1
|
Li F, Chen L, Jia Z, Zhang J, Zhao Z, Han Y, Wang Y. Core microbial taxonomies that maintain high organic carbon content in upland soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 939:173300. [PMID: 38810757 DOI: 10.1016/j.scitotenv.2024.173300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024]
Abstract
The accumulation of soil carbon (C) is crucial for the productivity and ecological function of farmland ecosystems. The balance between microbial carbon dioxide (CO2) emission and fixation determines the sustained accumulation potential of C in soil. Microorganisms involved in this process are highly obscure, thus hindering identification and further application of microorganisms with fertile soil function. In this study, a series of typical upland farmland soils were collected from 29 regions and their microbial community structure and soil C fractions were analyzed. Additionally, the rates of CO2 emission and fixation in each soil were measured. The results showed that the correlation between soil CO2 emissions and the SOC concentration was logarithmic, while that between CO2 fixation and SOC was linear. Bacterial and fungal diversity showed an upward trend with increasing soil C, and their α diversity was significantly correlated with CO2 fixation, but not correlated with CO2 emission. Fungi were more associated with soil C than bacteria, and the strength of linkage with soil C varied among the different phyla of microorganisms. Furthermore, the core microbial taxa in soils with low, medium and high SOC levels were identified by discarding redundant amplicon sequence variants, and their community differentiation was significantly driven by soil CO2 emission and fixation based on Mantel analysis. The high abundance of Chloroflexi, Nitrospirota, Actinobacteria, and Mortierellomycota in core taxa might indicate a high level of SOC level. This study highlights that SOC fluctuations are mainly driven by the core microbial taxa, rather than all microbial taxa in the agricultural system. Our research sheds light on the targeted regulation of the soil microbial community structure in upland farmland for soil fertility enhancement.
Collapse
Affiliation(s)
- Fang Li
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Lin Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhongjun Jia
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zhanhui Zhao
- School of Survey and Urban Spatial Information, Henan University of Urban Construction, Pingdingshan 467021, China
| | - Yanlai Han
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China; Co-construction State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.
| | - Yi Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China; Co-construction State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.
| |
Collapse
|
2
|
Luan H, Liu Y, Huang S, Qiao W, Chen J, Guo T, Zhang X, Guo S, Zhang X, Qi G. Successive walnut plantations alter soil carbon quantity and quality by modifying microbial communities and enzyme activities. Front Microbiol 2022; 13:953552. [PMID: 35958128 PMCID: PMC9358653 DOI: 10.3389/fmicb.2022.953552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
Knowledge of the spatial–temporal variations of soil organic carbon (SOC) quantity and quality and its microbial regulation mechanisms is essential for long-term SOC sequestration in agroecosystems; nevertheless, this information is lacking in the process of walnut plantations. Here, we used the modified Walkley-Black method, phospholipid fatty acid analysis, and micro-plate enzyme technique to analyze the evolution of SOC stocks and quality/lability as well as microbial communities and enzyme activities at different soil depths in walnut plantations with a chronosequence of 0-, 7-, 14-, and 21-years in the Eastern Taihang Mountains, China. The results indicated that long-term walnut plantations (14-and 21-years) enhanced SOC stocks, improved SOC quality/lability (as indicated by the lability index), and promoted microbial growth and activities (i.e., hydrolase and oxidase activities) in the 0–40 cm soil layers. Besides, these above-mentioned SOC-and microbial-related indices (except for oxidase activities) decreased with increasing soil depths, while oxidase activities were higher in deeper soils (40–60 cm) than in other soils (0–40 cm). The partial least squares path model also revealed that walnut plantation ages and soil depths had positive and negative effects on microbial attributes (e.g., enzyme activities, fungal and bacterial communities), respectively. Meanwhile, the SOC stocks were closely related to the fungal community; meanwhile, the bacterial community affected SOC quality/liability by regulating enzyme activities. Comprehensively, long-term walnut plantations were conducive to increasing SOC stocks and quality through altering microbial communities and activities in the East Taihang Mountains in Hebei, China.
Collapse
Affiliation(s)
- Haoan Luan
- College of Forestry, Hebei Agricultural University, Baoding, China
| | - Yingru Liu
- College of Agronomy, Hebei Agricultural University/North China Key Laboratory for Crop Germplasm Resources, Ministry of Education/State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Shaohui Huang
- Hebei Fertilizer Technology Innovation Centre, Institute of Agricultural Resources and Environment, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Wenyan Qiao
- College of Forestry, Hebei Agricultural University, Baoding, China
| | - Jie Chen
- Institute of Agricultural Resources and Regional Planning/Key Laboratory of Plant Nutrition and Fertilizer of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tengfei Guo
- Institution of Plant Nutrition and Environmental Resources, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaojia Zhang
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Suping Guo
- College of Forestry, Hebei Agricultural University, Baoding, China
| | - Xuemei Zhang
- College of Forestry, Hebei Agricultural University, Baoding, China
- *Correspondence: Xuemei Zhang,
| | - Guohui Qi
- College of Forestry, Hebei Agricultural University, Baoding, China
- Guohui Qi,
| |
Collapse
|
3
|
Dundore-Arias JP, Castle SC, Felice L, Dill-Macky R, Kinkel LL. Carbon Amendments Influence Composition and Functional Capacities of Indigenous Soil Microbiomes. Front Mol Biosci 2020; 6:151. [PMID: 31993439 PMCID: PMC6964746 DOI: 10.3389/fmolb.2019.00151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/10/2019] [Indexed: 02/01/2023] Open
Abstract
Soil nutrient amendments are recognized for their potential to improve microbial activity and biomass in the soil. However, the specific selective impacts of carbon amendments on indigenous microbiomes and their metabolic functions in agricultural soils remain poorly understood. We investigated the changes in soil chemical characteristics and phenotypes of Streptomyces communities following carbon amendments to soil. Mesocosms were established with soil from two field sites varying in soil organic matter content (low organic matter, LOM; high organic matter, HOM), that were amended at intervals over nine months with low or high dose solutions of glucose, fructose, malic acid, a mixture of these compounds, or water only (non-amended control). Significant shifts in soil chemical characteristics and antibiotic inhibitory capacities of indigenous Streptomyces were observed in response to carbon additions. All high dose carbon amendments consistently increased soil total carbon, while amendments with malic acid decreased soil pH. In LOM soils, higher frequencies of Streptomyces inhibitory phenotypes of the two plant pathogens, Streptomyces scabies and Fusarium oxysporum, were observed in response to soil carbon additions. Additionally, to determine if shifts in Streptomyces functional characteristics correlated with microbiome composition, we investigated whether shifts in functional characteristics of soil Streptomyces correlated with composition of soil bacterial communities, analyzed using 16S rRNA gene sequencing. Regardless of dose, community composition differed significantly among carbon-amended and non-amended soils from both sites. Carbon type and dose had significant effects on bacterial community composition in both LOM and HOM soils. Relationships among microbial community richness (observed species number), diversity, and soil characteristics varied among soils from different sites. These results suggest that manipulation of soil resource availability has the potential to selectively modify the functional capacities of soil microbiomes, and specifically to enhance pathogen inhibitory populations of high value to agricultural systems.
Collapse
Affiliation(s)
- José Pablo Dundore-Arias
- Department of Biology and Chemistry, California State University, Monterey Bay, Seaside, CA, United States.,Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Sarah C Castle
- Plant Science Research Unit, USDA-ARS, Saint Paul, MN, United States
| | - Laura Felice
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Linda L Kinkel
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| |
Collapse
|
4
|
Malik AA, Martiny JBH, Brodie EL, Martiny AC, Treseder KK, Allison SD. Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. THE ISME JOURNAL 2020; 14:1-9. [PMID: 31554911 PMCID: PMC6908601 DOI: 10.1038/s41396-019-0510-0] [Citation(s) in RCA: 248] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 06/07/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Ashish A Malik
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA.
| | - Jennifer B H Martiny
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Adam C Martiny
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Kathleen K Treseder
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
| | - Steven D Allison
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| |
Collapse
|
5
|
van der Waals MJ, Plugge C, Meima-Franke M, de Waard P, Bodelier PLE, Smidt H, Gerritse J. Ethyl tert-butyl ether (EtBE) degradation by an algal-bacterial culture obtained from contaminated groundwater. WATER RESEARCH 2019; 148:314-323. [PMID: 30391860 DOI: 10.1016/j.watres.2018.10.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/16/2018] [Accepted: 10/17/2018] [Indexed: 06/08/2023]
Abstract
EtBE is a fuel oxygenate that is synthesized from (bio)ethanol and fossil-based isobutylene, and replaces the fossil-based MtBE. Biodegradation of EtBE to harmless metabolites or end products can reduce the environmental and human health risks after accidental release. In this study, an algal-bacterial culture enriched from contaminated groundwater was used to (i) assess the potential for EtBE degradation, (ii) resolve the EtBE degradation pathway and (iii) characterize the phylogenetic composition of the bacterial community involved in EtBE degradation in contaminated groundwater. In an unamended microcosm, algal growth was observed after eight weeks when exposed to a day-night light cycle. In the fed-batch reactor, oxygen produced by the algae Scenedesmus and Chlorella was used by bacteria to degrade 50 μM EtBE replenishments with a cumulative total of 1250 μM in a day/night cycle (650 lux), over a period of 913 days. The microbial community in the fed-batch reactor degraded EtBE, using a P450 monooxygenase and 2-hydroxyisobutyryl-CoA mutase, to tert-butyl alcohol (TBA), ethanol and CO2 as determined using 13C nuclear magnetic resonance spectroscopy (NMR) and gas chromatography. Stable isotope probing (SIP) with 13C6 labeled EtBE in a fed-batch vessel showed no significant difference in community profiles of the 13C and 12C enriched DNA fractions, with representatives of the families Halomonadaceae, Shewanellaceae, Rhodocyclaceae, Oxalobacteraceae, Comamonadaceae, Sphingomonadaceae, Hyphomicrobiaceae, Candidatus Moranbacteria, Omnitrophica, Anaerolineaceae, Nocardiaceae, and Blastocatellaceae. This is the first study describing micro-oxic degradation of EtBE by an algal-bacterial culture. This algal-bacterial culture has advantages compared with conventional aerobic treatments: (i) a lower risk of EtBE evaporation and (ii) no need for external oxygen supply in the presence of light. This study provides novel leads towards future possibilities to implement algal-bacterial consortia in field-scale groundwater or wastewater treatment.
Collapse
Affiliation(s)
- Marcelle J van der Waals
- Deltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 BK, Utrecht, the Netherlands; Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, the Netherlands.
| | - Caroline Plugge
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Marion Meima-Franke
- The Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | - Pieter de Waard
- Wageningen University & Research, BioNanoTechnology, Bornse Weilanden 9, 6700 EK, Wageningen, the Netherlands
| | - Paul L E Bodelier
- The Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands
| | - Hauke Smidt
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, the Netherlands
| | - Jan Gerritse
- Deltares, Subsurface and Groundwater Systems, Daltonlaan 600, 3584 BK, Utrecht, the Netherlands
| |
Collapse
|
6
|
Moreno-Espíndola IP, Ferrara-Guerrero MJ, Luna-Guido ML, Ramírez-Villanueva DA, De León-Lorenzana AS, Gómez-Acata S, González-Terreros E, Ramírez-Barajas B, Navarro-Noya YE, Sánchez-Rodríguez LM, Fuentes-Ponce M, Macedas-Jímenez JU, Dendooven L. The Bacterial Community Structure and Microbial Activity in a Traditional Organic Milpa Farming System Under Different Soil Moisture Conditions. Front Microbiol 2018; 9:2737. [PMID: 30487784 PMCID: PMC6246654 DOI: 10.3389/fmicb.2018.02737] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/25/2018] [Indexed: 12/03/2022] Open
Abstract
Agricultural practices affect the bacterial community structure, but how they determine the response of the bacterial community to drought, is still largely unknown. Conventional cultivated soil, i.e., inorganic fertilization, tillage, crop residue removal and maize (Zea mays L.) monoculture, and traditional organic farmed soil “milpa,” i.e., minimum tillage, rotation of maize, pumpkin (Cucurbita sp.) and beans (Phaseolus vulgaris L.) and organic fertilization were sampled. Both soils from the central highlands of Mexico were characterized and incubated aerobically at 5% field capacity (5%FC) and 100% field capacity (FC) for 45 days, while the C and N mineralization, enzyme activity and the bacterial community structure were monitored. After applying the different agricultural practices 3 years, the organic C content was 1.8-times larger in the milpa than in the conventional cultivated soil, the microbial biomass C 1.3-times, and C and N mineralization 2.0-times (mean for soil incubated at 5%FC and FC). The dehydrogenase, activity was significantly higher in the conventional cultivated soil than in the milpa soil when incubated at 5%FC, but not when incubated at FC. The relative abundance of Gemmatimonadetes was larger in the conventional cultivated soil than in the milpa soil in soil both at 5%FC and FC, while that of Bacteroidetes showed an opposite trend. The relative abundance of other groups, such as Nitrospirae and Proteobacteria, was affected by cultivation technique, but controlled by soil water content. The relative abundance of other groups, e.g., FBP, Gemmatimonadetes and Proteobacteria, was affected by water content, but the effect depended on agricultural practice. For soil incubated at FC, the xenobiotics biodegradation and metabolism related functions were higher in the milpa soil than in the conventional cultivated soil, and carbohydrate metabolism showed an opposite trend. It was found that agricultural practices and soil water content had a strong effect on soil characteristics, C and N mineralization, enzyme activity, and the bacterial community structure and its functionality. Decreases or increases in the relative abundance of bacterial groups when the soil water content decreased, i.e., from FC to 5%FC, was defined often by the cultivation technique, and the larger organic matter content in the milpa soil did not prevent large changes in the bacterial community structure when the soil was dried.
Collapse
Affiliation(s)
- Iván P Moreno-Espíndola
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - María J Ferrara-Guerrero
- Departamento de El Hombre y su Ambiente, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - Marco L Luna-Guido
- Laboratory of Soil Ecology, ABACUS, Centro de Investigación y de Estudios Avanzados, Mexico City, Mexico
| | | | - Arit S De León-Lorenzana
- Laboratory of Soil Ecology, ABACUS, Centro de Investigación y de Estudios Avanzados, Mexico City, Mexico
| | - Selene Gómez-Acata
- Laboratory of Soil Ecology, ABACUS, Centro de Investigación y de Estudios Avanzados, Mexico City, Mexico
| | | | - Blanca Ramírez-Barajas
- Laboratory of Soil Ecology, ABACUS, Centro de Investigación y de Estudios Avanzados, Mexico City, Mexico
| | | | - Luis M Sánchez-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - Mariela Fuentes-Ponce
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - Juan U Macedas-Jímenez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, Centro de Investigación y de Estudios Avanzados, Mexico City, Mexico
| |
Collapse
|
7
|
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: 52] [Impact Index Per Article: 7.4] [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.
Collapse
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
| |
Collapse
|
8
|
de Carvalho TS, Jesus EDC, Barlow J, Gardner TA, Soares IC, Tiedje JM, Moreira FMDS. Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria. Ecology 2016; 97:2760-2771. [PMID: 27859123 DOI: 10.1002/ecy.1513] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 02/11/2016] [Accepted: 05/24/2016] [Indexed: 12/30/2022]
Abstract
Anthropogenic pressures on tropical forests are rapidly intensifying, but our understanding of their implications for biological diversity is still very limited, especially with regard to soil biota, and in particular soil bacterial communities. Here we evaluated bacterial community composition and diversity across a gradient of land use intensity in the eastern Amazon from undisturbed primary forest, through primary forests varyingly disturbed by fire, regenerating secondary forest, pasture, and mechanized agriculture. Soil bacteria were assessed by paired-end Illumina sequencing of 16S rRNA gene fragments (V4 region). The resulting sequences were clustered into operational taxonomic units (OTU) at a 97% similarity threshold. Land use intensification increased the observed bacterial diversity (both OTU richness and community heterogeneity across space) and this effect was strongly associated with changes in soil pH. Moreover, land use intensification and subsequent changes in soil fertility, especially pH, altered the bacterial community composition, with pastures and areas of mechanized agriculture displaying the most contrasting communities in relation to undisturbed primary forest. Together, these results indicate that tropical forest conversion impacts soil bacteria not through loss of diversity, as previously thought, but mainly by imposing marked shifts on bacterial community composition, with unknown yet potentially important implications for ecological functions and services performed by these communities.
Collapse
Affiliation(s)
- Teotonio Soares de Carvalho
- Departamento de Ciência do Solo, Universidade Federal de Lavras, Lavras, Minas Gerais, 37200-000, Brazil.,Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster, LA14YQ, United Kingdom
| | | | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster, LA14YQ, United Kingdom.,Museu Paraense Emilio Goeldi, Avenida Magalhães Barata, 376, Belém, Pará, Brazil
| | - Toby A Gardner
- Stockholm Environment Institute, Linnégatan 87D, Box 24218, Stockholm, 10451, Sweden
| | - Isaac Carvalho Soares
- Departamento de Ciência do Solo, Universidade Federal de Lavras, Lavras, Minas Gerais, 37200-000, Brazil
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan, 48824, USA
| | | |
Collapse
|
9
|
Hill R, Saetnan ER, Scullion J, Gwynn-Jones D, Ostle N, Edwards A. Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure. Environ Microbiol 2015; 18:1942-53. [DOI: 10.1111/1462-2920.13017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Richard Hill
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
- Interdisciplinary Centre for Environmental Microbiology; Aberystwyth University; Aberystwyth UK
| | - Eli R. Saetnan
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - John Scullion
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - Dylan Gwynn-Jones
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
| | - Nick Ostle
- Plant and Soil Ecology Laboratory; Lancaster Environmental Centre; Lancaster University; Lancaster LA1 4YQ UK
| | - Arwyn Edwards
- Institute of Biological, Rural and Environmental Sciences; Cledwyn Building; Aberystwyth University; Aberystwyth SY23 3FG UK
- Interdisciplinary Centre for Environmental Microbiology; Aberystwyth University; Aberystwyth UK
| |
Collapse
|
10
|
Malik AA, Dannert H, Griffiths RI, Thomson BC, Gleixner G. Rhizosphere bacterial carbon turnover is higher in nucleic acids than membrane lipids: implications for understanding soil carbon cycling. Front Microbiol 2015; 6:268. [PMID: 25914679 PMCID: PMC4391234 DOI: 10.3389/fmicb.2015.00268] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/18/2015] [Indexed: 11/13/2022] Open
Abstract
Using a pulse chase (13)CO2 plant labeling experiment we compared the flow of plant carbon into macromolecular fractions of rhizosphere soil microorganisms. Time dependent (13)C dilution patterns in microbial cellular fractions were used to calculate their turnover time. The turnover times of microbial biomolecules were found to vary: microbial RNA (19 h) and DNA (30 h) turned over fastest followed by chloroform fumigation extraction-derived soluble cell lysis products (14 days), while phospholipid fatty acids (PLFAs) had the slowest turnover (42 days). PLFA/NLFA (13)C analyses suggest that both mutualistic arbuscular mycorrhizal and saprophytic fungi are dominant in initial plant carbon uptake. In contrast, high initial (13)C enrichment in RNA hints at bacterial importance in initial C uptake due to the dominance of bacterial derived RNA in total extracts of soil RNA. To explain this discrepancy, we observed low renewal rate of bacterial lipids, which may therefore bias lipid fatty acid based interpretations of the role of bacteria in soil microbial food webs. Based on our findings, we question current assumptions regarding plant-microbe carbon flux and suggest that the rhizosphere bacterial contribution to plant assimilate uptake could be higher. This highlights the need for more detailed quantitative investigations with nucleic acid biomarkers to further validate these findings.
Collapse
Affiliation(s)
- Ashish A Malik
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry Jena, Germany
| | - Helena Dannert
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry Jena, Germany
| | | | | | - Gerd Gleixner
- Department of Biogeochemical Processes, Max Planck Institute for Biogeochemistry Jena, Germany
| |
Collapse
|
11
|
Rettedal EA, Brözel VS. Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H 218 O. Microbiologyopen 2015; 4:208-219. [PMID: 25650291 PMCID: PMC4398504 DOI: 10.1002/mbo3.230] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 11/08/2014] [Accepted: 11/17/2014] [Indexed: 11/10/2022] Open
Abstract
Current limitations in culture-based methods have lead to a reliance on culture-independent approaches, based principally on the comparative analysis of primary semantides such as ribosomal gene sequences. DNA can be remarkably stable in some environments, so its presence does not indicate live bacteria, but extracted ribosomal RNA (rRNA) has previously been viewed as an indicator of active cells. Stable isotope probing (SIP) involves the incorporation of heavy isotopes into newly synthesized nucleic acids, and can be used to separate newly synthesized from existing DNA or rRNA. H218 O is currently the only potential universal bacterial substrate suitable for SIP of entire bacterial communities. The aim of our work was to compare soil bacterial community composition as revealed by total versus SIP-labeled DNA and rRNA. Soil was supplemented with H218 O and after 38 days the DNA and RNA were co-extracted. Heavy nucleic acids were separated out by CsCl and CsTFA density centrifugation. The 16S rRNA gene pools were characterized by DGGE and pyrosequencing, and the sequence results analyzed using mothur. The majority of DNA (~60%) and RNA (~75%) from the microcosms incubated with H218 O were labeled by the isotope. The analysis indicated that total and active members of the same type of nucleic acid represented similar community structures, which suggested that most dominant OTUs in the total nucleic acid extracts contained active members. It also supported that H218 O was an effective universal label for SIP for both DNA and RNA. DNA and RNA-derived diversity was dissimilar. RNA from this soil more comprehensively recovered bacterial richness than DNA because the most abundant OTUs were less numerous in RNA than DNA-derived community data, and dominant OTU pools didn't mask rare OTUs as much in RNA.
Collapse
Affiliation(s)
- Elizabeth A Rettedal
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, South Dakota, 57007
| | - Volker S Brözel
- Department of Biology and Microbiology, South Dakota State UniversityBrookings, South Dakota, 57007
- Department of Microbiology and Plant Pathology, University of PretoriaPretoria, 0004, South Africa
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Rousk J, Bengtson P. Microbial regulation of global biogeochemical cycles. Front Microbiol 2014; 5:103. [PMID: 24672519 PMCID: PMC3954078 DOI: 10.3389/fmicb.2014.00103] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 02/27/2014] [Indexed: 11/21/2022] Open
Affiliation(s)
- Johannes Rousk
- Department of Biology/Microbial Ecology, Lund UniversityLund, Sweden
| | | |
Collapse
|