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Sipes K, Paul R, Fine A, Li P, Liang R, Boike J, Onstott TC, Vishnivetskaya TA, Schaeffer S, Lloyd KG. Permafrost Active Layer Microbes From Ny Ålesund, Svalbard (79°N) Show Autotrophic and Heterotrophic Metabolisms With Diverse Carbon-Degrading Enzymes. Front Microbiol 2022; 12:757812. [PMID: 35185810 PMCID: PMC8851200 DOI: 10.3389/fmicb.2021.757812] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/24/2021] [Indexed: 02/02/2023] Open
Abstract
The active layer of permafrost in Ny Ålesund, Svalbard (79°N) around the Bayelva River in the Leirhaugen glacier moraine is measured as a small net carbon sink at the brink of becoming a carbon source. In many permafrost-dominating ecosystems, microbes in the active layers have been shown to drive organic matter degradation and greenhouse gas production, creating positive feedback on climate change. However, the microbial metabolisms linking the environmental geochemical processes and the populations that perform them have not been fully characterized. In this paper, we present geochemical, enzymatic, and isotopic data paired with 10 Pseudomonas sp. cultures and metagenomic libraries of two active layer soil cores (BPF1 and BPF2) from Ny Ålesund, Svalbard, (79°N). Relative to BPF1, BPF2 had statistically higher C/N ratios (15 ± 1 for BPF1 vs. 29 ± 10 for BPF2; n = 30, p < 10–5), statistically lower organic carbon (2% ± 0.6% for BPF1 vs. 1.6% ± 0.4% for BPF2, p < 0.02), statistically lower nitrogen (0.1% ± 0.03% for BPF1 vs. 0.07% ± 0.02% for BPF2, p < 10–6). The d13C values for inorganic carbon did not correlate with those of organic carbon in BPF2, suggesting lower heterotrophic respiration. An increase in the δ13C of inorganic carbon with depth either reflects an autotrophic signal or mixing between a heterotrophic source at the surface and a lithotrophic source at depth. Potential enzyme activity of xylosidase and N-acetyl-β-D-glucosaminidase increases twofold at 15°C, relative to 25°C, indicating cold adaptation in the cultures and bulk soil. Potential enzyme activity of leucine aminopeptidase across soils and cultures was two orders of magnitude higher than other tested enzymes, implying that organisms use leucine as a nitrogen and carbon source in this nutrient-limited environment. Besides demonstrating large variability in carbon compositions of permafrost active layer soils only ∼84 m apart, results suggest that the Svalbard active layer microbes are often limited by organic carbon or nitrogen availability and have adaptations to the current environment, and metabolic flexibility to adapt to the warming climate.
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Affiliation(s)
- Katie Sipes
- Microbiology Department, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Raegan Paul
- Microbiology Department, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Aubrey Fine
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Peibo Li
- Microbiology Department, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Renxing Liang
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Julia Boike
- Alfred Wegener Institute, Potsdam, Germany.,Geography Department, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Tatiana A Vishnivetskaya
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sean Schaeffer
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Karen G Lloyd
- Microbiology Department, University of Tennessee, Knoxville, Knoxville, TN, United States
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Solon AJ, Mastrangelo C, Vimercati L, Sommers P, Darcy JL, Gendron EMS, Porazinska DL, Schmidt SK. Gullies and Moraines Are Islands of Biodiversity in an Arid, Mountain Landscape, Asgard Range, Antarctica. Front Microbiol 2021; 12:654135. [PMID: 34177836 PMCID: PMC8222675 DOI: 10.3389/fmicb.2021.654135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022] Open
Abstract
Cold, dry, and nutrient-poor, the McMurdo Dry Valleys of Antarctica are among the most extreme terrestrial environments on Earth. Numerous studies have described microbial communities of low elevation soils and streams below glaciers, while less is known about microbial communities in higher elevation soils above glaciers. We characterized microbial life in four landscape features (habitats) of a mountain in Taylor Valley. These habitats varied significantly in soil moisture and include moist soils of a (1) lateral glacial moraine, (2) gully that terminates at the moraine, and very dry soils on (3) a southeastern slope and (4) dry sites near the gully. Using rRNA gene PCR amplicon sequencing of Bacteria and Archaea (16S SSU) and eukaryotes (18S SSU), we found that all habitat types harbored significantly different bacterial and eukaryotic communities and that these differences were most apparent when comparing habitats that had macroscopically visible soil crusts (gully and moraine) to habitats with no visible crusts (near gully and slope). These differences were driven by a relative predominance of Actinobacteria and a Colpodella sp. in non-crust habitats, and by phototrophic bacteria and eukaryotes (e.g., a moss) and predators (e.g., tardigrades) in habitats with biological soil crusts (gully and moraine). The gully and moraine also had significantly higher 16S and 18S ESV richness than the other two habitat types. We further found that many of the phototrophic bacteria and eukaryotes of the gully and moraine share high sequence identity with phototrophs from moist and wet areas elsewhere in the Dry Valleys and other cold desert ecosystems. These include a Moss (Bryum sp.), several algae (e.g., a Chlorococcum sp.) and cyanobacteria (e.g., Nostoc and Phormidium spp.). Overall, the results reported here broaden the diversity of habitat types that have been studied in the Dry Valleys of Antarctica and suggest future avenues of research to more definitively understand the biogeography and factors controlling microbial diversity in this unique ecosystem.
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Affiliation(s)
- Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Claire Mastrangelo
- School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado-Anschutz Medical Campus, Denver, CO, United States
| | - Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States
| | - S K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
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Díaz-Puente FJ, Schmid T, Pelayo M, Rodríguez-Rastrero M, Herraiz MJS, O'Neill T, López-Martínez J. Abiotic factors influencing soil microbial activity in the northern Antarctic Peninsula region. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 750:141602. [PMID: 32882495 DOI: 10.1016/j.scitotenv.2020.141602] [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: 09/12/2019] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 06/11/2023]
Abstract
Microorganisms play a key role in the carbon (C) cycle through soil organic matter (SOM). The rate of SOM mineralization, the influence of abiotic factors on this rate and the potential behaviour of SOM are of particular interest in the northern Antarctic Peninsula and offshore islands. This is one of the most rapidly warming regions on Earth with numerous ice-free areas, some with abundant wildlife and with the greatest known soil organic carbon (SOC) storage in Antarctica. The latter implies extended Antarctic summer conditions promote increased terrestrial plant growth and soil microbial activity (SMA). SMA, determined by respirometry, is a measure of ecosystem function, and depends on microclimatic conditions and soil environmental properties. SMA and the effect of abiotic variables have been analysed in locations with different soil types, on Cierva Point (Antarctic Peninsula), Deception Island and Fildes Peninsula (King George Island). Soil microbial biomass carbon (SMBC) ranged from 5.66 to 196.6 mg SMBC kg-1and basal respiration (BR) from 2.86 to 160.67 mg CO2 kg-1 d-1. SMBC and BR values were higher in Cierva Point, followed by Fildes Peninsula and Deception Island, showing the same trend of SOM abundance. Except for Cierva Point, low nitrogen, phosphorus and C concentrations were observed. SMBC/total organic carbon (TOC) levels indicated that SOC was recalcitrant and SOM content was closely related to the extent of vegetation cover observed in situ. High metabolic quotient values obtained at Cierva Point and Deception Island (median values 7.27 and 6.53 mg C-CO2 g SMBC-1 h-1) and low SMBC/TOC in Cierva Point suggest a poor efficiency of the microbial populations in the consumption of the SOC. High SMBC/TOC values obtained in Deception Island indicates that SMBC may influence SOM stabilization. Mineralization rates were very low (negligible values to 1.44%) and sites with the lowest values had the highest SOM.
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Affiliation(s)
- F J Díaz-Puente
- CIEMAT - Department of Environment, Avda. Complutense, 40, 28040 Madrid, Spain.
| | - T Schmid
- CIEMAT - Department of Environment, Avda. Complutense, 40, 28040 Madrid, Spain
| | - M Pelayo
- CIEMAT - Department of Environment, Avda. Complutense, 40, 28040 Madrid, Spain
| | | | - M J Sierra Herraiz
- CIEMAT - Department of Environment, Avda. Complutense, 40, 28040 Madrid, Spain
| | - T O'Neill
- School of Sciences, University of Waikato, Private Bag 3105, Hamilton, New Zealand
| | - J López-Martínez
- Faculty of Sciences, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Geyer KM, Barrett JE. Unimodal productivity–diversity relationships among bacterial communities in a simple polar soil ecosystem. Environ Microbiol 2019; 21:2523-2532. [DOI: 10.1111/1462-2920.14639] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/20/2019] [Accepted: 04/23/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Kevin M. Geyer
- Department of Natural Resources and the EnvironmentUniversity of New Hampshire Durham New Hampshire USA
- Department of Biological SciencesVirginia Polytechnic Institute and State University Blacksburg Virginia USA
| | - John E. Barrett
- Department of Biological SciencesVirginia Polytechnic Institute and State University Blacksburg Virginia USA
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Feeser KL, Van Horn DJ, Buelow HN, Colman DR, McHugh TA, Okie JG, Schwartz E, Takacs-Vesbach CD. Local and Regional Scale Heterogeneity Drive Bacterial Community Diversity and Composition in a Polar Desert. Front Microbiol 2018; 9:1928. [PMID: 30186257 PMCID: PMC6110917 DOI: 10.3389/fmicb.2018.01928] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/30/2018] [Indexed: 02/01/2023] Open
Abstract
The distribution of organisms in an environment is neither uniform nor random but is instead spatially patterned. The factors that control this patterning are complex and the underlying mechanisms are poorly understood. Soil microbes are critical to ecosystem function but exhibit highly complex distributions and community dynamics due in large part to the scale-dependent effects of environmental heterogeneity. To better understand the impact of environmental heterogeneity on the distribution of soil microbes, we sequenced the 16S rRNA gene from bacterial communities in the microbe-dominated polar desert ecosystem of the McMurdo Dry Valleys (MDV), Antarctica. Significant differences in key edaphic variables and alpha diversity were observed among the three lake basins of the Taylor Valley (Kruskal-Wallis; pH: χ2 = 68.89, P < 0.001, conductivity: χ2 = 35.03, P < 0.001, observed species: χ2 = 7.98, P = 0.019 and inverse Simpson: χ2 = 18.52, P < 0.001) and each basin supported distinctive microbial communities (ANOSIM R = 0.466, P = 0.001, random forest ratio of 14.1). However, relationships between community structure and edaphic characteristics were highly variable and contextual, ranging in magnitude and direction across regional, basin, and local scales. Correlations among edaphic factors (pH and soil conductivity) and the relative abundance of specific phyla were most pronounced along local environmental gradients in the Lake Fryxell basin where Acidobacteria, Bacteroidetes, and Proteobacteria declined while Deinococcus-Thermus and Gemmatimonadetes increased with soil conductivity (all P < 0.1). Species richness was most strongly related to the soil conductivity gradient present within this study system. We suggest that the relative importance of pH versus soil conductivity in structuring microbial communities is related to the length of edaphic gradients and the spatial scale of sampling. These results highlight the importance of conducting studies over large ranges of key environmental gradients and across multiple spatial scales to assess the influence of environmental heterogeneity on the composition and diversity of microbial communities.
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Affiliation(s)
- Kelli L. Feeser
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - David J. Van Horn
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Heather N. Buelow
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Daniel R. Colman
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Theresa A. McHugh
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO, United States
| | - Jordan G. Okie
- School of Life Sciences, School of Earth and Space Exploration, Arizona State University, Tempe, AZ, United States
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States
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Darcy JL, Schmidt SK, Knelman JE, Cleveland CC, Castle SC, Nemergut DR. Phosphorus, not nitrogen, limits plants and microbial primary producers following glacial retreat. SCIENCE ADVANCES 2018; 4:eaaq0942. [PMID: 29806022 PMCID: PMC5966225 DOI: 10.1126/sciadv.aaq0942] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 04/11/2018] [Indexed: 06/08/2023]
Abstract
Current models of ecosystem development hold that low nitrogen availability limits the earliest stages of primary succession, but these models were developed from studies conducted in areas with temperate or wet climates. Global warming is now causing rapid glacial retreat even in inland areas with cold, dry climates, areas where ecological succession has not been adequately studied. We combine field and microcosm studies of both plant and microbial primary producers and show that phosphorus, not nitrogen, is the nutrient most limiting to the earliest stages of primary succession along glacial chronosequences in the Central Andes and central Alaska. We also show that phosphorus addition greatly accelerates the rate of succession for plants and for microbial phototrophs, even at the most extreme deglaciating site at over 5000 meters above sea level in the Andes of arid southern Peru. These results challenge the idea that nitrogen availability and a severe climate limit the rate of plant and microbial succession in cold-arid regions and will inform conservation efforts to mitigate the effects of global change on these fragile and threatened ecosystems.
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Affiliation(s)
- John L. Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Joey E. Knelman
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO 80309, USA
| | - Cory C. Cleveland
- Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT 59812, USA
| | - Sarah C. Castle
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55455, USA
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7
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Geyer KM, Takacs-Vesbach CD, Gooseff MN, Barrett JE. Primary productivity as a control over soil microbial diversity along environmental gradients in a polar desert ecosystem. PeerJ 2017; 5:e3377. [PMID: 28761776 PMCID: PMC5530992 DOI: 10.7717/peerj.3377] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/04/2017] [Indexed: 11/20/2022] Open
Abstract
Primary production is the fundamental source of energy to foodwebs and ecosystems, and is thus an important constraint on soil communities. This coupling is particularly evident in polar terrestrial ecosystems where biological diversity and activity is tightly constrained by edaphic gradients of productivity (e.g., soil moisture, organic carbon availability) and geochemical severity (e.g., pH, electrical conductivity). In the McMurdo Dry Valleys of Antarctica, environmental gradients determine numerous properties of soil communities and yet relatively few estimates of gross or net primary productivity (GPP, NPP) exist for this region. Here we describe a survey utilizing pulse amplitude modulation (PAM) fluorometry to estimate rates of GPP across a broad environmental gradient along with belowground microbial diversity and decomposition. PAM estimates of GPP ranged from an average of 0.27 μmol O2/m2/s in the most arid soils to an average of 6.97 μmol O2/m2/s in the most productive soils, the latter equivalent to 217 g C/m2/y in annual NPP assuming a 60 day growing season. A diversity index of four carbon-acquiring enzyme activities also increased with soil productivity, suggesting that the diversity of organic substrates in mesic environments may be an additional driver of microbial diversity. Overall, soil productivity was a stronger predictor of microbial diversity and enzymatic activity than any estimate of geochemical severity. These results highlight the fundamental role of environmental gradients to control community diversity and the dynamics of ecosystem-scale carbon pools in arid systems.
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Affiliation(s)
- Kevin M. Geyer
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | | | - Michael N. Gooseff
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA
- Department of Civil, Environmental and Architectural Engineering, University of Colorado, Boulder, CO, USA
| | - John E. Barrett
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
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Metagenomics and Single-Cell Omics Data Analysis for Human Microbiome Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 939:117-137. [PMID: 27807746 DOI: 10.1007/978-981-10-1503-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Microbes are ubiquitous on our planet, and it is well known that the total number of microbial cells on earth is huge. These organisms usually live in communities, and each of these communities has a different taxonomical structure. As such, microbial communities would serve as the largest reservoir of genes and genetic functions for a vast number of applications in "bio"-related disciplines, especially in biomedicine. Human microbiome is the area in which the relationships between ourselves as hosts and our microbiomes have been examined.In this chapter, we have first reviewed the researches in microbes on community, population and single-cell levels in general. Then we have focused on the effects of recent metagenomics and single-cell advances on human microbiome research, as well as their effects on translational biomedical research. We have also foreseen that with the advancement of big-data analysis techniques, deeper understanding of human microbiome, as well as its broader applications, could be realized.
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Pajares S, Escalante AE, Noguez AM, García-Oliva F, Martínez-Piedragil C, Cram SS, Eguiarte LE, Souza V. Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico. PeerJ 2016; 4:e2459. [PMID: 27652001 PMCID: PMC5018672 DOI: 10.7717/peerj.2459] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/17/2016] [Indexed: 11/20/2022] Open
Abstract
Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content) at local scale (meters) occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m2 plot and: (a) characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b) determined soil chemical parameters, and (c) identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca2, K+) and anions (HCO\documentclass[12pt]{minimal}
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}{}${}_{4}^{2-}$\end{document}42−) content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities.
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Affiliation(s)
- Silvia Pajares
- Instituto de Ciencias del Mar y Limnología, Unidad Académica de Ecología y Biodiversidad Acuática, Universidad Nacional Autónoma de México, Mexico City, Mexico; Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Mexico City, Mexico
| | - Ana E Escalante
- Instituto de Ecología, Laboratorio Nacional de Ciencias de la Sostenibilidad, Universidad Nacional Autónoma de México , Mexico City , Mexico
| | - Ana M Noguez
- Instituto de Ecología, Departamento de Ecología Evolutiva, Universidad Nacional Autónoma de México , Mexico City , Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México , Morelia , Michoacán , Mexico
| | - Celeste Martínez-Piedragil
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México , Morelia , Michoacán , Mexico
| | - Silke S Cram
- Instituto de Geografía, Universidad Nacional Autónoma de México , Mexico City , Mexico
| | - Luis Enrique Eguiarte
- Instituto de Ecología, Departamento de Ecología Evolutiva, Universidad Nacional Autónoma de México , Mexico City , Mexico
| | - Valeria Souza
- Instituto de Ecología, Departamento de Ecología Evolutiva, Universidad Nacional Autónoma de México , Mexico City , Mexico
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Buelow HN, Winter AS, Van Horn DJ, Barrett JE, Gooseff MN, Schwartz E, Takacs-Vesbach CD. Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica. Front Microbiol 2016; 7:1040. [PMID: 27486436 PMCID: PMC4947590 DOI: 10.3389/fmicb.2016.01040] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/21/2016] [Indexed: 11/27/2022] Open
Abstract
The soils of the McMurdo Dry Valleys, Antarctica are an extreme polar desert, inhabited exclusively by microscopic taxa. This region is on the threshold of anticipated climate change, with glacial melt, permafrost thaw, and the melting of massive buried ice increasing liquid water availability and mobilizing soil nutrients. Experimental water and organic matter (OM) amendments were applied to investigate how these climate change effects may impact the soil communities. To identify active taxa and their functions, total community RNA transcripts were sequenced and annotated, and amended soils were compared with unamended control soils using differential abundance and expression analyses. Overall, taxonomic diversity declined with amendments of water and OM. The domain Bacteria increased with both amendments while Eukaryota declined from 38% of all taxa in control soils to 8 and 11% in water and OM amended soils, respectively. Among bacterial phyla, Actinobacteria (59%) dominated water-amended soils and Firmicutes (45%) dominated OM amended soils. Three bacterial phyla (Actinobacteria, Proteobacteria, and Firmicutes) were primarily responsible for the observed positive functional responses, while eukaryotic taxa experienced the majority (27 of 34) of significant transcript losses. These results indicated that as climate changes in this region, a replacement of endemic taxa adapted to dry, oligotrophic conditions by generalist, copiotrophic taxa is likely.
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Affiliation(s)
- Heather N Buelow
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - Ara S Winter
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - David J Van Horn
- Department of Biology, University of New Mexico Albuquerque, NM, USA
| | - John E Barrett
- Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA
| | - Michael N Gooseff
- Department of Civil, Architectural, and Environmental Engineering, Institute of Arctic and Alpine Research, University of Colorado Boulder Boulder, CO, USA
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University Flagstaff, AZ, USA
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11
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Biogeochemical Stoichiometry Reveals P and N Limitation Across the Post-glacial Landscape of Denali National Park, Alaska. Ecosystems 2016. [DOI: 10.1007/s10021-016-9992-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Zeglin LH, Wang B, Waythomas C, Rainey F, Talbot SL. Organic matter quantity and source affects microbial community structure and function following volcanic eruption on Kasatochi Island, Alaska. Environ Microbiol 2015; 18:146-58. [DOI: 10.1111/1462-2920.12924] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/26/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Lydia H. Zeglin
- Alaska Science Center; U. S. Geological Survey; Anchorage AK USA
| | - Bronwen Wang
- Alaska Science Center; U. S. Geological Survey; Anchorage AK USA
| | | | - Frederick Rainey
- Department of Biological Sciences; University of Alaska Anchorage; Anchorage AK USA
| | - Sandra L. Talbot
- Alaska Science Center; U. S. Geological Survey; Anchorage AK USA
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13
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Ochoa-Hueso R, Arróniz-Crespo M, Bowker MA, Maestre FT, Pérez-Corona ME, Theobald MR, Vivanco MG, Manrique E. Biogeochemical indicators of elevated nitrogen deposition in semiarid Mediterranean ecosystems. ENVIRONMENTAL MONITORING AND ASSESSMENT 2014; 186:5831-42. [PMID: 24894911 PMCID: PMC4427508 DOI: 10.1007/s10661-014-3822-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 05/09/2014] [Indexed: 05/24/2023]
Abstract
Nitrogen (N) deposition has doubled the natural N inputs received by ecosystems through biological N fixation and is currently a global problem that is affecting the Mediterranean regions. We evaluated the existing relationships between increased atmospheric N deposition and biogeochemical indicators related to soil chemical factors and cryptogam species across semiarid central, southern, and eastern Spain. The cryptogam species studied were the biocrust-forming species Pleurochaete squarrosa (moss) and Cladonia foliacea (lichen). Sampling sites were chosen in Quercus coccifera (kermes oak) shrublands and Pinus halepensis (Aleppo pine) forests to cover a range of inorganic N deposition representative of the levels found in the Iberian Peninsula (between 4.4 and 8.1 kg N ha(-1) year(-1)). We extended the ambient N deposition gradient by including experimental plots to which N had been added for 3 years at rates of 10, 20, and 50 kg N ha(-1) year(-1). Overall, N deposition (extant plus simulated) increased soil inorganic N availability and caused soil acidification. Nitrogen deposition increased phosphomonoesterase (PME) enzyme activity and PME/nitrate reductase (NR) ratio in both species, whereas the NR activity was reduced only in the moss. Responses of PME and NR activities were attributed to an induced N to phosphorus imbalance and to N saturation, respectively. When only considering the ambient N deposition, soil organic C and N contents were positively related to N deposition, a response driven by pine forests. The PME/NR ratios of the moss were better predictors of N deposition rates than PME or NR activities alone in shrublands, whereas no correlation between N deposition and the lichen physiology was observed. We conclude that integrative physiological measurements, such as PME/NR ratios, measured on sensitive species such as P. squarrosa, can provide useful data for national-scale biomonitoring programs, whereas soil acidification and soil C and N storage could be useful as additional corroborating ecosystem indicators of chronic N pollution.
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Affiliation(s)
- Raúl Ochoa-Hueso
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, New South Wales, 2751, Australia,
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Abstract
Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost features and between sites. Some microorganisms are even active at subzero temperatures in permafrost. An emerging concern is the impact of climate change and the possibility of subsequent permafrost thaw promoting microbial activity in permafrost, resulting in increased potential for greenhouse-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles.
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Affiliation(s)
- Janet K Jansson
- 1] Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 70A-3317 Berkeley, California 94720, USA. [2] Joint Genome Institute (JGI), 2800 Mitchell Drive, Walnut Creek, California 94598, USA. [3] Joint BioEnergy Institute (JBEI), 5885 Hollis Street, Emeryville, California 94608, USA. [4] Danish Center for Permafrost (CENPERM), University of Copenhagen, Oester Voldgade 10, DK-1350 Copenhagen, Denmark. [5] Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, California 94720-3102, USA
| | - Neslihan Taş
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 70A-3317 Berkeley, California 94720, USA
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Soil microbial responses to increased moisture and organic resources along a salinity gradient in a polar desert. Appl Environ Microbiol 2014; 80:3034-43. [PMID: 24610850 DOI: 10.1128/aem.03414-13] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Microbial communities in extreme environments often have low diversity and specialized physiologies suggesting a limited resistance to change. The McMurdo Dry Valleys (MDV) are a microbially dominated, extreme ecosystem currently undergoing climate change-induced disturbances, including the melting of massive buried ice, cutting through of permafrost by streams, and warming events. These processes are increasing moisture across the landscape, altering conditions for soil communities by mobilizing nutrients and salts and stimulating autotrophic carbon inputs to soils. The goal of this study was to determine the effects of resource addition (water/organic matter) on the composition and function of microbial communities in the MDV along a natural salinity gradient representing an additional gradient of stress in an already extreme environment. Soil respiration and the activity of carbon-acquiring extracellular enzymes increased significantly (P < 0.05) with the addition of resources at the low- and moderate-salinity sites but not the high-salinity site. The bacterial community composition was altered, with an increase in Proteobacteria and Firmicutes with water and organic matter additions at the low- and moderate-salinity sites and a near dominance of Firmicutes at the high-salinity site. Principal coordinate analyses of all samples using a phylogenetically informed distance matrix (UniFrac) demonstrated discrete clustering among sites (analysis of similarity [ANOSIM], P < 0.05 and R > 0.40) and among most treatments within sites. The results from this experimental work suggest that microbial communities in this environment will undergo rapid change in response to the altered resources resulting from climate change impacts occurring in this region.
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Sokol ER, Herbold CW, Lee CK, Cary SC, Barrett JE. Local and regional influences over soil microbial metacommunities in the Transantarctic Mountains. Ecosphere 2013. [DOI: 10.1890/es13-00136.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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17
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Geyer KM, Altrichter AE, Van Horn DJ, Takacs-Vesbach CD, Gooseff MN, Barrett JE. Environmental controls over bacterial communities in polar desert soils. Ecosphere 2013. [DOI: 10.1890/es13-00048.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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18
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Factors Controlling Soil Microbial Biomass and Bacterial Diversity and Community Composition in a Cold Desert Ecosystem: Role of Geographic Scale. PLoS One 2013; 8:e66103. [PMID: 23824063 PMCID: PMC3688848 DOI: 10.1371/journal.pone.0066103] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/02/2013] [Indexed: 02/01/2023] Open
Abstract
Understanding controls over the distribution of soil bacteria is a fundamental step toward describing soil ecosystems, understanding their functional capabilities, and predicting their responses to environmental change. This study investigated the controls on the biomass, species richness, and community structure and composition of soil bacterial communities in the McMurdo Dry Valleys, Antarctica, at local and regional scales. The goals of the study were to describe the relationships between abiotic characteristics and soil bacteria in this unique, microbially dominated environment, and to test the scale dependence of these relationships in a low complexity ecosystem. Samples were collected from dry mineral soils associated with snow patches, which are a significant source of water in this desert environment, at six sites located in the major basins of the Taylor and Wright Valleys. Samples were analyzed for a suite of characteristics including soil moisture, pH, electrical conductivity, soil organic matter, major nutrients and ions, microbial biomass, 16 S rRNA gene richness, and bacterial community structure and composition. Snow patches created local biogeochemical gradients while inter-basin comparisons encompassed landscape scale gradients enabling comparisons of microbial controls at two distinct spatial scales. At the organic carbon rich, mesic, low elevation sites Acidobacteria and Actinobacteria were prevalent, while Firmicutes and Proteobacteria were dominant at the high elevation, low moisture and biomass sites. Microbial parameters were significantly related with soil water content and edaphic characteristics including soil pH, organic matter, and sulfate. However, the magnitude and even the direction of these relationships varied across basins and the application of mixed effects models revealed evidence of significant contextual effects at local and regional scales. The results highlight the importance of the geographic scale of sampling when determining the controls on soil microbial community characteristics.
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Lynch RC, King AJ, Farías ME, Sowell P, Vitry C, Schmidt SK. The potential for microbial life in the highest-elevation (>6000 m.a.s.l.) mineral soils of the Atacama region. ACTA ACUST UNITED AC 2012. [DOI: 10.1029/2012jg001961] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Niederberger TD, Sohm JA, Tirindelli J, Gunderson T, Capone DG, Carpenter EJ, Cary SC. Diverse and highly active diazotrophic assemblages inhabit ephemerally wetted soils of the Antarctic Dry Valleys. FEMS Microbiol Ecol 2012; 82:376-90. [PMID: 22500944 DOI: 10.1111/j.1574-6941.2012.01390.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 04/04/2012] [Accepted: 04/10/2012] [Indexed: 11/28/2022] Open
Abstract
Eolian transport of biomass from ephemerally wetted soils, associated with summer glacial meltwater runoffs and lake edges, to low-productivity areas of the Antarctic Dry Valleys (DV) has been postulated to be an important source of organic matter (fixed nitrogen and fixed carbon) to the entire DV ecosystem. However, descriptions and identification of the microbial members responsible for N(2) fixation within these wetted sites are limited. In this study, N(2) fixers from wetted soils were identified by direct nifH gene sequencing and their in situ N(2) fixation activities documented via acetylene reduction and RNA-based quantitative PCR assays. Shannon-index nifH diversity levels ranged between 1.8 and 2.6 and included the expected cyanobacterial signatures and a large number of phylotypes related to the gamma-, beta-, alpha-, and delta-proteobacteria. N(2) fixation rates ranged between approximately 0.5 and 6 nmol N cm(-3) h(-1) with measurements indicating that approximately 50% of this activity was linked with sulfate reduction at some sites. Comparisons with proximal dry soils also suggested that these communities are not ubiquitously distributed, and conditions unrelated to moisture content may define the composition, diversity, or habitat suitability of the microbial communities within wetted soils of the DVs.
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Stomeo F, Makhalanyane TP, Valverde A, Pointing SB, Stevens MI, Cary CS, Tuffin MI, Cowan DA. Abiotic factors influence microbial diversity in permanently cold soil horizons of a maritime-associated Antarctic Dry Valley. FEMS Microbiol Ecol 2012; 82:326-40. [DOI: 10.1111/j.1574-6941.2012.01360.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 03/06/2012] [Accepted: 03/06/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Francesca Stomeo
- Institute for Microbial Biotechnology and Metagenomics; University of the Western Cape; Cape Town; South Africa
| | - Thulani P. Makhalanyane
- Institute for Microbial Biotechnology and Metagenomics; University of the Western Cape; Cape Town; South Africa
| | - Angel Valverde
- Institute for Microbial Biotechnology and Metagenomics; University of the Western Cape; Cape Town; South Africa
| | - Stephen B. Pointing
- School of Biological Sciences; The University of Hong Kong; Hong Kong; China
| | - Mark I. Stevens
- South Australian Museum and School of Earth and Environmental Sciences; University of Adelaide; Adelaide; SA; Australia
| | - Craig S. Cary
- Department of Biological Sciences; University of Waikato; Hamilton; New Zealand
| | - Marla I. Tuffin
- Institute for Microbial Biotechnology and Metagenomics; University of the Western Cape; Cape Town; South Africa
| | - Don A. Cowan
- Institute for Microbial Biotechnology and Metagenomics; University of the Western Cape; Cape Town; South Africa
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Frossard A, Gerull L, Mutz M, Gessner MO. Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors. ISME JOURNAL 2011; 6:680-91. [PMID: 22030674 DOI: 10.1038/ismej.2011.134] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A fundamental issue in microbial and general ecology is the question to what extent environmental conditions dictate the structure of communities and the linkages with functional properties of ecosystems (that is, ecosystem function). We approached this question by taking advantage of environmental gradients established in soil and sediments of small stream corridors in a recently created, early successional catchment. Specifically, we determined spatial and temporal patterns of bacterial community structure and their linkages with potential microbial enzyme activities along the hydrological flow paths of the catchment. Soil and sediments were sampled in a total of 15 sites on four occasions spread throughout a year. Denaturing gradient gel electrophoresis (DGGE) was used to characterize bacterial communities, and substrate analogs linked to fluorescent molecules served to track 10 different enzymes as specific measures of ecosystem function. Potential enzyme activities varied little among sites, despite contrasting environmental conditions, especially in terms of water availability. Temporal changes, in contrast, were pronounced and remarkably variable among the enzymes tested. This suggests much greater importance of temporal dynamics than spatial heterogeneity in affecting specific ecosystem functions. Most strikingly, bacterial community structure revealed neither temporal nor spatial patterns. The resulting disconnect between bacterial community structure and potential enzyme activities indicates high functional redundancy within microbial communities even in the physically and biologically simplified stream corridors of early successional landscapes.
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Affiliation(s)
- Aline Frossard
- Department of Aquatic Ecology, Eawag (Swiss Federal Institute of Aquatic Science and Technology), Dübendorf, Switzerland.
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23
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Zeglin LH, Dahm CN, Barrett JE, Gooseff MN, Fitpatrick SK, Takacs-Vesbach CD. Bacterial community structure along moisture gradients in the parafluvial sediments of two ephemeral desert streams. MICROBIAL ECOLOGY 2011; 61:543-556. [PMID: 21153024 DOI: 10.1007/s00248-010-9782-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Accepted: 11/18/2010] [Indexed: 05/30/2023]
Abstract
Microorganisms inhabiting stream sediments mediate biogeochemical processes of importance to both aquatic and terrestrial ecosystems. In deserts, the lateral margins of ephemeral stream channels (parafluvial sediments) are dried and rewetted, creating periodically wet conditions that typically enhance microbial activity. However, the influence of water content on microbial community composition and diversity in desert stream sediments is unclear. We sampled stream margins along gradients of wet to dry sediments, measuring geochemistry and bacterial 16S rRNA gene composition, at streams in both a cold (McMurdo Dry Valleys, Antarctica) and hot (Chihuahuan Desert, New Mexico, USA) desert. Across the gradients, sediment water content spanned a wide range (1.6-37.9% w/w), and conductivity was highly variable (12.3-1,380 μS cm(-2)). Bacterial diversity (at 97% sequence similarity) was high and variable, but did not differ significantly between the hot and cold desert and was not correlated with sediment water content. Instead, conductivity was most strongly related to diversity. Water content was strongly related to bacterial 16S rRNA gene community composition, though samples were distributed in wet and dry clusters rather than as assemblages shifting along a gradient. Phylogenetic analyses showed that many taxa from wet sediments at the hot and cold desert site were related to, respectively, halotolerant Gammaproteobacteria, and one family within the Sphingobacteriales (Bacteroidetes), while dry sediments at both sites contained a high proportion of taxa related to the Acidobacteria. These results suggest that bacterial diversity and composition in desert stream sediments is more strongly affected by hydrology and conductivity than temperature.
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Affiliation(s)
- Lydia H Zeglin
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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Austin AT. Has water limited our imagination for aridland biogeochemistry? Trends Ecol Evol 2011; 26:229-35. [PMID: 21397975 DOI: 10.1016/j.tree.2011.02.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 02/08/2011] [Accepted: 02/09/2011] [Indexed: 10/18/2022]
Abstract
The classic ecological paradigm for deserts, that all processes are controlled by water availability, has limited our imagination for exploring other controls on the cycling of carbon and nutrients in aridland ecosystems. This review of recent studies identifies alternative mechanisms that challenge the idea that all soil processes in aridlands are proximately water-limited, and highlights the significance of photodegradation of aboveground litter and the overriding importance of spatial heterogeneity as a modulator of biotic responses to water availability. Aridlands currently occupy >30% of the terrestrial land surface and are expanding. It is therefore critical to incorporate these previously unappreciated mechanisms in our understanding of aridland biogeochemistry to mitigate the effects of desertification and global change.
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Affiliation(s)
- Amy T Austin
- Instituto de Investigaciones Ecológicas y Fisiológicas Vinculadas a la Agricultura (IFEVA-CONICET), Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453 Buenos Aires, (C1417DSE) Argentina.
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