101
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Jurburg SD, Nunes I, Brejnrod A, Jacquiod S, Priemé A, Sørensen SJ, Van Elsas JD, Salles JF. Legacy Effects on the Recovery of Soil Bacterial Communities from Extreme Temperature Perturbation. Front Microbiol 2017; 8:1832. [PMID: 28993764 PMCID: PMC5622210 DOI: 10.3389/fmicb.2017.01832] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/06/2017] [Indexed: 02/01/2023] Open
Abstract
The type and frequency of disturbances experienced by soil microbiomes is expected to increase given predicted global climate change scenarios and intensified anthropogenic pressures on ecosystems. While the direct effect of multiple disturbances to soil microbes has been explored in terms of function, their effect on the recovery of microbial community composition remains unclear. Here, we used soil microcosm experiments and multiple model disturbances to explore their short-term effect on the recovery of soil microbiota after identical or novel stresses. Soil microcosms were exposed to a heat shock to create an initial effect. Upon initial community recovery (25 days after stress), they were subjected to a second stress, either a heat or a cold shock, and they were monitored for additional 25 days. To carefully verify the bacterial response to the disturbances, we monitored changes in community composition throughout the experiment using 16S rRNA gene transcript amplicon sequencing. The application of a heat shock to soils with or without the initial heat shock resulted in similar successional dynamics, but these dynamics were faster in soils with a prior heat shock. The application of a cold shock had negligible effects on previously undisturbed soils but, in combination with an initial heat shock, caused the largest shift in the community composition. Our findings show that compounded perturbation affects bacterial community recovery by altering community structure and thus, the community's response during succession. By altering dominance patterns, disturbance legacy affects the microbiome's ability to recover from further perturbation within the 25 days studied. Our results highlight the need to consider the soil's disturbance history in the development of soil management practices in order to maintain the system's resilience.
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Affiliation(s)
- Stephanie D. Jurburg
- Microbial Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands
- Bioinformatics group, Bioveterinary Institute, Wageningen University and ResearchWageningen, Netherlands
| | - Inês Nunes
- Section of Microbiology, University of CopenhagenCopenhagen, Denmark
- Microbe Technology Department, NovozymesCopenhagen, Denmark
| | - Asker Brejnrod
- Section of Microbiology, University of CopenhagenCopenhagen, Denmark
| | - Samuel Jacquiod
- Section of Microbiology, University of CopenhagenCopenhagen, Denmark
| | - Anders Priemé
- Section of Microbiology, University of CopenhagenCopenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, University of CopenhagenCopenhagen, Denmark
| | - Jan Dirk Van Elsas
- Microbial Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands
| | - Joana F. Salles
- Microbial Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands
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102
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Kaisermann A, de Vries FT, Griffiths RI, Bardgett RD. Legacy effects of drought on plant-soil feedbacks and plant-plant interactions. THE NEW PHYTOLOGIST 2017. [PMID: 28621813 DOI: 10.1111/nph.14661] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Interactions between aboveground and belowground biota have the potential to modify ecosystem responses to climate change, yet little is known about how drought influences plant-soil feedbacks with respect to microbial mediation of plant community dynamics. We tested the hypothesis that drought modifies plant-soil feedback with consequences for plant competition. We measured net pairwise plant-soil feedbacks for two grassland plant species grown in monoculture and competition in soils that had or had not been subjected to a previous drought; these were then exposed to a subsequent drought. To investigate the mechanisms involved, we assessed treatment responses of soil microbial communities and nutrient availability. We found that previous drought had a legacy effect on bacterial and fungal community composition that decreased plant growth in conspecific soils and had knock-on effects for plant competitive interactions. Moreover, plant and microbial responses to subsequent drought were dependent on a legacy effect of the previous drought on plant-soil interactions. We show that drought has lasting effects on belowground communities with consequences for plant-soil feedbacks and plant-plant interactions. This suggests that drought, which is predicted to increase in frequency with climate change, may change soil functioning and plant community composition via the modification of plant-soil feedbacks.
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Affiliation(s)
- Aurore Kaisermann
- School of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Manchester, M13 9PT, UK
- UMR 1391 Interaction Sol-Plante-Atmosphere, INRA Centre Bordeaux-Aquitaine, CS20032, 71 Avenue Edouard Bourlaux, Villenave d'Ornon Cedex, 33882, France
| | - Franciska T de Vries
- School of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Manchester, M13 9PT, UK
| | - Robert I Griffiths
- Centre of Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, OX10 8BB, UK
| | - Richard D Bardgett
- School of Earth and Environmental Sciences, The University of Manchester, Michael Smith Building, Manchester, M13 9PT, UK
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103
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Starke R, Bastida F, Abadía J, García C, Nicolás E, Jehmlich N. Ecological and functional adaptations to water management in a semiarid agroecosystem: a soil metaproteomics approach. Sci Rep 2017; 7:10221. [PMID: 28860535 PMCID: PMC5579227 DOI: 10.1038/s41598-017-09973-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 08/02/2017] [Indexed: 01/14/2023] Open
Abstract
Climate change models point to a decrease in water availability in semiarid areas that would compromise the maintenance of sustainable agriculture. Here, we used a grapefruit agroecosystem model to evaluate the responses of the active soil microbial community – as a microbial subset directly involved in soil functionality- undergoing strategies to cope with the low water availability in south-east Spain. For this purpose, we tested the impacts of: (i) water quality: transfer-water from a river (TW) or reclaimed-water from a wastewater-treatment plant (RW); and (ii) water quantity: continuous optimal amount of water or reduced irrigation (RDI) in the temporal frame when the crop is less sensitive; and their interactions. Metaproteomics revealed that the phylogenetic diversity of the active community and its functional diversity were lowered in soils with RW. RDI lowered soil respiration and functional diversity while the phylogenetic diversity remained constant. The reestablishment of full irrigation after RDI led to a recovery of soil respiration that was accompanied by an enhanced abundance of resilient bacterial populations. Bacterial populations displayed molecular mechanisms against water stress that have been conserved evolutionarily in plants. Protein-based studies shed light on ecological and functional mechanisms that govern the adaptive responses of soil microbial communities to climate-change friendly water management.
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Affiliation(s)
- Robert Starke
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Felipe Bastida
- Centro de Edafología y Biología Aplicada del Segura. Spanish Research Council (CEBAS-CSIC). Campus Universitario de Espinardo, CP 30100 PO Box 164, Murcia, Spain.
| | - Joaquín Abadía
- Centro de Edafología y Biología Aplicada del Segura. Spanish Research Council (CEBAS-CSIC). Campus Universitario de Espinardo, CP 30100 PO Box 164, Murcia, Spain
| | - Carlos García
- Centro de Edafología y Biología Aplicada del Segura. Spanish Research Council (CEBAS-CSIC). Campus Universitario de Espinardo, CP 30100 PO Box 164, Murcia, Spain
| | - Emilio Nicolás
- Centro de Edafología y Biología Aplicada del Segura. Spanish Research Council (CEBAS-CSIC). Campus Universitario de Espinardo, CP 30100 PO Box 164, Murcia, Spain
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Permoserstrasse 15, 04318, Leipzig, Germany
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104
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Dal Bello M, Rindi L, Benedetti-Cecchi L. Legacy effects and memory loss: how contingencies moderate the response of rocky intertidal biofilms to present and past extreme events. GLOBAL CHANGE BIOLOGY 2017; 23:3259-3268. [PMID: 28181716 DOI: 10.1111/gcb.13656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/24/2017] [Accepted: 01/25/2017] [Indexed: 06/06/2023]
Abstract
Understanding how historical processes modulate the response of ecosystems to perturbations is becoming increasingly important. In contrast to the growing interest in projecting biodiversity and ecosystem functioning under future climate scenarios, how legacy effects originating from historical conditions drive change in ecosystems remains largely unexplored. Using experiments in combination with stochastic antecedent modelling, we evaluated how extreme warming, sediment deposition and grazing events modulated the ecological memory of rocky intertidal epilithic microphytobenthos (EMPB). We found memory effects in the non-clustered scenario of disturbance (60 days apart), where EMPB biomass fluctuated in time, but not under clustered disturbances (15 days apart), where EMPB biomass was consistently low. A massive grazing event impacted on EMPB biomass in a second run of the experiment, also muting ecological memory. Our results provide empirical support to the theoretical expectation that stochastic fluctuations promote ecological memory, but also show that contingencies may lead to memory loss.
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Affiliation(s)
- Martina Dal Bello
- Department of Biology, University of Pisa, CoNISMa, Via Derna 1, Pisa, Italy
| | - Luca Rindi
- Department of Biology, University of Pisa, CoNISMa, Via Derna 1, Pisa, Italy
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105
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Berga M, Zha Y, Székely AJ, Langenheder S. Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes. Front Microbiol 2017. [PMID: 28642735 PMCID: PMC5463035 DOI: 10.3389/fmicb.2017.00948] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Disturbances and environmental change are important factors determining the diversity, composition, and functioning of communities. However, knowledge about how natural bacterial communities are affected by such perturbations is still sparse. We performed a whole ecosystem manipulation experiment with freshwater rock pools where we applied salinity disturbances of different intensities. The aim was to test how the compositional and functional resistance and resilience of bacterial communities, alpha- and beta-diversity and the relative importance of stochastic and deterministic community assembly processes changed along a disturbance intensity gradient. We found that bacterial communities were functionally resistant to all salinity levels (3, 6, and 12 psu) and compositionally resistant to a salinity increase to 3 psu and resilient to increases of 6 and 12 psu. Increasing salinities had no effect on local richness and evenness, beta-diversity and the proportion of deterministically vs. stochastically assembled communities. Our results show a high functional and compositional stability of bacterial communities to salinity changes of different intensities both at local and regional scales, which possibly reflects long-term adaptation to environmental conditions in the study system.
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Affiliation(s)
- Mercè Berga
- Department of Ecology and Genetics/Limnology, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden.,Biological Oceanography, Leibniz Institute for Baltic Sea Research WarnemündeRostock, Germany
| | - Yinghua Zha
- Department of Ecology and Genetics/Limnology, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden
| | - Anna J Székely
- Department of Ecology and Genetics/Limnology, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden
| | - Silke Langenheder
- Department of Ecology and Genetics/Limnology, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden
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106
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Historical climate controls soil respiration responses to current soil moisture. Proc Natl Acad Sci U S A 2017; 114:6322-6327. [PMID: 28559315 DOI: 10.1073/pnas.1620811114] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ecosystem carbon losses from soil microbial respiration are a key component of global carbon cycling, resulting in the transfer of 40-70 Pg carbon from soil to the atmosphere each year. Because these microbial processes can feed back to climate change, understanding respiration responses to environmental factors is necessary for improved projections. We focus on respiration responses to soil moisture, which remain unresolved in ecosystem models. A common assumption of large-scale models is that soil microorganisms respond to moisture in the same way, regardless of location or climate. Here, we show that soil respiration is constrained by historical climate. We find that historical rainfall controls both the moisture dependence and sensitivity of respiration. Moisture sensitivity, defined as the slope of respiration vs. moisture, increased fourfold across a 480-mm rainfall gradient, resulting in twofold greater carbon loss on average in historically wetter soils compared with historically drier soils. The respiration-moisture relationship was resistant to environmental change in field common gardens and field rainfall manipulations, supporting a persistent effect of historical climate on microbial respiration. Based on these results, predicting future carbon cycling with climate change will require an understanding of the spatial variation and temporal lags in microbial responses created by historical rainfall.
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107
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Dispersal timing and drought history influence the response of bacterioplankton to drying-rewetting stress. ISME JOURNAL 2017; 11:1764-1776. [PMID: 28440801 DOI: 10.1038/ismej.2017.55] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/21/2017] [Accepted: 03/03/2017] [Indexed: 01/06/2023]
Abstract
The extent and frequency of drought episodes is expected to increase in the following decades making it a crucial stress factor for smaller water bodies. However, very little is known about how bacterioplankton is affected by increased evaporation and how these communities reassemble after rewetting. Here, we present results from a microcosm experiment that assessed the effect of drying-rewetting stress on bacterioplankton in the light of the stress history and the rate and timing of dispersal after the rewetting. We found that the drying phase resulted mainly in a change of function, whereas the complete desiccation and rewetting processes strongly affected both composition and function, which were, however, influenced by the initial conditions and stress history of the communities. Effects of dispersal were generally stronger when it occurred at an early stage after the rewetting. At this stage, selective establishment of dispersed bacteria coupled with enhanced compositional and functional recovery was found, whereas effects of dispersal were neutral, that is, predictable by dispersal rates, at later stages. Our studies therefore show that both the stress history and the timing of dispersal are important factors that influence the response of bacterial communities to environmental change and stress events.
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108
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Jurburg SD, Nunes I, Stegen JC, Le Roux X, Priemé A, Sørensen SJ, Salles JF. Autogenic succession and deterministic recovery following disturbance in soil bacterial communities. Sci Rep 2017; 7:45691. [PMID: 28383027 PMCID: PMC5382530 DOI: 10.1038/srep45691] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 03/03/2017] [Indexed: 01/23/2023] Open
Abstract
The response of bacterial communities to environmental change may affect local to global nutrient cycles. However the dynamics of these communities following disturbance are poorly understood, given that they are often evaluated over macro-ecological time scales and end-point measurements. In order to understand the successional trajectory of soil bacterial communities following disturbances and the mechanisms controlling these dynamics at a scale relevant for these organisms, we subjected soil microcosms to a heat disturbance and followed the community composition of active bacteria over 50 days. The disturbance imposed a strong selective pressure that persisted for up to 10 days, after which the importance of stochastic processes increased. Three successional stages were detected: a primary response in which surviving taxa increased in abundance; a secondary response phase during which community dynamics slowed down, and a stability phase (after 29 days), during which the community tended towards its original composition. Phylogenetic turnover patterns indicated that the community experienced stronger deterministic selection during recovery. Thus, soil bacterial communities, despite their extreme diversity and functional redundancy, respond to disturbances like many macro-ecological systems and exhibit path-dependent, autogenic dynamics during secondary succession. These results highlight the role of autogenic factors and successional dynamics in microbial recovery.
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Affiliation(s)
- Stephanie D Jurburg
- Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands
| | - Inês Nunes
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - James C Stegen
- Earth and Biological Sciences, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xavier Le Roux
- Microbial Ecology Center, INRA (UMR 1418), CNRS, Université Lyon1, Université de Lyon, 69622 Villeurbanne, France
| | - Anders Priemé
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, Denmark
| | - Joana Falcão Salles
- Genomic Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, Groningen, 9747 AG, The Netherlands
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109
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Kumaresan D, Cross AT, Moreira-Grez B, Kariman K, Nevill P, Stevens J, Allcock RJN, O'Donnell AG, Dixon KW, Whiteley AS. Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration. Sci Rep 2017; 7:564. [PMID: 28373716 PMCID: PMC5428872 DOI: 10.1038/s41598-017-00650-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/07/2017] [Indexed: 11/21/2022] Open
Abstract
Mining of mineral resources produces substantial volumes of crushed rock based wastes that are characterised by poor physical structure and hydrology, unstable geochemistry and potentially toxic chemical conditions. Recycling of these substrates is desirable and can be achieved by blending waste with native soil to form a ‘novel substrate’ which may be used in future landscape restoration. However, these post-mining substrate based ‘soils’ are likely to contain significant abiotic constraints for both plant and microbial growth. Effective use of these novel substrates for ecosystem restoration will depend on the efficacy of stored topsoil as a potential microbial inoculum as well as the subsequent generation of key microbial soil functions originally apparent in local pristine sites. Here, using both marker gene and shotgun metagenome sequencing, we show that topsoil storage and the blending of soil and waste substrates to form planting substrates gives rise to variable bacterial and archaeal phylogenetic composition but a high degree of metabolic conservation at the community metagenome level. Our data indicates that whilst low phylogenetic conservation is apparent across substrate blends we observe high functional redundancy in relation to key soil microbial pathways, allowing the potential for functional recovery of key belowground pathways under targeted management.
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Affiliation(s)
- Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Adam T Cross
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Kings Park and Botanic Garden, 1 Kattidj Close, Kings Park, WA, 6005, Australia
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Khalil Kariman
- UWA School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Paul Nevill
- Department of Environment and Agriculture, Curtin University, GPO Box U1987, Bentley, WA, 6102, Australia
| | - Jason Stevens
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Kings Park and Botanic Garden, 1 Kattidj Close, Kings Park, WA, 6005, Australia
| | - Richard J N Allcock
- School of Pathology and Laboratory Medicine, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Pathwest Laboratory Medicine WA, QEII Medical Centre, Monash Avenue, Nedlands, WA, 6009, Australia
| | - Anthony G O'Donnell
- Faculty of Science, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Kingsley W Dixon
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.,Department of Environment and Agriculture, Curtin University, GPO Box U1987, Bentley, WA, 6102, Australia
| | - Andrew S Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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110
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Gliksman D, Rey A, Seligmann R, Dumbur R, Sperling O, Navon Y, Haenel S, De Angelis P, Arnone JA, Grünzweig JM. Biotic degradation at night, abiotic degradation at day: positive feedbacks on litter decomposition in drylands. GLOBAL CHANGE BIOLOGY 2017; 23:1564-1574. [PMID: 27520482 DOI: 10.1111/gcb.13465] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 06/02/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
The arid and semi-arid drylands of the world are increasingly recognized for their role in the terrestrial net carbon dioxide (CO2 ) uptake, which depends largely on plant litter decomposition and the subsequent release of CO2 back to the atmosphere. Observed decomposition rates in drylands are higher than predictions by biogeochemical models, which are traditionally based on microbial (biotic) degradation enabled by precipitation as the main mechanism of litter decomposition. Consequently, recent research in drylands has focused on abiotic mechanisms, mainly photochemical and thermal degradation, but they only partly explain litter decomposition under dry conditions, suggesting the operation of an additional mechanism. Here we show that in the absence of precipitation, absorption of dew and water vapor by litter in the field enables microbial degradation at night. By experimentally manipulating solar irradiance and nighttime air humidity, we estimated that most of the litter CO2 efflux and decay occurring in the dry season was due to nighttime microbial degradation, with considerable additional contributions from photochemical and thermal degradation during the daytime. In a complementary study, at three sites across the Mediterranean Basin, litter CO2 efflux was largely explained by litter moisture driving microbial degradation and ultraviolet radiation driving photodegradation. We further observed mutual enhancement of microbial activity and photodegradation at a daily scale. Identifying the interplay of decay mechanisms enhances our understanding of carbon turnover in drylands, which should improve the predictions of the long-term trend of global carbon sequestration.
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Affiliation(s)
- Daniel Gliksman
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 7610001, Israel
| | - Ana Rey
- Department of Biogeography and Global Change, National Museum of Natural History, Spanish Scientific Council (CSIC), C/Serrano 115bis, 28006, Madrid, Spain
| | - Ron Seligmann
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 7610001, Israel
| | - Rita Dumbur
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 7610001, Israel
| | - Or Sperling
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Yael Navon
- Ramat Hanadiv Nature Park, Zichron Yakov, Israel
| | - Sabine Haenel
- Faculty of Agriculture/Landscape Management, University of Applied Sciences HTW-Dresden, Pillnitzer Platz 2, 01326, Dresden, Germany
| | - Paolo De Angelis
- DIBAF (Department for Innovation in Biological, Agro-Food and Forest Systems), University of Tuscia, Via San Camillo de Lellis, 01100, Viterbo, Italy
| | - John A Arnone
- Desert Research Institute, 2215 Raggio Pkwy, Reno, NV, 89512, USA
| | - José M Grünzweig
- Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 7610001, Israel
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111
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Martiny JBH, Martiny AC, Weihe C, Lu Y, Berlemont R, Brodie EL, Goulden ML, Treseder KK, Allison SD. Microbial legacies alter decomposition in response to simulated global change. THE ISME JOURNAL 2017; 11:490-499. [PMID: 27740610 PMCID: PMC5270563 DOI: 10.1038/ismej.2016.122] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/11/2016] [Accepted: 08/05/2016] [Indexed: 01/19/2023]
Abstract
Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungal composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities.
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Affiliation(s)
- Jennifer BH Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Claudia Weihe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Ying Lu
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Renaud Berlemont
- Department of Earth System Science, University of California, Irvine, CA, USA
- Department of Biology, California State University, Long Beach, CA, USA
| | - Eoin L Brodie
- Ecology Department, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Michael L Goulden
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
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112
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Graham EB, Crump AR, Resch CT, Fansler S, Arntzen E, Kennedy DW, Fredrickson JK, Stegen JC. Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism. Front Microbiol 2016; 7:1949. [PMID: 28123379 PMCID: PMC5226446 DOI: 10.3389/fmicb.2016.01949] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/21/2016] [Indexed: 11/13/2022] Open
Abstract
Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures-imposed by sediment and porewater physicochemistry-integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.
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Affiliation(s)
- Emily B Graham
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Alex R Crump
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Charles T Resch
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Sarah Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Evan Arntzen
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - David W Kennedy
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - Jim K Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
| | - James C Stegen
- Biological Sciences Division, Pacific Northwest National Laboratory Richland, WA, USA
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113
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Fodelianakis S, Moustakas A, Papageorgiou N, Manoli O, Tsikopoulou I, Michoud G, Daffonchio D, Karakassis I, Ladoukakis ED. Modified niche optima and breadths explain the historical contingency of bacterial community responses to eutrophication in coastal sediments. Mol Ecol 2016; 26:2006-2018. [DOI: 10.1111/mec.13842] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 08/30/2016] [Accepted: 09/14/2016] [Indexed: 01/06/2023]
Affiliation(s)
- S. Fodelianakis
- Biological and Environmental Sciences and Engineering Department King Abdullah University of Science and Technology (KAUST) Thuwal 23955‐6900 Saudi Arabia
- Department of Biology University of Crete Voutes University Campus 70013 Heraklion Crete Greece
| | - A. Moustakas
- School of Biological and Chemical Sciences Queen Mary University of London Mile End Road London E1 4NS UK
| | - N. Papageorgiou
- Department of Biology University of Crete Voutes University Campus 70013 Heraklion Crete Greece
| | - O. Manoli
- Department of Biology University of Crete Voutes University Campus 70013 Heraklion Crete Greece
| | - I. Tsikopoulou
- Department of Biology University of Crete Voutes University Campus 70013 Heraklion Crete Greece
| | - G. Michoud
- Biological and Environmental Sciences and Engineering Department King Abdullah University of Science and Technology (KAUST) Thuwal 23955‐6900 Saudi Arabia
| | - D. Daffonchio
- Biological and Environmental Sciences and Engineering Department King Abdullah University of Science and Technology (KAUST) Thuwal 23955‐6900 Saudi Arabia
| | - I. Karakassis
- Department of Biology University of Crete Voutes University Campus 70013 Heraklion Crete Greece
| | - E. D. Ladoukakis
- Department of Biology University of Crete Voutes University Campus 70013 Heraklion Crete Greece
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114
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Fuchslueger L, Bahn M, Hasibeder R, Kienzl S, Fritz K, Schmitt M, Watzka M, Richter A. Drought history affects grassland plant and microbial carbon turnover during and after a subsequent drought event. THE JOURNAL OF ECOLOGY 2016; 104:1453-1465. [PMID: 27609992 PMCID: PMC4996329 DOI: 10.1111/1365-2745.12593] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 04/18/2016] [Indexed: 05/07/2023]
Abstract
Drought periods are projected to become more severe and more frequent in many European regions. While effects of single strong droughts on plant and microbial carbon (C) dynamics have been studied in some detail, impacts of recurrent drought events are still little understood.We tested whether the legacy of extreme experimental drought affects responses of plant and microbial C and nitrogen (N) turnover to further drought and rewetting. In a mountain grassland, we conducted a 13C pulse-chase experiment during a naturally occurring drought and rewetting event in plots previously exposed to experimental droughts and in ambient controls (AC). After labelling, we traced 13C below-ground allocation and incorporation into soil microbes using phospholipid fatty acid biomarkers.Drought history (DH) had no effects on the standing shoot and fine root plant biomass. However, plants with experimental DH displayed decreased shoot N concentrations and increased fine root N concentrations relative to those in AC. During the natural drought, plants with DH assimilated and allocated less 13C below-ground; moreover, fine root respiration was reduced and not fuelled by fresh C compared to plants in AC.Regardless of DH, microbial biomass remained stable during natural drought and rewetting. Although microbial communities initially differed in their composition between soils with and without DH, they responded to the natural drought and rewetting in a similar way: gram-positive bacteria increased, while fungal and gram-negative bacteria remained stable. In soils with DH, a strongly reduced uptake of recent plant-derived 13C in microbial biomarkers was observed during the natural drought, pointing to a smaller fraction of active microbes or to a microbial community that is less dependent on plant C. Synthesis. Drought history can induce changes in above- vs. below-ground plant N concentrations and affect the response of plant C turnover to further droughts and rewetting by decreasing plant C uptake and below-ground allocation. DH does not affect the responses of the microbial community to further droughts and rewetting, but alters microbial functioning, particularly the turnover of recent plant-derived carbon, during and after further drought periods.
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Affiliation(s)
- Lucia Fuchslueger
- Department of Microbiology and Ecosystem Science University of Vienna Althanstrasse 14A-1090 Vienna Austria; Present address: National Institute for Amazonian Research (INPA) Av. André Araujo 2936 Aleixo Manaus Amazonas CEP: 69067-375 Brazil
| | - Michael Bahn
- Institute of Ecology University of Innsbruck Sternwartestrasse 15 A-6020 Innsbruck Austria
| | - Roland Hasibeder
- Institute of Ecology University of Innsbruck Sternwartestrasse 15 A-6020 Innsbruck Austria
| | - Sandra Kienzl
- Department of Microbiology and Ecosystem Science University of Vienna Althanstrasse 14 A-1090 Vienna Austria
| | - Karina Fritz
- Institute of Ecology University of Innsbruck Sternwartestrasse 15 A-6020 Innsbruck Austria
| | - Michael Schmitt
- Institute of Ecology University of Innsbruck Sternwartestrasse 15 A-6020 Innsbruck Austria
| | - Margarete Watzka
- Department of Microbiology and Ecosystem Science University of Vienna Althanstrasse 14 A-1090 Vienna Austria
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science University of Vienna Althanstrasse 14 A-1090 Vienna Austria
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115
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Bastida F, Jehmlich N. It's all about functionality: How can metaproteomics help us to discuss the attributes of ecological relevance in soil? J Proteomics 2016; 144:159-61. [DOI: 10.1016/j.jprot.2016.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 06/01/2016] [Indexed: 10/21/2022]
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116
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Sheng Y, Bibby K, Grettenberger C, Kaley B, Macalady JL, Wang G, Burgos WD. Geochemical and Temporal Influences on the Enrichment of Acidophilic Iron-Oxidizing Bacterial Communities. Appl Environ Microbiol 2016; 82:3611-3621. [PMID: 27084004 PMCID: PMC4959181 DOI: 10.1128/aem.00917-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 02/01/2023] Open
Abstract
UNLABELLED Two acid mine drainage (AMD) sites in the Appalachian bituminous coal basin were selected to enrich for Fe(II)-oxidizing microbes and measure rates of low-pH Fe(II) oxidation in chemostatic bioreactors. Microbial communities were enriched for 74 to 128 days in fed-batch mode, then switched to flowthrough mode (additional 52 to 138 d) to measure rates of Fe(II) oxidation as a function of pH (2.1 to 4.2) and influent Fe(II) concentration (80 to 2,400 mg/liter). Biofilm samples were collected throughout these operations, and the microbial community structure was analyzed to evaluate impacts of geochemistry and incubation time. Alpha diversity decreased as the pH decreased and as the Fe(II) concentration increased, coincident with conditions that attained the highest rates of Fe(II) oxidation. The distribution of the seven most abundant bacterial genera could be explained by a combination of pH and Fe(II) concentration. Acidithiobacillus, Ferrovum, Gallionella, Leptospirillum, Ferrimicrobium, Acidiphilium, and Acidocella were all found to be restricted within specific bounds of pH and Fe(II) concentration. Temporal distance, defined as the cumulative number of pore volumes from the start of flowthrough mode, appeared to be as important as geochemical conditions in controlling microbial community structure. Both alpha and beta diversities of microbial communities were significantly correlated to temporal distance in the flowthrough experiments. Even after long-term operation under nearly identical geochemical conditions, microbial communities enriched from the different sites remained distinct. While these microbial communities were enriched from sites that displayed markedly different field rates of Fe(II) oxidation, rates of Fe(II) oxidation measured in laboratory bioreactors were essentially the same. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup. IMPORTANCE This study showed that different microbial communities enriched from two sites maintained distinct microbial community traits inherited from their respective seed materials. Long-term operation (up to 128 days of fed-batch enrichment followed by up to 138 days of flowthrough experiments) of these two systems did not lead to the same, or even more similar, microbial communities. However, these bioreactors did oxidize Fe(II) and remove total iron [Fe(T)] at very similar rates. These results suggest that the performance of suspended-growth bioreactors for AMD treatment may not be strongly dependent on the inoculum used for reactor startup. This would be advantageous, because system performance should be well constrained and predictable for many different sites.
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Affiliation(s)
- Yizhi Sheng
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
- School of Water Resources and Environment, China University of Geosciences, Beijing, China
| | - Kyle Bibby
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Christen Grettenberger
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Bradley Kaley
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jennifer L Macalady
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Guangcai Wang
- School of Water Resources and Environment, China University of Geosciences, Beijing, China
| | - William D Burgos
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, Pennsylvania, USA
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117
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Trivedi P, Delgado-Baquerizo M, Trivedi C, Hu H, Anderson IC, Jeffries TC, Zhou J, Singh BK. Microbial regulation of the soil carbon cycle: evidence from gene-enzyme relationships. ISME JOURNAL 2016; 10:2593-2604. [PMID: 27168143 DOI: 10.1038/ismej.2016.65] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/31/2022]
Abstract
A lack of empirical evidence for the microbial regulation of ecosystem processes, including carbon (C) degradation, hinders our ability to develop a framework to directly incorporate the genetic composition of microbial communities in the enzyme-driven Earth system models. Herein we evaluated the linkage between microbial functional genes and extracellular enzyme activity in soil samples collected across three geographical regions of Australia. We found a strong relationship between different functional genes and their corresponding enzyme activities. This relationship was maintained after considering microbial community structure, total C and soil pH using structural equation modelling. Results showed that the variations in the activity of enzymes involved in C degradation were predicted by the functional gene abundance of the soil microbial community (R2>0.90 in all cases). Our findings provide a strong framework for improved predictions on soil C dynamics that could be achieved by adopting a gene-centric approach incorporating the abundance of functional genes into process models.
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Affiliation(s)
- Pankaj Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Chanda Trivedi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Hangwei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Thomas C Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Botany and Microbiology, The University of Oklahoma, Norman, OK, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith South, New South Wales, Australia.,Global Centre for Land Based Innovation, Western Sydney University, Penrith South, New South Wales, Australia
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118
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Averill C, Waring BG, Hawkes CV. Historical precipitation predictably alters the shape and magnitude of microbial functional response to soil moisture. GLOBAL CHANGE BIOLOGY 2016; 22:1957-64. [PMID: 26748720 DOI: 10.1111/gcb.13219] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/26/2015] [Indexed: 05/03/2023]
Abstract
Soil moisture constrains the activity of decomposer soil microorganisms, and in turn the rate at which soil carbon returns to the atmosphere. While increases in soil moisture are generally associated with increased microbial activity, historical climate may constrain current microbial responses to moisture. However, it is not known if variation in the shape and magnitude of microbial functional responses to soil moisture can be predicted from historical climate at regional scales. To address this problem, we measured soil enzyme activity at 12 sites across a broad climate gradient spanning 442-887 mm mean annual precipitation. Measurements were made eight times over 21 months to maximize sampling during different moisture conditions. We then fit saturating functions of enzyme activity to soil moisture and extracted half saturation and maximum activity parameter values from model fits. We found that 50% of the variation in maximum activity parameters across sites could be predicted by 30-year mean annual precipitation, an indicator of historical climate, and that the effect is independent of variation in temperature, soil texture, or soil carbon concentration. Based on this finding, we suggest that variation in the shape and magnitude of soil microbial response to soil moisture due to historical climate may be remarkably predictable at regional scales, and this approach may extend to other systems. If historical contingencies on microbial activities prove to be persistent in the face of environmental change, this approach also provides a framework for incorporating historical climate effects into biogeochemical models simulating future global change scenarios.
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Affiliation(s)
- Colin Averill
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Bonnie G Waring
- Department of Ecology Evolution and Behavior, University of Minnesota, St. Paul, MN, 55455, USA
| | - Christine V Hawkes
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
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119
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Revillini D, Gehring CA, Johnson NC. The role of locally adapted mycorrhizas and rhizobacteria in plant–soil feedback systems. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12668] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Revillini
- Department of Biological Sciences Northern Arizona University PO Box 5640 Flagstaff AZ 86011 USA
| | - Catherine A. Gehring
- Department of Biological Sciences Northern Arizona University PO Box 5640 Flagstaff AZ 86011 USA
| | - Nancy Collins Johnson
- Department of Biological Sciences Northern Arizona University PO Box 5640 Flagstaff AZ 86011 USA
- School of Earth Sciences and Environmental Sustainability Northern Arizona University PO Box 5694 Flagstaff AZ 86011 USA
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120
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Renslow RS, Lindemann SR, Song HS. A Generalized Spatial Measure for Resilience of Microbial Systems. Front Microbiol 2016; 7:443. [PMID: 27092116 PMCID: PMC4823267 DOI: 10.3389/fmicb.2016.00443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 03/18/2016] [Indexed: 11/29/2022] Open
Abstract
The emergent property of resilience is the ability of a system to return to an original state after a disturbance. Resilience may be used as an early warning system for significant or irreversible community transition; that is, a community with diminishing or low resilience may be close to catastrophic shift in function or an irreversible collapse. Typically, resilience is quantified using recovery time, which may be difficult or impossible to directly measure in microbial systems. A recent study in the literature showed that under certain conditions, a set of spatial-based metrics termed recovery length, can be correlated to recovery time, and thus may be a reasonable alternative measure of resilience. However, this spatial metric of resilience is limited to use for step-change perturbations. Building upon the concept of recovery length, we propose a more general form of the spatial metric of resilience that can be applied to any shape of perturbation profiles (for example, either sharp or smooth gradients). We termed this new spatial measure “perturbation-adjusted spatial metric of resilience” (PASMORE). We demonstrate the applicability of the proposed metric using a mathematical model of a microbial mat.
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Affiliation(s)
- Ryan S Renslow
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA, USA
| | - Stephen R Lindemann
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA, USA
| | - Hyun-Seob Song
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland WA, USA
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121
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Stolpovsky K, Fetzer I, Van Cappellen P, Thullner M. Influence of dormancy on microbial competition under intermittent substrate supply: insights from model simulations. FEMS Microbiol Ecol 2016; 92:fiw071. [DOI: 10.1093/femsec/fiw071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/01/2016] [Indexed: 12/14/2022] Open
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122
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Rebollar EA, Antwis RE, Becker MH, Belden LK, Bletz MC, Brucker RM, Harrison XA, Hughey MC, Kueneman JG, Loudon AH, McKenzie V, Medina D, Minbiole KPC, Rollins-Smith LA, Walke JB, Weiss S, Woodhams DC, Harris RN. Using "Omics" and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases. Front Microbiol 2016; 7:68. [PMID: 26870025 PMCID: PMC4735675 DOI: 10.3389/fmicb.2016.00068] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 01/14/2016] [Indexed: 12/20/2022] Open
Abstract
Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called "omics," are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the Kolmogorov-Smirnov Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics, or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.
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Affiliation(s)
- Eria A. Rebollar
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
| | - Rachael E. Antwis
- Unit for Environmental Sciences and Management, North-West UniversityPotchefstroom, South Africa
- Institute of Zoology, Zoological Society of LondonLondon, UK
- School of Environment and Life Sciences, University of SalfordSalford, UK
| | - Matthew H. Becker
- Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological ParkWashington, DC, USA
| | - Lisa K. Belden
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Molly C. Bletz
- Zoological Institute, Technische Universität BraunschweigBraunschweig, Germany
| | | | | | - Myra C. Hughey
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Jordan G. Kueneman
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Andrew H. Loudon
- Department of Zoology, Biodiversity Research Centre, University of British ColumbiaVancouver, BC, Canada
| | - Valerie McKenzie
- Department of Ecology and Evolutionary Biology, University of ColoradoBoulder, CO, USA
| | - Daniel Medina
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | | | - Louise A. Rollins-Smith
- Department of Pathology, Microbiology and Immunology and Department of Pediatrics, Vanderbilt University School of Medicine, Department of Biological Sciences, Vanderbilt UniversityNashville, TN, USA
| | - Jenifer B. Walke
- Department of Biological Sciences, Virginia TechBlacksburg, VA, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado at BoulderBoulder, CO, USA
| | | | - Reid N. Harris
- Department of Biology, James Madison UniversityHarrisonburg, VA, USA
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123
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Mueller RC, Belnap J, Kuske CR. Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland. Front Microbiol 2015; 6:891. [PMID: 26388845 PMCID: PMC4559666 DOI: 10.3389/fmicb.2015.00891] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/17/2015] [Indexed: 11/13/2022] Open
Abstract
Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0-0.5 or 0-10 cm) across the N-amendment gradient (0, 7, and 15 kg ha(-1) yr(-1)). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.
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Affiliation(s)
- Rebecca C Mueller
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
| | - Jayne Belnap
- Southwest Biological Science Center, United States Geological Survey Moab, UT, USA
| | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory Los Alamos, NM, USA
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