201
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Rastelli E, Corinaldesi C, Dell'Anno A, Tangherlini M, Martorelli E, Ingrassia M, Chiocci FL, Lo Martire M, Danovaro R. High potential for temperate viruses to drive carbon cycling in chemoautotrophy-dominated shallow-water hydrothermal vents. Environ Microbiol 2017; 19:4432-4446. [DOI: 10.1111/1462-2920.13890] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/06/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Eugenio Rastelli
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn; Villa Comunale; Naples 80121 Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Michael Tangherlini
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Eleonora Martorelli
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
| | - Michela Ingrassia
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
- Department of Earth Science; University of Rome Sapienza; Rome Italy
| | - Francesco L. Chiocci
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
- Department of Earth Science; University of Rome Sapienza; Rome Italy
| | - Marco Lo Martire
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn; Villa Comunale; Naples 80121 Italy
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202
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Sarker JR, Singh BP, He X, Fang Y, Li GD, Collins D, Cowie AL. Tillage and nitrogen fertilization enhanced belowground carbon allocation and plant nitrogen uptake in a semi-arid canola crop-soil system. Sci Rep 2017; 7:10726. [PMID: 28878351 PMCID: PMC5587530 DOI: 10.1038/s41598-017-11190-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 08/16/2017] [Indexed: 12/04/2022] Open
Abstract
Carbon (C) and nitrogen (N) allocation and assimilation are coupled processes, likely influencing C accumulation, N use efficiency and plant productivity in agro-ecosystems. However, dynamics and responses of these processes to management practices in semi-arid agro-ecosystems are poorly understood. A field-based 13CO2 and urea-15N pulse labelling experiment was conducted to track how C and N allocation and assimilation during canola growth from flowering to maturity were affected by short-term (2-year) tillage (T) and no-till (NT) with or without 100 kg urea-N ha-1 (T-0, T-100, NT-0, NT-100) on a Luvisol in an Australian semi-arid region. The T-100 caused greater (P < 0.05) belowground C allocation and higher (P < 0.05) translocation of soil N to shoots and seeds, compared to other treatments. Microbial N uptake was rapid and greatest in the fertilized (cf. non-fertilized) treatments, followed by a rapid release of microbial immobilized N, thus increasing N availability for plant uptake. In contrast, management practices had insignificant impact on soil C and N stocks, aggregate stability, microbial biomass, and 13C retention in aggregate-size fractions. In conclusion, tillage and N fertilization increased belowground C allocation and crop N uptake and yield, possibly via enhancing root-microbial interactions, with minimal impact on soil properties.
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Affiliation(s)
- Jharna Rani Sarker
- University of New England, Armidale, NSW 2351, Australia
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, NSW 2568, Australia
| | - Bhupinder Pal Singh
- University of New England, Armidale, NSW 2351, Australia.
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, NSW 2568, Australia.
| | - Xinhua He
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, NSW 2568, Australia
- College of Resources and Environment, Southwest University, Chongqing, 400715, China
| | - Yunying Fang
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, NSW 2568, Australia
| | - Guangdi D Li
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - Damian Collins
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, NSW 2568, Australia
| | - Annette L Cowie
- University of New England, Armidale, NSW 2351, Australia
- NSW Department of Primary Industries, Beef Industry Centre, Trevenna Road, Armidale, NSW 2351, Australia
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203
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Soares M, Kritzberg ES, Rousk J. Labile carbon ‘primes’ fungal use of nitrogen from submerged leaf litter. FEMS Microbiol Ecol 2017; 93:4104630. [DOI: 10.1093/femsec/fix110] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/04/2017] [Indexed: 11/12/2022] Open
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204
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Zornoza R, Gómez-Garrido M, Martínez-Martínez S, Gómez-López MD, Faz Á. Bioaugmentaton in Technosols created in abandoned pyritic tailings can contribute to enhance soil C sequestration and plant colonization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 593-594:357-367. [PMID: 28346909 DOI: 10.1016/j.scitotenv.2017.03.154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 03/16/2017] [Accepted: 03/16/2017] [Indexed: 06/06/2023]
Abstract
Creation of Technosols in combination with phytostabilization may be a sustainable strategy to minimize the environmental and human health hazards derived from mine tailings. Bioaugmentation can facilitate plant establishment and growth for efficient phytostabilization. In order to assess if bioaugmentation can increase soil quality and fertility, decrease metal(loid) mobility and accelerate plant colonization, a one-year field experiment was designed with creation of Technosols in two tailings ponds with different pH (acidic (AT) and neutral (NT)), with addition of marble waste (MaW) and two organic materials (pig manure (PM) and sewage sludge (SS), without or with inoculation of effective microorganisms (EM) at three rates. Results showed that MaW was the main factor responsible for maintaining pH ~7 in AT and ~8 in NT, decreasing salinity, and decreasing the soluble fraction of metals (70-99%). The soluble fraction of As decreased ~45% in AT, related to increases in pH up to neutrality, while increased ~90% in NT with PM due to pH>8 and higher content of organic compounds. The addition of PM and SS significantly increased soil organic C (SOC), nutrient contents and microbial biomass and activity in both tailings, being PM more effective. However, a positive priming effect was observed in NT with SS addition likely due to higher C/N ratio and lack of nutrients. There was a significant effect of EM rate on inorganic C, SOC, N, K and microbial biomass and activity, with higher values as rate increased. Vegetation richness and density directly increased with increasing EM rate. Multivariate analyses showed that the most important properties contributing to increase richness and plant density were microbial biomass and N. Thus, bioaugmentation contributed to soil C sequestration (as organic and inorganic C) and soil fertility, related to high soil microbial biomass and activity, which facilitated an effective colonization of vegetation.
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Affiliation(s)
- Raúl Zornoza
- Sustainable Use, Management, and Reclamation of Soil and Water Research Group, Technical School of Agricultural Engineering, Universidad Politécnica de Cartagena, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain.
| | - Melisa Gómez-Garrido
- Sustainable Use, Management, and Reclamation of Soil and Water Research Group, Technical School of Agricultural Engineering, Universidad Politécnica de Cartagena, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain
| | - Silvia Martínez-Martínez
- Sustainable Use, Management, and Reclamation of Soil and Water Research Group, Technical School of Agricultural Engineering, Universidad Politécnica de Cartagena, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain
| | - María Dolores Gómez-López
- Sustainable Use, Management, and Reclamation of Soil and Water Research Group, Technical School of Agricultural Engineering, Universidad Politécnica de Cartagena, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain
| | - Ángel Faz
- Sustainable Use, Management, and Reclamation of Soil and Water Research Group, Technical School of Agricultural Engineering, Universidad Politécnica de Cartagena, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain
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205
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Effects of different nitrogen additions on soil microbial communities in different seasons in a boreal forest. Ecosphere 2017. [DOI: 10.1002/ecs2.1879] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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206
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Xu Y, Chen Z, Ding W, Fan J. Responses of manure decomposition to nitrogen addition: Role of chemical composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 587-588:11-21. [PMID: 28187939 DOI: 10.1016/j.scitotenv.2017.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/05/2017] [Accepted: 02/05/2017] [Indexed: 06/06/2023]
Abstract
Understanding the interactions among organic manure chemical composition, decomposition and nitrogen (N) fertilization is critical for sustainable agriculture management. Six organic manures were incubated in a cultivated black soil with or without N addition for one year, and carbon dioxide (CO2) emissions from these organic manures were monitored. Chemical compositions of the organic manures were determined by elemental analysis, proximate chemical analysis, and carbon (C)-13 nuclear magnetic resonance spectroscopy, and evaluated after cupric-oxide oxidation for lignin biomarkers. During the experimental period, 19-44% of manure C was decomposed without N addition, which decreased to 17-35% with N addition, except for the composted furfural residue with rice dregs. However, during different decomposition stages, N effect changed from stimulation to inhibition, or behaved as increasing inhibition. During stage 1 (days 0-100) when N stimulation effect reached a maximum, CO2 emissions from manure had positive relationships with labile C fraction indicators, including total sugars, soluble polyphenols, and lignin cinnamyl/vanillyl ratio regardless of N addition. N effect on manure decomposition was related to the C/N ratio and labile organic C content. During stage 2 (days 101-267), N effect shifted to inhibition, with CO2 emissions from manure negatively related to lignin vanillyl-units content. The magnitude of N inhibition increased linearly with the aromaticity of dissolved organic C, and was strengthened by nitrate in manure. Finally, N inhibition effect reached a maximum during stage 3 (days 268-365), increasing with higher aromatic C in manure. Critical factors for manure decomposition shifted from total sugars, soluble polyphenols, and lignin cinnamyl-units to recalcitrant lignin vanillyl-units and aromatic C fraction, which mediated the type and magnitude of N effect on decomposition. Our results suggested that the potential for enhancing soil C sequestration with organic manures would magnify under combined application with N fertilizer in the long term.
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Affiliation(s)
- Yehong Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zengming Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Jianling Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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207
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Ehtesham E, Bengtson P. Decoupling of soil carbon and nitrogen turnover partly explains increased net ecosystem production in response to nitrogen fertilization. Sci Rep 2017; 7:46286. [PMID: 28406242 PMCID: PMC5390271 DOI: 10.1038/srep46286] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 03/15/2017] [Indexed: 11/09/2022] Open
Abstract
During the last decade there has been an ongoing controversy regarding the extent to which nitrogen fertilization can increase carbon sequestration and net ecosystem production in forest ecosystems. The debate is complicated by the fact that increased nitrogen availability caused by nitrogen deposition has coincided with increasing atmospheric carbon dioxide concentrations. The latter could further stimulate primary production but also result in increased allocation of carbon to root exudates, which could potentially 'prime' the decomposition of soil organic matter. Here we show that increased input of labile carbon to forest soil caused a decoupling of soil carbon and nitrogen cycling, which was manifested as a reduction in respiration of soil organic matter that coincided with a substantial increase in gross nitrogen mineralization. An estimate of the magnitude of the effect demonstrates that the decoupling could potentially result in an increase in net ecosystem production by up to 51 kg C ha-1 day-1 in nitrogen fertilized stands during peak summer. Even if the effect is several times lower on an annual basis, the results still suggest that nitrogen fertilization can have a much stronger influence on net ecosystem production than can be expected from a direct stimulation of primary production alone.
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Affiliation(s)
- Emad Ehtesham
- Department of Biology – Microbial Ecology, Lund University, Lund, Sweden
| | - Per Bengtson
- Department of Biology – Microbial Ecology, Lund University, Lund, Sweden
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208
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Morrissey EM, Mau RL, Schwartz E, McHugh TA, Dijkstra P, Koch BJ, Marks JC, Hungate BA. Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter. ISME JOURNAL 2017; 11:1890-1899. [PMID: 28387774 DOI: 10.1038/ismej.2017.43] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/06/2017] [Accepted: 02/14/2017] [Indexed: 12/26/2022]
Abstract
Microorganisms perform most decomposition on Earth, mediating carbon (C) loss from ecosystems, and thereby influencing climate. Yet, how variation in the identity and composition of microbial communities influences ecosystem C balance is far from clear. Using quantitative stable isotope probing of DNA, we show how individual bacterial taxa influence soil C cycling following the addition of labile C (glucose). Specifically, we show that increased decomposition of soil C in response to added glucose (positive priming) occurs as a phylogenetically diverse group of taxa, accounting for a large proportion of the bacterial community, shift toward additional soil C use for growth. Our findings suggest that many microbial taxa exhibit C use plasticity, as most taxa altered their use of glucose and soil organic matter depending upon environmental conditions. In contrast, bacteria that exhibit other responses to glucose (reduced growth or reliance on glucose for additional growth) clustered strongly by phylogeny. These results suggest that positive priming is likely the prototypical response of bacteria to sustained labile C addition, consistent with the widespread occurrence of the positive priming effect in nature.
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Affiliation(s)
- Ember M Morrissey
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, USA
| | - Rebecca L Mau
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Theresa A McHugh
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO, USA
| | - Paul Dijkstra
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA
| | - Jane C Marks
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.,Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA
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209
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Schmidt J, Fester T, Schulz E, Michalzik B, Buscot F, Gutknecht J. Effects of plant-symbiotic relationships on the living soil microbial community and microbial necromass in a long-term agro-ecosystem. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 581-582:756-765. [PMID: 28082056 DOI: 10.1016/j.scitotenv.2017.01.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/30/2016] [Accepted: 01/01/2017] [Indexed: 06/06/2023]
Abstract
We examined the impact of arbuscular mycorrhizal fungi and rhizobia on the living microbial community and microbial necromass under different long-term fertilization treatments at the long-term Static Fertilization Experiment Bad Lauchstädt (Germany). Phospholipid fatty acids (PLFA) and amino sugars plus muramic acid, were used as biomarkers for soil microbial bio- and necromass, respectively, and analyzed from six treatments imposed on two crop rotations, varying only in the inclusion/non-inclusion of a legume. Treatments included: two levels of only farmyard manure (FYM), only mineral fertilizer (NPK), the combined application of both fertilizer types and a non-fertilized control. PLFA profiles differed clearly between the investigated crop rotations and were significantly related to labile C, mineral N, and soil pH. This emphasizes the role of carbon, and of mycorrhizal and rhizobial symbioses, as driver for changes in the microbial community composition due to effects on the living conditions in soil. We found some evidence that legume associated symbiosis with arbuscular mycorrhizal fungi and rhizobia act as a buffer, reducing the impact of varying inputs of mineral nutrients on the decomposer community. While our results support former findings that living microbial populations vary within short-term periods and are reflective of a given crop grown in a given year, soil necromass composition indicates longer term changes across the two crop rotation types, mainly shaped by fertilizer related effects on the community composition and C turnover. However, there was some evidence that specifically the presence of a legume, affects the soil necromass composition not only over the whole crop rotation but even in the short-term.
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Affiliation(s)
- J Schmidt
- UFZ - Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle, Germany.
| | - T Fester
- UFZ - Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, D-04318 Leipzig, Germany
| | - E Schulz
- UFZ - Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle, Germany
| | - B Michalzik
- Friedrich-Schiller-University of Jena, Institute of Geography, Löbdergraben 32, D-07743 Jena, Germany
| | - F Buscot
- UFZ - Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle, Germany; German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103 Leipzig, Germany
| | - J Gutknecht
- UFZ - Helmholtz Centre for Environmental Research, Department of Soil Ecology, Theodor-Lieser-Str. 4, D-06120 Halle, Germany; University of Minnesota, Twin Cities, Department of Soil, Water, and Climate, 439 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
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210
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Bohacz J. Lignocellulose-degrading enzymes, free-radical transformations during composting of lignocellulosic waste and biothermal phases in small-scale reactors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 580:744-754. [PMID: 27986311 DOI: 10.1016/j.scitotenv.2016.12.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/16/2016] [Accepted: 12/03/2016] [Indexed: 05/23/2023]
Abstract
Environmentally friendly strategies of waste management are both part of legal solutions currently in place and a focus of interest worldwide. Large-scale composting plants are set up across various regions while home composting is becoming increasingly popular. A variety of microbial groups are successively at work during composting and enzymatic activities detected in the composting mass fluctuate accordingly. Changes in the activities of oxidoreductases and hydrolases, i.e. glucose oxidase, horseradish peroxidase, lignin peroxidase, laccase, xylanase, superoxide dismutase and keratinase, low-molecular weight compounds, i.e. methoxyphenolic and hydroxyphenolic compounds, and the relative level of superoxide radicals and glucose were determined periodically in water extracts of composts to investigate the process of biochemical transformations of ligninocellulose in relation to biothermal phases and to identify a potential priming effect in two composts containing different ratios of lignocellulosic waste and chicken feathers. Composting was conducted for 30weeks. An important aim of the study was to demonstrate that a positive priming effect was induced during composting of a variety of lignocellulosic waste types using native keratin (chicken feathers) as a source of N. The effect was more evident in compost containing grass, which was related to a more rapid depletion of easily available sources of C and energy (glucose) during composting. Ligninolytic enzymes known to biodegrade recalcitrant organic matter were induced in subsequent biothermal phases of composting. Compost I enriched with grass (pine bark, grass, sawdust and chicken feathers) exhibited a higher enzymatic activity than compost II which did not contain any grass but which had a greater number of hardly-degradable components (pine bark, wheat straw, sawdust, chicken feathers). Similar observations were made for the concentrations of low-molecular weight compounds. The enzymes activities and concentration of low-molecular weight compounds listed above can be used to estimate the biodegradation of lignocellulose during composting.
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Affiliation(s)
- Justyna Bohacz
- University of Life Sciences, Faculty of Agrobioengineering, Department of Environmental Microbiology, Laboratory of Mycology, 7 Leszczyńskiego Street, 20-069 Lublin, Poland.
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211
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Naranjo-Ortíz MA, Brock M, Brunke S, Hube B, Marcet-Houben M, Gabaldón T. Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes. Front Microbiol 2016; 7:2001. [PMID: 28066338 PMCID: PMC5169069 DOI: 10.3389/fmicb.2016.02001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/29/2016] [Indexed: 01/22/2023] Open
Abstract
Analysis of the growing number of available fully-sequenced genomes has shown that Horizontal Gene Transfer (HGT) in eukaryotes is more common than previously thought. It has been proposed that genes with certain functions may be more prone to HGT than others, but we still have a very poor understanding of the selective forces driving eukaryotic HGT. Recent work uncovered that d-amino acid racemases have been commonly transferred from bacteria to fungi, but their role in the receiving organisms is currently unknown. Here, we set out to assess whether d-amino acid racemases are commonly transferred to and between eukaryotic groups. For this we performed a global survey that used a novel automated phylogeny-based HGT-detection algorithm (Abaccus). Our results revealed that at least 7.0% of the total eukaryotic racemase repertoire is the result of inter- or intra-domain HGT. These transfers are significantly enriched in plant-associated fungi. For these, we hypothesize a possible role for the acquired racemases allowing to exploit minoritary nitrogen sources in plant biomass, a nitrogen-poor environment. Finally, we performed experiments on a transferred aspartate-glutamate racemase in the fungal human pathogen Candida glabrata, which however revealed no obvious biological role.
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Affiliation(s)
- Miguel A Naranjo-Ortíz
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Matthias Brock
- Fungal Genetics and Biology Group, School of Life Sciences, University of Nottingham Nottingham, UK
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Hans Knoell Institute Jena Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Hans Knoell Institute JenaJena, Germany; Friedrich Schiller UniversityJena, Germany; Center for Sepsis Control and Care, University HospitalJena, Germany
| | - Marina Marcet-Houben
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation, The Barcelona Institute of Science and TechnologyBarcelona, Spain; Universitat Pompeu FabraBarcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA)Barcelona, Spain
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212
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Rousk K, Michelsen A, Rousk J. Microbial control of soil organic matter mineralization responses to labile carbon in subarctic climate change treatments. GLOBAL CHANGE BIOLOGY 2016; 22:4150-4161. [PMID: 27010358 DOI: 10.1111/gcb.13296] [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: 01/18/2016] [Revised: 02/17/2016] [Accepted: 03/11/2016] [Indexed: 06/05/2023]
Abstract
Half the global soil carbon (C) is held in high-latitude systems. Climate change will expose these to warming and a shift towards plant communities with more labile C input. Labile C can also increase the rate of loss of native soil organic matter (SOM); a phenomenon termed 'priming'. We investigated how warming (+1.1 °C over ambient using open top chambers) and litter addition (90 g m-2 yr-1 ) treatments in the subarctic influenced the susceptibility of SOM mineralization to priming, and its microbial underpinnings. Labile C appeared to inhibit the mineralization of C from SOM by up to 60% within hours. In contrast, the mineralization of N from SOM was stimulated by up to 300%. These responses occurred rapidly and were unrelated to microbial successional dynamics, suggesting catabolic responses. Considered separately, the labile C inhibited C mineralization is compatible with previously reported findings termed 'preferential substrate utilization' or 'negative apparent priming', while the stimulated N mineralization responses echo recent reports of 'real priming' of SOM mineralization. However, C and N mineralization responses derived from the same SOM source must be interpreted together: This suggested that the microbial SOM-use decreased in magnitude and shifted to components richer in N. This finding highlights that only considering SOM in terms of C may be simplistic, and will not capture all changes in SOM decomposition. The selective mining for N increased in climate change treatments with higher fungal dominance. In conclusion, labile C appeared to trigger catabolic responses of the resident microbial community that shifted the SOM mining to N-rich components; an effect that increased with higher fungal dominance. Extrapolating from these findings, the predicted shrub expansion in the subarctic could result in an altered microbial use of SOM, selectively mining it for N-rich components, and leading to a reduced total SOM-use.
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Affiliation(s)
- Kathrin Rousk
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, 1350, Copenhagen, Denmark
| | - Anders Michelsen
- Terrestrial Ecology Section, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, 1350, Copenhagen, Denmark
| | - Johannes Rousk
- Section of Microbial Ecology, Department of Biology, Lund University, 22362, Lund, Sweden
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213
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Emsens WJ, Aggenbach CJS, Grootjans AP, Nfor EE, Schoelynck J, Struyf E, van Diggelen R. Eutrophication triggers contrasting multilevel feedbacks on litter accumulation and decomposition in fens. Ecology 2016; 97:2680-2690. [PMID: 27859133 DOI: 10.1002/ecy.1482] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/13/2016] [Accepted: 05/25/2016] [Indexed: 11/06/2022]
Abstract
Eutrophication is a major threat for the persistence of nutrient-poor fens, as multilevel feedbacks on decomposition rates could trigger carbon loss and increase nutrient cycling. Here, we experimentally investigate the effects of macronutrient (NPK) enrichment on litter quality of six species of sedge (Carex sp.), which we relate to litter decomposition rates in a nutrient-poor and nutrient-rich environment. Our research focused on four levels: we examined how eutrophication alters (1) fresh litter production ("productivity shift"), (2) litter stoichiometry within the same species ("intraspecific shift"), (3) overall litter stoichiometry of the vegetation under the prediction that low-competitive species are outcompeted by fast-growing competitors ("interspecific shift"), and (4) litter decomposition rates due to an altered external environment (e.g., shifts in microbial activity; "exogenous shift"). Eutrophication triggered a strong increase in fresh litter production. Moreover, individuals of the same species produced litter with lower C:N and C:P ratios, higher K contents, and lower lignin, Ca and Mg contents (intraspecific shift), which increased litter decomposability. In addition, species typical for eutrophic conditions produced more easily degradable litter than did species typical for nutrient-poor conditions (interspecific shift). However, the effects of nutrient loading of the external environment (exogenous shift) were contradictory. Here, interactions between litter type and ambient nutrient level indicate that the (exogenous) effects of eutrophication on litter decomposition rates are strongly dependent of litter quality. Moreover, parameters of litter quality only correlated with decomposition rates for litter incubated in nutrient-poor environments, but not in eutrophic environments. This suggests that rates of litter decomposition can be uncoupled from litter stoichiometry under eutrophic conditions. In conclusion, our results show that eutrophication affects litter accumulation and -decomposition at multiple levels, in which stimulatory and inhibitory effects interact. The cumulative effect of these interactions ultimately determine whether peatlands remain sinks or become sources of carbon under eutrophic conditions.
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Affiliation(s)
- W-J Emsens
- Ecosystem Management Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1C, Wilrijk, 2610, Belgium
| | - C J S Aggenbach
- Ecosystem Management Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1C, Wilrijk, 2610, Belgium.,KWR Watercycle Research Institute, PO Box 1072, Nieuwegein, 3430 BB, the Netherlands
| | - A P Grootjans
- Centre for Energy and Environmental Studies, University of Groningen, Groningen, the Netherlands.,Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - E E Nfor
- Ecosystem Management Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1C, Wilrijk, 2610, Belgium
| | - J Schoelynck
- Ecosystem Management Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1C, Wilrijk, 2610, Belgium
| | - E Struyf
- Ecosystem Management Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1C, Wilrijk, 2610, Belgium
| | - R van Diggelen
- Ecosystem Management Research Group, Department of Biology, University of Antwerp, Universiteitsplein 1C, Wilrijk, 2610, Belgium
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214
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Wang Q, He T, Liu J. Litter input decreased the response of soil organic matter decomposition to warming in two subtropical forest soils. Sci Rep 2016; 6:33814. [PMID: 27644258 PMCID: PMC5028766 DOI: 10.1038/srep33814] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/02/2016] [Indexed: 11/17/2022] Open
Abstract
Interaction effect of temperature and litter input on SOM decomposition is poor understood, restricting accurate prediction of the dynamics and stocks of soil organic carbon under global warming. To address this knowledge gap, we conducted an incubation experiment by adding 13C labeled leaf-litter into a coniferous forest (CF) soil and a broadleaved forest (BF) soil. In this experiment, response of the temperature sensitivity (Q10) of SOM decomposition to the increase in litter input was investigated. The temperature dependences of priming effect (PE) and soil microbial community were analyzed. The Q10 for CF soil significantly decreased from 2.41 in no-litter treatment to 2.05 in litter-added treatment and for BF soil from 2.14 to 1.82, suggesting that litter addition decreases the Q10. PE in the CF soil was 24.9% at 20 °C and 6.2% at 30 °C, and in the BF soil the PE was 8.8% at 20 °C and −7.0% at 30 °C, suggesting that PE decreases with increasing temperature. Relative PE was positively related to the concentrations of Gram-negative bacterial and fungal PLFAs. This study moves a step forward in understanding warming effect on forest carbon cycling by highlighting interaction effect of litter input and warming on soil carbon cycling.
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Affiliation(s)
- Qingkui Wang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, P. R. China.,Huitong Experimental Station of Forest Ecology, Chinese Academy of Sciences, Huitong 418307, P.R. China
| | - Tongxin He
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, P. R. China
| | - Jing Liu
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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215
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Souza HA, Parent SÉ, Rozane DE, Amorim DA, Modesto VC, Natale W, Parent LE. Guava Waste to Sustain Guava (Psidium guajava) Agroecosystem: Nutrient "Balance" Concepts. FRONTIERS IN PLANT SCIENCE 2016; 7:1252. [PMID: 27621735 PMCID: PMC5002492 DOI: 10.3389/fpls.2016.01252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/08/2016] [Indexed: 05/26/2023]
Abstract
The Brazilian guava processing industry generates 5.5 M Mg guava waste year(-1) that could be recycled sustainably in guava agro-ecosystems as slow-release fertilizer. Our objectives were to elaborate nutrient budgets and to diagnose soil, foliar, and fruit nutrient balances in guava orchards fertilized with guava waste. We hypothesized that (1) guava waste are balanced fertilizer sources that can sustain crop yield and soil nutrient stocks, and (2) guava agroecosystems remain productive within narrow ranges of nutrient balances. A 6-year experiment was conducted in 8-year old guava orchard applying 0-9-18-27-36 Mg ha(-1) guava waste (dry mass basis) and the locally recommended mineral fertilization. Nutrient budgets were compiled as balance sheets. Foliar and fruit nutrient balances were computed as isometric log ratios to avoid data redundancy or resonance due to nutrient interactions and the closure to measurement unit. The N, P, and several other nutrients were applied in excess of crop removal while K was in deficit whatever the guava waste treatment. The foliar diagnostic accuracy reached 93% using isometric log ratios and knn classification, generating reliable foliar nutrient and concentration ranges at high yield level. The plant mined the soil K reserves without any significant effect on fruit yield and foliar nutrient balances involving K. High guava productivity can be reached at lower soil test K and P values than thought before. Parsimonious dosage of fresh guava waste should be supplemented with mineral K fertilizers to recycle guava waste sustainably in guava agroecosystems. Brazilian growers can benefit from this research by lowering soil test P and K threshold values to avoid over-fertilization and using fresh guava waste supplemented with mineral fertilizers, especially K. Because yield was negatively correlated with fruit acidity and Brix index, balanced plant nutrition and fertilization diagnosis will have to consider not only fruit yield targets but also fruit quality to meet requirements for guava processing.
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Affiliation(s)
- Henrique A. Souza
- Empresa Brasileira de Pesquisa Agropecuária - Embrapa Meio-NorteTeresina, Brazil
| | - Serge-Étienne Parent
- Department of Soils and Agrifood Engineering, Université Laval, QuébecCA, Canada
| | - Danilo E. Rozane
- Cursos de Engenharia Agronômica e Engenharia de Pesca, Universidade Estadual Paulista “Júlio de Mesquita Filho,”Registro, Brazil
| | - Daniel A. Amorim
- Empresa de Pesquisa Agropecuária de Minas Gerais - EPAMIG OesteUberaba, Brazil
| | - Viviane C. Modesto
- Faculdade de Engenharia, Universidade Estadual Paulista “Júlio de Mesquita Filho,”Ilha Solteira, Brazil
| | - William Natale
- Departamento de Fitotecnia, Universidade Federal do CearáFortaleza, Brazil
| | - Leon E. Parent
- Department of Soils and Agrifood Engineering, Université Laval, QuébecCA, Canada
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216
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Louis BP, Maron PA, Menasseri-Aubry S, Sarr A, Lévêque J, Mathieu O, Jolivet C, Leterme P, Viaud V. Microbial Diversity Indexes Can Explain Soil Carbon Dynamics as a Function of Carbon Source. PLoS One 2016; 11:e0161251. [PMID: 27551779 PMCID: PMC4995005 DOI: 10.1371/journal.pone.0161251] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 08/02/2016] [Indexed: 11/19/2022] Open
Abstract
Mathematical models do not explicitly represent the influence of soil microbial diversity on soil organic carbon (SOC) dynamics despite recent evidence of relationships between them. The objective of the present study was to statistically investigate relationships between bacterial and fungal diversity indexes (richness, evenness, Shannon index, inverse Simpson index) and decomposition of different pools of soil organic carbon by measuring dynamics of CO2 emissions under controlled conditions. To this end, 20 soils from two different land uses (cropland and grassland) were incubated with or without incorporation of 13C-labelled wheat-straw residue. 13C-labelling allowed us to study residue mineralisation, basal respiration and the priming effect independently. An innovative data-mining approach was applied, based on generalized additive models and a predictive criterion. Results showed that microbial diversity indexes can be good covariates to integrate in SOC dynamics models, depending on the C source and the processes considered (native soil organic carbon vs. fresh wheat residue). Specifically, microbial diversity indexes were good candidates to help explain mineralisation of native soil organic carbon, while priming effect processes seemed to be explained much more by microbial composition, and no microbial diversity indexes were found associated with residue mineralisation. Investigation of relationships between diversity and mineralisation showed that higher diversity, as measured by the microbial diversity indexes, seemed to be related to decreased CO2 emissions in the control soil. We suggest that this relationship can be explained by an increase in carbon yield assimilation as microbial diversity increases. Thus, the parameter for carbon yield assimilation in mathematical models could be calculated as a function of microbial diversity indexes. Nonetheless, given limitations of the methods used, these observations should be considered with caution and confirmed with more experimental studies. Overall, along with other studies on relationships between microbial community composition and SOM dynamics, this study suggests that overall measures of microbial diversity may constitute relevant ways to include microbial diversity in models of SOM dynamics.
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Affiliation(s)
- Benjamin P. Louis
- UMR SAS 1069, AGROCAMPUS OUEST, Rennes, France
- UMR SAS 1069, INRA, Rennes, France
| | | | | | | | - Jean Lévêque
- Biogeosciences, University Bourgogne Franche-Comté, CNRS, Dijon, France
| | - Olivier Mathieu
- Biogeosciences, University Bourgogne Franche-Comté, CNRS, Dijon, France
| | | | - Philippe Leterme
- UMR SAS 1069, AGROCAMPUS OUEST, Rennes, France
- UMR SAS 1069, INRA, Rennes, France
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217
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Pajares S, Bohannan BJM. Ecology of Nitrogen Fixing, Nitrifying, and Denitrifying Microorganisms in Tropical Forest Soils. Front Microbiol 2016; 7:1045. [PMID: 27468277 PMCID: PMC4932190 DOI: 10.3389/fmicb.2016.01045] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/22/2016] [Indexed: 01/08/2023] Open
Abstract
Soil microorganisms play important roles in nitrogen cycling within forest ecosystems. Current research has revealed that a wider variety of microorganisms, with unexpected diversity in their functions and phylogenies, are involved in the nitrogen cycle than previously thought, including nitrogen-fixing bacteria, ammonia-oxidizing bacteria and archaea, heterotrophic nitrifying microorganisms, and anammox bacteria, as well as denitrifying bacteria, archaea, and fungi. However, the vast majority of this research has been focused in temperate regions, and relatively little is known regarding the ecology of nitrogen-cycling microorganisms within tropical and subtropical ecosystems. Tropical forests are characterized by relatively high precipitation, low annual temperature fluctuation, high heterogeneity in plant diversity, large amounts of plant litter, and unique soil chemistry. For these reasons, regulation of the nitrogen cycle in tropical forests may be very different from that of temperate ecosystems. This is of great importance because of growing concerns regarding the effect of land use change and chronic-elevated nitrogen deposition on nitrogen-cycling processes in tropical forests. In the context of global change, it is crucial to understand how environmental factors and land use changes in tropical ecosystems influence the composition, abundance and activity of key players in the nitrogen cycle. In this review, we synthesize the limited currently available information regarding the microbial communities involved in nitrogen fixation, nitrification and denitrification, to provide deeper insight into the mechanisms regulating nitrogen cycling in tropical forest ecosystems. We also highlight the large gaps in our understanding of microbially mediated nitrogen processes in tropical forest soils and identify important areas for future research.
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Affiliation(s)
- Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de MéxicoCoyoacán, Mexico
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218
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Qiu Q, Wu L, Ouyang Z, Li B, Xu Y. Different effects of plant-derived dissolved organic matter (DOM) and urea on the priming of soil organic carbon. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2016; 18:330-341. [PMID: 26791412 DOI: 10.1039/c5em00446b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Soil organic carbon (SOC) mineralization is important for the regulation of the global climate and soil fertility. Decomposition of SOC may be significantly affected by the supply of plant-derived labile carbon (C). To investigate the impact of plant-derived dissolved organic matter (DOM) and urea (N) additions on the decomposition of native SOC as well as to elucidate the underlying mechanisms of priming effects (PEs), a batch of incubation experiments was conducted for 250 days by application of (13)C-labeled plant-derived DOM and urea to soils. The direction of PE induced by the addition of DOM was different from the addition of N, i.e. it switched from negative to positive in DOM-amended soils, whereas in the N-treated soil it switched from positive to negative. Adding DOM alone was favorable for soil C sequestration (59 ± 5 mg C per kg soil), whereas adding N alone or together with DOM accelerated the decomposition of native SOC, causing net C losses (-62 ± 4 and -34 ± 31 mg C per kg soil, respectively). These findings indicate that N addition and its interaction with DOM are not favorable for soil C sequestration. Adding DOM alone increased the level of dissolved organic carbon (DOC), but it did not increase the level of soil mineral N. Changes in the ratio of microbial biomass carbon (MBC) to microbial biomass nitrogen (MBN) and microbial metabolic quotient (qCO2) after the addition of DOM and N suggest that a possible shift in the microbial community composition may occur in the present study. Adding DOM with or without N increased the activities of β-glucosidase and urease. Changes in the direction and magnitude of PE were closely related to changes in soil C and N availability. Soil C and N availability might influence the PE through affecting the microbial biomass and extracellular enzyme activity as well as causing a possible shift in the microbial community composition.
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Affiliation(s)
- Qingyan Qiu
- Yucheng Comprehensive Experiment Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanfang Wu
- Yucheng Comprehensive Experiment Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhu Ouyang
- Yucheng Comprehensive Experiment Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Binbin Li
- Yucheng Comprehensive Experiment Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yanyan Xu
- Yucheng Comprehensive Experiment Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China. and University of Chinese Academy of Sciences, Beijing 100049, China
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219
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Qiao N, Xu X, Hu Y, Blagodatskaya E, Liu Y, Schaefer D, Kuzyakov Y. Carbon and nitrogen additions induce distinct priming effects along an organic-matter decay continuum. Sci Rep 2016; 6:19865. [PMID: 26806914 PMCID: PMC4726261 DOI: 10.1038/srep19865] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 10/30/2015] [Indexed: 12/19/2022] Open
Abstract
Decomposition of organic matter (OM) in soil, affecting carbon (C) cycling and climate feedbacks, depends on microbial activities driven by C and nitrogen (N) availability. However, it remains unknown how decomposition of various OMs vary across global supplies and ratios of C and N inputs. We examined OM decomposition by incubating four types of OM (leaf litter, wood, organic matter from organic and mineral horizons) from a decay continuum in a subtropical forest at Ailao Mountain, China with labile C and N additions. Decomposition of wood with high C:N decreased for 3.9 to 29% with these additions, while leaf decomposition was accelerated only within a narrow C:N range of added C and N. Decomposition of OM from organic horizon was accelerated by high C:N and suppressed by low C:N, but mineral soil was almost entirely controlled by high C:N. These divergent responses to C and N inputs show that mechanisms for priming (i.e. acceleration or retardation of OM decomposition by labile inputs) vary along this decay continuum. We conclude that besides C:N ratios of OM, those of labile inputs control the OM decay in the litter horizons, while energy (labile C) regulates decomposition in mineral soil. This suggests that OM decomposition can be predicted from its intrinsic C:N ratios and those of labile inputs.
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Affiliation(s)
- Na Qiao
- Key Laboratory of Tropical Forest Ecology, Chinese Academy of Sciences, Xishuangbanna Tropical Botanical Garden, Menglun, Mengla, Yunnan 666303, China.,Graduate School of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xingliang Xu
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 11A Datun Road, Chaoyang District, Beijing 100101, China
| | - Yuehua Hu
- Key Laboratory of Tropical Forest Ecology, Chinese Academy of Sciences, Xishuangbanna Tropical Botanical Garden, Menglun, Mengla, Yunnan 666303, China
| | - Evgenia Blagodatskaya
- Department of Soil Science of Temperate Ecosystems, and Department of Agricultural Soil Science, University of Göttingen, Göttingen, Germany.,Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Institutskaya, 26 Pushchino, Moscow Region, Russia, 142290
| | - Yongwen Liu
- Key Laboratory for Earth Surface Processes, Ministry of Education, Peking University, Beijing 100871, China
| | - Douglas Schaefer
- Key Laboratory of Tropical Forest Ecology, Chinese Academy of Sciences, Xishuangbanna Tropical Botanical Garden, Menglun, Mengla, Yunnan 666303, China
| | - Yakov Kuzyakov
- Department of Soil Science of Temperate Ecosystems, and Department of Agricultural Soil Science, University of Göttingen, Göttingen, Germany
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220
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Craig ME, Pearson SM, Fraterrigo JM. Grass invasion effects on forest soil carbon depend on landscape-level land use patterns. Ecology 2015; 96:2265-79. [PMID: 26405751 DOI: 10.1890/14-1770.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Plant invasions can alter the quality and quantity of detrital and root-derived inputs entering a system, thereby influencing the activities of microbial decomposers and affecting the soil carbon cycle. The effect of these inputs on soil carbon storage is often conflicting, suggesting strong context dependency in the plant-decomposer relationship. Whether there is a generalizable pattern that explains this dependency remains relatively unexplored. Here, we (1) examine how invasion by the exotic grass Microstegium vimineum affects carbon cycling across a land use gradient, and (2) evaluate the importance of inorganic nitrogen availability and other environmental variables for explaining patterns in soil carbon. Using paired invaded and uninvaded plots, we quantified invasion effects on belowground carbon pools, extracellular enzyme activities, and native leaf litter decomposition in forests embedded in an urban, agricultural, or forested landscape matrix. Compared to the urban matrix, invasion-associated declines in total soil organic carbon in the forested and agricultural landscapes were 3.5 and 2.5 times greater, respectively. Inorganic nitrogen availability and M. vimineum biomass interacted to explain these patterns: when both nitrogen availability and M. vimineum biomass were high, invaded soils exhibited higher total organic carbon, unchanged particulate organic matter carbon, and higher mineral-associated organic matter carbon compared to adjacent uninvaded soils. Consistent with these patterns, activities of carbon-mineralizing enzymes were lower in invaded than in uninvaded soils when both nitrogen availability and M. vimineum biomass were high. By contrast,. decomposition of native leaf litter was faster when inorganic nitrogen availability and M. vimineum biomass were high. Our findings suggest that, although this invader may accelerate carbon cycling in forest soils, its effects on soil carbon storage largely depend on nitrogen availability and invader biomass, which can be altered by landscape-level patterns of land use. Additional research is needed to determine whether land use or other broad-scale processes such as atmospheric nitrogen deposition can explain context dependence in plant invasion effects on other ecosystem processes.
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221
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Redmile-Gordon M, Evershed R, Hirsch P, White R, Goulding K. Soil organic matter and the extracellular microbial matrix show contrasting responses to C and N availability. SOIL BIOLOGY & BIOCHEMISTRY 2015; 88:257-267. [PMID: 26339106 PMCID: PMC4534311 DOI: 10.1016/j.soilbio.2015.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/08/2015] [Accepted: 05/26/2015] [Indexed: 05/24/2023]
Abstract
An emerging paradigm in soil science suggests microbes can perform 'N mining' from recalcitrant soil organic matter (SOM) in conditions of low N availability. However, this requires the production of extracellular structures rich in N (including enzymes and structural components) and thus defies stoichiometric expectation. We set out to extract newly synthesised peptides from the extracellular matrix in soil and compare the amino acid (AA) profiles, N incorporation and AA dynamics in response to labile inputs of contrasting C/N ratio. Glycerol was added both with and without an inorganic source of N (10% 15N labelled NH4NO3) to a soil already containing a large pool of refractory SOM and incubated for 10 days. The resulting total soil peptide (TSP) and extracellular pools were compared using colorimetric methods, gas chromatography, and isotope ratio mass spectrometry. N isotope compositions showed that the extracellular polymeric substance (EPS) contained a greater proportion of products formed de novo than did TSP, with hydrophobic EPS-AAs (leucine, isoleucine, phenylalanine, hydroxyproline and tyrosine) deriving substantially more N from the inorganic source provided. Quantitative comparison between extracts showed that the EPS contained greater relative proportions of alanine, glycine, proline, phenylalanine and tyrosine. The greatest increases in EPS-peptide and EPS-polysaccharide concentrations occurred at the highest C/N ratios. All EPS-AAs responded similarly to treatment whereas the responses of TSP were more complex. The results suggest that extracellular investment of N (as EPS peptides) is a microbial survival mechanism in conditions of low N/high C which, from an evolutionary perspective, must ultimately lead to the tendency for increased N returns to the microbial biomass. A conceptual model is proposed that describes the dynamics of the extracellular matrix in response to the C/N ratio of labile inputs.
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Affiliation(s)
- M.A. Redmile-Gordon
- Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
- Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, BS8 1TS, UK
| | - R.P. Evershed
- Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, BS8 1TS, UK
| | - P.R. Hirsch
- Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - R.P. White
- Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
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222
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Nottingham AT, Whitaker J, Turner BL, Salinas N, Zimmermann M, Malhi Y, Meir P. Climate Warming and Soil Carbon in Tropical Forests: Insights from an Elevation Gradient in the Peruvian Andes. Bioscience 2015; 65:906-921. [PMID: 26955086 PMCID: PMC4777015 DOI: 10.1093/biosci/biv109] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The temperature sensitivity of soil organic matter (SOM) decomposition in tropical forests will influence future climate. Studies of a 3.5-kilometer elevation gradient in the Peruvian Andes, including short-term translocation experiments and the examination of the long-term adaptation of biota to local thermal and edaphic conditions, have revealed several factors that may regulate this sensitivity. Collectively this work suggests that, in the absence of a moisture constraint, the temperature sensitivity of decomposition is regulated by the chemical composition of plant debris (litter) and both the physical and chemical composition of preexisting SOM: higher temperature sensitivities are found in litter or SOM that is more chemically complex and in SOM that is less occluded within aggregates. In addition, the temperature sensitivity of SOM in tropical montane forests may be larger than previously recognized because of the presence of "cold-adapted" and nitrogen-limited microbial decomposers and the possible future alterations in plant and microbial communities associated with warming. Studies along elevation transects, such as those reviewed here, can reveal factors that will regulate the temperature sensitivity of SOM. They can also complement and guide in situ soil-warming experiments, which will be needed to understand how this vulnerability to temperature may be mediated by altered plant productivity under future climatic change.
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Affiliation(s)
- Andrew T Nottingham
- Andrew T. Nottingham ( ) is affiliated with the School of Geosciences at the University of Edinburgh, in the United Kingdom. Jeanette Whitaker is with the Centre for Ecology and Hydrology at the Lancaster Environment Centre, in Lancaster, United Kingdom. Benjamin L. Turner is affiliated with the Smithsonian Tropical Research Institute, in Balboa, Ancon, Republic of Panama. Norma Salinas is with the Seccion Química at the Universidad La Católica, in Lima, Peru. Michael Zimmermann is affiliated with the University of Natural Resources and Applied Life Sciences, in Vienna, Austria. Yadvinder Malhi is with the Environmental Change Institute in the School of Geography and the Environment at the University of Oxford, in the United Kingdom. Patrick Meir is affiliated with the Research School of Biology at Australian National University, in Canberra, and with the School of Geosciences at the University of Edinburgh, in the United Kingdom
| | - Jeanette Whitaker
- Andrew T. Nottingham ( ) is affiliated with the School of Geosciences at the University of Edinburgh, in the United Kingdom. Jeanette Whitaker is with the Centre for Ecology and Hydrology at the Lancaster Environment Centre, in Lancaster, United Kingdom. Benjamin L. Turner is affiliated with the Smithsonian Tropical Research Institute, in Balboa, Ancon, Republic of Panama. Norma Salinas is with the Seccion Química at the Universidad La Católica, in Lima, Peru. Michael Zimmermann is affiliated with the University of Natural Resources and Applied Life Sciences, in Vienna, Austria. Yadvinder Malhi is with the Environmental Change Institute in the School of Geography and the Environment at the University of Oxford, in the United Kingdom. Patrick Meir is affiliated with the Research School of Biology at Australian National University, in Canberra, and with the School of Geosciences at the University of Edinburgh, in the United Kingdom
| | - Benjamin L Turner
- Andrew T. Nottingham ( ) is affiliated with the School of Geosciences at the University of Edinburgh, in the United Kingdom. Jeanette Whitaker is with the Centre for Ecology and Hydrology at the Lancaster Environment Centre, in Lancaster, United Kingdom. Benjamin L. Turner is affiliated with the Smithsonian Tropical Research Institute, in Balboa, Ancon, Republic of Panama. Norma Salinas is with the Seccion Química at the Universidad La Católica, in Lima, Peru. Michael Zimmermann is affiliated with the University of Natural Resources and Applied Life Sciences, in Vienna, Austria. Yadvinder Malhi is with the Environmental Change Institute in the School of Geography and the Environment at the University of Oxford, in the United Kingdom. Patrick Meir is affiliated with the Research School of Biology at Australian National University, in Canberra, and with the School of Geosciences at the University of Edinburgh, in the United Kingdom
| | - Norma Salinas
- Andrew T. Nottingham ( ) is affiliated with the School of Geosciences at the University of Edinburgh, in the United Kingdom. Jeanette Whitaker is with the Centre for Ecology and Hydrology at the Lancaster Environment Centre, in Lancaster, United Kingdom. Benjamin L. Turner is affiliated with the Smithsonian Tropical Research Institute, in Balboa, Ancon, Republic of Panama. Norma Salinas is with the Seccion Química at the Universidad La Católica, in Lima, Peru. Michael Zimmermann is affiliated with the University of Natural Resources and Applied Life Sciences, in Vienna, Austria. Yadvinder Malhi is with the Environmental Change Institute in the School of Geography and the Environment at the University of Oxford, in the United Kingdom. Patrick Meir is affiliated with the Research School of Biology at Australian National University, in Canberra, and with the School of Geosciences at the University of Edinburgh, in the United Kingdom
| | - Michael Zimmermann
- Andrew T. Nottingham ( ) is affiliated with the School of Geosciences at the University of Edinburgh, in the United Kingdom. Jeanette Whitaker is with the Centre for Ecology and Hydrology at the Lancaster Environment Centre, in Lancaster, United Kingdom. Benjamin L. Turner is affiliated with the Smithsonian Tropical Research Institute, in Balboa, Ancon, Republic of Panama. Norma Salinas is with the Seccion Química at the Universidad La Católica, in Lima, Peru. Michael Zimmermann is affiliated with the University of Natural Resources and Applied Life Sciences, in Vienna, Austria. Yadvinder Malhi is with the Environmental Change Institute in the School of Geography and the Environment at the University of Oxford, in the United Kingdom. Patrick Meir is affiliated with the Research School of Biology at Australian National University, in Canberra, and with the School of Geosciences at the University of Edinburgh, in the United Kingdom
| | - Yadvinder Malhi
- Andrew T. Nottingham ( ) is affiliated with the School of Geosciences at the University of Edinburgh, in the United Kingdom. Jeanette Whitaker is with the Centre for Ecology and Hydrology at the Lancaster Environment Centre, in Lancaster, United Kingdom. Benjamin L. Turner is affiliated with the Smithsonian Tropical Research Institute, in Balboa, Ancon, Republic of Panama. Norma Salinas is with the Seccion Química at the Universidad La Católica, in Lima, Peru. Michael Zimmermann is affiliated with the University of Natural Resources and Applied Life Sciences, in Vienna, Austria. Yadvinder Malhi is with the Environmental Change Institute in the School of Geography and the Environment at the University of Oxford, in the United Kingdom. Patrick Meir is affiliated with the Research School of Biology at Australian National University, in Canberra, and with the School of Geosciences at the University of Edinburgh, in the United Kingdom
| | - Patrick Meir
- Andrew T. Nottingham ( ) is affiliated with the School of Geosciences at the University of Edinburgh, in the United Kingdom. Jeanette Whitaker is with the Centre for Ecology and Hydrology at the Lancaster Environment Centre, in Lancaster, United Kingdom. Benjamin L. Turner is affiliated with the Smithsonian Tropical Research Institute, in Balboa, Ancon, Republic of Panama. Norma Salinas is with the Seccion Química at the Universidad La Católica, in Lima, Peru. Michael Zimmermann is affiliated with the University of Natural Resources and Applied Life Sciences, in Vienna, Austria. Yadvinder Malhi is with the Environmental Change Institute in the School of Geography and the Environment at the University of Oxford, in the United Kingdom. Patrick Meir is affiliated with the Research School of Biology at Australian National University, in Canberra, and with the School of Geosciences at the University of Edinburgh, in the United Kingdom
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Wang H, Boutton TW, Xu W, Hu G, Jiang P, Bai E. Quality of fresh organic matter affects priming of soil organic matter and substrate utilization patterns of microbes. Sci Rep 2015; 5:10102. [PMID: 25960162 PMCID: PMC4426597 DOI: 10.1038/srep10102] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/30/2015] [Indexed: 11/09/2022] Open
Abstract
Changes in biogeochemical cycles and the climate system due to human activities are expected to change the quantity and quality of plant litter inputs to soils. How changing quality of fresh organic matter (FOM) might influence the priming effect (PE) on soil organic matter (SOM) mineralization is still under debate. Here we determined the PE induced by two (13)C-labeled FOMs with contrasting nutritional quality (leaf vs. stalk of Zea mays L.). Soils from two different forest types yielded consistent results: soils amended with leaf tissue switched faster from negative PE to positive PE due to greater microbial growth compared to soils amended with stalks. However, after 16 d of incubation, soils amended with stalks had a higher PE than those amended with leaf. Phospholipid fatty acid (PLFA) results suggested that microbial demand for carbon and other nutrients was one of the major determinants of the PE observed. Therefore, consideration of both microbial demands for nutrients and FOM supply simultaneously is essential to understand the underlying mechanisms of PE. Our study provided evidence that changes in FOM quality could affect microbial utilization of substrate and PE on SOM mineralization, which may exacerbate global warming problems under future climate change.
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Affiliation(s)
- Hui Wang
- 1] State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China [2] University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Thomas W Boutton
- Department of Ecosystem Science and Management, Texas A&M University, College Station, TX 77843-2138, USA
| | - Wenhua Xu
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Guoqing Hu
- 1] State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China [2] University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Jiang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Edith Bai
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
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224
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Finzi AC, Abramoff RZ, Spiller KS, Brzostek ER, Darby BA, Kramer MA, Phillips RP. Rhizosphere processes are quantitatively important components of terrestrial carbon and nutrient cycles. GLOBAL CHANGE BIOLOGY 2015; 21:2082-94. [PMID: 25421798 DOI: 10.1111/gcb.12816] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/28/2014] [Accepted: 10/31/2014] [Indexed: 05/23/2023]
Abstract
While there is an emerging view that roots and their associated microbes actively alter resource availability and soil organic matter (SOM) decomposition, the ecosystem consequences of such rhizosphere effects have rarely been quantified. Using a meta-analysis, we show that multiple indices of microbially mediated C and nitrogen (N) cycling, including SOM decomposition, are significantly enhanced in the rhizospheres of diverse vegetation types. Then, using a numerical model that combines rhizosphere effect sizes with fine root morphology and depth distributions, we show that root-accelerated mineralization and priming can account for up to one-third of the total C and N mineralized in temperate forest soils. Finally, using a stoichiometrically constrained microbial decomposition model, we show that these effects can be induced by relatively modest fluxes of root-derived C, on the order of 4% and 6% of gross and net primary production, respectively. Collectively, our results indicate that rhizosphere processes are a widespread, quantitatively important driver of SOM decomposition and nutrient release at the ecosystem scale, with potential consequences for global C stocks and vegetation feedbacks to climate.
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Affiliation(s)
- Adrien C Finzi
- Department of Biology and PhD Program in Biogeoscience, Boston University, Boston, MA, 02215, USA
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225
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The priming effect of soluble carbon inputs in organic and mineral soils from a temperate forest. Oecologia 2015; 178:1239-50. [DOI: 10.1007/s00442-015-3290-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
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226
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Whitaker J, Ostle N, McNamara NP, Nottingham AT, Stott AW, Bardgett RD, Salinas N, Ccahuana AJQ, Meir P. Microbial carbon mineralization in tropical lowland and montane forest soils of Peru. Front Microbiol 2014; 5:720. [PMID: 25566230 PMCID: PMC4270188 DOI: 10.3389/fmicb.2014.00720] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/02/2014] [Indexed: 11/13/2022] Open
Abstract
Climate change is affecting the amount and complexity of plant inputs to tropical forest soils. This is likely to influence the carbon (C) balance of these ecosystems by altering decomposition processes e.g., "positive priming effects" that accelerate soil organic matter mineralization. However, the mechanisms determining the magnitude of priming effects are poorly understood. We investigated potential mechanisms by adding (13)C labeled substrates, as surrogates of plant inputs, to soils from an elevation gradient of tropical lowland and montane forests. We hypothesized that priming effects would increase with elevation due to increasing microbial nitrogen limitation, and that microbial community composition would strongly influence the magnitude of priming effects. Quantifying the sources of respired C (substrate or soil organic matter) in response to substrate addition revealed no consistent patterns in priming effects with elevation. Instead we found that substrate quality (complexity and nitrogen content) was the dominant factor controlling priming effects. For example a nitrogenous substrate induced a large increase in soil organic matter mineralization whilst a complex C substrate caused negligible change. Differences in the functional capacity of specific microbial groups, rather than microbial community composition per se, were responsible for these substrate-driven differences in priming effects. Our findings suggest that the microbial pathways by which plant inputs and soil organic matter are mineralized are determined primarily by the quality of plant inputs and the functional capacity of microbial taxa, rather than the abiotic properties of the soil. Changes in the complexity and stoichiometry of plant inputs to soil in response to climate change may therefore be important in regulating soil C dynamics in tropical forest soils.
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Affiliation(s)
- Jeanette Whitaker
- Centre for Ecology & Hydrology, Lancaster Environment Centre Lancaster, UK
| | - Nicholas Ostle
- Soil and Ecosystem Laboratory, Lancaster Environment Centre, Lancaster University Lancaster, UK
| | - Niall P McNamara
- Centre for Ecology & Hydrology, Lancaster Environment Centre Lancaster, UK
| | | | - Andrew W Stott
- Centre for Ecology & Hydrology, Lancaster Environment Centre Lancaster, UK
| | | | - Norma Salinas
- Seccion Química, Pontificia Universidad Católica del Perú Lima, Peru ; School of Geography and the Environment, Environmental Change Institute, University of Oxford Oxford, UK
| | - Adan J Q Ccahuana
- Facultad de Ciencias Biologicas, Universidad Nacional de San Antonio Abad Cusco, Peru
| | - Patrick Meir
- School of Geosciences, University of Edinburgh Edinburgh, UK
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227
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Rousk J, Hill PW, Jones DL. Priming of the decomposition of ageing soil organic matter: concentration dependence and microbial control. Funct Ecol 2014. [DOI: 10.1111/1365-2435.12377] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Johannes Rousk
- Section of Microbial Ecology Department of Biology Lund University Lund Sweden
| | - Paul W. Hill
- School of Environment Natural Resources and Geography Bangor University Bangor UK
| | - Davey L. Jones
- School of Environment Natural Resources and Geography Bangor University Bangor UK
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