Glomeromycota, Cercozoa and Chytridiomycota were the most abundant fungal phyla across the elevation gradient. Our study also provides valuable indications of relations between fungal communities and an array of soil chemical properties, and variations in fungal taxonomic diversity across a substantial elevation gradient.
Collapse
|
25
|
Afouda P, Dubourg G, Raoult D. Archeomicrobiology applied to environmental samples. Microb Pathog 2020; 143:104140. [DOI: 10.1016/j.micpath.2020.104140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
|
26
|
Steger K, Kim AT, Ganzert L, Grossart HP, Smart DR. Floodplain soil and its bacterial composition are strongly affected by depth. FEMS Microbiol Ecol 2020; 95:5300135. [PMID: 30690447 DOI: 10.1093/femsec/fiz014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 01/23/2019] [Indexed: 11/14/2022] Open
Abstract
We studied bacterial abundance and community structure of five soil cores using high-throughput sequencing of the 16S rRNA gene. Shifts in the soil bacterial composition were more pronounced within a vertical profile than across the landscape. Soil organic carbon (SOC) and nitrogen (N) concentrations decreased exponentially with soil depth and revealed a buried carbon-rich horizon between 0.8 and 1.3 m across all soil cores. This buried horizon was phylogenetically similar to its surrounding subsoils supporting the idea that the type of carbon, not necessarily the amount of carbon was driving the apparent similarities. In contrast to other studies, Nitrospirae was one of our major phyla with relatively high abundances throughout the soil profile except for the surface soil. Although depth is the major driver shaping soil bacterial community structure, positive correlations with SOC and N concentrations, however, were revealed with the bacterial abundance of Acidobacteria, one of the major, and Gemmatimonadetes, one of the minor phyla in our study. Our study showed that bacterial diversity in soils below 2.0 m can be still as high if not higher than in the above laying subsurface soil suggesting that various bacteria throughout the soil profile influence major biogeochemical processes in floodplain soils.
Collapse
Affiliation(s)
- Kristin Steger
- College of Agricultural and Environmental Sciences, Department of Viticulture and Enology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Amy Taeyen Kim
- Department of Statistics, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Lars Ganzert
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Experimental Limnology, Alte Fischerhütte 2, 16775 Stechlin, Germany.,GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Telegrafenberg C-422, 14473 Potsdam, Germany.,University of Göttingen, Experimental Phycology and Culture Collection of Algae (EPSAG), Nikolausberger Weg 18, 37073 Göttingen, Germany
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Experimental Limnology, Alte Fischerhütte 2, 16775 Stechlin, Germany.,Potsdam University, Institute for Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam, Germany
| | - David R Smart
- College of Agricultural and Environmental Sciences, Department of Viticulture and Enology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| |
Collapse
|
27
|
Rowles LS, Hossain AI, Aggarwal S, Kirisits MJ, Saleh NB. Water quality and associated microbial ecology in selected Alaska Native communities: Challenges in off-the-grid water supplies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:134450. [PMID: 31812391 DOI: 10.1016/j.scitotenv.2019.134450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/20/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
The availability of safe water for potable purposes in Alaska Native communities is limited due to naturally occurring metals and contaminants released from anthropogenic activities, such as drilling and mining. The impacts of climate change are magnified in the arctic and sub-arctic regions and thus have the potential to mobilize contaminants and exacerbate the water contamination problem. Alaska Native communities are vulnerable to such changes in their water quality because of their remote location and limited access to resources. This study initiates an assessment of water quality, including its microbial ecology, in off-the-grid Alaskan water supplies (i.e., primarily groundwater wells). In particular, water quality data were collected from nine communities (22 ground water wells). Water quality analyses included basic water quality parameters, a suite of metals relevant to human health, and microbial community composition. Results revealed location-specific elevated arsenic concentrations based on the underlying geological formation, particularly in the areas located in the geological formation of the McHugh Complex. Diverse microbial communities were observed, and the grouping appeared to be based on elevation. These findings present evidence of compromised water quality in an understudied area in the United States. The results from this study should be considered as a snapshot in time, which highlight the importance for further systematic studies in similar off-the-grid communities.
Collapse
Affiliation(s)
- Lewis Stetson Rowles
- Department of Civil, Architectural, and Environmental Engineering, University of Texas, Austin, TX 78712, United States
| | - Areeb I Hossain
- Department of Biology, University of Texas, Austin, TX 78712, United States
| | - Srijan Aggarwal
- Department of Civil and Environmental Engineering, University of Alaska Fairbanks, Fairbanks, AK 99775, United States
| | - Mary Jo Kirisits
- Department of Civil, Architectural, and Environmental Engineering, University of Texas, Austin, TX 78712, United States
| | - Navid B Saleh
- Department of Civil, Architectural, and Environmental Engineering, University of Texas, Austin, TX 78712, United States.
| |
Collapse
|
28
|
Effects of the Freezing–Thawing Cycle Mode on Alpine Vegetation in the Nagqu River Basin of the Qinghai–Tibet Plateau. WATER 2019. [DOI: 10.3390/w11102122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The freezing–thawing cycle is a basic feature of a frozen soil ecosystem, and it affects the growth of alpine vegetation both directly and indirectly. As the climate changes, the freezing–thawing mode, along with its impact on frozen soil ecosystems, also changes. In this research, the freezing–thawing cycle of the Nagqu River Basin in the Qinghai–Tibet Plateau was studied. Vegetation growth characteristics and microbial abundance were analyzed under different freezing–thawing modes. The direct and indirect effects of the freezing–thawing cycle mode on alpine vegetation in the Nagqu River Basin are presented, and the changing trends and hazards of the freezing–thawing cycle mode due to climate change are discussed. The results highlight two major findings. First, the freezing–thawing cycle in the Nagqu River Basin has a high-frequency mode (HFM) and a low-frequency mode (LFM). With the influence of climate change, the LFM is gradually shifting to the HFM. Second, the alpine vegetation biomass in the HFM is lower than that in the LFM. Frequent freezing–thawing cycles reduce root cell activity and can even lead to root cell death. On the other hand, frequent freezing–thawing cycles increase microbial (Bradyrhizobium, Mesorhizobium, and Pseudomonas) death, weaken symbiotic nitrogen fixation and the disease resistance of vegetation, accelerate soil nutrient loss, reduce the soil water holding capacity and soil moisture, and hinder root growth. This study provides a complete response mechanism of alpine vegetation to the freezing–thawing cycle frequency while providing a theoretical basis for studying the change direction and impact on the frozen soil ecosystem due to climate change.
Collapse
|
29
|
Actinobacterial community in Shuanghe Cave using culture-dependent and -independent approaches. World J Microbiol Biotechnol 2019; 35:153. [PMID: 31576426 DOI: 10.1007/s11274-019-2713-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/11/2019] [Indexed: 12/12/2022]
Abstract
Karst caves, considering to be the "arks" of biodiversity, often contain high levels of endemism. In the present study, the actinobacterial community in Shuanghe Cave, the longest cave in Asia, was analyzed for the first-time using culture-dependent and -independent (16S rRNA amplicon sequencing) approaches. The amplicon sequencing analysis revealed a broad taxonomic diversity in Shuanghe Cave, including 19 phyla (predominantly Actinobacteria) and 264 different genera. While the culture-dependent method got the unrepresentative but supplemental result, a total of 239 actinomycetes were isolated and were identified to seven genera based on culture features and 16S rRNA tests. Among the three habitats (soil, rock soil, and bat guano), the dominant phyla did not differ significantly, while the dominant genus community varied among different habitats, and the richness in soil and rock soil samples was higher than that in bat guano. Furthermore, 16 isolate strains showed antimicrobial activity, especially, the strain S142 (Streptomyces badius) and S761 (Actinoplanes friuliensis) exhibited the most promising activity against various pathogens. Overall, this work showed the abundant bacterial diversity and the antimicrobial potential of the isolates from the Shuanghe Cave.
Collapse
|
30
|
Sayed AM, Hassan MHA, Alhadrami HA, Hassan HM, Goodfellow M, Rateb ME. Extreme environments: microbiology leading to specialized metabolites. J Appl Microbiol 2019; 128:630-657. [PMID: 31310419 DOI: 10.1111/jam.14386] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/18/2019] [Accepted: 07/10/2019] [Indexed: 12/19/2022]
Abstract
The prevalence of multidrug-resistant microbial pathogens due to the continued misuse and overuse of antibiotics in agriculture and medicine is raising the prospect of a return to the preantibiotic days of medicine at the time of diminishing numbers of drug leads. The good news is that an increased understanding of the nature and extent of microbial diversity in natural habitats coupled with the application of new technologies in microbiology and chemistry is opening up new strategies in the search for new specialized products with therapeutic properties. This review explores the premise that harsh environmental conditions in extreme biomes, notably in deserts, permafrost soils and deep-sea sediments select for micro-organisms, especially actinobacteria, cyanobacteria and fungi, with the potential to synthesize new druggable molecules. There is evidence over the past decade that micro-organisms adapted to life in extreme habitats are a rich source of new specialized metabolites. Extreme habitats by their very nature tend to be fragile hence there is a need to conserve those known to be hot-spots of novel gifted micro-organisms needed to drive drug discovery campaigns and innovative biotechnology. This review also provides an overview of microbial-derived molecules and their biological activities focusing on the period from 2010 until 2018, over this time 186 novel structures were isolated from 129 representatives of microbial taxa recovered from extreme habitats.
Collapse
Affiliation(s)
- A M Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - M H A Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - H A Alhadrami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.,Special Infectious Agent Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - H M Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt.,Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - M Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley, UK
| |
Collapse
|
31
|
Altshuler I, Hamel J, Turney S, Magnuson E, Lévesque R, Greer CW, Whyte LG. Species interactions and distinct microbial communities in high Arctic permafrost affected cryosols are associated with the CH 4 and CO 2 gas fluxes. Environ Microbiol 2019; 21:3711-3727. [PMID: 31206918 DOI: 10.1111/1462-2920.14715] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 05/27/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022]
Abstract
Microbial metabolism of the thawing organic carbon stores in permafrost results in a positive feedback loop of greenhouse gas emissions. CO2 and CH4 fluxes and the associated microbial communities in Arctic cryosols are important in predicting future warming potential of the Arctic. We demonstrate that topography had an impact on CH4 and CO2 flux at a high Arctic ice-wedge polygon terrain site, with higher CO2 emissions and lower CH4 uptake at troughs compared to polygon interior soils. The pmoA sequencing suggested that USCα cluster of uncultured methanotrophs is likely responsible for observed methane sink. Community profiling revealed distinct assemblages across the terrain at different depths. Deeper soils contained higher abundances of Verrucomicrobia and Gemmatimonadetes, whereas the polygon interior had higher Acidobacteria and lower Betaproteobacteria and Deltaproteobacteria abundances. Genome sequencing of isolates from the terrain revealed presence of carbon cycling genes including ones involved in serine and ribulose monophosphate pathways. A novel hybrid network analysis identified key members that had positive and negative impacts on other species. Operational Taxonomic Units (OTUs) with numerous positive interactions corresponded to Proteobacteria, Candidatus Rokubacteria and Actinobacteria phyla, while Verrucomicrobia and Acidobacteria members had negative impacts on other species. Results indicate that topography and microbial interactions impact community composition.
Collapse
Affiliation(s)
- Ianina Altshuler
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Jérémie Hamel
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, QC, Québec, Canada
| | - Shaun Turney
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Elisse Magnuson
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Roger Lévesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, QC, Québec, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada.,National Research Council of Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| |
Collapse
|
32
|
Day NJ, Dunfield KE, Johnstone JF, Mack MC, Turetsky MR, Walker XJ, White AL, Baltzer JL. Wildfire severity reduces richness and alters composition of soil fungal communities in boreal forests of western Canada. GLOBAL CHANGE BIOLOGY 2019; 25:2310-2324. [PMID: 30951220 DOI: 10.1111/gcb.14641] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 02/27/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Wildfire is the dominant disturbance in boreal forests and fire activity is increasing in these regions. Soil fungal communities are important for plant growth and nutrient cycling postfire but there is little understanding of how fires impact fungal communities across landscapes, fire severity gradients, and stand types in boreal forests. Understanding relationships between fungal community composition, particularly mycorrhizas, and understory plant composition is therefore important in predicting how future fire regimes may affect vegetation. We used an extreme wildfire event in boreal forests of Canada's Northwest Territories to test drivers of fungal communities and assess relationships with plant communities. We sampled soils from 39 plots 1 year after fire and 8 unburned plots. High-throughput sequencing (MiSeq, ITS) revealed 2,034 fungal operational taxonomic units. We found soil pH and fire severity (proportion soil organic layer combusted), and interactions between these drivers were important for fungal community structure (composition, richness, diversity, functional groups). Where fire severity was low, samples with low pH had higher total fungal, mycorrhizal, and saprotroph richness compared to where severity was high. Increased fire severity caused declines in richness of total fungi, mycorrhizas, and saprotrophs, and declines in diversity of total fungi and mycorrhizas. The importance of stand age (a surrogate for fire return interval) for fungal composition suggests we could detect long-term successional patterns even after fire. Mycorrhizal and plant community composition, richness, and diversity were weakly but significantly correlated. These weak relationships and the distribution of fungi across plots suggest that the underlying driver of fungal community structure is pH, which is modified by fire severity. This study shows the importance of edaphic factors in determining fungal community structure at large scales, but suggests these patterns are mediated by interactions between fire and forest stand composition.
Collapse
Affiliation(s)
- Nicola J Day
- Wilfrid Laurier University, Waterloo, Ontario, Canada
| | | | - Jill F Johnstone
- University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- University of Alaska Fairbanks, Fairbanks, Alaska
| | | | | | | | | | | |
Collapse
|
33
|
Tripathi BM, Kim HM, Jung JY, Nam S, Ju HT, Kim M, Lee YK. Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska. Front Microbiol 2019; 10:1442. [PMID: 31316487 PMCID: PMC6610311 DOI: 10.3389/fmicb.2019.01442] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Permafrost-underlain tundra soils in Northern Hemisphere are one of the largest reservoirs of terrestrial carbon, which are highly sensitive to microbial decomposition due to climate warming. However, knowledge about the taxonomy and functions of microbiome residing in different horizons of permafrost-underlain tundra soils is still limited. Here we compared the taxonomic and functional composition of microbiome between different horizons of soil cores from a moist tussock tundra ecosystem in Council, Alaska, using 16S rRNA gene and shotgun metagenomic sequencing. The composition, diversity, and functions of microbiome varied significantly between soil horizons, with top soil horizon harboring more diverse communities than sub-soil horizons. The vertical gradient in soil physico-chemical parameters were strongly associated with composition of microbial communities across permafrost soil horizons; however, a large fraction of the variation in microbial communities remained unexplained. The genes associated with carbon mineralization were more abundant in top soil horizon, while genes involved in acetogenesis, fermentation, methane metabolism (methanogenesis and methanotrophy), and N cycling were dominant in sub-soil horizons. The results of phylogenetic null modeling analysis showed that stochastic processes strongly influenced the composition of the microbiome in different soil horizons, except the bacterial community composition in top soil horizon, which was largely governed by homogeneous selection. Our study expands the knowledge on the structure and functional potential of microbiome associated with different horizons of permafrost soil, which could be useful in understanding the effects of environmental change on microbial responses in tundra ecosystems.
Collapse
Affiliation(s)
| | - Hye Min Kim
- Environmental Safety Research Institute, NeoEnBiz, Bucheon, South Korea
| | - Ji Young Jung
- Korea Polar Research Institute, Incheon, South Korea
| | - Sungjin Nam
- Korea Polar Research Institute, Incheon, South Korea
| | - Hyeon Tae Ju
- Korea Polar Research Institute, Incheon, South Korea
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon, South Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon, South Korea
| |
Collapse
|
34
|
Wang N, Guo Y, Li G, Xia Y, Ma M, Zang J, Ma Y, Yin X, Han W, Lv J, Cao H. Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics. Microbes Environ 2019; 34:180-190. [PMID: 31178526 PMCID: PMC6594734 DOI: 10.1264/jsme2.me18091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 02/23/2019] [Indexed: 11/27/2022] Open
Abstract
Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3-V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.
Collapse
Affiliation(s)
- Nengfei Wang
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic AdministrationQingdao 266061China
| | - Yudong Guo
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science & TechnologyQingdao 266042China
| | - Gaoyang Li
- College of Computer Science and Technology, Jilin UniversityChangchun, Jilin 100012China
| | - Yan Xia
- Jilin University First HospitalChangchun, Jilin 100012China
| | - Mingyang Ma
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic AdministrationQingdao 266061China
| | - Jiaye Zang
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic AdministrationQingdao 266061China
| | - Yue Ma
- Department of Bioengineering, College of Marine Sciences and Biological Engineering, Qingdao University of Science & TechnologyQingdao 266042China
| | - Xiaofei Yin
- Key Lab of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic AdministrationQingdao 266061China
| | - Wenbing Han
- College of Chemistry and Chemical Engineering, Qingdao UniversityQingdao 266071China
| | - Jinjiang Lv
- College of Chemistry and Chemical Engineering, Qingdao UniversityQingdao 266071China
| | - Huansheng Cao
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State UniversityTempe, AZ 85287USA
| |
Collapse
|
35
|
Kramshøj M, Albers CN, Svendsen SH, Björkman MP, Lindwall F, Björk RG, Rinnan R. Volatile emissions from thawing permafrost soils are influenced by meltwater drainage conditions. GLOBAL CHANGE BIOLOGY 2019; 25:1704-1716. [PMID: 30806027 DOI: 10.1111/gcb.14582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
Vast amounts of carbon are bound in both active layer and permafrost soils in the Arctic. As a consequence of climate warming, the depth of the active layer is increasing in size and permafrost soils are thawing. We hypothesize that pulses of biogenic volatile organic compounds are released from the near-surface active layer during spring, and during late summer season from thawing permafrost, while the subsequent biogeochemical processes occurring in thawed soils also lead to emissions. Biogenic volatile organic compounds are reactive gases that have both negative and positive climate forcing impacts when introduced to the Arctic atmosphere, and the knowledge of their emission magnitude and pattern is necessary to construct reliable climate models. However, it is unclear how different ecosystems and environmental factors such as drainage conditions upon permafrost thaw affect the emission and compound composition. Here we show that incubations of frozen B horizon of the active layer and permafrost soils collected from a High Arctic heath and fen release a range of biogenic volatile organic compounds upon thaw and during subsequent incubation experiments at temperatures of 10°C and 20°C. Meltwater drainage in the fen soils increased emission rates nine times, while having no effect in the drier heath soils. Emissions generally increased with temperature, and emission profiles for the fen soils were dominated by benzenoids and alkanes, while benzenoids, ketones, and alcohols dominated in heath soils. Our results emphasize that future changes affecting the drainage conditions of the Arctic tundra will have a large influence on volatile emissions from thawing permafrost soils - particularly in wetland/fen areas.
Collapse
Affiliation(s)
- Magnus Kramshøj
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Christian N Albers
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
- Department of Geochemistry, Geological Survey of Denmark and Greenland (GEUS), Copenhagen, Denmark
| | - Sarah H Svendsen
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Mats P Björkman
- Department of Earth Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Frida Lindwall
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Robert G Björk
- Department of Earth Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Riikka Rinnan
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Center for Permafrost (CENPERM), Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
36
|
Altshuler I, Ronholm J, Layton A, Onstott TC, W. Greer C, Whyte LG. Denitrifiers, nitrogen-fixing bacteria and N2O soil gas flux in high Arctic ice-wedge polygon cryosols. FEMS Microbiol Ecol 2019; 95:5481522. [DOI: 10.1093/femsec/fiz049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 04/24/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ianina Altshuler
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21,111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Jennifer Ronholm
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21,111 Lakeshore Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21,111 Lakeshore Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Alice Layton
- Center for Environmental Biotechnology, University of Tennessee – Knoxville, 676 Dabney-Buehler Hall, 1416 Circle Drive, TN 37996-1605, USA
| | - Tullis C Onstott
- Geomicrobiology, Geosciences, Princeton University, Princeton, NJ 08544, USA
| | - Charles W. Greer
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21,111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
- National Research Council of Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, 21,111 Lakeshore Rd, Ste Anne-de-Bellevue, QC, H9X 3V9, Canada
| |
Collapse
|
37
|
Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence. Appl Environ Microbiol 2019; 85:AEM.02646-18. [PMID: 30683748 PMCID: PMC6585489 DOI: 10.1128/aem.02646-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/21/2019] [Indexed: 01/31/2023] Open
Abstract
Permafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains. Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of the Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost. IMPORTANCE Permafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.
Collapse
|
38
|
Schostag M, Priemé A, Jacquiod S, Russel J, Ekelund F, Jacobsen CS. Bacterial and protozoan dynamics upon thawing and freezing of an active layer permafrost soil. ISME JOURNAL 2019; 13:1345-1359. [PMID: 30692629 DOI: 10.1038/s41396-019-0351-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/17/2018] [Accepted: 12/23/2018] [Indexed: 11/09/2022]
Abstract
The active layer of soil overlaying permafrost in the Arctic is subjected to annual changes in temperature and soil chemistry, which we hypothesize to affect the overall soil microbial community. We investigated changes in soil microorganisms at different temperatures during warming and freezing of the active layer soil from Svalbard, Norway. Soil community data were obtained by direct shotgun sequencing of total extracted RNA. No changes in soil microbial communities were detected when warming from -10 to -2 °C or when freezing from -2 to -10 °C. In contrast, within a few days we observed changes when warming from -2 to +2 °C with a decrease in fungal rRNA and an increase in several OTUs belonging to Gemmatimonadetes, Bacteroidetes and Betaproteobacteria. Even more substantial changes occurred when incubating at 2 °C for 16 days, with declines in total fungal potential activity and decreases in oligotrophic members from Actinobacteria and Acidobacteria. Additionally, we detected an increase in transcriptome sequences of bacterial phyla Bacteriodetes, Firmicutes, Betaproteobacteria and Gammaproteobacteria-collectively presumed to be copiotrophic. Furthermore, we detected an increase in putative bacterivorous heterotrophic flagellates, likely due to predation upon the bacterial community via grazing. Although this grazing activity may explain relatively large changes in the bacterial community composition, no changes in total 16S rRNA gene copy number were observed and the total RNA level remained stable during the incubation. Together, these results are showing the first comprehensive ecological evaluation across prokaryotic and eukaryotic microbial communities on thawing and freezing of soil by application of the TotalRNA technique.
Collapse
Affiliation(s)
- Morten Schostag
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Anders Priemé
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Samuel Jacquiod
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.,INRA Dijon, UMR1347 Agroécologie, Dijon, France
| | - Jakob Russel
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Flemming Ekelund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Suhr Jacobsen
- Department of Geosciences and Natural Resource Management, Center for Permafrost, University of Copenhagen, Copenhagen, Denmark. .,Geological Survey of Denmark and Greenland, Copenhagen, Denmark. .,Department of Environmental Science, Aarhus University, Roskilde, Denmark.
| |
Collapse
|
39
|
Dynamics of microbial communities and CO 2 and CH 4 fluxes in the tundra ecosystems of the changing Arctic. J Microbiol 2019; 57:325-336. [PMID: 30656588 DOI: 10.1007/s12275-019-8661-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 10/27/2022]
Abstract
Arctic tundra ecosystems are rapidly changing due to the amplified effects of global warming within the northern high latitudes. Warming has the potential to increase the thawing of the permafrost and to change the landscape and its geochemical characteristics, as well as terrestrial biota. It is important to investigate microbial processes and community structures, since soil microorganisms play a significant role in decomposing soil organic carbon in the Arctic tundra. In addition, the feedback from tundra ecosystems to climate change, including the emission of greenhouse gases into the atmosphere, is substantially dependent on the compositional and functional changes in the soil microbiome. This article reviews the current state of knowledge of the soil microbiome and the two most abundant greenhouse gas (CO2 and CH4) emissions, and summarizes permafrost thaw-induced changes in the Arctic tundra. Furthermore, we discuss future directions in microbial ecological research coupled with its link to CO2 and CH4 emissions.
Collapse
|
40
|
Malard LA, Pearce DA. Microbial diversity and biogeography in Arctic soils. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:611-625. [PMID: 30028082 DOI: 10.1111/1758-2229.12680] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 06/08/2023]
Abstract
Microorganisms dominate terrestrial environments in the polar regions and Arctic soils are known to harbour significant microbial diversity, far more diverse and numerous in the region than was once thought. Furthermore, the geographic distribution and structure of Arctic microbial communities remains elusive, despite their important roles in both biogeochemical cycling and in the generation and decomposition of climate active gases. Critically, Arctic soils are estimated to store over 1500 Pg of carbon and, thus, have the potential to generate positive feedback within the climate system. As the Arctic region is currently undergoing rapid change, the likelihood of faster release of greenhouse gases such as CO2 , CH4 and N2 O is increasing. Understanding the microbial communities in the region, in terms of their diversity, abundance and functional activity, is key to producing accurate models of greenhouse gas release. This review brings together existing data to determine what we know about microbial diversity and biogeography in Arctic soils.
Collapse
Affiliation(s)
- Lucie A Malard
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, NE1 8ST, UK
| | - David A Pearce
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, NE1 8ST, UK
| |
Collapse
|
41
|
Li Q, Liu C, Wang X, Jin Z, Song A, Liang Y, Cao J, Müller WEG. Influence of Altered Microbes on Soil Organic Carbon Availability in Karst Agricultural Soils Contaminated by Pb-Zn Tailings. Front Microbiol 2018; 9:2062. [PMID: 30233539 PMCID: PMC6127319 DOI: 10.3389/fmicb.2018.02062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
Soil organic carbon (SOC) availability is determined via a complex bio-mediated process, and Pb-Zn tailings are toxic to the soil microbes that are involved in this process. Here, Pb-Zn-tailings- contaminated karst soils with different levels (paddy field > corn field > citrus field > control group) were collected to explore the intrinsic relationship between Pb-Zn tailings and microbes due to the limited microbial abundance in these soils. The SOC concentration in the paddy fields is the highest. However, based on the soil microbial diversity and sole-carbon-source utilization profiles, the rate of SOC availability, McIntosh index, Shannon-Wiener diversity index, Simpson's diversity index and species richness are the lowest in the rice paddy soils. According to the results of Illumina sequencing of the 16S rRNA gene, Acidobacteria and Proteobacteria are the dominant phyla in all samples, accounting for more than 70% of the reads, while the majority of the remaining reads belong to the phyla Verrucomicrobia, Chloroflexi, Actinobacteria, Bacteroidetes, and Nitrospirae. We also observed that their class, order, family, genus and operational taxonomic units (OTUs) were dependent on SOC availability. Pearson correlation analysis reveals that L-asparagine utilization profiles show significant positive correlation with OTUs 24, 75, and 109 (r = 0.383, 0.350, and 0.292, respectively), and malic acid utilization profiles show significant positive correlation with OTUs 4, 5, 19, 27 (Bradyrhizobium), 32 (Burkholderia), 75 and 109 (r = 0.286, 0.361, 0.387, 0.384, 0.363, 0.285, and 0.301, respectively), as also evidenced by the redundancy analysis (RDA) biplot and heat map. These results indicate that the most abundant groups of bacteria, especially the uncultured facultative Deltaproteobacteria GR-WP33-30 (OTU 24), after long-term acclimation in heavy metal-contaminated soil, are associated with the variance of labile carbon source such as L-asparagine and may have considerable control over the stability of the vast SOC pool in karst surface soils with different agricultural land-use practices. These findings can expand our understanding of global soil-carbon sequestration and storage via changes in microbial community structure of the most abundant species.
Collapse
Affiliation(s)
- Qiang Li
- Key Laboratory of Karst Dynamics, Ministry of Land and Resources & Guangxi Zhuang Autonomous Region, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China
- The International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Chang Liu
- Key Laboratory of Karst Dynamics, Ministry of Land and Resources & Guangxi Zhuang Autonomous Region, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China
| | - Xiaohong Wang
- ERC Advanced Investigator Grant Research Group at Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Zhenjiang Jin
- Environmental Sciences and Engineering College, Guilin University of Technology, Guilin, China
| | - Ang Song
- Key Laboratory of Karst Dynamics, Ministry of Land and Resources & Guangxi Zhuang Autonomous Region, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China
| | - Yueming Liang
- Key Laboratory of Karst Dynamics, Ministry of Land and Resources & Guangxi Zhuang Autonomous Region, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China
| | - Jianhua Cao
- Key Laboratory of Karst Dynamics, Ministry of Land and Resources & Guangxi Zhuang Autonomous Region, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin, China
- The International Research Center on Karst under the Auspices of UNESCO, Guilin, China
| | - Werner E. G. Müller
- ERC Advanced Investigator Grant Research Group at Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| |
Collapse
|
42
|
Suleiman AKA, Lourenço KS, Pitombo LM, Mendes LW, Roesch LFW, Pijl A, Carmo JB, Cantarella H, Kuramae EE. Recycling organic residues in agriculture impacts soil-borne microbial community structure, function and N 2O emissions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 631-632:1089-1099. [PMID: 29727935 DOI: 10.1016/j.scitotenv.2018.03.116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 03/10/2018] [Accepted: 03/10/2018] [Indexed: 06/08/2023]
Abstract
Recycling residues is a sustainable alternative to improve soil structure and increase the stock of nutrients. However, information about the magnitude and duration of disturbances caused by crop and industrial wastes on soil microbial community structure and function is still scarce. The objective of this study was to investigate how added residues from industry and crops together with nitrogen (N) fertiliser affect the microbial community structure and function, and nitrous oxide (N2O) emissions. The experimental sugarcane field had the following treatments: (I) control with nitrogen, phosphorus, and potassium (NPK), (II) sugarcane straw with NPK, (III) vinasse (by-product of ethanol industry) with NP, and (IV) vinasse plus sugarcane straw with NP. Soil samples were collected on days 1, 3, 6, 11, 24 and 46 of the experiment for DNA extraction and metagenome sequencing. N2O emissions were also measured. Treatments with straw and vinasse residues induced changes in soil microbial composition and potential functions. The change in the microbial community was highest in the treatments with straw addition with functions related to decomposition of different ranges of C-compounds overrepresented while in vinasse treatment, the functions related to spore-producing microorganisms were overrepresented. Furthermore, all additional residues increased microorganisms related to the nitrogen metabolism and vinasse with straw had a synergetic effect on the highest N2O emissions. The results highlight the importance of residues and fertiliser management in sustainable agriculture.
Collapse
Affiliation(s)
- Afnan Khalil Ahmad Suleiman
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Késia Silva Lourenço
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, SP, Brazil; Institute of Biology Leiden, Leiden University, Netherlands
| | - Leonardo Machado Pitombo
- Department of Environmental Sciences, Federal University of São Carlos (UFSCar), Rod. João Leme dos Santos Km 110, 18052-780 Sorocaba, SP, Brazil
| | - Lucas William Mendes
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Luiz Fernando Wurdig Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa (UNIPAMPA), Avenida Antônio Trilha 1847, 97300-000 São Gabriel, Brazil
| | - Agata Pijl
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Janaína Braga Carmo
- Department of Environmental Sciences, Federal University of São Carlos (UFSCar), Rod. João Leme dos Santos Km 110, 18052-780 Sorocaba, SP, Brazil
| | - Heitor Cantarella
- Soils and Environmental Resources Center, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, SP, Brazil
| | - Eiko Eurya Kuramae
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.
| |
Collapse
|
43
|
Gentsch N, Wild B, Mikutta R, Čapek P, Diáková K, Schrumpf M, Turner S, Minnich C, Schaarschmidt F, Shibistova O, Schnecker J, Urich T, Gittel A, Šantrůčková H, Bárta J, Lashchinskiy N, Fuß R, Richter A, Guggenberger G. Temperature response of permafrost soil carbon is attenuated by mineral protection. GLOBAL CHANGE BIOLOGY 2018; 24:3401-3415. [PMID: 29774972 DOI: 10.1111/gcb.14316] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 03/19/2018] [Accepted: 04/16/2018] [Indexed: 06/08/2023]
Abstract
Climate change in Arctic ecosystems fosters permafrost thaw and makes massive amounts of ancient soil organic carbon (OC) available to microbial breakdown. However, fractions of the organic matter (OM) may be protected from rapid decomposition by their association with minerals. Little is known about the effects of mineral-organic associations (MOA) on the microbial accessibility of OM in permafrost soils and it is not clear which factors control its temperature sensitivity. In order to investigate if and how permafrost soil OC turnover is affected by mineral controls, the heavy fraction (HF) representing mostly MOA was obtained by density fractionation from 27 permafrost soil profiles of the Siberian Arctic. In parallel laboratory incubations, the unfractionated soils (bulk) and their HF were comparatively incubated for 175 days at 5 and 15°C. The HF was equivalent to 70 ± 9% of the bulk CO2 respiration as compared to a share of 63 ± 1% of bulk OC that was stored in the HF. Significant reduction of OC mineralization was found in all treatments with increasing OC content of the HF (HF-OC), clay-size minerals and Fe or Al oxyhydroxides. Temperature sensitivity (Q10) decreased with increasing soil depth from 2.4 to 1.4 in the bulk soil and from 2.9 to 1.5 in the HF. A concurrent increase in the metal-to-HF-OC ratios with soil depth suggests a stronger bonding of OM to minerals in the subsoil. There, the younger 14 C signature in CO2 than that of the OC indicates a preferential decomposition of the more recent OM and the existence of a MOA fraction with limited access of OM to decomposers. These results indicate strong mineral controls on the decomposability of OM after permafrost thaw and on its temperature sensitivity. Thus, we here provide evidence that OM temperature sensitivity can be attenuated by MOA in permafrost soils.
Collapse
Affiliation(s)
- Norman Gentsch
- Institute of Soil Science, Leibniz Universität Hannover, Hannover, Germany
| | - Birgit Wild
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Robert Mikutta
- Institute of Soil Science, Leibniz Universität Hannover, Hannover, Germany
- Soil Science and Soil Protection, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Petr Čapek
- Department of Ecosystems Biology, University of South Bohemia, České Budéjovice, Czech Republic
| | - Katka Diáková
- Department of Ecosystems Biology, University of South Bohemia, České Budéjovice, Czech Republic
| | | | - Stephanie Turner
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Cynthia Minnich
- Institute of Soil Science, Leibniz Universität Hannover, Hannover, Germany
- Soil Ecology, University of Bayreuth, Bayreuth, Germany
| | | | - Olga Shibistova
- Institute of Soil Science, Leibniz Universität Hannover, Hannover, Germany
- V.N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Jörg Schnecker
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire
| | - Tim Urich
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Institute of Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany
| | - Antje Gittel
- Department of Biology, Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Bioscience, Centre for Geomicrobiology, Aarhus, Denmark
| | - Hana Šantrůčková
- Department of Ecosystems Biology, University of South Bohemia, České Budéjovice, Czech Republic
| | - Jiři Bárta
- Department of Ecosystems Biology, University of South Bohemia, České Budéjovice, Czech Republic
| | - Nikolay Lashchinskiy
- Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Roland Fuß
- Thünen Institute of Climate-Smart Agriculture, Braunschweig, Germany
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Georg Guggenberger
- Institute of Soil Science, Leibniz Universität Hannover, Hannover, Germany
- V.N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, Russia
| |
Collapse
|
44
|
Müller O, Bang-Andreasen T, White RA, Elberling B, Taş N, Kneafsey T, Jansson JK, Øvreås L. Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates. Environ Microbiol 2018; 20:4328-4342. [PMID: 29971895 DOI: 10.1111/1462-2920.14348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 11/28/2022]
Abstract
Thawing permafrost can stimulate microbial activity, leading to faster decomposition of formerly preserved organic matter and CO2 release. Detailed knowledge about the vertical distribution of the responsible microbial community that is changing with increasing soil depth is limited. In this study, we determined the microbial community composition from cores sampled in a high Arctic heath at Svalbard, Norway; spanning from the active layer (AL) into the permafrost layer (PL). A special aim has been on identifying a layer of recently thawed soil, the transition zone (TZ), which might provide new insights into the fate of thawing permafrost. A unique sampling strategy allowed us to observe a diverse and gradually shifting microbial community in the AL, a Bacteroidetes dominated community in the TZ and throughout the PL, a community strongly dominated by a single Actinobacteria family (Intrasporangiaceae). The contrasting abundances of these two taxa caused a community difference of about 60%, just within 3 cm from TZ to PL. We incubated subsamples at about 5°C and measured highest CO2 production rates under aerobic incubations, yet contrasting for five different layers and correlating to the microbial community composition. This high resolution strategy provides new insights on how microbial communities are structured in permafrost and a better understanding of how they respond to thaw.
Collapse
Affiliation(s)
- Oliver Müller
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway
| | - Toke Bang-Andreasen
- Department of Environmental Science, Aarhus University, DK-4000, Roskilde, Denmark.,Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | | | - Bo Elberling
- Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, DK-1350, Copenhagen, Denmark
| | - Neslihan Taş
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Janet K Jansson
- Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, N-5020, Bergen, Norway.,University Center in Svalbard, UNIS, N-9171, Longyearbyen, Norway
| |
Collapse
|
45
|
Oulehle F, Tahovská K, Chuman T, Evans CD, Hruška J, Růžek M, Bárta J. Comparison of the impacts of acid and nitrogen additions on carbon fluxes in European conifer and broadleaf forests. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 238:884-893. [PMID: 29631233 DOI: 10.1016/j.envpol.2018.03.081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 06/08/2023]
Abstract
Increased reactive nitrogen (N) loadings to terrestrial ecosystems are believed to have positive effects on ecosystem carbon (C) sequestration. Global "hot spots" of N deposition are often associated with currently or formerly high deposition of sulphur (S); C fluxes in these regions might therefore not be responding solely to N loading, and could be undergoing transient change as S inputs change. In a four-year, two-forest stand (mature Norway spruce and European beech) replicated field experiment involving acidity manipulation (sulphuric acid addition), N addition (NH4NO3) and combined treatments, we tested the extent to which altered soil solution acidity or/and soil N availability affected the concentration of soil dissolved organic carbon (DOC), soil respiration (Rs), microbial community characteristics (respiration, biomass, fungi and bacteria abundances) and enzyme activity. We demonstrated a large and consistent suppression of soil water DOC concentration driven by chemical changes associated with increased hydrogen ion concentrations under acid treatments, independent of forest type. Soil respiration was suppressed by sulphuric acid addition in the spruce forest, accompanied by reduced microbial biomass, increased fungal:bacterial ratios and increased C to N enzyme ratios. We did not observe equivalent effects of sulphuric acid treatments on Rs in the beech forest, where microbial activity appeared to be more tightly linked to N acquisition. The only changes in C cycling following N addition were increased C to N enzyme ratios, with no impact on C fluxes (either Rs or DOC). We conclude that C accumulation previously attributed solely to N deposition could be partly attributable to their simultaneous acidification.
Collapse
Affiliation(s)
- Filip Oulehle
- Czech Geological Survey, Klárov 3, 118 21 Prague, Czech Republic; Global Change Research Institute, AS CR, Bělidla 986/4a, 60300 Brno, Czech Republic.
| | - Karolina Tahovská
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Tomáš Chuman
- Czech Geological Survey, Klárov 3, 118 21 Prague, Czech Republic; Department of Physical Geography, Faculty of Science, Charles University, Albertov 6, 128 43 Prague, Czech Republic
| | - Chris D Evans
- Centre for Ecology and Hydrology, Environmental Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - Jakub Hruška
- Czech Geological Survey, Klárov 3, 118 21 Prague, Czech Republic; Global Change Research Institute, AS CR, Bělidla 986/4a, 60300 Brno, Czech Republic
| | - Michal Růžek
- Czech Geological Survey, Klárov 3, 118 21 Prague, Czech Republic; Department of Physical Geography, Faculty of Science, Charles University, Albertov 6, 128 43 Prague, Czech Republic
| | - Jiří Bárta
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| |
Collapse
|
46
|
Mello A, Balestrini R. Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions. Front Microbiol 2018; 9:216. [PMID: 29497408 PMCID: PMC5818412 DOI: 10.3389/fmicb.2018.00216] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/30/2018] [Indexed: 12/21/2022] Open
Abstract
The roots of most terrestrial plants are colonized by mycorrhizal fungi. They play a key role in terrestrial environments influencing soil structure and ecosystem functionality. Around them a peculiar region, the mycorrhizosphere, develops. This is a very dynamic environment where plants, soil and microorganisms interact. Interest in this fascinating environment has increased over the years. For a long period the knowledge of the microbial populations in the rhizosphere has been limited, because they have always been studied by traditional culture-based techniques. These methods, which only allow the study of cultured microorganisms, do not allow the characterization of most organisms existing in nature. The introduction in the last few years of methodologies that are independent of culture techniques has bypassed this limitation. This together with the development of high-throughput molecular tools has given new insights into the biology, evolution, and biodiversity of mycorrhizal associations, as well as, the molecular dialog between plants and fungi. The genomes of many mycorrhizal fungal species have been sequenced so far allowing to better understanding the lifestyle of these fungi, their sexual reproduction modalities and metabolic functions. The possibility to detect the mycelium and the mycorrhizae of heterothallic fungi has also allowed to follow the spatial and temporal distributional patterns of strains of different mating types. On the other hand, the availability of the genome sequencing from several mycorrhizal fungi with a different lifestyle, or belonging to different groups, allowed to verify the common feature of the mycorrhizal symbiosis as well as the differences on how different mycorrhizal species interact and dialog with the plant. Here, we will consider the aspects described before, mainly focusing on ectomycorrhizal fungi and their interactions with plants and other soil microorganisms.
Collapse
Affiliation(s)
- Antonietta Mello
- Institute for Sustainable Plant Protection (IPSP), Torino Unit, National Research Council, Turin, Italy
| | | |
Collapse
|
47
|
Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores. Sci Rep 2018; 8:504. [PMID: 29323168 PMCID: PMC5765012 DOI: 10.1038/s41598-017-18777-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022] Open
Abstract
Understating the microbial communities and ecological processes that influence their structure in permafrost soils is crucial for predicting the consequences of climate change. In this study we investigated the bacterial and archaeal communities along depth profiles of four soil cores collected across Alaska. The bacterial and archaeal diversity (amplicon sequencing) overall decreased along the soil depth but the depth-wise pattern of their abundances (qPCR) varied by sites. The community structure of bacteria and archaea displayed site-specific pattern, with a greater role of soil geochemical characteristics rather than soil depth. In particular, we found significant positive correlations between methane trapped in cores and relative abundance of methanogenic archaeal genera, indicating a strong association between microbial activity and methane production in subsurface soils. We observed that bacterial phylogenetic community assembly tended to be more clustered in surface soils than in deeper soils. Analyses of phylogenetic community turnover among depth profiles across cores indicated that the relative influence of deterministic and stochastic processes was mainly determined by soil properties rather than depth. Overall, our findings emphasize that the vertical distributions of bacterial and archaeal communities in permafrost soils are to a large extent determined by the variation in site-specific soil properties.
Collapse
|
48
|
Chen YL, Deng Y, Ding JZ, Hu HW, Xu TL, Li F, Yang GB, Yang YH. Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau. Mol Ecol 2017; 26:6608-6620. [DOI: 10.1111/mec.14396] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 09/29/2017] [Accepted: 10/13/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Yong-Liang Chen
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Jin-Zhi Ding
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Tian-Le Xu
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Fei Li
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Gui-Biao Yang
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- Faculty of Veterinary and Agricultural Sciences; The University of Melbourne; Parkville Melbourne Vic. Australia
| | - Yuan-He Yang
- State Key Laboratory of Vegetation and Environmental Change; Institute of Botany; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| |
Collapse
|
49
|
Eukaryotic microbial richness increases with latitude and decreasing temperature in the Pacific Subarctic domain in late winter. Polar Biol 2017. [DOI: 10.1007/s00300-017-2131-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
50
|
Lewin GR, Carlos C, Chevrette MG, Horn HA, McDonald BR, Stankey RJ, Fox BG, Currie CR. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications. Annu Rev Microbiol 2017; 70:235-54. [PMID: 27607553 DOI: 10.1146/annurev-micro-102215-095748] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.
Collapse
Affiliation(s)
- Gina R Lewin
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Heidi A Horn
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706;
| | - Bradon R McDonald
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Robert J Stankey
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Brian G Fox
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726.,Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| |
Collapse
|